Multiple Evolutionary Pathways Research Articles

Comparative genomics in the Asteraceae reveals little evidence for parallel evolutionary change in invasive taxa.

Asteraceae, the largest family of flowering plants, has given rise to many notorious invasive species. Using publicly available transcriptome assemblies from 35 Asteraceae, including six major invasive species, we examined evidence for micro- and macro-evolutionary genomic changes associated with invasion. To detect episodes of positive selection repeated across multiple introductions, we conducted comparisons between native and introduced genotypes from six focal species and identified genes with elevated rates of amino acid change (dN/dS). We then looked for evidence of positive selection at a broader phylogenetic scale across all taxa. As invasive species may experience founder events during colonization and spread, we also looked for evidence of increased genetic load in introduced genotypes. We rarely found evidence for parallel changes in orthologous genes in the intraspecific comparisons, but in some cases we identified changes in members of the same gene family. Using among-species comparisons, we detected positive selection in 0.003-0.69% and 2.4-7.8% of the genes using site and stochastic branch-site models, respectively. These genes had diverse putative functions, including defence response, stress response and herbicide resistance, although there was no clear pattern in the GO terms. There was no indication that introduced genotypes have a higher proportion of deleterious alleles than native genotypes in the six focal species, suggesting multiple introductions and admixture mitigated the impact of drift. Our findings provide little evidence for common genomic responses in invasive taxa of the Asteraceae and hence suggest that multiple evolutionary pathways may lead to adaptation during introduction and spread in these species.

A DEEPSPITZERSURVEY OF CIRCUMSTELLAR DISKS IN THE YOUNG DOUBLE CLUSTER, h AND χ PERSEI

We analyze very deep IRAC and MIPS photometry of $\sim$ 12,500 members of the 14 Myr old Double Cluster, h and $\chi$ Persei, building upon on our earlier, shallower Spitzer studies (Currie et al. 2007a, 2008a). Numerous likely members show infrared (IR) excesses at 8 {\mu}m and 24 $\mu$m indicative of circumstellar dust. The frequency of stars with 8 $\mu$m excess is at least 2% for our entire sample, slightly lower (higher) for B/A stars (later type, lower-mass stars). Optical spectroscopy also identifies gas in about 2% of systems but with no clear trend between the presence of dust and gas. Spectral energy distribution (SED) modeling of 18 sources with detections at optical wavelengths through MIPS 24 $\mu m$ reveals a diverse set of disk evolutionary states, including a high fraction of transitional disks, although similar data for all disk-bearing members would provide better constraints. We combine our results with those for other young clusters to study the global evolution of dust/gas disks. For nominal cluster ages, the e-folding times ($\tau_{o}$) for the frequency of warm dust and gas are 2.75 Myr and 1.75 Myr respectively. Assuming a revised set of ages for some clusters (e.g. Bell et al. 2013), these timescales increase to 5.75 and 3.75 Myr, respectively, implying a significantly longer typical protoplanetary disk lifetime. The transitional disk duration, averaged over multiple evolutionary pathways, is $\sim$ 1 Myr. Finally, 24 $\mu$m excess frequencies for 4-6 M$_{\odot}$ stars appear lower than for 1-2.5 M$_{\odot}$ stars in other 10-30 Myr old clusters.

Evolution of the Genomic Landscape in Non-Small Cell Lung Cancer

ABSTRACT Aim: Few studies have investigated the clonal architecture of non-small cell lung cancer (NSCLC) and its evolution over time. With increasing evidence for the potential impact of intratumour heterogeneity (ITH) on clinical outcome, and its recognition as a driver of cancer progression, there is an unmet need to elicit the implications of ITH for biomarker validation, therapeutic response, and therefore survival. Methods: In a cohort of 11 primary NSCLC tumours, multi-region whole-exome sequencing at a mean depth of 214x was performed on a total of 37 tumour regions. Single nucleotide variants, indels and copy number data were identified using VarScan2 (v2.3.6). Non-silent mutations were validated using ultra-deep amplicon sequencing (mean depth 1189x). The subclonal composition of each tumor was used to construct phylogenetic trees. Candidate driver genes were selected by referencing large-scale lung cancer or pan-cancer sequencing studies, and the Catalogue of Somatic Mutations in Cancer (COSMIC) gene census. Results: ITH was evident in all tumours, with a median of 33% heterogeneous mutations (range 5–61%). Phylogenetic tree analysis revealed branched tumour evolution, with mutations in potential driver genes occurring both early (trunk) and late (branch). Thirty-five percent (range 8-67%) of mutations in potential driver genes were heterogeneous, and included TP53, EGFR, KRAS, BRAF, ALK and ROS1. Overall, heterogeneous non-silent somatic mutations and copy number aberrations occurred frequently. Conclusions: This study demonstrates spatial and temporal heterogeneity of both driver mutations and copy number events, suggesting that NSCLCs may follow multiple distinct evolutionary pathways simultaneously. Knowledge of these pathways may help identify novel therapeutic targets to improve clinical outcomes, and large-scale longitudinal genomic studies, such as TRACERx (TRAcking NSCLC Evolution through therapy (Rx), NCT01888601), may become a central component to the delivery of precision cancer medicine. Disclosure: All authors have declared no conflicts of interest.

Evolutionary implications of deception in mimicry and masquerade

Abstract Aggressive mimicry occurs when an organism resembles some aspect of another organism (the model) in order to obtain prey through its deceptive resemblance. This may function either through the overt response of the receiver or through the lack of response of the receiver. Reviewing selected examples, I discuss some of the difficulties in ascribing a model for the mimic. I also discuss how a single animal can have multiple ploys in its armoury of deceptive signals, thus belonging within two or more categories of deceptive signalling. In addition to aggressive mimicry, these may include crypsis or camouflage, masquerade (mimicry of inanimate objects), and Batesian or protective mimicry. Each of these examples of deception has multiple evolutionary pathways, and some deceptive signals may be more costly to receivers than others, but no single organism is subject to a single selection pressure, leading to the reality that many evolutionary pathways contribute to the diversity we see around us. New technologies are opening new channels of investigation into deceptive signaling in many different sensory modalities, and this is reflected in the recent increase in studies investigating the structure and function of deceptive signals. In turn, these studies are beginning to expose the fascinating complexity of deceptive signaling systems, allowing us to discover the myriad, non-mutually exclusive, solutions that can be selected for to obtain prey.

Are all red algal parasites cut from the same cloth?

Parasitism is a common life strategy throughout the eukaryotic tree of life. Many devastating human pathogens, including the causative agents of malaria and toxoplasmosis, have evolved from a photosynthetic ancestor. However, how an organism transitions from a photosynthetic to a parasitic life history strategy remains mostly unknown. This is largely because few systems present the opportunity to make meaningful comparisons between a parasite and a close free-living relative. Parasites have independently evolved dozens of times throughout the Florideophyceae (Rhodophyta), and often infect close relatives. The accepted evolutionary paradigm proposes that red algal parasites arise by first infecting a close relative and over time diversify and infect more distantly related species. This provides a natural evolutionary gradient of relationships between hosts and parasites that share a photosynthetic common ancestor. Elegant microscopic work in the late 20th century provided detailed insight into the infection cycle of red algal parasites and the cellular interactions between parasites and their hosts. Those studies led to the use of molecular work to further investigate the origins of the parasite organelles and reveal the evolutionary relationships between hosts and their parasites. Here we synthesize the research detailing the infection methods and cellular interactions between red algal parasites and their hosts. We offer an alternative hypothesis to the current dogma of red algal parasite evolution and propose that red algae can adopt a parasitic life strategy through multiple evolutionary pathways, including direct infection of distant relatives. Furthermore, we highlight potential directions for future research to further evaluate parasite evolution in red algae.

Ordering copy number alteration data to analyze colorectal cancer progression

Ordering copy number alteration data to analyze colorectal cancer progression

Biodiversity studies of myxomycetes in Madagascar

The results of the first comprehensive study of myxomycetes from the island of Madagascar, a world biodiversity hotspot, are reported in this paper. The island is of continental origin, the fourth largest in the world, and has been geographically isolated for more than 160 million years, since its separation from Gondwanaland. The isolation, size and topography of Madagascar have triggered the development of a great variety of different habitats and favoured multiple evolutionary pathways, resulting in many animals and plants that exist nowhere else on earth. Fieldwork for the biodiversity survey of the central and southern parts of the island took place in May 2009, to coincide with the end of the rainy season. Tropical moist forest, sclerophyll forest and dry forest were selected for sampling in Ranomafana, Andringitra, Andohahela and L’Isalo National Parks. Some unique vegetation was sampled in the spiny dry forest and succulent scrub with plants from the genera Alluaudia, Euphorbia, Kalanchoe and Pachypodium. The survey produced 124 species from 22 different genera in more than 750 myxomycete collections. In this paper one species, Perichaena madagascariensis, is described as new to science, 21 species are new records for Africa, and 106 are reported for the first time from Madagascar. Some unusual collections included Physarum lakhanpalii that appeared on Ravenala madagascariensis, Fuligo intermedia and Licea nannengae found on Adansonia grandidieri, Perichaena pulcherrima, Physarum dictyosporum, and P. echinosporum on Euphorbia and Licea rufocuprea on bark. The scope, methods and results of this survey are included in this paper, and comments are made on the ecology, distribution and substrate association of the myxomycetes of these areas of Madagascar. Macrographs, micrographs and SEM images of interesting species are included. The results indicate that the island of Madagascar has a unique assemblage of species of myxomycetes, different from neighbouring islands and from similar but distant environments.

Directed Evolution of Ionizing Radiation Resistance in Escherichia coli

We have generated extreme ionizing radiation resistance in a relatively sensitive bacterial species, Escherichia coli, by directed evolution. Four populations of Escherichia coli K-12 were derived independently from strain MG1655, with each specifically adapted to survive exposure to high doses of ionizing radiation. D(37) values for strains isolated from two of the populations approached that exhibited by Deinococcus radiodurans. Complete genomic sequencing was carried out on nine purified strains derived from these populations. Clear mutational patterns were observed that both pointed to key underlying mechanisms and guided further characterization of the strains. In these evolved populations, passive genomic protection is not in evidence. Instead, enhanced recombinational DNA repair makes a prominent but probably not exclusive contribution to genome reconstitution. Multiple genes, multiple alleles of some genes, multiple mechanisms, and multiple evolutionary pathways all play a role in the evolutionary acquisition of extreme radiation resistance. Several mutations in the recA gene and a deletion of the e14 prophage both demonstrably contribute to and partially explain the new phenotype. Mutations in additional components of the bacterial recombinational repair system and the replication restart primosome are also prominent, as are mutations in genes involved in cell division, protein turnover, and glutamate transport. At least some evolutionary pathways to extreme radiation resistance are constrained by the temporally ordered appearance of specific alleles.

Striking convergence in the mouthpart evolution of stream-living algae grazers

This scanning-electron microscopic study demonstrates the convergent evolution of the mouthparts of various herbivorous stream animals (insects from different orders, an isopod, snails, fish, and a tadpole) feeding on epilithic algal pastures. This food source is rich but is often difficult to harvest. Nevertheless, a large number of species can live on it because they have evolved highly specialized mouthparts. There are four functional problems that an algae grazer has to solve: the algae must be removed from the stone, they have to be collected and crushed, and a current shield is needed to prevent the water flow sweeping away the food. Among the 30 algae grazers examined in this study, a limited number of morphological solutions have been found for each of these adaptational problems. There are multiple evolutionary pathways for mouthpart adaptation and even closely related species have often evolved different types of tools for the same function. This refects the existence of a certain amount of evolutionary scope. Such freedom of evolution is present, however, only at the beginning of the adaptiogenesis of an algae grazer. Once one of the evolutionary pathways is taken, further improvement of the mouthparts is possible only by the refinement of the ‘chosen’ type of tools. The consequence of this is that a large number of astonishing convergences have occurred in algae grazers that have independently trodden the same evolutionary pathway.

EVOLUTION OF SEXUAL DICHROMATISM. 2. CAROTENOIDS AND MELANINS CONTRIBUTE TO SEXUAL DICHROMATISM IN NEW WORLD ORIOLES (ICTERUSSPP.)

Abstract Several recent studies have investigated how different proximate mechanisms of color production contribute to sexual dichromatism. These studies suggest that carotenoid pigments—which are frequently subject to sexual selection—are more strongly associated with sexual dichromatism than melanins. This reasoning implicitly assumes that increased male elaboration leads to sexual dichromatism. However, sexual dichromatism can be generated through multiple evolutionary pathways, including decreases in female elaboration. We examined whether evolutionary changes in carotenoid- and melanin-based plumage were correlated within New World orioles (Icterus spp.), a genus in which male elaboration is ancestral and only female elaboration varies. We found a significant correlation between evolutionary changes in the degree of carotenoid and eumelanin sexual dichromatism. These findings differ from those of previous comparative studies and suggest the possibility of interesting differences when different evolut...

MULTIPLE DIRECT TRANSITIONS FROM SEXUAL REPRODUCTION TO APOMICTIC PARTHENOGENESIS INTIMEMASTICK INSECTS

Transitions from sexual reproduction to parthenogenesis may occur along multiple evolutionary pathways and involve various cytological mechanisms to produce diploid eggs. Here, we investigate routes to parthenogenesis in Timema stick insects, a genus comprising five obligate parthenogens. By combining information from microsatellites and karyotypes with a previously published mitochondrial phylogeny, we show that all five parthenogens likely evolved spontaneously from sexually reproducing species, and that the sexual ancestor of one of the five parthenogens was probably of hybrid origin. The complete maintenance of heterozygosity between generations in the five parthenogens strongly suggests that eggs are produced by apomixis. Virgin females of the sexual species were also able to produce parthenogenetic offspring, but these females produced eggs by automixis. High heterozygosity levels stemming from conserved ancestral alleles in the parthenogens suggest, however, that automixis has not generated the current parthenogenetic Timema lineages but that apomixis appeared abruptly in several sexual species. A direct transition from sexual reproduction to (at least functional) apomixis results in a relatively high level of allelic diversity and high efficiency for parthenogenesis. Because both of these traits should positively affect the demographic success of asexual lineages, spontaneous apomixis may have contributed to the origin and maintenance of asexuality in Timema.

Comparative analysis of eight Arthrobacter plasmids

Despite the prevalence of Arthrobacter in the environment little is known about their plasmids, or the capacity of Arthrobacter plasmids to mediate horizontal gene transfer. In this study, we compared eight plasmids from five Arthrobacter strains in order to identify putative core maintenance genes for replication, segregation, and conjugation. Iteron like sequences were identified on some of the plasmids; however, no genes with obvious similarity to known replication sequences such as an origin of replication, or rep genes were identified. All eight plasmids contained a putative conjugation system. Genes with similarity to a relaxase, coupling protein, and various components of a type IV secretion system were identified on each plasmid; it appears that three different systems may be present. Putative parA partitioning genes were found in all of the plasmids. Each of the Arthrobacter strains examined contained a putative parB gene; however, of the three plasmids in Arthrobacter strain FB24 only one plasmid had a putative parB gene. Cluster analysis of many of the Arthrobacter genes suggested that they often formed branches within existing families of plasmid maintenance genes. Comparison of a concatenation of all the maintenance genes from each plasmid suggests that the eight Arthrobacter plasmids represent multiple evolutionary pathways.

Development of the supralaryngeal vocal tract in Japanese macaques: Implications for the evolution of the descent of the larynx

The configuration of the supralaryngeal vocal tract depends on the nonuniform growth of the oral and pharyngeal portion. The human pharynx develops to form a unique configuration, with the epiglottis losing contact with the velum. This configuration develops from the great descent of the larynx relative to the palate, which is accomplished through both the descent of the laryngeal skeleton relative to the hyoid and the descent of the hyoid relative to the palate. Chimpanzees show both processes of laryngeal descent, as in humans, but the evolutionary path before the divergence of the human and chimpanzee lineages is unclear. The development of laryngeal descent in six living Japanese macaque monkeys, Macaca fuscata, was examined monthly during the first three years of life using magnetic resonance imaging, to delineate the present or absence of these two processes and their contributions to the development of the pharyngeal topology. The macaque shows descent of the hyoid relative to the palate, but lacks the descent of the laryngeal skeleton relative to the hyoid and that of the EG from the VL. We argue that the former descent is simply a morphological consequence of mandibular growth and that the latter pair of descents arose in a common ancestor of extant hominoids. Thus, the evolutionary path of the great descent of the larynx is likely to be explained by a model comprising multiple and mosaic evolutionary pathways, wherein these developmental phenomena may have contributed secondarily to the faculty of speech in the human lineage.

Chromosomal abnormalities of adenocarcinoma of the pancreas: identifying early and late changes

The high level of karyotypic complexity found in epithelial neoplasms hinders the characterization of their cytogenetic evolution. Derivation of such pathways in adenocarcinoma of the pancreas has been particularly limited, because only a few pancreatic carcinomas are resected at an early stage of disease and so the number of primary carcinomas for which analysis of abnormal karyotypes has been reported is small. Here we report the clonal karyotypic abnormalities identified by G-banding analysis of 36 primary pancreatic carcinomas obtained from patients undergoing a Whipple resection with curative intent. The majority of the 36 carcinomas were diploid or triploid (33 of 36; 91%). Numerical alterations were found in all carcinomas for which a complete karyotype was determined. All the chromosomes were involved in gain, loss, or both gain and loss of the entire chromosome, in at least 8 and up to 28 of the carcinomas. Most commonly lost were chromosomes 18 (in 78% of the 36 carcinomas), 17 (56%), 6 (44%), 21 (42%), 22 (42%), Y (36%), and 4 (33%). Gain of chromosome 20 was observed in 10 of the 36 carcinomas. Structural abnormalities were common, resulting in partial chromosomal gains and losses, with a median number of 7 partial imbalances per carcinoma (range, 1–15). Sixteen carcinomas contained double-minute chromosomes, homogeneously staining regions, or both, indicating gene amplification. Pooling data for these 36 carcinomas with the primary carcinomas with karyotypes published in the Mitelman database ( http://cgap.nci.nih.gov/Chromosomes/Mitelman), we defined pathways of karyotypic evolution. The most frequent chromosomal imbalances were −18 (67.6%), −10 (34.3%), −4 (31.4%), +20 (31.4%), −15p (23.8%), −14p (22.9%), +2 (21.9%), −5 (21.9%), −13p (20%), +16 (20%), −21p (19%), −17p (19%), +1q (19.0%). Recurrent imbalances identified as occurring early were −1p, −15p, −18, −7q, −8p, −17p, and −5; late recurrent imbalances were +11q, +7q, +6p, −19p, and +2. In contrast to reports from similar analyses in other epithelial carcinomas, we did not find evidence for multiple karyotypic evolutionary pathways.

Diversity in structural ultraviolet coloration among female sulphur butterflies (Coliadinae, Pieridae)

In some species of sulphur butterflies (Pieridae: Coliadinae) females as well as males display bright structural reflectance on their dorsal wing surfaces, although comparatively little attention has been paid to this coloration in females. We examined the spectral properties of female dorsal coloration and scale structure in three species of sulphurs for which published images show bright UV reflectance in females: the Neotropical Anteos clorinde and two species of Indo-Australian Eurema, E. hecabe and E. candida. In A. clorinde and E. hecabe, female UV reflectance is iridescent and produced by thin film interference in a system of ridges and lamellae, as it is in conspecific males. Female A. clorinde exhibit the same spatial distribution and chromaticity of UV reflectance as seen in males, but the UV reflectance in female E. hecabe is much smaller in area compared to that of conspecific males and is both less bright and less chromatic than observed in males. In contrast, UV reflectance in E. candida females is diffuse, and arises from a lack of pterin pigments in the wings, which permits a broad-band scattered reflection to be seen. This is the mechanism that is known to produce bright UV reflectance in females of the confamilial whites. Our results highlight the diversity of UV reflectances and underlying mechanisms in sulphurs and suggest multiple evolutionary pathways leading to this diversity in female sulphur butterflies.

Learning Multiple Evolutionary Pathways from Cross-Sectional Data

We introduce a mixture model of trees to describe evolutionary processes that are characterized by the ordered accumulation of permanent genetic changes. The basic building block of the model is a directed weighted tree that generates a probability distribution on the set of all patterns of genetic events. We present an EM-like algorithm for learning a mixture model of K trees and show how to determine K with a maximum likelihood approach. As a case study, we consider the accumulation of mutations in the HIV-1 reverse transcriptase that are associated with drug resistance. The fitted model is statistically validated as a density estimator, and the stability of the model topology is analyzed. We obtain a generative probabilistic model for the development of drug resistance in HIV that agrees with biological knowledge. Further applications and extensions of the model are discussed.

Evolution of a unique Plasmodium falciparum chloroquine-resistance phenotype in association with pfcrt polymorphism in Papua New Guinea and South America.

The mechanistic basis for chloroquine resistance (CQR) in Plasmodium falciparum recently has been linked to the polymorphic gene pfcrt. Alleles associated with CQR in natural parasite isolates harbor threonine (T), as opposed to lysine (K) at amino acid 76. P. falciparum CQR strains of African and Southeast Asian origin carry pfcrt alleles encoding an amino acid haplotype of CVIET (residues 72-76), whereas most South American CQR strains studied carry an allele encoding an SVMNT haplotype; chloroquine-sensitive strains from malarious regions around the world carry a CVMNK haplotype. Upon investigating the origin of pfcrt alleles in Papua New Guinean (PNG) P. falciparum we found either the chloroquine-sensitive-associated CVMNK or CQR-associated SVMNT haplotypes previously seen in Brazilian isolates. Remarkably we did not find the CVIET haplotype observed in CQR strains from Southeast Asian regions more proximal to PNG. Further we found a previously undescribed CQR phenotype to be associated with the SVMNT haplotype from PNG and South America. This CQR phenotype is significantly less responsive to verapamil chemosensitization compared with the effect associated with the CVIET haplotype. Consistent with this, we observed that verapamil treatment of P. falciparum isolates carrying pfcrt SVMNT is associated with an attenuated increase in digestive vacuole pH relative to CVIET pfcrt-carrying isolates. These data suggest a key role for pH-dependent changes in hematin receptor concentration in the P. falciparum CQR mechanism. Our findings also suggest that P. falciparum CQR has arisen through multiple evolutionary pathways associated with pfcrt K76T.

EVOLUTIONARY TRADE-OFFS UNDER CONDITIONS OF RESOURCE ABUNDANCE AND SCARCITY: EXPERIMENTS WITH BACTERIA

It is often hypothesized that bacteria that are superior competitors when resources are abundant must be inferior competitors when resources are scarce, and vice versa. Most previous studies that sought to test this trade-off hypothesis compared kinetic parameters of extant strains of bacteria, with mixed results. We employed an experimental approach in which bacterial populations were propagated for many generations under two distinct regimes and their evolutionary responses were monitored. Thirty-six populations of bacteria were allowed to adapt evolutionarily to either abundant (batch culture) or scarce (chemostat culture) resource regimes. The competitive fitness of each derived line, relative to its ancestor, was then measured under both regimes. The trade-off hypothesis predicts that adaptation to either selective regime causes a concomitant loss of fitness under the alternative regime. Overall, our findings failed to support this hypothesis, and several cases contradict it. Only two derived lines showed clear trade-offs, having significantly adapted to the selective regime while becoming significantly less fit in the alternative regime. By contrast, five derived lines significantly improved in the alternative regime even as they adapted to their selective regime. Summing over all 36 derived lines (including those for which the observed fitness changes were nonsignificant under one or both regimes), 15 cases support the trade-off hypothesis, whereas 21 indicate the opposite result. These data therefore refute the necessity, or even general tendency, for evolutionary trade-offs in performance under conditions of resource abundance vs. scarcity. Instead, these data suggest that bacteria are able to adapt to a particular level of resource via multiple evolutionary pathways, which may produce either gains or losses in fitness at some different level of resource.

Evolutionary Trade-Offs under Conditions of Resource Abundance and Scarcity: Experiments with Bacteria

It is often hypothesized that bacteria that are superior competitors when resources are abundant must be inferior competitors when resources are scarce, and vice versa. Most previous studies that sought to test this trade-off hypothesis compared kinetic parameters of extant strains of bacteria, with mixed results. We employed an experimental approach in which bacterial populations were propagated for many generations under two distinct regimes and their evolutionary responses were monitored. Thirty-six populations of bacteria were allowed to adapt evolutionarily to either abundant (batch culture) or scarce (chemostat culture) resource regimes. The competitive fitness of each derived line, relative to its ancestor, was then measured under both regimes. The trade-off hypothesis predicts that adaptation to either selective regime causes a concomitant loss of fitness under the alternative regime. Overall, our findings failed to support this hypothesis, and several cases contradict it. Only two derived lines showed clear trade-offs, having significantly adapted to the selective regime while becoming significantly less fit in the alternative regime. By contrast, five derived lines significantly improved in the alternative regime even as they adapted to their selective regime. Summing over all 36 derived lines (including those for which the observed fitness changes were nonsignificant under one or both regimes), 15 cases support the trade-off hypothesis, whereas 21 indicate the opposite result. These data therefore refute the necessity, or even general tendency, for evolutionary trade-offs in performance under conditions of resource abundance vs. scarcity. Instead, these data suggest that bacteria are able to adapt to a particular level of resource via multiple evolutionary pathways, which may produce either gains or losses in fitness at some different level of resource.

Mechanism and evolution of protein dimerization.

We have investigated the mechanism and the evolutionary pathway of protein dimerization through analysis of experimental structures of dimers. We propose that the evolution of dimers may have multiple pathways, including (1) formation of a functional dimer directly without going through an ancestor monomer, (2) formation of a stable monomer as an intermediate followed by mutations of its surface residues, and (3), a domain swapping mechanism, replacing one segment in a monomer by an equivalent segment from an identical chain in the dimer. Some of the dimers which are governed by a domain swapping mechanism may have evolved at an earlier stage of evolution via the second mechanism. Here, we follow the theory that the kinetic pathway reflects the evolutionary pathway. We analyze the structure-kinetics-evolution relationship for a collection of symmetric homodimers classified into three groups: (1) 14 dimers, which were referred to as domain swapping dimers in the literature; (2) nine 2-state dimers, which have no measurable intermediates in equilibrium denaturation; and (3), eight 3-state dimers, which have stable intermediates in equilibrium denaturation. The analysis consists of the following stages: (i) The dimer is divided into two structural units, which have twofold symmetry. Each unit contains a contiguous segment from one polypeptide chain of the dimer, and its complementary contiguous segment from the other chain. (ii) The division is repeated progressively, with different combinations of the two segments in each unit. (iii) The coefficient of compactness is calculated for the units in all divisions. The coefficients obtained for different cuttings of a dimer form a compactness profile. The profile probes the structural organization of the two chains in a dimer and the stability of the monomeric state. We describe the features of the compactness profiles in each of the three dimer groups. The profiles identify the swapping segments in domain swapping dimers, and can usually predict whether a dimer has domain swapping. The kinetics of dimerization indicates that some dimers which have been assigned in the literature as domain swapping cases, dimerize through the 2-state kinetics, rather than through swapping segments of performed monomers. The compactness profiles indicate a wide spectrum in the kinetics of dimerization: dimers having no intermediate stable monomers; dimers having an intermediate with a stable monomer structure; and dimers having an intermediate with a stable structure in part of the monomer. These correspond to the multiple evolutionary pathways for dimer formation. The evolutionary mechanisms proposed here for dimers are applicable to other oligomers as well.