Short Evolutionary Timescales Research Articles

Molecular Evolution across the Asteraceae: Micro- and Macroevolutionary Processes

The Asteraceae (Compositae) is a large family of over 20,000 wild, weedy, and domesticated species that comprise approximately 10% of all angiosperms, including annual and perennial herbs, shrubs and trees, and species on every continent except Antarctica. As a result, the Asteraceae provide a unique opportunity to understand the evolutionary genomics of lineage radiation and diversification at numerous phylogenetic scales. Using publicly available expressed sequence tags from 22 species representing four of the major Asteraceae lineages, we assessed neutral and nonneutral evolutionary processes across this diverse plant family. We used bioinformatic tools to identify candidate genes under selection in each species. Evolution at silent and coding sites were assessed for different Gene Ontology functional categories to compare rates of evolution over both short and long evolutionary timescales. Our results indicate that patterns of molecular change across the family are surprisingly consistent on a macroevolutionary timescale and much more so more than would be predicted from the analysis of one (or many) examples of microevolution. These analyses also point to particular classes of genes that may be crucial in shaping the radiation of this diverse plant family. Similar analyses of nuclear and chloroplast genes in six other plant families confirm that many of these patterns are common features of the plant kingdom.

Molecular Evolution from AGB Stars to Planetary Nebulae

AbstractThe late stages of stellar evolution from the Asymptotic Giant Branch (AGB) to planetary nebulae represent the most active phase of molecular synthesis in a star's life. Over 60 molecular species, including inorganics, organics, radicals, chains, rings, and molecular ions have been detected in the circumstellar envelopes of evolved stars. Most interestingly, complex organic compounds of aromatic and aliphatic structures are synthesized over very short time intervals after the end of the AGB. Also appeared during the post-AGB evolution are the unidentified 21 and 30 μm emission features, which are believed to originate from carbonaceous compounds.The circumstellar environment is an ideal laboratory for the testing of theories of chemical synthesis. The distinct spectral behavior among AGB stars, proto-planetary nebulae (PPN), and planetary nebulae (PN) and the short evolutionary time scales that separate these stages pose severe constraints on models. In this paper, we will present an observational summary of the chemical synthesis in the late stages of stellar evolution, discuss chemical and physical processes at work, and speculate on the possible effects these chemical products have on the Galaxy and the Solar System.

Evolutionary Lability of Integration in Cambrian Ptychoparioid Trilobites

Phenotypic integration can influence evolutionary rate and direction by channeling variation into few dimensions. The extent to which that channeling serves as a constraint over macroevolutionary timescales is determined in part by the evolutionary lability of phenotypic integration. Evolutionary change in patterns of pleiotropy, potentially reducing that constraint, is thought to be more readily achieved when pleiotropy is structured by variation arising in parallel along different developmental pathways rather than by variation arising from direct interactions within and between those pathways. Herein we test two predictions that follow from that hypothesis: (1) that clades undergoing dramatic diversification are characterized by integration that is weakly influenced by direct interactions; and (2) that the structure of integration arising from direct interactions is more conservative than that arising from parallel variation. We examine integration of the cranidium of two Cambrian ptychoparioid trilobites, Crassifimbra walcotti and Eokochaspis nodosa, comparing them to each other and to a previously studied species, C.? metalaspis. Shape variation is decomposed into components representing variation among individuals and variation due to direct interactions. In all three species, variation among individuals was only weakly influenced by direct interactions, suggesting that integration was unlikely to have been a long-term constraint on the Cambrian diversification of ptychoparioids. Phenotypic integration of E. nodosa is no more similar than expected by chance to either Crassifimbra species, but the component due to direct interactions is more similar than expected by chance to that of C.? metalaspis. Conversely, the two Crassifimbra species are generally similar (although not identical) in phenotypic integration, but markedly differ in their structure of direct interactions. Integration arising from direct interactions was therefore not immune to restructuring over even short evolutionary timescales, and was not always more conservative than that arising from parallel variation.

Rapid Acquisition of Gigapascal-High-Pressure Resistance by Escherichia coli

Pressure and temperature are important environmental variables that influence living systems. However, while they vary over a considerable range on Earth and other planets, it has hardly been addressed how straightforwardly and to what extent cellular life can acquire resistance to extremes of these parameters within a defined genomic context and a limited number of generations. Nevertheless, this is a very pertinent question with respect to the penetration of life in allegedly inhospitable environments. In this study, directed evolution was used to reveal the potential of the nonsporulating and mesophilic model bacterium Escherichia coli to develop the ability to survive exposure to high temperature or pressure. While heat resistance could only marginally be increased, our data show that piezoresistance could readily and reproducibly be extended into the GPa range, thereby greatly exceeding the currently recognized maximum for growth or survival.

Studying the Evolution of Promoter Sequences: A Waiting Time Problem

To gain a better understanding of the evolutionary dynamics of regulatory DNA sequences, we address the following questions: (1) How long does it take until a given transcription factor (TF) binding site emerges at random in a promoter sequence? and (2) How does the composition of a TF binding site affect this waiting time? Using two different probabilistic models (an i.i.d. model and a neighbor dependent model), we can compute the expected waiting time for every k-mer, k ranging from 5 to 10, until it appears in a promoter of a species. Our findings indicate that new TF binding sites can be created on a short evolutionary time scale, i.e. in a time span below the speciation time of human and chimp. Furthermore, one can conclude that the composition of a TF binding site plays a crucial role concerning the waiting time until it appears and that the CpG methylation-deamination substitution process probably accelerates the creation of new TF binding sites. A screening of existing TF binding sites moreover reveals that k-mers predicted to have short waiting times occur more frequently than others. Supplementary Material is available at www.libertonline.com/cmb .

Sexual Dimorphism Increases Evolvability in a Genetic Regulatory Network

The majority of work on genetic regulatory networks has focused on environmental and mutational robustness, and much less attention has been paid to the conditions under which a network may produce an evolvable phenotype. Sexually dimorphic characters often show rapid rates of change over short evolutionary time scales and while this is thought to be due to the strength of sexual selection acting on the trait, a dimorphic character with an underlying pleiotropic architecture may also influence the evolution of the regulatory network that controls the character and affect evolvability. As evolvability indicates a capacity for phenotypic change and mutational robustness refers to a capacity for phenotypic stasis, increases in evolvability may show a negative relationship with mutational robustness. I tested this with a computational model of a genetic regulatory network and found that, contrary to expectation, sexually dimorphic characters exhibited both higher mutational robustness and higher evolvability. Decomposition of the results revealed that linkage disequilibrium within sex and linkage disequilibrium between sexes, two of the three primary components of additive genetic variance and evolvability in quantitative genetics models, contributed to the differences in evolvability between sexually dimorphic and monomorphic populations. These results indicate that producing two pleiotropically linked characters did not constrain either the production of a robust phenotype or adaptive potential. Instead, the genetic system evolved to maximize both quantities.

Genetic Diversity within the Japanese Badgers (Meles anakuma), as Revealed by Microsatellite Analysis

To further understand the population structures of the Japanese badgers (Meles anakuma) on the Japanese islands, we analyzed their bi-parentally inherited microsatellites. Based on genotypes of nine microsatellite loci, the badgers were divided into five discrete clusters: three clusters from the Honshu Island, one from Kyushu and one from Shikoku. We propose that this genetic differentiation among badgers from the Honshu, Shikoku and Kyushu Islands is as a consequence of geographical isolation caused by the Seto Inland Sea. Furthermore, the cluster containing individuals from Shikoku was more differentiated from the other clusters, plausibly attributable to the earlier geological separation of the Shikoku Island from the Honshu and Kyushu Islands. The three clusters in Honshu, however, did not correspond precisely with geographical locations. As indicated in previous studies, based on mitochondrial DNA analysis, the genetic relationships within the Japanese badgers might reflect recent population expansion, occurring over a relatively short evolutionary time-scale. The findings preliminarily indicate that the Japanese badgers do not possess the high levels of philopatry seen in the European badger (Meles meles), a closely related species, although further analyses using balanced sample sizes from a wider range is required.

Recent speciation associated with the evolution of selfing inCapsella

The evolution from outcrossing to predominant self-fertilization represents one of the most common transitions in flowering plant evolution. This shift in mating system is almost universally associated with the "selfing syndrome," characterized by marked reduction in flower size and a breakdown of the morphological and genetic mechanisms that prevent self-fertilization. In general, the timescale in which these transitions occur, and the evolutionary dynamics associated with the evolution of the selfing syndrome are poorly known. We investigated the origin and evolution of selfing in the annual plant Capsella rubella from its self-incompatible, outcrossing progenitor Capsella grandiflora by characterizing multilocus patterns of DNA sequence variation at nuclear genes. We estimate that the transition to selfing and subsequent geographic expansion have taken place during the past 20,000 years. This transition was probably associated with a shift from stable equilibrium toward a near-complete population bottleneck causing a major reduction in effective population size. The timing and severe founder event support the hypothesis that selfing was favored during colonization as new habitats emerged after the last glaciation and the expansion of agriculture. These results suggest that natural selection for reproductive assurance can lead to major morphological evolution and speciation on relatively short evolutionary timescales.

Distant horizontal gene transfer is rare for multiple families of prokaryotic insertion sequences

Horizontal gene transfer in prokaryotes is rampant on short and intermediate evolutionary time scales. It poses a fundamental problem to our ability to reconstruct the evolutionary tree of life. Is it also frequent over long evolutionary distances? To address this question, we analyzed the evolution of 2,091 insertion sequences from all 20 major families in 438 completely sequenced prokaryotic genomes. Specifically, we mapped insertion sequence occurrence on a 16S rDNA tree of the genomes we analyzed, and we also constructed phylogenetic trees of the insertion sequence transposase coding sequences. We found only 30 cases of likely horizontal transfer among distantly related prokaryotic clades. Most of these horizontal transfer events are ancient. Only seven events are recent. Almost all of these transfer events occur between pairs of human pathogens or commensals. If true also for other, non-mobile DNA, the rarity of distant horizontal transfer increases the odds of reliable phylogenetic inference from sequence data.

The core endodermal gene network of vertebrates: combining developmental precision with evolutionary flexibility

Embryonic development combines paradoxical properties: it has great precision, it is usually conducted at breakneck speed and it is flexible on relatively short evolutionary time scales, particularly at early stages. While these features appear mutually exclusive, we consider how they may be reconciled by the properties of key early regulatory networks. We illustrate these ideas with the network that controls development of endoderm progenitors. We argue that this network enables precision because of its intrinsic stability, self propagation and dependence on signalling. The network enables high developmental speed because it is rapidly established by maternal inputs at multiple points. In turn these properties confer flexibility on an evolutionary time scale because they can be initiated in many ways, while buffering essential progenitor cell populations against changes in their embryonic environment on both evolutionary and developmental time scales. Although stable, these networks must be capable of rapid dissolution as cell differentiation progresses. While we focus on the core early endodermal network of vertebrates, we argue that these properties are likely to be general in early embryonic stem cell populations, such as mammalian ES cells.

EVOLUTION OF THE GENOMIC RATE OF RECOMBINATION IN MAMMALS

Rates of recombination vary considerably between species. Despite the significance of this observation for evolutionary biology and genetics, the evolutionary mechanisms that contribute to these interspecific differences are unclear. On fine physical scales, recombination rates appear to evolve rapidly between closely related species, but the mode and tempo of recombination rate evolution on the broader scale is poorly understood. Here, we use phylogenetic comparative methods to begin to characterize the evolutionary processes underlying average genomic recombination rates in mammals. We document a strong phylogenetic effect in recombination rates, indicating that more closely related species tend to have more similar average rates of recombination. We demonstrate that this phylogenetic signal is not an artifact of errors in recombination rate estimation and show that it is robust to uncertainty in the mammalian phylogeny. Neutral evolutionary models present good fits to the data and we find no evidence for heterogeneity in the rate of evolution in recombination across the mammalian tree. These results suggest that observed interspecific variation in average genomic rates of recombination is largely attributable to the steady accumulation of neutral mutations over evolutionary time. Although single recombination hotspots may live and die on short evolutionary time scales, the strong phylogenetic signal in genomic recombination rates indicates that the pace of evolution on this scale may be considerably slower.

Recombination diversifies chloroplast trnF pseudogenes in Arabidopsis lyrata

Extensive intraspecific variation in the chloroplast trnL(UAA)-trnF(GAA) spacer of model plant Arabidopsis lyrata is caused by multiple copies of a tandemly repeated trnF pseudogene undergoing parallel independent changes in copy number. Linkage disequilibrium and secondary structure analyses indicate that the diversification of pseudogene copies is driven by complex processes of structurally mediated illegitimate recombination. Disperse repeats sharing similar secondary structures interact, facilitating reciprocal exchange of structural motifs between copies via intramolecular and intermolecular recombinations, forming chimeric sequences and iterative expansion and contraction in pseudogene copy numbers. Widely held assumptions that chloroplast sequence evolution is simple and structural changes are informative are violated. Our findings have important implications for the use of this highly variable region in Brassicaceae studies. The reticulate evolution and nonindependent nucleotide substitution render the pseudogene inappropriate for standard phylogenetic reconstruction, but over short evolutionary timescales they may be useful for assessing gene flow, hybridization and introgression.

Ventral coloration differentiation and mitochondrial sequences of the Chinese Cobra (Naja atra) in Taiwan

Differences in coloration between eastern and western populations of the Chinese cobra (Naja atra) in Taiwan have been noted by snake collectors, snake keepers, and users of Chinese traditional medicine, but have never been verified by scientific research. In this study, we quantified the amount of black pigment on ventral scales, and found prominent differences in ventral coloration of populations across Taiwan; populations in eastern Taiwan have black ventral scales while populations in the west are predominantly white. Previous studies have shown a similar east-west population differentiation in regards to venom components. We supplement these data with mitochondrial control region sequences, which show extremely low nucleotide diversity. Black-ventral and white-ventral snakes share major haplotypes and show no genetic differentiation. Nevertheless, moderate Fst and low Nm values between populations indicate low levels of gene flow. With a morphological fixation earlier than mitochondrial sequences on a relatively short evolutionary time scale, ventral coloration is potentially a result of local adaptation. Based upon the results of this study, along with traditional observations, we strongly recommend treating each of the four populations of the Chinese cobra in Taiwan as distinct ESUs. Reintroducing confiscated snakes from the illegal trade back into the wild needs to be halted to prevent artifical gene flow.

Genetically idiosyncratic responses of Drosophila melanogaster populations to selection for improved learning ability

To what extent is adaptive evolution over short timescales repeatable? To address this question, we studied the performance of crosses between replicate Drosophila melanogaster lines previously subject to selection for improved learning response in the context of oviposition substrate choice. Of the 10 pairwise F1 crosses among the five selection lines, four performed in the original learning assay similarly to the parental lines, whereas the remaining six showed learning scores significantly below the average of the parental lines. In particular, four F1 crosses (three involving the same line) showed no detectable learning, on a par with unselected control lines. This indicates that the response to selection in some lines involved allelic substitutions at different loci. Additional assays of crosses between two selection lines indicated that the loss of performance in hybrids generalized to another type of learning assay, and held for both short- and long-term memory. Joint analysis of first- and second-generation crosses between these two lines supported the hypothesis that the response to selection in these different lines was based on the spread of recessive alleles at different loci. These results show that the evolutionary trajectories of populations of the same origin subject to uniform selection may sometimes diverge over very short evolutionary timescales.

Co-evolution of transcription factors and their targets depends on mode of regulation

Analysis of transcription regulatory networks in γ-proteobacteria reveals that repressors co-evolve tightly with their target genes, whereas activators can be lost independently of their targets.

Bacterial genome size reduction by experimental evolution

Bacterial evolution toward endosymbiosis with eukaryotic cells is associated with extensive bacterial genome reduction and loss of metabolic and regulatory capabilities. Here we examined the rate and process of genome reduction in the bacterium Salmonella enterica by a serial passage experimental evolution procedure. The initial rate of DNA loss was estimated to be 0.05 bp per chromosome per generation for a WT bacterium and approximately 50-fold higher for a mutS mutant defective in methyl-directed DNA mismatch repair. The endpoints were identified for seven chromosomal deletions isolated during serial passage and in two separate genetic selections. Deletions ranged in size from 1 to 202 kb, and most of them were not associated with DNA repeats, indicating that they were formed via RecA-independent recombination events. These results suggest that extensive genome reduction can occur on a short evolutionary time scale and that RecA-dependent homologous recombination only plays a limited role in this process of jettisoning superfluous DNA.

Past and Future Evolution of Sakurai's Object

We present a stellar evolution model sequence of the past and future evolution of the post-AGB born again star Sakurai's object (V 4334 Sgr). In order to match the short evolutionary time scale we have to assume that the convective ingestion of hydrogen-rich envelope material into the He-flash convection zone proceeds slower than predicted by the mixing length theory. For the future we predict a swift second evolution through the central star region before a second born-again evolution occurs.

Formation of Mildly Recycled Low‐Mass Binary Pulsars from Intermediate‐Mass X‐Ray Binaries

Binary and millisecond pulsars (BMSPs) with He white dwarf companions are generally thought to be recycled in low-mass X-ray binaries (LMXBs). Here we investigate the formation of three recently discovered binary pulsars: PSRs J1232-6501, J1810-2005, and J1904+0412. These pulsars are in circular orbits with low-mass white dwarf companions, but their spin periods and period derivatives are considerably larger than that of most BMSPs. It has been suggested that these mildly recycled pulsars are descendants of intermediate-mass X-ray binaries (IMXBs), in which, due to higher mass transfer rates and shorter evolutionary timescales, smaller amounts of mass may be accreted by the neutron stars than in LMXBs. As a demonstration, we calculate the evolution of the possible IMXB progenitor system: a binary consisting of a 1.3 M☉ neutron star and a 3.0 M☉ main-sequence star. The results show that after a short, rapid mass transfer phase, the binary evolves into an LMXB, with nearly all of the transferred mass accreted by the neutron star. Thus, low-mass binary pulsars born in this way should have masses (and hence spin periods and magnetic fields) comparable to those from LMXBs. To account for the discrepancy between the mildly recycled pulsars and BMSPs, we suggest that the accretion disks in some IMXBs may suffer thermal-viscous instability when they evolve to low-mass systems and the mass transfer rate declines. This may greatly reduce the active X-ray time and the amount of mass transferred onto the neutron stars and help alleviate the LMXB-BMSP birthrate problem.

How do chromosomal changes fit in?

11 review on the process of speciation brings to my mind several comments that I would like to make as to what is accomplished by the approach he advocates. 11 proposal is to update the biological species concept (BSC) by in fact revising what he considers as a consensual notion of reproductive isolation (RI), i.e. complete reproductive isolation. Many interpretations exist of the BSC and I am not convinced that the adherence to this particular definition has been as strict among biologists as 11 contends. It is clear that few biologists would argue against the designation of taxa as species when they occur in sympatry and between which the barrier to gene exchange is absolute. But, as this is an end product in the process of speciation, it does not tell us much about how the process originated. That incipient species can and do exchange genes is evident from the numerous studies on hybrid zones and examples of horizontal transfer through introgression between what appear to be full-fledged species (5; 4). However, 11 strongest contribution is to provide a conceptual framework of the process of speciation based on a mosaic nature of incipient species genomes, although the task is no less arduous experimentally. This should spur additional empirical and theoretical studies on gene flow taking into account the selective differential in permeability of genomes. 11 wishes to refocus the concept of speciation away from RI and onto the process of differential adaptation. In doing so, I find his argumentation sometimes confusing leading to statements such as ‘…the very essence (of speciation) does not have to include RI…’ (p. 8). In fact, implicit in his definition of species is that they are differentially adapted groups that upon contact are not able to share genes controlling the adaptive characters. Given this, how will they maintain this divergence if not by a barrier to gene exchange? The extensive discussion on the nature of the barrier to gene exchange in 11 paper is worthwhile, in that it emphasizes the shift in focus that has occurred in recent studies from models of speciation by mutation and drift to those analysing the contribution of differential adaptative traits to RI. However, a potential drawback of this shift in emphasis as argued by 11 may be the setting aside of the role of chromosomal rearrangements in reducing gene flow. This issue is somewhat dodged with an analogy dealing with the status of lineages differing solely by the presence a toxin gene and its repressor in one and their absence in the other, leading to hybrid inviability of their progeny. What then of karyotypically divergent taxa such as the chromosomal races of the house mouse, the interbreeding between at least some of which can produce sterile hybrids (6; 2). It is evident as stated by 11 that the study of RI and its consequences are required to assess the extent of the barrier to gene exchange, and this applies to this case as well. However, these chromosomal races clearly illustrate three aspects of karyotypic change: (i) chromosomal divergence can have an effect on hybrid fertility and thus on the extent of gene flow, (ii) this type of change can occur very rapidly over a short evolutionary time scale, and (iii) it is not genic, which means that it would have been completely overlooked in any gene-based study of reproductive isolation. The point I would like to make is that this type of change exists and may have consequences for the rates of evolutionary pathways to speciation. Because this process includes RI leading to differential adaptation which 11 wishes to de-emphasize, does not mean that it should be minimized as a field of research. Although the emphasis has moved away from models of chromosomal speciation as expounded by 10, interest in the consequences of chromosomal change as a barrier to gene flow has been renewed by the exciting studies on sunflowers and Drosophila (9; Noor et al., 2001). Such analyses argue for a role of chromosomal rearrangements in reducing gene flow through suppression of recombination (see 8). When linked to some chromosomal rearrangements, isolation genes decrease gene flow in larger regions of the genome than in those where the former are absent. Although additional data are required to assess the relative importance of this role of chromosomal rearrangements, these results are totally germane to the mosaic genome view of species of 11. Who knows, future research in this field may even indicate that rearrangements are isolating mechanisms in the sense that they would be selected for by their effect on recombination, or that they are adaptive traits in that a change in structure may modify gene expression during interphase (3; 1; 8).

Evolutionary adaptations of cochlear function in Jamaican mormoopid bats

Mormoopid bat species have their echolocation system adapted to different hunting strategies. To study the corresponding mechanical properties of their inner ear, we measured distortion-product otoacoustic emissions to assess cochlear sensitivity and tuning. Mormoops blainvillii, Pteronotus macleayii and P. quadridens use frequency-modulated echolocation signals, sometimes preceded by a short narrowband signal component. Their distortion-product otoacoustic emission-threshold curves are most sensitive between 30 and 50 kHz and show no adaptation to the narrowband echolocation components. In contrast, the constant-frequency bat P. parnellii always uses long constant-frequency call components. Its inner ear is maximally sensitive at 62 kHz, the echo-frequency of the dominant constant-frequency component, and pronounced insensitivities at 61 and 93 kHz (CF2 and CF3 call frequency) are the major evolutionary change in comparison to its relatives. Furthermore, in P. parnellii, the optimum cochlear frequency separation is minimal at 62 and 93 kHz, associated with enhanced cochlear tuning, while for the other mormoopids there is no indication of enhanced tuning. The phylogeny of mormoopids, assessed by mitochondrial DNA analysis, shows a close relationship between the Pteronotus species. This suggests that major cochlear redesign, associated with the acquisition of echolocation-call specific cochlear processing in P. parnellii, has occurred within a relatively short evolutionary time scale.