Past Evolutionary History Research Articles

Distinguishing Cophylogenetic Signal from Phylogenetic Congruence Clarifies the Interplay Between Evolutionary History and Species Interactions.

Interspecific interactions, including host-symbiont associations, can profoundly affect the evolution of the interacting species. Given the phylogenies of host and symbiont clades and knowledge of which host species interact with which symbiont, two questions are often asked: "Do closely related hosts interact with closely related symbionts?" and "Do host and symbiont phylogenies mirror one another?." These questions are intertwined and can even collapse under specific situations, such that they are often confused one with the other. However, in most situations, a positive answer to the first question, hereafter referred to as "cophylogenetic signal," does not imply a close match between the host and symbiont phylogenies. It suggests only that past evolutionary history has contributed to shaping present-day interactions, which can arise, for example, through present-day trait matching, or from a single ancient vicariance event that increases the probability that closely related species overlap geographically. A positive answer to the second, referred to as "phylogenetic congruence," is more restrictive as it suggests a close match between the two phylogenies, which may happen, for example, if symbiont diversification tracks host diversification or if the diversifications of the two clades were subject to the same succession of vicariance events. Here we apply a set of methods (ParaFit, PACo, and eMPRess), whose significance is often interpreted as evidence for phylogenetic congruence, to simulations under 3 biologically realistic scenarios of trait matching, a single ancient vicariance event, and phylogenetic tracking with frequent cospeciation events. The latter is the only scenario that generates phylogenetic congruence, whereas the first 2 generate a cophylogenetic signal in the absence of phylogenetic congruence. We find that tests of global-fit methods (ParaFit and PACo) are significant under the 3 scenarios, whereas tests of event-based methods (eMPRess) are only significant under the scenario of phylogenetic tracking. Therefore, significant results from global-fit methods should be interpreted in terms of cophylogenetic signal and not phylogenetic congruence; such significant results can arise under scenarios when hosts and symbionts had independent evolutionary histories. Conversely, significant results from event-based methods suggest a strong form of dependency between hosts and symbionts evolutionary histories. Clarifying the patterns detected by different cophylogenetic methods is key to understanding how interspecific interactions shape and are shaped by evolution.

ConDoR: tumor phylogeny inference with a copy-number constrained mutation loss model

A tumor contains a diverse collection of somatic mutations that reflect its past evolutionary history and that range in scale from single nucleotide variants (SNVs) to large-scale copy-number aberrations (CNAs). However, no current single-cell DNA sequencing (scDNA-seq) technology produces accurate measurements of both SNVs and CNAs, complicating the inference of tumor phylogenies. We introduce a new evolutionary model, the constrainedk-Dollo model, that uses SNVs as phylogenetic markers but constrains losses of SNVs according to clusters of cells. We derive an algorithm, ConDoR, that infers phylogenies from targeted scDNA-seq data using this model. We demonstrate the advantages of ConDoR on simulated and real scDNA-seq data.

Preceding Host History of Conjugative Resistance Plasmids Affects Intra- and Interspecific Transfer Potential from Biofilm.

Conjugative plasmids can confer antimicrobial resistance (AMR) to their host bacterium. The plasmids disperse even between distantly related host species, rescuing the host from otherwise detrimental effects of antibiotics. Little is known about the role of these plasmids in the spread of AMR during antibiotic treatment. One unstudied question is whether the past evolutionary history of a plasmid in a particular species creates host specificity in its rescue potential or if interspecific coevolution can improve interspecific rescues. To study this, we coevolved the plasmid RP4 under three different host settings; solely Escherichia coli or Klebsiella pneumoniae, or alternating between both of them. The ability of evolved plasmids in bacterial biofilm to rescue susceptible planktonic host bacteria of either the same or different species during beta-lactam treatment was tested. The interspecific coevolution seemed to decrease rescue potential for the RP4 plasmid, while the K. pneumoniae evolved plasmid became more host specific. Large deletion in the region encoding the mating pair formation (Tra2) apparatus was detected in the plasmids evolved with K. pneumoniae. This adaptation resulted in the exapted evolution of resistance against a plasmid-dependent bacteriophage PRD1. Further, previous studies have suggested that mutations in this region completely abolish the plasmid's ability to conjugate; however, our study shows it is not essential for conjugation but rather affects the host-specific conjugation efficiency. Overall, the results suggest that previous evolutionary history can result in the separation of host-specific plasmid lineages that may be further amplified by unselected exaptations such as phage resistance. IMPORTANCE Antimicrobial resistance (AMR) is a major global public health threat which can rapidly spread in microbial communities via conjugative plasmids. Here, we advance with evolutionary rescue via conjugation in a more natural setting, namely, biofilm, and incorporate a broad-host range plasmid RP4 to test whether intra- and interspecific host histories affect its transfer potential. Escherichia coli and Klebsiella pneumoniae hosts were seen to elicit different evolutionary influences on the RP4 plasmid, leading to clear differences in the rescue potential and underlining the significant role of the plasmid-host interactions in the spread of AMR. We also contradicted previous reports that established certain conjugal transfer genes of RP4 as essential. This work enhances the understanding of how plasmid host range evolve in different host settings and further, the potential effects it may have on the horizontal spread of AMR in complex environments such as biofilms.

Detecting Local Adaptation between North and South European Atlantic Salmon Populations.

Simple SummaryAtlantic salmon is a diadromous species that has the particularity that it returns to reproduce to its river of birth. This means that, in most cases, each river can be considered a population and that these populations can be adapted to the characteristics of the river. The Atlantic Salmon in the rivers of the Iberian Peninsula has been in decline since the 80’s of the last century. At that time, to alleviate the decline in the number of individuals, the rivers were stocked with salmon from Scotland and other northern European rivers, but the result was not positive. In this work, we studied eight salmon populations using a 220,000 high-density SNP array (Affymetrix) specific to Atlantic salmon. Our results revealed potential evidence of local adaptation for North Spanish and Scottish populations, which may be the cause of the failure of restocking programs. In addition, by performing a review of previous studies, we demonstrated that, as suggested, NADP-dependent malic enzyme-2 is a candidate for local adaptation in salmon from the Iberian Peninsula.Pollution and other anthropogenic effects have driven a decrease in Atlantic salmon (Salmo salar) in the Iberian Peninsula. The restocking effort carried out in the 1980s, with salmon from northern latitudes with the aim of mitigating the decline of native populations, failed, probably due to the deficiency in adaptation of foreign salmon from northern Europe to the warm waters of the Iberian Peninsula. This result would imply that the Iberian populations of Atlantic salmon have experienced local adaptation in their past evolutionary history, as has been described for other populations of this species and other salmonids. Local adaptation can occur by divergent selections between environments, favoring the fixation of alleles that increase the fitness of a population in the environment it inhabits relative to other alleles favored in another population. In this work, we compared the genomes of different populations from the Iberian Peninsula (Atlantic and Cantabric basins) and Scotland in order to provide tentative evidence of candidate SNPs responsible for the adaptive differences between populations, which may explain the failures of restocking carried out during the 1980s. For this purpose, the samples were genotyped with a 220,000 high-density SNP array (Affymetrix) specific to Atlantic salmon. Our results revealed potential evidence of local adaptation for North Spanish and Scottish populations. As expected, most differences concerned the comparison of the Iberian Peninsula with Scotland, although there were also differences between Atlantic and Cantabric populations. A high proportion of the genes identified are related to development and cellular metabolism, DNA transcription and anatomical structure. A particular SNP was identified within the NADP-dependent malic enzyme-2 (mMEP-2*), previously reported by independent studies as a candidate for local adaptation in salmon from the Iberian Peninsula. Interestingly, the corresponding SNP within the mMEP-2* region was consistent with a genomic pattern of divergent selection.

Analysing diversification dynamics using barcoding data: Thecase of an obligate mycorrhizal symbiont.

Analysing diversification dynamics is key to understanding the past evolutionary history of clades that led to present‐day biodiversity patterns. While such analyses are widespread in well‐characterized groups of species, they are much more challenging in groups for which diversity is mostly known through molecular techniques. Here, we use the largest global database on the small subunit (SSU) rRNA gene of Glomeromycotina, a subphylum of microscopic arbuscular mycorrhizal fungi that provide mineral nutrients to most land plants by forming one of the oldest terrestrial symbioses, to analyse the diversification dynamics of this clade in the past 500 million years. We perform a range of sensitivity analyses and simulations to control for potential biases linked to the nature of the data. We find that Glomeromycotina tend to have low speciation rates compared to other eukaryotes. After a peak of speciations between 200 and 100 million years ago, they experienced an important decline in speciation rates toward the present. Such a decline could be at least partially related to a shrinking of their mycorrhizal niches and to their limited ability to colonize new niches. Our analyses identify patterns of diversification in a group of obligate symbionts of major ecological and evolutionary importance and illustrate that short molecular markers combined with intensive sensitivity analyses can be useful for studying diversification dynamics in microbial groups.

DeCiFering the elusive cancer cell fraction in tumor heterogeneity and evolution

The cancer cell fraction (CCF), or proportion of cancerous cells in a tumor containing a single-nucleotide variant (SNV), is a fundamental statistic used to quantify tumor heterogeneity and evolution. Existing CCF estimation methods from bulk DNA sequencing data assume that every cell with an SNV contains the same number of copies of the SNV. This assumption is unrealistic in tumors with copy-number aberrations that alter SNV multiplicities. Furthermore, the CCF does not account for SNV losses due to copy-number aberrations, confounding downstream phylogenetic analyses. We introduce DeCiFer, an algorithm that overcomes these limitations by clustering SNVs using a novel statistic, the descendant cell fraction (DCF). The DCF quantifies both the prevalence of an SNV at the present time and its past evolutionary history using an evolutionary model that allows mutation losses. We show that DeCiFer yields more parsimonious reconstructions of tumor evolution than previously reported for 49 prostate cancer samples.

A genome-wide association study identifies Arabidopsis thaliana genes that contribute to differences in the outcome of infection with two Turnip mosaic potyvirus strains that differ in their evolutionary history and degree of host specialization.

Viruses lie in a continuum between generalism and specialism depending on their ability to infect more or less hosts. While generalists are able to successfully infect a wide variety of hosts, specialists are limited to one or a few. Even though generalists seem to gain an advantage due to their wide host range, they usually pay a pleiotropic fitness cost within each host. On the contrary, a specialist has maximal fitness within its own host. A relevant yet poorly explored question is whether viruses differ in the way they interact with their hosts’ gene expression depending on their degree of specialization. Using a genome-wide association study approach, we have identified host genes whose expression depends on whether hosts were infected with more or less specialized viral strains. Four hundred fifty natural accessions of Arabidopsis thaliana were inoculated with Turnip mosaic potyvirus strains with different past evolutionary histories and that shown different degrees of specialization. Three disease-related traits were measured and associated with different sets of host genes for each strain. The genetic architectures of these traits differed among viral strains and, in the case of the more specialized virus, also varied along the duration of infection. While most of the mapped loci were strain specific, one shared locus was mapped for both strains, a disease-resistance TIR-NBS-LRR class protein. Likewise, only putative cysteine-rich receptor-like protein kinases were involved in all three traits. The impact on disease progress of 10 selected genes was validated by studying the infection phenotypes of loss-of-function mutant plants. Nine of these mutants have altered the disease progress and/or symptoms intensity between both strains. Compared to wild-type plants six had an effect on both viral strains, three had an effect only on the more specialized, and two were significant during infection with the less specialized.

Domestic chicken diversity: Origin, distribution, and adaptation.

Chicken is the most numerous among the domesticated livestock species. Across cultures, religions, and societies, chicken is widely accepted with little or no taboo compared to other domestic animals. Its adaptability to diverse environmental conditions and demonstrated potential for breeding improvement provide a unique genetic resource for addressing the challenges of food security in a world impacted by climatic change and human population growth. Recent studies, shedding new knowledge on the chicken genomes, have helped reconstruct its past evolutionary history. Here, we review the literature concerning the origin, dispersion, and adaptation of domestic chicken. We highlight the role of human and natural selection in shaping the diversity of the species and provide a few examples of knowledge gaps that may be the focus of future research.

Additional Hybridization Studies of Genomic Compatibility and Phenotypic Expression in the Genus Speyeria (Nymphalidae: Argynnini)

The genetic compatibility of the most divergent species within the genus Speyeria was tested in 25 different hybrid crosses and back-crosses. In addition, the inheritance and expression of various phenotypic characters of wing pattern and coloration were studied including examples of extreme sexual dimorphism in certain species. These characters are important for the taxonomic diagnosis and identification of the various Speyeria taxa. Most of these characters or traits appear to have a complex polygenic inheritance with more continuous ranges of variation that have often become fixated at one end of the continuum for many taxa. However, other characters show a simpler Mendelian inheritance of dominant or recessive expressions. Some color pattern traits appear to be unique for one or two species, but most characters appear to be widely shared among many different Speyeria taxa. The results of these hybrid crosses suggest that extensive interspecies gene flow through natural hybridization may have been important in shaping the past evolutionary history of this genus. Also, the extensive clinal intergradation between highly divergent eastern and western subspecies of S. atlantis is documented in northwestern Minnesota.

Does past evolutionary history under different mating regimes influence the demographic dynamics of interspecific competition?

Interspecific interactions are contingent upon organism phenotypes, and thus phenotypic evolution can modify interspecific interactions and affect ecological dynamics. Recent studies have suggested that male–male competition within a species selects for capability to reproductively interfere with a closely related species. Here, we examine the effect of past evolutionary history under different mating regimes on the demographic dynamics of interspecific competition in Callosobruchus seed beetles. We used previously established experimental evolution lines of Callosobruchus chinensis that evolved under either forced lifelong monogamy or polygamy for 17 generations, and examined the demographic dynamics of competition between these C. chinensis lines and a congener, Callosobruchus maculatus. Callosobruchus chinensis was competitively excluded by C. maculatus in all trials. Time series data analyses suggested that reproductive interference from C. chinensis was relatively more important in the trials involving polygamous C. chinensis than those involving monogamous C. chinensis, in accordance with the potentially higher reproductive interference capability of polygamous C. chinensis. However, the estimated signs and magnitudes of interspecific interactions were not fully consistent with this explanation, implying the evolution of not only reproductive interference but also other interaction mechanisms. Our study thus suggests multifaceted effects of sexually selected traits on interspecific competitive dynamics.

V643 Orionis: A detached, evolved, post-mass-exchange eclipsing binary

Context. One of the greatest uncertainties in modelling the mass-exchange phases during the evolution of a binary system is the quantity of mass and angular momentum that has been lost from the system. To constrain this problem, a favourable, evolved, and detached real binary system is valuable as an example of the end result of this process. Aims. We study the 52-day post-mass-exchange eclipsing binary V643 Ori from complete uvby light curves and high-resolution spectra. V643 Ori is double-lined and shows total primary eclipses. The orbit is accurately circular and the rotation of the two stars is synchronised with the orbit, but the photometry from a single year (1993) shows signs of weak spot activity (0.02 mag) around the primary eclipse. Results. We determined accurate masses of 3.3 and 1.9 M⊙ from the spectroscopic orbit and solved the four light curves to determine radii of 16 and 21 R⊙, using the Wilson-Devinney photometric code. The rotational velocities from the cross-correlation profiles agree well with those computed from the known radii and orbital parameters. All observable parameters are thus very precisely determined, but the masses and radii of V643 Ori are incompatible with undisturbed post-main-sequence evolution. Conclusions. We have attempted to simulate the past evolutionary history of V643 Ori under both conservative and non-conservative Case B mass transfer scenarios. In the non-conservative case we varied the amounts of mass and angular momentum loss needed to arrive at the present masses in a circular 52-day orbit, keeping the two stars detached and synchronised as now observed, but without following the evolution of other stellar properties in any detail. Multiple possible solutions were found. Further attempts were made using both the BSE formalism and the binary MESA code in order to track stellar evolution more closely, and make use of the measured radii and temperatures as important additional constraints. Those efforts yielded no satisfactory solutions, possibly due to limitations in handling mass transfer in evolved stars such as these. We remain hopeful that future theoreticians can more fully model the system under realistic conditions.

Climatic influences on the genetic structure and distribution of the common vole and field vole in Europe

The purpose of this study was to examine the influence of climate on the distribution and present-day genetic structure of the common vole (Microtus arvalis) and the field vole (Microtus agrestis). In this study, we used previously published data on the genetic structure (using microsatellite DNA) of the common and field vole in Central Europe and a set of climatic variables to conduct binomial generalized linear and environmental niche modeling. In terms of present-day genetic structure, climate is an important factor shaping the patterns of distribution of the identified genetic groups, with the average minimum temperature in January being a significant factor for both species. For the field vole, average annual precipitation was an important factor also and consistent with the species’ preference for wet habitats. Therefore, this study has provided indirect evidence that (1) climate can shape the genetic structure and distribution of species at both broad and local scales and (2) using genetic data and species distribution modeling can be an effective approach to establish locations of putative glacial refugia for different species in Europe and to explore their past evolutionary history.

The divergence history of European blue mussel species reconstructed from Approximate Bayesian Computation: the effects of sequencing techniques and sampling strategies.

Genome-scale diversity data are increasingly available in a variety of biological systems, and can be used to reconstruct the past evolutionary history of species divergence. However, extracting the full demographic information from these data is not trivial, and requires inferential methods that account for the diversity of coalescent histories throughout the genome. Here, we evaluate the potential and limitations of one such approach. We reexamine a well-known system of mussel sister species, using the joint site frequency spectrum (jSFS) of synonymous mutations computed either from exome capture or RNA-seq, in an Approximate Bayesian Computation (ABC) framework. We first assess the best sampling strategy (number of: individuals, loci, and bins in the jSFS), and show that model selection is robust to variation in the number of individuals and loci. In contrast, different binning choices when summarizing the jSFS, strongly affect the results: including classes of low and high frequency shared polymorphisms can more effectively reveal recent migration events. We then take advantage of the flexibility of ABC to compare more realistic models of speciation, including variation in migration rates through time (i.e., periodic connectivity) and across genes (i.e., genome-wide heterogeneity in migration rates). We show that these models were consistently selected as the most probable, suggesting that mussels have experienced a complex history of gene flow during divergence and that the species boundary is semi-permeable. Our work provides a comprehensive evaluation of ABC demographic inference in mussels based on the coding jSFS, and supplies guidelines for employing different sequencing techniques and sampling strategies. We emphasize, perhaps surprisingly, that inferences are less limited by the volume of data, than by the way in which they are analyzed.

Implications and future prospects for evolutionary analyses of DNA in historical herbarium collections

Global herbarium collections house a vast number of plant specimens stretching back over centuries. They include rare and extinct species, important historical collections, and valuable type specimens that could help to resolve long-standing taxonomic issues. Historical plant collections also provide unique windows into past evolutionary processes and population histories that do not exist with modern data alone. However, because the DNA in such specimens is often degraded and scarce, manipulation and analysis of their genetic material can be challenging. Recent developments in non-destructive genetic sampling and working with very small quantities of genomic DNA, especially in next-generation sequencing and bioinformatic analysis of ancient DNA, now make the majority of herbarium specimens potentially accessible to phylogenetic, population genetic, and barcoding studies. For example, studies of DNA from long time series of Ipomoea batatas and Anacamptis palustris collections revealed linkages between anthropogenic activity and changes in haplotype distribution. These time series also enable the identification of genes under recent selection in the genomes of both the plants and their pathogens, as was shown for Phytophthora infestans, a microbial pathogen of Solanum tuberosum. Here, we summarize the major challenges in using historical plant DNA in evolutionary studies and review genetic studies integrating herbarium specimens. We expect future genetic studies of historical herbarium specimens to use genomic, metagenomic, and population genetic approaches to: investigate how plant populations respond to environmental change; infer temporal changes in genetic diversity; identify genes under recent selection; and investigate past plant pathogen epidemics.

Interactions retain the co‐phylogenetic matching that communities lost

Both species and their interactions are affected by changes that occur at evolutionary time‐scales, and these changes shape both ecological communities and their phylogenetic structure. That said, extant ecological community structure is contingent upon random chance, environmental filters and local effects. It is therefore unclear how much ecological signal local communities should retain. Here we show that, in a host–parasite system where species interactions vary substantially over a continental gradient, the ecological significance of individual interactions is maintained across different scales. Notably, this occurs despite the fact that observed community variation at the local scale frequently tends to weaken or remove community‐wide phylogenetic signal. When considered in terms of the interplay between community ecology and coevolutionary theory, our results demonstrate that individual interactions are capable and indeed likely to show a consistent signature of past evolutionary history even when woven into communities that do not.

A molecular approach to the reconstruction of the pre-Lessepsian fauna of the Isthmus of Suez: The case of the interstitial flatworm Monocelis lineata sensu lato (Platyhelminthes: Proseriata)

Since the opening of the Suez Canal in 1869 the Mediterranean Sea has been affected by a gradually increasing influx of species of Erythraean origin, which significantly modified species composition and ecological interactions of entire communities. Most studies have focused on macrofaunal species. Nevertheless, given the sandy nature of its shores, the Suez Canal is an ideal habitat for many interstitial taxa, whose study has been so far neglected. During a number of sampling campaigns, aimed to appreciate interstitial flatworms fauna in the Suez Canal, specimens of the Monocelis lineata (Platyhelminthes: Proseriata) species complex were collected in Lake Timsah.Here we performed molecular analyses by using the 18S and 28S nuclear rDNA genes. Species delimitation methods agree in considering this population as a distinct entity (Monocelis sp. nov.). Molecular phylogeny places Monocelis sp. nov. as the sister taxon of the Mediterranean populations of the Monocelis lineata species complex. Molecular dating results based on a minimum age calibration point, date the common ancestor of Monocelis sp. nov. and Mediterranean populations around the Bramertonian Interglacial optimum (1.8–2.3myr ago). In that stage, due to high eustatic sea levels, the geographic limit in the Isthmus of Suez shifted southward, with a new biogeographic barrier placed about the southern edge of the Gulf of Suez. It is thus conceivable that the ancestor of present-day Monocelis sp. nov. became isolated from its Mediterranean counterparts in the following regression, during the Pre-Pastonian glaciation. Data presented here suggest that populations inhabiting the Isthmus should be carefully screened as they may reveal a long history of persistence in the area and help to reconstruct past evolutionary histories of Mediterranean and Red Sea species. Considering the recent project aimed to widen the Suez Canal, which may significantly modify present ecological conditions, gathering of genetic data from populations of the water bodies of the Isthmus becomes an urgent task, before they are lost forever.

Phylogeography and Coevolution of Bamboo Mosaic Virus and Its Associated Satellite RNA.

Bamboo mosaic virus (BaMV), a plant potexvirus, has been found only in infected bamboo species. It is frequently associated with a large, linear single-stranded satellite RNA (satBaMV) that encodes a non-structural protein. Decades of collecting across a wide geographic area in Asia have accumulated a sizable number of BaMV and satBaMV isolates. In this study, we reconstructed the BaMV phylogeny and satBaMV phylogeny with partial coat protein gene sequences and partial genomic sequences, respectively. The evolutionary relationships allowed us to infer the phylogeography of BaMV and satBaMV on the Asian continent and its outlying islands. The BaMV phylogeny suggests that the BaMV isolates from Taiwan, unsurprisingly, are most likely derived from China. Interestingly, the newly available satBaMV isolates from China were found to be most closely related to the previously established Clade III, which is found in India. The general pattern of clustering along the China/India and Taiwan divide led us to hypothesize that the Taiwan Strait has been a physical barrier to gene flow in the past evolutionary history of both BaMV and satBaMV. Lastly, cophylogeny analyses revealed a complex association pattern between BaMV and satBaMV isolates from China. In general, closely related BaMV sequences tend to carry closely related satBaMV sequences as well; but instances of mismatching with distantly related satBaMV isolates were also found. We hypothesize plausible scenarios of infection and superinfection of bamboo hosts that may be responsible for the observed association pattern. However, a more systematic sampling throughout the geographic distribution of various bamboo species is needed to unambiguously establish the origin, movement, and evolution of BaMV and satBaMV.

The unfolding of the historical style in modern cosmology: Emergence, evolution, entrenchment

This paper traces the emergence, evolution and subsequent entrenchment of the historical style in the shifting scene of modern cosmological inquiry. It argues that the historical style in cosmology was forged in the early decades of the 20th century and continued to evolve in the century that followed. Over time, the scene of cosmological inquiry has gradually become dominated and entirely constituted by historicist explanations. Practices such as forwards and backwards temporal extrapolation (thinking about the past evolutionary history of the universe with different initial conditions and other parameters) are now commonplace. The non-static geometrization of the cosmos in the early 20th century led to inquires thinking about the cosmos in evolutionary terms. Drawing on the historical approach of Gamow (and contrasting this with the ahistorical approach of Bondi), the paper then argues that the historical style became a major force as inquirers began scouring the universe for fossils and other relics as a new form of scientific practice—cosmic palaeontology. By the 1970s the historical style became the bedrock of the discipline and the presupposition of new lines of inquiry. By the end of the 20th century, the historical style was pushed to its very limits as temporal reasoning began to occur beyond a linear historical narrative. With the atemporal ‘ensemble’ type multiverse proposals, a certain type of ahistorical reasoning has been reintroduced to cosmological discourse, which, in a sense, represents a radical de-historicization of the historical style in cosmology. Some are now even attempting to explain the laws of physics in terms of their historicity.

Phylogenetic context determines the role of competition in adaptive radiation.

Understanding ecological mechanisms regulating the evolution of biodiversity is of much interest to ecologists and evolutionary biologists. Adaptive radiation constitutes an important evolutionary process that generates biodiversity. Competition has long been thought to influence adaptive radiation, but the directionality of its effect and associated mechanisms remain ambiguous. Here, we report a rigorous experimental test of the role of competition on adaptive radiation using the rapidly evolving bacterium Pseudomonas fluorescens SBW25 interacting with multiple bacterial species that differed in their phylogenetic distance to the diversifying bacterium. We showed that the inhibitive effect of competitors on the adaptive radiation of P. fluorescens decreased as their phylogenetic distance increased. To explain this phylogenetic dependency of adaptive radiation, we linked the phylogenetic distance between P. fluorescens and its competitors to their niche and competitive fitness differences. Competitive fitness differences, which showed weak phylogenetic signal, reduced P. fluorescens abundance and thus diversification, whereas phylogenetically conserved niche differences promoted diversification. These results demonstrate the context dependency of competitive effects on adaptive radiation, and highlight the importance of past evolutionary history for ongoing evolutionary processes.

Repeated evolution and the impact of evolutionary history on adaptation.

BackgroundWhether natural selection can erase the imprint of past evolutionary history from phenotypes has been a topic of much debate. A key source of evidence that present-day selection can override historically contingent effects comes from the repeated evolution of similar adaptations in different taxa. Yet classic examples of repeated evolution are often among closely related taxa, suggesting the likelihood that similar adaptations evolve is contingent on the length of time separating taxa. To resolve this, we performed a meta-analysis of published reports of repeated evolution.ResultsOverall, repeated evolution was far more likely to be documented among closely related than distantly related taxa. However, not all forms of adaptation seemed to exhibit the same pattern. The evolution of similar behavior and physiology seemed frequent in distantly related and closely related taxa, while the repeated evolution of morphology was heavily skewed towards closely related taxa. Functionally redundant characteristics—alternative phenotypes that achieve the same functional outcome—also appeared less contingent.ConclusionsIf the literature provides a reasonable reflection of the incidence of repeated evolution in nature, our findings suggest that natural selection can overcome contingent effects to an extent, but it depends heavily on the aspect of the phenotype targeted by selection.Electronic supplementary materialThe online version of this article (doi:10.1186/s12862-015-0424-z) contains supplementary material, which is available to authorized users.