The Evolution of Vocal Communication: Inertia and Divergence in Two Closely Related Primates

International Journal of Primatology - Primate vocal repertoires change slowly over evolutionary time, making them good indicators of phylogenetic relatedness. Occasionally, however,...     

Historical Biogeography: Evolution in Time and Space

Biogeography is the discipline of biology that studies the present and past distribution patterns of biological diversity and their underlying environmental and historical causes. For most of its history, biogeography has been divided into proponents of vicariance explanations, who defend that distribution patterns can mainly be explained by geological, tectonic-isolating events; and dispersalists, who argue that current distribution patterns are largely the result of recent migration events. This paper provides an overview of the evolution of the discipline from methods focused on finding general patterns of distribution (cladistic biogeography), to those that integrate biogeographic processes (event-based biogeography), to modern probabilistic approaches (parametric biogeography). The latter allows incorporating into biogeographic inference estimates of the divergence time between lineages (usually based on DNA sequences) and external sources of evidence, such as information on past climate and geography, the organism fossil record, or its ecological tolerance. This has revolutionized the discipline, allowing it to escape the dispersal versus vicariance dilemma and to address a wider range of evolutionary questions, including the role of ecological and historical factors in the construction of biomes or the existence of contrasting patterns of range evolution in animals and plants.     

Evolution of the Hedgehog Gene Family

Effective intercellular communication is an important feature in the development of multicellular organisms. Secreted hedgehog (hh) protein is essential for both long- and short-range cellular signaling required for body pattern formation in animals. In a molecular evolutionary study, we find that the vertebrate homologs of the Drosophila hh gene arose by two gene duplications: the first gave rise to Desert hh, whereas the second produced the Indian and Sonic hh genes. Both duplications occurred before the emergence of vertebrates and probably before the evolution of chordates. The amino-terminal fragment of the hh precursor, crucial in long- and short-range intercellular communication, evolves two to four times slower than the carboxyl-terminal fragment in both Drosophila hh and its vertebrate homologues, suggesting conservation of mechanism of hh action in animals. A majority of amino acid substitutions in the amino- and carboxyl-terminal fragments are conservative, but the carboxyl-terminal domain has undergone extensive insertion-deletion events while maintaining its autocleavage protease activity. Our results point to similarity of evolutionary constraints among sites of Drosophila and vertebrate hh homologs and suggest some future directions for understanding the role of hh genes in the evolution of developmental complexity in animals.     

Molecular Evolution of the Myeloperoxidase Family

Animal myeloperoxidase and its relatives constitute a diverse protein family, which includes myeloperoxidase, eosinophil peroxidase, thyroid peroxidase, salivary peroxidase, lactoperoxidase, ovoperoxidase, peroxidasin, peroxinectin, cyclooxygenase, and others. The members of this protein family share a catalytic domain of about 500 amino acid residues in length, although some members have distinctive mosaic structures. To investigate the evolution of the protein family, we performed a comparative analysis of its members, using the amino acid sequences and the coordinate data available today. The results obtained in this study are as follows: (1) 60 amino acid sequences belonging to this family were collected by database searching. We found a new member of the myeloperoxidase family derived from a bacterium. This is the first report of a bacterial member of this family. (2) An unrooted phylogenetic tree of the family was constructed according to the alignment. Considering the branching pattern in the obtained phylogenetic tree, together with the mosaic features in the primary structures, 60 members of the myeloperoxidase family were classified into 16 subfamilies. (3) We found two molecular features that distinguish cyclooxygenase from the other members of the protein family. (4) Several structurally deviated segments were identified by a structural comparison between cyclooxygenase and myeloperoxidase. Some of the segments seemed to be associated with the functional and/or structural differences between the enzymes. Received: 25 January 2000 / Accepted: 19 July 2000     

The Dynamics of Nestedness Predicts the Evolution of Industrial Ecosystems

In economic systems, the mix of products that countries make or export has been shown to be a strong leading indicator of economic growth. Hence, methods to characterize and predict the structure of the network connecting countries to the products that they export are relevant for understanding the dynamics of economic development. Here we study the presence and absence of industries in international and domestic economies and show that these networks are significantly nested. This means that the less filled rows and columns of these networks'' adjacency matrices tend to be subsets of the fuller rows and columns. Moreover, we show that their nestedness remains constant over time and that it is sustained by both, a bias for industries that deviate from the networks'' nestedness to disappear, and a bias for the industries that are missing according to nestedness to appear. This makes the appearance and disappearance of individual industries in each location predictable. We interpret the high level of nestedness observed in these networks in the context of the neutral model of development introduced by Hidalgo and Hausmann (2009). We show that the model can reproduce the high level of nestedness observed in these networks only when we assume a high level of heterogeneity in the distribution of capabilities available in countries and required by products. In the context of the neutral model, this implies that the high level of nestedness observed in these economic networks emerges as a combination of both, the complementarity of inputs and heterogeneity in the number of capabilities available in countries and required by products. The stability of nestedness in industrial ecosystems, and the predictability implied by it, demonstrates the importance of the study of network properties in the evolution of economic networks.     

The Evolution and Expression of the Moth Visual Opsin Family

Because visual genes likely evolved in response to their ambient photic environment, the dichotomy between closely related nocturnal moths and diurnal butterflies forms an ideal basis for investigating their evolution. To investigate whether the visual genes of moths are associated with nocturnal dim-light environments or not, we cloned long-wavelength (R), blue (B) and ultraviolet (UV) opsin genes from 12 species of wild-captured moths and examined their evolutionary functions. Strong purifying selection appeared to constrain the functions of the genes. Dark-treatment altered the levels of mRNA expression in Helicoverpa armigera such that R and UV opsins were up-regulated after dark-treatment, the latter faster than the former. In contrast, B opsins were not significantly up-regulated. Diel changes of opsin mRNA levels in both wild-captured and lab-reared individuals showed no significant fluctuation within the same group. However, the former group had significantly elevated levels of expression compared with the latter. Consequently, environmental conditions appeared to affect the patterns of expression. These findings and the proportional expression of opsins suggested that moths potentially possessed color vision and the visual system played a more important role in the ecology of moths than previously appreciated. This aspect did not differ much from that of diurnal butterflies.     

Evolution of the Australian flora through the Tertiary

The evolution of the Australian flora through the Tertiary has not been reviewed by a megafossil palaeobotanist for almost a century. Based on material available and published studies, the Australian Tertiary can be considered in three units: Eocene, Oligo-Miocene, and Pliocene. Key taxa in the Eocene includeCasuarinaceae, Proteaceae, Fagaceae, Podocarpaceae, andLauraceae. Many known Eocene deposits are interpreted as warm, humid rainforests.Oligo-Miocene floras reflect a climatic deterioration, with greater occurrence of sclerophylly and xerophylly. A reduction of tropical taxa is seen with an increase ofMyrtaceae and earliest records ofMimosaceae, Chenopodiaceae, andPoaceae. These trends continue into the Pliocene, which is not well represented in Australia.Problems needing to be addressed include the discrepancy between the pollen and megafossil records ofNothofagus, the origins of Australia's wet tropical taxa, and the role of fire in the early evolution of the Australian flora.     

The Evolution of the Calpain Family as Reflected in Paralogous Chromosome Regions

Calpains, the Ca²⁺-dependent intracellular proteinases, are involved in the regulation of distinct cellular pathways including signal transduction and processing, cytoskeleton dynamics, and muscle homeostasis. To investigate the evolutionary origin of diverse calpain subfamilies, a phylogenetic study was carried out. The topology of the calpain phylogenetic tree has shown that some of the gene duplications occurred before the divergence of the protostome and deuterostome lineages. Other gene doublings, leading to vertebrate-specific calpain forms, took place during early chordate evolution and coincided with genome duplications as disclosed by the localization of calpain genes to paralogous chromosome regions in the human genome. On the basis of the phylogenetic tree, the time of gene duplications, and the localization of calpain genes, we propose a model of tandem and chromosome duplications for the evolution of vertebrate-specific calpain forms. The data presented here are consistent with scenarios proposed for the evolution of other multigene families. Received: 17 November 1998 / Accepted: 30 April 1999     

Evolution of a Neuropeptide Family: Gonadotropin-Releasing Hormone

SYNOPSIS. Gonadotropin-releasing hormone (GnRH), a small peptidein the brain, is essential for reproduction. It is now clearthat GnRH is part of a family of closely related molecules.The primary structure has been identified for 4 GnRH molecules:mammalian, chicken I, chicken II and salmon. During evolutionthe molecule has been conserved in length, terminal amino acidstructure, 70–90% of amino acid sequence and the His²Trp³residues,residues, which are important in the release of gonadotropin.Alterations have occurred in positions 5, 7 and 8, regions thoughtto be involved in receptor binding. The receptors for GnRH haveapparently evolved also in that the mammalian and avian receptorsvary considerably in their ability to bind different GnRH molecules.Other GnRH family members have been distinguished indirectlyby chromatographic or immunological means; 3 different GnRH-likemolecules are present, respectively, in lamprey, sturgeon andsalmon (a second form). Several GnRH-like molecules includingthose in chondrichthyes have not yet been distinguished fromthe proposed salmon II molecule. The lamprey GnRH-like moleculemay be a nodal point inthe analysis of the ancestral molecule;hagfish do not contain a detectable GnRH molecule. The elucidationof the GnRH precursor molecule in human placenta showed thepresence of a 53-amino-acid gene-related peptide of unknownfunction, but did not reveal the basis for expression of multipleGnRH forms in many nonmammalian species. GnRH has a varietyof novel functions in addition to release of gonadotropin fromthe pituitary. During evolution certain functions such as thosein the retina and sympathetic ganglia have apparently disappearedin amniotes, but GnRH placental functions have appeared in mammals.     

The Dynamics of Sex Ratio Evolution: From the Gene Perspective to Multilevel Selection

The new dynamical game theoretic model of sex ratio evolution emphasizes the role of males as passive carriers of sex ratio genes. This shows inconsistency between population genetic models of sex ratio evolution and classical strategic models. In this work a novel technique of change of coordinates will be applied to the new model. This will reveal new aspects of the modelled phenomenon which cannot be shown or proven in the original formulation. The underlying goal is to describe the dynamics of selection of particular genes in the entire population, instead of in the same sex subpopulation, as in the previous paper and earlier population genetics approaches. This allows for analytical derivation of the unbiased strategic model from the model with rigorous non-simplified genetics. In effect, an alternative system of replicator equations is derived. It contains two subsystems: the first describes changes in gene frequencies (this is an alternative unbiased formalization of the Fisher-Dusing argument), whereas the second describes changes in the sex ratios in subpopulations of carriers of genes for each strategy. An intriguing analytical result of this work is that the fitness of a gene depends on the current sex ratio in the subpopulation of its carriers, not on the encoded individual strategy. Thus, the argument of the gene fitness function is not constant but is determined by the trajectory of the sex ratio among carriers of that gene. This aspect of the modelled phenomenon cannot be revealed by the static analysis. Dynamics of the sex ratio among gene carriers is driven by a dynamic “tug of war” between female carriers expressing the encoded strategic trait value and random partners of male carriers expressing the average population strategy (a primary sex ratio). This mechanism can be called “double-level selection”. Therefore, gene interest perspective leads to multi-level selection.     

The Molecular Evolution of the Pif Family Proteins in Various Species of Mollusks

Various novel proteins have been identified from many kinds of mollusk shells. Although such matrix proteins are believed to play important roles in the calcium carbonate crystal formation of shells, no common proteins that interact with calcium carbonate or that are involved in the molecular mechanisms behind shell formation have been identified. Pif consists of two proteins, Pif 80 and Pif 97, which are encoded by a single mRNA. Pif 80 was identified as a key acidic protein that regulates the formation of the nacreous layer in Pinctada fucata, while Pif 97 has von Willebrand factor type A (VWA) and chitin-binding domains. In this study, we identified Pif homologues from Pinctada margaritifera, Pinctada maxima, Pteria penguin, Mytilus galloprovincialis, and in the genome database of Lottia gigantea in order to compare their primary protein sequences. The VWA and chitin-binding domains are conserved in all Pif 97 homologues, whereas the amino acid sequences of the Pif 80 regions differ markedly among the species. Sequence alignment revealed the presence of a novel significantly conserved sequence between the chitin-binding domain and the C-terminus of Pif 97. Further examination of the Pif 80 regions suggested that they share a sequence that is similar to the laminin G domain. These results indicate that all Pif molecules in bivalves and gastropods may be derived from a common ancestral gene. These comparisons may shed light on the correlation between molecular evolution and morphology in mollusk shell microstructure.     

Evolution of the Relaxin/Insulin-like Gene Family in Placental Mammals: Implications for Its Early Evolution

The relaxin (RLN) and insulin-like (INSL) gene family is a group of genes involved in a variety of physiological roles that includes bone formation, testicular descent, trophoblast development, and cell differentiation. This family appears to have expanded in vertebrates relative to non-vertebrate chordates, but the relative contribution of whole genome duplications (WGDs) and tandem duplications to the observed diversity of genes is still an open question. Results from our comparative analyses favor a model of divergence post vertebrate WGDs in which a single-copy progenitor found in the last common ancestor of vertebrates experienced two rounds of WGDs before the functional differentiation that gave rise to the RLN and INSL genes. One of the resulting paralogs was subsequently lost, resulting in three proto-RLN/INSL genes on three separate chromosomes. Subsequent rounds of tandem gene duplication and divergence originated the set of paralogs found on a given cluster in extant vertebrates. Our study supports the hypothesis that differentiation of the RLN and INSL genes took place independently in each RLN/INSL cluster after the two WGDs during the evolutionary history of vertebrates. In addition, we show that INSL4 represents a relatively old gene that has been apparently lost independently in all Euarchontoglires other than apes and Old World monkeys, and that RLN2 derives from an ape-specific duplication.     

Stasis is an Inevitable Consequence of Every Successful Evolution

Evolutionary stasis is discussed in light of the idea that the common output of every successful evolution is the creation of the entities that are increasingly resistant to further change. The moving force of evolution is entropy. This general aspiration for chaos is a cause of the mortality of organisms and extinction of species. However, being a prerequisite for any motion, entropy generates (by chance) novelties, which may happen to be (by chance) more resistant to further decay and thus survive. The entities that change rapidly disappear. All existing entities are endowed with an ability to resist further change. In simple organisms, the stasis is primarily achieved by means of the high fidelity of DNA reproduction. In organisms with a large genome and complex development, the achievable fidelity of genome reproduction fails to guarantee homeorhetic reproduction: there is more mutation than reproduction. Such species must be capable of surviving and remain phenotypically unchanged at continuous changes of their genes. This capability (canalization or robustness) reflects a global degeneracy of the link structure-function: there are more genotypes than phenotypes. Hence, function (i.e. meaning), not structure, is selected. The selection for successful ontogenesis in a varying environment creates developmental robustness to mutational and environmental perturbations and, consequently, to the halt of evolution. Evolution is resistance to entropy, the adaptation to environment being only one of the means of this resistance. Everything essential in biology is determined not by physical causality but by semantic rules and goal-directed programs. This principal operates on various levels of biological organization.     

Mutation Rate Evolution in Replicator Dynamics

The mutation rate of an organism is itself evolvable. In stable environments, if faithful replication is costless, theory predicts that mutation rates will evolve to zero. However, positive mutation rates can evolve in novel or fluctuating environments, as analytical and empirical studies have shown. Previous work on this question has focused on environments that fluctuate independently of the evolving population. Here we consider fluctuations that arise from frequency-dependent selection in the evolving population itself. We investigate how the dynamics of competing traits can induce selective pressure on the rates of mutation between these traits. To address this question, we introduce a theoretical framework combining replicator dynamics and adaptive dynamics. We suppose that changes in mutation rates are rare, compared to changes in the traits under direct selection, so that the expected evolutionary trajectories of mutation rates can be obtained from analysis of pairwise competition between strains of different rates. Depending on the nature of frequency-dependent trait dynamics, we demonstrate three possible outcomes of this competition. First, if trait frequencies are at a mutation–selection equilibrium, lower mutation rates can displace higher ones. Second, if trait dynamics converge to a heteroclinic cycle—arising, for example, from “rock-paper-scissors” interactions—mutator strains succeed against non-mutators. Third, in cases where selection alone maintains all traits at positive frequencies, zero and nonzero mutation rates can coexist indefinitely. Our second result suggests that relatively high mutation rates may be observed for traits subject to cyclical frequency-dependent dynamics.