Convergence and divergence in the evolution of transport proteins

Different families of transport proteins catalyze transmembrane solute translocation, employing different mechanisms and energy sources. Several of these functionally dissimilar proteins nevertheless exhibit similar strutural units, consisting of six tightly packed α-helices which may comprise all or part of a transmembrane channel. It is now recognized that some of these families arose independently of each other by convergence, while others arose from common precursors by divergence. The former families apparently arose at different times in evolutionary history, in different groups of organisms, employing different routes.     

Genomic evidence for convergent evolution of a key trait underlying divergence in island birds

Reproductive isolation can be initiated by changes in one or a few key traits that prevent random mating among individuals in a population. During the early stages of speciation, when isolation is often incomplete, there will be a heterogeneous pattern of differentiation across regions of the genome between diverging populations, with loci controlling these key traits appearing the most distinct as a result of strong diversifying selection. In this study, we used Illumina‐sequenced ddRAD tags to identify genomewide patterns of differentiation in three recently diverged island populations of the Monarcha castaneiventris flycatcher of the Solomon Islands. Populations of this species have diverged in plumage colour, and these differences in plumage colour, in turn, are used in conspecific recognition and likely important in reproductive isolation. Previous candidate gene sequencing identified point mutations in MC1R and ASIP, both known pigmentation genes, to be associated with the difference in plumage colour between islands. Here, we show that background levels of genomic differentiation based on over 70,000 SNPs are extremely low between populations of distinct plumage colour, with no loci reaching the level of differentiation found in either candidate gene. Further, we found that a phylogenetic analysis based on these SNPs produced a taxonomy wherein the two melanic populations appear to have evolved convergently, rather than from a single common ancestor, in contrast to their original classification as a single subspecies. Finally, we found evidence that the pattern of low genomic differentiation is the result of both incomplete lineage sorting and gene flow between populations.     

Convergence and divergence in the evolution of cat skulls: temporal and spatial patterns of morphological diversity

Background

Studies of biological shape evolution are greatly enhanced when framed in a phylogenetic perspective. Inclusion of fossils amplifies the scope of macroevolutionary research, offers a deep-time perspective on tempo and mode of radiations, and elucidates life-trait changes. We explore the evolution of skull shape in felids (cats) through morphometric analyses of linear variables, phylogenetic comparative methods, and a new cladistic study of saber-toothed cats.

Methodology/Principal Findings

A new phylogenetic analysis supports the monophyly of saber-toothed cats (Machairodontinae) exclusive of Felinae and some basal felids, but does not support the monophyly of various saber-toothed tribes and genera. We quantified skull shape variation in 34 extant and 18 extinct species using size-adjusted linear variables. These distinguish taxonomic group membership with high accuracy. Patterns of morphospace occupation are consistent with previous analyses, for example, in showing a size gradient along the primary axis of shape variation and a separation between large and small-medium cats. By combining the new phylogeny with a molecular tree of extant Felinae, we built a chronophylomorphospace (a phylogeny superimposed onto a two-dimensional morphospace through time). The evolutionary history of cats was characterized by two major episodes of morphological divergence, one marking the separation between saber-toothed and modern cats, the other marking the split between large and small-medium cats.

Conclusions/Significance

Ancestors of large cats in the ‘Panthera’ lineage tend to occupy, at a much later stage, morphospace regions previously occupied by saber-toothed cats. The latter radiated out into new morphospace regions peripheral to those of extant large cats. The separation between large and small-medium cats was marked by considerable morphologically divergent trajectories early in feline evolution. A chronophylomorphospace has wider applications in reconstructing temporal transitions across two-dimensional trait spaces, can be used in ecophenotypical and functional diversity studies, and may reveal novel patterns of morphospace occupation.     

Convergence and divergence of the signaling pathways for insulin and phosphoinositolglycans.

Phosphoinositolglycan molecules isolated from insulin-sensitive mammalian tissues have been demonstrated in numerous in vitro studies to exert partial insulin-mimetic activity on glucose and lipid metabolism in insulin-sensitive cells. However, their ill-defined structures, heterogeneous nature, and limited availability have prohibited the analysis of the underlying molecular mechanism. Phosphoinositolglycan-peptide (PIG-P) of defined and homogeneous structure prepared in large scale from the core glycan of a glycosyl-phosphatidylinositol-anchored membrane protein from Saccharomyces cerevisiae has recently been shown to stimulate glucose transport as well as a number of glucose-metabolizing enzymes and pathways to up to 90% (at 2 to 10 microns) of the maximal insulin effect in isolated rat adipocytes, cardiomyocytes, and diaphragms (G. Müller et al., 1997, Endocrinology 138: 3459-3476). Consequently, we used this PIG-P for the present study in which we compare its intracellular signaling with that of insulin. The activation of glucose transport by both PIG-P and insulin in isolated rat adipocytes and diaphragms was found to require stimulation of phosphatidylinositol (PI) 3-kinase but to be independent of functional p70S6kinase and mitogen-activated protein kinase. The increase in glycerol-3-phosphate acyltransferase activity in rat adipocytes in response to PIG-P and insulin was dependent on both PI 3-kinase and p70S6kinase. This suggest that the signaling pathways for PIG-P and insulin to glucose transport and metabolism converage at the level of PI 3-kinase. A component of the PIG-P signaling pathway located up-stream of PI 3-kinase was identified by desensitization of isolated rat adipocytes for PIG-P action by combined treatment with trypsin and NaCl under conditions that preserved cell viability and the insulin-mimetic activity of sodium vanadate but completely blunted the insulin response. Incubation of the cells with either trypsin or NaCl alone was ineffective. The desensitized adipocytes were reconstituted for stimulation of lipogenesis by PIG-P by addition of the concentrated trypsin/salt extract. The reconstituted adipocytes exhibited 65-75% of the maximal PIG-P response and similar EC50 values for PIG-P (2 to 5 microns) compared with control cells. A proteinaceous N-ethylmaleimide (NEM)-sensitive component contained in the trypsin/salt extract was demonstrated to bind in a functional manner to the adipocyte plasma membrane of desensitized adipocytes via bipolar interactions. An excess of trypsin/salt extract inhibited PIG-P action in untreated adipocytes in a competitive fashion compatible with a receptor function for PIG-P of this protein. The presence of the putative PIG-P receptor protein in detergent-insoluble complexes prepared from isolated rat adipocytes suggests that caveolae/detergent-insoluble complexes of the plasma membrane may play a role in insulin-mimetic signaling by PIG-P. Furthermore, treatment of isolated rat diaphragms and adipocytes with PIG-P as well as with other agents exerting partially insulin-mimetic activity, such as PI-specific phospholipase C (PLC) and the sulfonylurea glimepiride, triggered tyrosine phosphorylation of the caveolar marker protein caveolin, which was apparently correlated with stimulation of lipogenesis. Strikingly, in adipocytes subjected to combined trypsin/salt treatment, PIG-P, PI-specific PLC, and glimepiride failed completely to provoke insulin-mimetic effects. A working model is presented for a signaling pathway in insulin-sensitive cells used by PIG(-P) molecules which involves GPI structures, the trypsin/salt- and NEM-sensitive receptor protein for PIG-P, and additional proteins located in caveolae/detergent-insoluble complexes.     

Differential rates of morphological divergence in birds

There are more small-bodied bird species than there are large-bodied, even on a logarithmic scale. In birds this pattern, which is also found in other higher taxa, appears not to be due to neutral evolution. It has often been suggested that the skew of body size frequency distributions is the result of a relationship between body size and the net rate of speciation, but phylogenetic analyses so far have rejected the hypothesis that small-bodied species are subject to higher net rates of speciation. On the contrary, we show that there exists a relationship between body size and its own evolutionary variability: avian families of small body size show less interspecific variation in body size than large-bodied families of similar age and species richness.     

Convergence and divergence in lizard colour polymorphisms

Colour polymorphic species are model systems for examining the evolutionary processes that generate and maintain discrete phenotypic variation in natural populations. Lizards have repeatedly evolved strikingly similar polymorphic sexual signals in distantly related lineages, providing an opportunity to examine convergence and divergence in colour polymorphism, correlated traits and associated evolutionary processes. Herein, we synthesise the extensive literature on lizard colour polymorphisms in both sexes, including recent advances in understanding of the underlying biochemical, cellular and genetic mechanisms, and correlated behavioural, physiological and life-history traits. Male throat, head or ventral colour morphs generally consist of red/orange, yellow and white/blue morphs, and sometimes mixed morphs with combinations of two colours. Despite these convergent phenotypes, there is marked divergence in correlated behavioural, physiological and life-history traits. We discuss the need for coherence in morph classification, particularly in relation to ‘mixed’ morphs. We highlight future research directions such as the genetic basis of convergent phenotypes and the role of environmental variation in the maintenance of polymorphism. Research in this very active field promises to continue to provide novel insights with broad significance to evolutionary biologists.     

Convergence and divergence in Diana monkey vocalizations

Individually distinct vocalizations are widespread among social animals, presumably caused by variation in vocal tract anatomy. A less-explored source of individual variation is due to learned movement patterns of the vocal tract, which can lead to vocal convergence or divergence in social groups. We studied patterns of acoustic similarity in a social call produced by 14 female Diana monkeys (Cercopithecus diana) in two free-ranging groups. Calls showed variability in fundamental frequency contours owing to individual identity and external context. Vocal divergence increased significantly between females during poor visibility and tended to increase in the presence of neighbours. In contrast, vocal convergence increased significantly between females during vocal interactions, because females matched the frequency contour of their own call with another female's preceding call. Our findings demonstrate that these primates have some control over the acoustic fine structure of their most important social vocalization. Vocal convergence and divergence are two opposing processes that enable callers to ensure spatial proximity and social cohesion with other group members.     

Strychnine poisoning of aquatic birds

Strychnine poisoning was diagnosed in free-flying mallards (Anas platyrhynchos) and a ring-billed gull (Larus delawarensis) found dead on a pond in a zoo. The probable source of toxin was improperly applied strychnine-treated grain used for control of rodents on adjacent farm land. Ingesta of the birds contained 19.7-85.1 mg/kg of strychnine.     

Avian coronavirus in wild aquatic birds

We detected a high prevalence (12.5%) of novel avian coronaviruses in aquatic wild birds. Phylogenetic analyses of these coronaviruses suggest that there is a diversity of gammacoronaviruses and deltacoronaviruses circulating in birds. Gammacoronaviruses were found predominantly in Anseriformes birds, whereas deltacoronaviruses could be detected in Ciconiiformes, Pelecaniformes, and Anseriformes birds in this study. We observed that there are frequent interspecies transmissions of gammacoronaviruses between duck species. In contrast, deltacoronaviruses may have more stringent host specificities. Our analysis of these avian viral and host mitochondrial DNA sequences also suggests that some, but not all, coronaviruses may have coevolved with birds from the same order.     

Allozyme divergence and evolution in the genusLens

The genusLens includes 5 taxonomic species:L. culinaris is cultivated andL. orientalis, L. odemensis, L. ervoides, andL. nigricans are wild. All the species are annual and almost exlusively selfers. The wild lentils are distributed over a large geographical area and form small disjunct populations which are composed of a small number of plants. 67Lens populations were assayed electrophoretically for 9 enzyme systems; 15 enzymic genes with 37 alleles were identified. The genetic distances (D) measured between the pairs of populations indicated a significantly greater similarity between populations belonging to the same taxonomic species. Assuming the populations represent a random sample of the variability in each of the species the genetic distances (D) between the 5 taxa were calculated. The shortest genetic distance was found betweenL. orientalis andL. culinaris. Another significant feature of the data is the apparent isolation ofL. nigricans from the other 4 species. The genetic distances between theLens species are compared to the patterns of crossability barriers between them.     

Isolation of Vibrio cholerae from aquatic birds in Colorado and Utah.

Vibrio cholerae was isolated from cloacal swabs and freshly voided feces collected from 20 species of aquatic birds in Colorado and Utah during 1986 and 1987. About 17% (198 of 1,131) fecal specimens collected from July 1986 through August 1987 contained the organism. Both O1 and non-O1 V. cholerae strains were isolated from the fecal specimens. Isolates from eight birds (representing five species) agglutinated in O group 1 antiserum. Supernatants of broth cultures from three isolates which typed as V. cholerae O1 serotype Ogawa gave reactions typical of cholera toxin when tested on Y-1 mouse adrenal cell cultures. Several serovars of non-O1 V. cholerae were isolated from the fecal specimens; serovar 22 was the most prevalent type. All non-O1 isolates were cytotoxic to Y-1 mouse adrenal cells. Only non-O1 V. cholerae was detected in water samples collected from the habitat of the birds. The results of this study suggest that aquatic birds serve as carriers and disseminate V. cholerae over a wide area.     

Feather function and the evolution of birds

The ability of feathers to perform many functions either simultaneously or at different times throughout the year or life of a bird is integral to the evolutionary history of birds. Many studies focus on single functions of feathers, but any given feather performs many functions over its lifetime. These functions necessarily interact with each other throughout the evolution and development of birds, so our knowledge of avian evolution is incomplete without understanding the multifunctionality of feathers, and how different functions may act synergistically or antagonistically during natural selection. Here, we review how feather functions interact with avian evolution, with a focus on recent technological and discovery-based advances. By synthesising research into feather functions over hierarchical scales (pattern, arrangement, macrostructure, microstructure, nanostructure, molecules), we aim to provide a broad context for how the adaptability and multifunctionality of feathers have allowed birds to diversify into an astounding array of environments and life-history strategies. We suggest that future research into avian evolution involving feather function should consider multiple aspects of a feather, including multiple functions, seasonal wear and renewal, and ecological or mechanical interactions. With this more holistic view, processes such as the evolution of avian coloration and flight can be understood in a broader and more nuanced context.     

Hominid divergence and speech evolution

Hominids evolved from a population which diverged from other hominoids during the Mio-Pliocene. This population was perhaps forced by ecological conditions and competitive exclusion to rely more on tools, gathering, hunting, vocal communication and memory, under whose mutually positively reinforcing effects the hominids diverged. The ape ancestors may have been forced into the forests (or they may have forced hominids onto the savanna), while hominids adapted to a plains, hunting econiche.Speech was selected for because verbal symbols served as retrieval cues for a large number of complex concepts and were transmissible, and thus could be used to influence food-getting and other behavior by the social group.Speech is dependent on three inherited entities: (1) anatomical and neurological adaptations which allow vocalization of a wide range of phonemes in rapid succession and which allow for (2) duality of patterning, thereby promoting a large number of words, and (3) encoding, which greatly increases the rate at which verbal information transfer can occur. Speech may have evolved through small hominid groups using progressively more phonemes in an increasingly blended manner, with encoding subsequently being selected for. Neandertals apparently could not encode speech and could speak only a restricted range of phonemes. Their expanded cranial capacity may have been selected for to store ambiguous and slowly transmitted verbal data.     

Calibrating molecular estimates of substitution rates and divergence times in birds

Many evolutionary studies of birds rely on the estimation of molecular divergence times and substitution rates. In order to perform such analyses, it is necessary to incorporate some form of calibration information: a known substitution rate, radiometric ages of heterochronous sequences, or inferred ages of lineage splitting events. All three of these techniques have been employed in avian molecular studies, but their usage has not been entirely satisfactory. For example, the 'traditional' avian mitochondrial substitution rate of 2% per million years is frequently adopted without acknowledgement of the associated uncertainty. Similarly, fossil and biogeographic information is almost always converted into an errorless calibration point. In both cases, the resulting estimates of divergence times and substitution rates will be artificially precise, which has a considerable impact on hypothesis testing. In addition, using such a simplistic approach to calibration discards much of the information offered by the fossil record. A number of more sophisticated calibration methods have recently been introduced, culminating in the development of probability distribution-based calibrations. In this article, I discuss the use of this new class of methods and offer guidelines for choosing a calibration technique.     

Genome evolution and functional divergence in Yersinia

The steadily increasing number of prokaryotic genomes has accelerated the study of genome evolution; in particular, the availability of sets of genomes from closely related bacteria has made exploration of questions surrounding the evolution of pathogenesis tractable. Here we present the results of a detailed comparison of the genomes of Yersinia pseudotuberculosis IP32593 and three strains of Yersinia pestis (CO92, KIM10, and 91001). There appear to be between 241 and 275 multigene families in these organisms. There are 2,568 genes that are identical in the three Y. pestis strains, but differ from the Y. pseudotuberculosis strain. The changes found in some of these families, such as the kinases, proteases, and transporters, are illustrative of how the evolutionary jump from the free-living enteropathogen Y. pseudotuberculosis to the obligate host-borne blood pathogen Y. pestis was achieved. We discuss the composition of some of the most important families and discuss the observed divergence between Y. pseudotuberculosis and Y. pestis homologs.     

The evolution of concepts on the evolution of endothermy in birds and mammals

Warm-blooded animals, mammals and birds, are unique not because they are endothermic in the strict sense of the term but because they use an extravagant economy: they have high energy budgets and spend a large part of their energy resources on basic maintenance. Although several advantages of endothermy are easy to indicate, mechanisms behind evolution of such a wasteful life strategy remain unclear and have been subject to intensive debate. For two decades, the aerobic capacity model has been widely recognized as a promising hypothesis and has catalyzed a new direction in ecological and evolutionary physiology--the study of correlated evolution of behavioral and morphophysiological traits. Recently, two alternative models have been proposed, both of which see evolution of high metabolic rates in birds and mammals as an element in evolution of intensive parental care. Unlike previous models, which treated individuals as static objects of fixed properties, the parental care models explicitly incorporate life histories into a evolutionary-physiology research program. The aim of this article was to outline the process of evolution of major concepts in the field, which reflects development of the paradigm of modern evolutionary physiology.     

Gene duplication and divergence in the early evolution of vertebrates

The duplication-degeneration-complementation model of duplicate gene preservation by subfunctionalisation is currently the best explanation for the high level of retention of duplicate genes in early vertebrate evolution. But a direct test of the applicability of this model to such ancient evolutionary events may be difficult. More likely, recent duplications in other lineages will allow us to establish general principles concerning the fate of genes of different types that are duplicated in different ways. These principles may be then extrapolated to understanding the early evolution of the vertebrates.     

Isolation of Candida albicans and halophilic Vibrio spp. from aquatic birds in Connecticut and Florida.

Halophilic vibrios were recovered from feces of six types of aquatic birds (gulls, pelicans, Canada geese, swans, egrets, cormorants) from Connecticut and/or Florida shorelines. Candida albicans was isolated from gulls and Canada geese in Connecticut and from gulls and cormorants in Florida.