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PubMed2002

Testing the neutral theory of molecular evolution with genomic data from Drosophila.

Although positive selection has been detected in many genes, its overall contribution to protein evolution is debatable. If the bulk of molecular evolution is neutral, then the ratio of amino-acid (A) to synonymous (S) polymorphism should, on average, equal that of divergence. A comparison of the A/S ratio of polymorphism in Drosophila melanogaster with that of divergence from Drosophila simulans shows that the A/S ratio of divergence is twice as high---a difference that is often attributed to positive selection. But an increase in selective constraint owing to an increase in effective population size could also explain this observation, and, if so, all genes should be affected similarly. Here we show that the difference between polymorphism and divergence is limited to only a fraction of the genes, which are also evolving more rapidly, and this implies that positive selection is responsible. A higher A/S ratio of divergence than of polymorphism is also observed in other species, which suggests a rate of adaptive evolution that is far higher than permitted by the neutral theory of molecular evolution.

Animals↗

PubMed1995

Evolution of the rDNA spacer, ITS 2, in the ticks Ixodes scapularis and I. pacificus (Acari: Ixodidae).

Evolution of the rDNA spacer, ITS 2, is examined by comparing 17 DNA sequences of the ticks, Ixodes scapularis and I. pacificus. The distribution of fixed interspecific differences and the relative frequency of base changes vs. insertions/deletions (indels) matches the distribution and relative frequency for intraspecifically variable sites. This suggests that most intraspecific variation is not effectively selected against. The base composition of the ITS 2 transcript is G- and U-biased. But, 5-base regions enriched (> 80 per cent) for A or U occur more frequently than expected while G- and C-enriched regions occur less frequently than expected. Enriched sequences may be prone to replication slippage, accounting for the A/T bias in insertions. Slippage-mediated gains and losses of A/T-rich tandem repeats apparently account for most indels. Minimum-energy conformations of the two species' folded transcripts share major structural features. Structural inertia arises from intramolecular base pairing within stems that allows most mutations to be absorbed as new bulges off stems. Yet, there is evidence of selection to maintain the conformation. First, intraspecifically variable sites are concentrated at the ends of stems in loops and intersections, structures that do not contribute to intramolecular base pairing. Moreover, some indels that have become fixed in one species compensate for the presence of conformation-destabilizing indels. However, high rates of sequence evolution within stems and absence of compensatory base evolution contraindicates selective constraint. Degenerate dispersed and tandem copies of two subrepeats, each approximately 20 bases long, may account for much of the ITS 2 sequence. These are approximately inverses of each other and are, consequently, capable of significant intramolecular hydrogen bonding to produce folded transcripts of low energy. Evolution of the ITS 2 sequence may largely entail replication slippage-mediated gains and losses of these repeats or their composite subrepeats.

Animals↗

PubMed2002

Contemporary fisherian life-history evolution in small salmonid populations.

The relative importance of natural selection and random drift in phenotypic evolution has been discussed since the introduction of the first population genetic models. The empirical evidence used to evaluate the evolutionary theories of Fisher and Wright remains obscure because formal tests for neutral divergence or sensitive attempts to separate the effects of selection and drift are scarce, subject to error, and have not been interpreted in the light of well-known population demography. We combined quantitative genetic and microsatellite DNA analyses to investigate the determinants of contemporary life-history evolution in isolated populations of grayling (Thymallus thymallus, Salmonidae) that originated from a common source 80-120 years ago. Here we show that natural selection was the dominant diversifying agent in the evolution of the quantitative traits. However, the populations were founded by a small number of individuals, exhibit very low microsatellite-based effective sizes and show genetic imprints of severe 'bottlenecks'; which are conditions often suggested to constrain selection and favour drift. This study demonstrates a very clear case of fisherian evolution in small natural populations across a contemporary timescale.

Animals↗

PubMed2004

Population density drives the local evolution of a threshold dimorphism.

Evolution can favour more than one reproductive tactic among conspecifics of the same sex. Under the conditional evolutionarily stable strategy, individuals adopt the tactic that generates the highest fitness return for their status: large males guard females, whereas small males sneak copulations. Tactics change at the status at which fitness benefits switch from favouring one tactic to favouring the alternative. This 'switchpoint' is expressed in many species as a threshold between divergent morphologies. Environmental and demographic parameters that influence the relative fitness of male tactics are predicted to determine a population's switchpoint and consequently whether the population is monomorphic or dimorphic. Here we show threshold evolution in the forceps dimorphism of the European earwig Forficula auricularia and document the transition from completely monomorphic to classical male-dimorphic populations over a distance of only 40 km. Because the superior fighting ability of the dominant morph will be more frequently rewarded at high encounter rates, population density is likely to be a key determinant of the relative fitness of the alternative tactics, and consequently the threshold. We show that, as predicted, population density correlates strongly with the shift in threshold, and that this factor drives the local evolution of the male dimorphism in these island populations. Our data provide evidence for the origin of phenotypic diversity within populations, through the evolution of a switchpoint in a conditional strategy that has responded to local population density.

Animals↗

PubMed2003

Molecular evolution meets the genomics revolution.

Changes in technology in the past decade have had such an impact on the way that molecular evolution research is done that it is difficult now to imagine working in a world without genomics or the Internet. In 1992, GenBank was less than a hundredth of its current size and was updated every three months on a huge spool of tape. Homology searches took 30 minutes and rarely found a hit. Now it is difficult to find sequences with only a few homologs to use as examples for teaching bioinformatics. For molecular evolution researchers, the genomics revolution has showered us with raw data and the information revolution has given us the wherewithal to analyze it. In broad terms, the most significant outcome from these changes has been our newfound ability to examine the evolution of genomes as a whole, enabling us to infer genome-wide evolutionary patterns and to identify subsets of genes whose evolution has been in some way atypical.

Animals↗

PubMed1997

Male-driven evolution of DNA sequences in birds.

Assuming that new mutations arise mainly during DNA replication, sequence evolution in mammals has been seen as 'male driven' (ref. 1) because of the many more cell divisions in spermatogenesis than in oogenesis. Molecular support for this idea has been obtained from the observation of higher substitution rates in genes on the Y than on the X chromosome of primates and rodents, which are species with male heterogamety, but has not been confirmed by the reciprocal analysis of organisms with female heterogamety. The recent suggestion that an intrinsic reduction in the X-chromosome mutation rate may be confounded with male effects in previous comparisons, and the paradoxical finding of low levels of polymorphism on the primate Y chromosome indicate that the idea of male-biased mutation rate needs to be re-examined. We have analysed the molecular evolution of the gene CHD, which is present on the Z and W sex chromosomes of birds. The substitution rate at synonymous positions, as well as in intron DNA, was considerably higher on the Z chromosome than on the female-specific W chromosome, with an estimated male-to-female bias in mutation rate (alpha m) of 3.9-6.5. Thus, evolution appears to be male driven in birds--a situation that supports a neutral model of molecular evolution.

Animals↗

PubMed2004

Rate of molecular evolution of the seminal protein gene SEMG2 correlates with levels of female promiscuity.

Postcopulatory sperm competition is a key aspect of sexual selection and is believed to drive the rapid evolution of both reproductive physiology and reproduction-related genes. It is well-established that mating behavior determines the intensity of sperm competition, with polyandry (i.e., female promiscuity) leading to fiercer sperm competition than monandry. Studies in mammals, particularly primates, showed that, owing to greater sperm competition, polyandrous taxa generally have physiological traits that make them better adapted for fertilization than monandrous species, including bigger testes, larger seminal vesicles, higher sperm counts, richer mitochondrial loading in sperm and more prominent semen coagulation. Here, we show that the degree of polyandry can also impact the dynamics of molecular evolution. Specifically, we show that the evolution of SEMG2, the gene encoding semenogelin II, a main structural component of semen coagulum, is accelerated in polyandrous primates relative to monandrous primates. Our study showcases the intimate relationship between sexual selection and the molecular evolution of reproductive genes.

Animals↗

PubMed2006

The evolution of spliceosomal introns: patterns, puzzles and progress.

The origins and importance of spliceosomal introns comprise one of the longest-abiding mysteries of molecular evolution. Considerable debate remains over several aspects of the evolution of spliceosomal introns, including the timing of intron origin and proliferation, the mechanisms by which introns are lost and gained, and the forces that have shaped intron evolution. Recent important progress has been made in each of these areas. Patterns of intron-position correspondence between widely diverged eukaryotic species have provided insights into the origins of the vast differences in intron number between eukaryotic species, and studies of specific cases of intron loss and gain have led to progress in understanding the underlying molecular mechanisms and the forces that control intron evolution.

Animals↗

PubMed2026

Rapid and repeated evolution of increased competitive ability in a global invader.

Rapid adaptive evolution can increase the competitive ability of invasive species in their non-native ranges. However, whether this increase is a general response and what drives it remain uncertain because the evidence is largely based on studies with limited sampling, inadequate consideration of population co-ancestry, and oversimplified estimates of competitive ability. We conduct a large-scale glasshouse experiment testing the effects of competition and drought on 100 native and 165 non-native populations of Erigeron canadensis, all genotyped to account for co-ancestry. Plants from non-native populations are significantly more competitive against other species than the conspecifics from native populations under both mesic and dry conditions. Genetic clustering indicates that the rapid evolution of competitive ability occurs independently in two out of four clusters in the non-native range. This advantage is present only during interspecific interactions and is absent during intraspecific competition. Repeated evolution of increased competitive ability suggests that adaptation following introduction can reshape species interactions and promote invasion success, even under future drought conditions, highlighting the importance of rapid evolution in determining the ecological impacts of invasive plants.

Biological Evolution↗

PubMed2000

The evolution of haplodiploidy under inbreeding.

Although haplodiploid organisms tend to be inbred, previous models of the evolution of haplodiploidy have assumed outbred populations. Here a model for the evolution of haplodiploidy is developed which incorporates sib mating, deleterious mutations generated by mutation, and fitness differences between haploids and diploids. Simulations of the model allow an assessment of the effect of inbreeding on the deleterious mutation and maternal transmission theories for the evolution of haplodiploidy. As expected from intuitive arguments, inbreeding favours haplodiploidy under the deleterious mutation hypothesis but disfavours haplodiploidy under the maternal transmission hypothesis. It appears that the effect of inbreeding is greater on the maternal transmission theory, and thus inbreeding may restrict the evolution of haplodiploidy.

Animals↗

PubMed2002

Bacterial resistance evolution by recruitment of super-integron gene cassettes.

The capture and spread of antibiotic resistance determinants by integrons underlies the rapid evolution of multiple antibiotic resistance among diverse Gram-negative clinical isolates. The association of multiple resistance integrons (MRIs) with mobile DNA elements facilitates their transit across phylogenetic boundaries and augments the potential impact of integrons on bacterial evolution. Recently, ancestral chromosomal versions, the super-integrons (SIs), were found to be genuine components of the genomes of diverse bacterial species. SIs possess evolutionary characteristics and stockpiles of adaptive functions, including cassettes related to antibiotic resistance determinants previously characterized in clinical isolates, which suggest that MRIs and their resistance genes were originally recruited from SIs and their pool of amassed genes. However, the recombination activity of integrons has never been demonstrated in a bacterium other than Escherichia coli. We introduced a naturally occurring MRI (TpR, SulR) on a conjugative plasmid into Vibrio cholerae, a species known to harbour a SI. We show that MRIs can randomly recruit genes directly from the cache of SI cassettes. By applying a selective constraint for the development of antibiotic resistance, we demonstrate bacterial resistance evolution through the recruitment a novel, but phenotypically silent, chloramphenicol acetyltransferase gene from the V. cholerae SI and its precise insertion into the MRI. The resulting resistance profile (CmR, TpR, SulR) could then be disseminated by conjugation to other clinically relevant pathogens at high frequency. These results demonstrate that otherwise phenotypically sensitive strains may still be a genetic source for the evolution of resistance to clinically relevant antibiotics through integron-mediated recombination events.

Amino Acid Sequence↗

PubMed1995

Molecular evolution of plant beta-glucan endohydrolases.

The evolutionary relationships of two classes of plant beta-glucan endohydrolases have been examined by comparison of their substrate specificities, their three-dimensional conformations and the structural features of their corresponding genes. These comparative studies provide compelling evidence that the (1-->3)-beta-glucanases and (1-->3,1-->4)-beta-glucanases from higher plants share a common ancestry and, in all likelihood, that the (1-->3,1-->4)-beta-glucanases diverged from the (1-->3)-beta-glucanases during the appearance of the graminaceous monocotyledons. The evolution of (1-->3,1-->4)-beta-glucanases from (1-->3)-beta-glucanases does not appear to have invoked 'modular' mechanisms of change, such as those caused by exon shuffling or recombination. Instead, the shift in specificity has been acquired through a limited number of point mutations that have resulted in amino acid substitutions along the substrate-binding cleft. This is consistent with current theories that the evolution of new enzymic activity is often achieved through duplication of the gene encoding an existing enzyme which is capable of performing the required chemistry, in this case the hydrolysis of a glycosidic linkage, followed by the mutational alteration and fine-tuning of substrate specificity. The evolution of a new specificity has enabled a dramatic shift in the functional capabilities of the enzymes. (1-->3)-beta-Glucanases that play a major role, inter alia, in the protection of the plant against pathogenic microorganisms through their ability to hydrolyse the (1-->3)-beta-glucans of fungal cell walls, appear to have been recruited to generate (1-->3,1-->4)-beta-glucanases, which quite specifically hydrolyse plant cell wall (1-->3,1-->4)-beta-glucans in the graminaceous monocotyledons during normal wall metabolism. Thus, one class of beta-glucan endohydrolase can degrade beta-glucans in fungal walls, while the other hydrolyses structurally distinct beta-glucans of plant cell walls. Detailed information on the three-dimensional structures of the enzymes and the identification of catalytic amino acids now present opportunities to explore the precise molecular and atomic details of substrate-binding, catalytic mechanisms and the sequence of molecular events that resulted in the evolution of the substrate specificities of the two classes of enzyme.

Amino Acid Sequence↗

PubMedDate not supplied

The Evolution of Developmental Mechanisms. Proceedings of a symposium. London, United Kingdom, January 2001.

In 1829, von Baer proposed four principles of development, the first of which states that the embryos of a large group of animals have most in common at early stages of development, the specialised features of different subgroups only emerging later. After the publication of Darwin's The Origin of Species in 1859, the relevance of von Baer's principles to evolution was clear to many biologists, who assessed evolutionary relationships on the basis of similarities and differences between early embryos. The validity of these comparisons, carried out more than a century ago, has been confirmed by recent molecular analyses. These new gene-based comparisons have in turn led to a renewed interest in the scientific literature of the first half of the 20th century, which documented in great detail comparative anatomical studies of living and fossil animals. The past decade has seen a growing synergy between developmental biology and evolutionary studies. As a result, not only is an evolutionary perspective now integral to developmental studies, but palaeontologists have become deeply interested in embryos. This integration was the subject of the symposium of the Winter Meeting of the Anatomical Society, held in London in January 2001, entitled 'The Evolution of Developmental Mechanisms'. It was a very stimulating and enjoyable meeting that addressed the theme at a number of levels, ranging from the major evolutionary changes resulting from gene duplication to the fine detail of insect wing vein evolution. These two ends of the spectrum of topics reflect Darwin's perspective on von Baer's principles, i.e. his recognition that homologies between different phyla are to be seen in early embryonic and larval structures, while adaptations that enable an organism to survive in its particular environment are the result of changes acting late in development. The reviews brought together in this volume represent a thoughtful and thought-provoking synthesis of data collected over many years. They show the rewards of detailed and long-term study of embryos that in some cases are difficult to obtain, but represent living clues to the mechanisms underlying important evolutionary transitions. We feel privileged to have had the responsibility for editing this impressive issue of the Journal of Anatomy, which will, we have no doubt, be a significant landmark in the ongoing story of development and evolution, and will be widely cited.

Animals↗

PubMedDate not supplied

The scale independence of evolution.

In this paper, I argue that the ultimate causes of morphological, and hence developmental, evolution are scale independent. In other words, micro- and macroevolutionary patterns show fundamental similarities and therefore are most simply explained as being caused by the same kinds of evolutionary forces. I begin by examining the evolution of single lineages and argue that dynamics of adaptive evolution are the same for bacteria in test-tube evolution experiments and fossil lineages. Similarly, I argue that the essential features of adaptive radiations large and small can be attributed to conventional forces such as mutation and diversifying natural selection due to competition. I then address recent claims that the molecular features of metazoan development are the result of clade-level selection for evolvability, and suggest that these features can be more easily explained by conventional individual-level selection for the suppression of deleterious pleiotropic effects. Finally, I ask what must be known if we are to understand the ultimate causes of molecular and developmental diversity.

Biological Evolution↗

PubMedDate not supplied

Developmental genetics and arthropod evolution: part 1, on legs.

Developmental genetic information as it relates to the ontogeny of limbs can help evaluate various scenarios of arthropod evolution proposed in the past, as well as help frame other alternatives. First, the cascade of genetic expressions, which controls the development of the arthropod limb, suggests that a postulated evolution of the crustacean coxa from a proximal endite, a structure seen on certain Cambrian crustaceomorphs, might not be correct. Alternative hypotheses could explain the fossil anatomy, and the genetic patterns of expression demand that we at least be cautious in interpreting the Orsten material. Second, recognition of three distinct models of limb formation in arthropods would appear to preclude Rehbachiella, from the Cambrian Orsten, and Lepidocaris, from the Devonian Rhynie Chert, as members of the crown-group Branchiopoda. The recognition of a distinct Artemia Model of limb induction within living anostracans, notostracans, cladocerans, and conchostracans requires that such a model be part of the ground pattern of the Branchiopoda, a pattern that does not appear to have been possible in the fossil species. Finally, the suggestion that a large number of leg segments must be a plesiomorphic condition in arthropods should be considered cautiously. A sequential occurrence of mutations including, for example, a recessive loss-of-function mutant of a Hox-gene like Antennapedia could have resulted in the apomorphic evolution of long, multisegmented limbs within different groups of arthropods. The need for more comprehensive phylogenetic studies using as many taxa and characters possible is obvious both for the generation of scenarios of evolution, as well as in testing multiple alternative hypotheses of relationships.

Animals↗

PubMedDate not supplied

Starting from fins: parallelism in the evolution of limbs and genitalia: the fin-to-genitalia transition.

Organizers of the symposium Starting from Fins: Parallelism in the Evolution of Limbs and Genitalia intended it 1) to begin debates and discussions about parallelism, serial homology and transitions in development, as well as evolution of gene function and theories of origins and 2) to examine closely the potential significance of serial homology in understanding the evolution of morphology. This issue of Evolution and Development focuses on unpaired fin to genitalia transitions; the July-August issue will focus on paired fins to limbs, revisit the issues raised in the symposium, and point to future directions. Minelli's opening presentation introduced the central theme of the symposium by suggesting that body appendages such as arthropod and vertebrate limbs, chordate tails and external genitalia are evolutionarily divergent duplicates (paramorphs) of the main body axis. Suzuki's and Podlasek's presentations focused on the development of mammalian genitalia. Suzuki presented Suzuki et al investigations of the role of fibroblast growth factor (Fgf) and Sonic hedgehog (Shh) as signaling molecules during murine external genitalia formation, and Podlasek presented Podlasek et al investigations to elucidate a rudimentary pathway of essential developmental genes and transcriptional regulators such as Hox genes, Sonic hedgehog (Shh), and Bone morphogenetic proteins 2 and 4 (BMP-2; BMP-4), found in the limb. Discussions and questions emerging from the symposium point to the need to recognize that claims of phylogenetic cause must be based on something more than similarities; research must focus on the extent to which comparisons can be taken as well as on the evolutionary significance of similarities.

Animals↗

PubMedDate not supplied

Starting from fins: parallelism in the evolution of limbs and genitalia. The fin-to-limb transition.

The March/April 2002 issue of Evolution and Development focused on three presentations made at the Starting from Fins: Parallelism in the Evolution of Limbs and Genitalia symposium held as part of the 2001 Chicago meeting of the Society of Integrative and Comparative Biology. The intention of the symposium and the publication of the presentations was to extend discussion of the potential and the limits of using serial homologues to understand developmental aspects of morphological evolution. The March/April 2002 issue concentrated on unpaired fin to genitalia transitions. This issue focuses on paired fins to limbs and highlights the need for developmental data to be integrated with data from fossil materal, phylogenetic analysis, and explicitly comparative studies. Coates et al. use phylogenetic methods to explore the limb/fin characters of taxa, but their analysis departs somewhat from the usual in that the reference group for organisms includes sister group taxa not usually considered true tetrapods. They state that including finned taxa from the stem group permits an attempt to distinguish the primitive condition of the characteristics demonstrated by the crown group, that is, "limbed tetrapods." In focusing on limb characters specifically and including aspects of the appendicular girdles, Coates et al. highlight morphological details and trends within a given phylogeny. They also demonstrate the degree of relevance of limb characters during the establishment of lineages and their branching patterns by using only limb characters to generate a tree and use a direct comparison of serial versus special homologies to explore the degree of evolutionary parallelism between fore-and hindlimbs. The preliminary conclusions indicate a high level of independence between the serially homologous fore-and hindlimb. Innes et al. present outcomes from the use of cutting edge molecular genetic approaches to understand developmental aspects of limb morphology. In a manner conceptually similar to Coates et al.'s use of fossil characters, Innes et al. use the serial analysis of gene expression to sort differences from similarities in the gene expression profiles of fore-and hindlimbs of the same embryos. Although these gene expression pattems are likely to reflect the serial homology of the paired limbs, they are silent in terms of our understanding both the profound and subtle differences between fore- and hindlimbs in any given species. Innes et al. point out the volume of data generated by SAGE far exceeds our ability to interpret its biological meaning. The studies presented here and in the March/April issue are excellent examples of the need to interpret complex data in light of collective knowledge of evolutionary history. We hope the insights gained from the symposium and papers contribute to a dialogue on how to integrate different approaches and assist in moving forward the field of Evolution and Development.

Animals↗

PubMed2004

Type I MADS-box genes have experienced faster birth-and-death evolution than type II MADS-box genes in angiosperms.

Plant MADS-box genes form a large gene family for transcription factors and are involved in various aspects of developmental processes, including flower development. They are known to be subject to birth-and-death evolution, but the detailed features of this mode of evolution remain unclear. To have a deeper insight into the evolutionary pattern of this gene family, we enumerated all available functional and nonfunctional (pseudogene) MADS-box genes from the Arabidopsis and rice genomes. Plant MADS-box genes can be classified into types I and II genes on the basis of phylogenetic analysis. Conducting extensive homology search and phylogenetic analysis, we found 64 presumed functional and 37 nonfunctional type I genes and 43 presumed functional and 4 nonfunctional type II genes in Arabidopsis. We also found 24 presumed functional and 6 nonfunctional type I genes and 47 presumed functional and 1 nonfunctional type II genes in rice. Our phylogenetic analysis indicated there were at least about four to eight type I genes and approximately 15-20 type II genes in the most recent common ancestor of Arabidopsis and rice. It has also been suggested that type I genes have experienced a higher rate of birth-and-death evolution than type II genes in angiosperms. Furthermore, the higher rate of birth-and-death evolution in type I genes appeared partly due to a higher frequency of segmental gene duplication and weaker purifying selection in type I than in type II genes.

Arabidopsis↗