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How and why genetic diversity varies among species is a long-standing question in evolutionary biology. Life history traits have been shown to explain a large part of observed diversity. Among them, mating systems have one of the strongest impacts on genetic diversity, with selfing species usually exhibiting much lower diversity than outcrossing relatives. Theory predicts that a high rate of selfing amplifies selection at linked sites, reducing genetic diversity genome-wide, but frequent bottlenecks and rapid population turn-over could also explain low genetic diversity in selfers. However, how linked selection varies with mating systems and whether it is sufficient to explain the observed difference between selfers and outcrossers has never been tested. Here, we used the Aegilops / Triticum grass species, a group characterized by contrasted mating systems (from obligate outcrossing to high selfing) and marked recombination rate variation across the genome, to quantify the effects of mating system and linked selection on patterns of neutral and selected polymorphism. By analyzing phenotypic and transcriptomic data of 13 species, we show that selfing strongly affects genetic diversity and the efficacy of selection by amplifying the intensity of linked selection genome-wide. In particular, signatures of adaptation were only found in the highly recombining regions in outcrossing species. These results bear implications for the evolution of mating systems and, more generally, for our understanding of the fundamental drivers of genetic diversity. [ABSTRACT FROM AUTHOR]

Consider a scenario where a quantum particle is initially prepared in some bounded region of space and left to propagate freely. After some time, we verify if the particle has reached some distant target region. We find that there exist 'ultrafast' ('ultraslow') quantum states, whose probability of arrival is greater (smaller) than that of any classical particle prepared in the same region with the same momentum distribution. For both projectiles and rockets, we prove that the quantum advantage, quantified by the difference between the quantum and optimal classical arrival probabilities, is limited by the Bracken-Melloy constant cbm, originally introduced to study the phenomenon of quantum backflow. In this regard, we substantiate the 29-year-old conjecture that cbm ≈ 0.038 by proving the bounds 0.0315 ≤ cbm ≤ 0.072. Finally, we show that, in a modified projectile scenario where the initial position distribution of the particle is also fixed, the quantum advantage can reach 0.1262. [ABSTRACT FROM AUTHOR]

Analyses of the genetic bases of plant adaptation to climate changes, using genome-scan approaches, are often conducted on natural populations, under hypothesis of out-crossing reproductive regime. We report here on a study based on diachronic sampling (1980 and 2011) of the autogamous crop species, Oryza sativa and Oryza glaberrima, in the tropical forest and the Sudanian savannah of West Africa. First, using historical meteorological data we confirmed changes in temperatures (+ 1 °C on average) and rainfall regime (less predictable and reduced amount) in the target areas. Second, phenotyping the populations for phenology, we observed significantly earlier heading time in the 2010 samples. Third, implementing two genome-scan methods (one of which specially developed for selfing species) on genotyping by sequencing genotypic data of the two populations, we detected 31 independent selection footprints. Gene ontology analysis detected significant enrichment of these selection footprints in genes involved in reproductive processes. Some of them bore known heading time QTLs and genes, including OsGI, Hd1 and OsphyB. This rapid adaptive evolution, originated from subtle changes in the standing variation in genetic network regulating heading time, did not translate into predominance of multilocus genotypes, as it is often the case in selfing plants, and into notable selective sweeps. The high adaptive potential observed results from the multiline genetic structure of the rice landraces, and the rather large and imbricated genetic diversity of the rice meta-population at the farm, the village and the region levels, that hosted the adaptive variants in multiple genetic backgrounds before the advent of the environmental selective pressure. Our results illustrate the evolution of in situ diversity through processes of human and natural selection, and provide a model for rice breeding and cultivars deployment strategies aiming resilience to climate changes. It also calls for further development of population genetic models for adaptation of plant populations to environmental changes. To our best knowledge, this is the first study dealing with climate-changes' selective footprint in crops. [ABSTRACT FROM AUTHOR]

The original article can be found online at https://doi.org/10.1038/s41534-022-00598-0.Correction to: npj Quantum Informationhttps://doi.org/10.1038/s41534-022-00598-0, published online 26 July 2022In this article the grant from the CN2021 project "Optimized detection of high-dimensional entanglement" relating to OeAD for Miguel Navascués was omitted. The original article has been corrected.By Kaiyan Yang; Xiao Zeng; Yujing Luo; Guowu Yang; Lan Shu; Miguel Navascués and Zizhu WangReported by Author; Author; Author; Author; Author; Author; Author [Extracted from the article]

In recent years there has been a growing interest in treating many-body systems as Bell scenarios, where lattice sites play the role of distant parties and only near-neighbor statistics are accessible. We investigate contextuality arising from three Bell scenarios in infinite, translation-invariant 1D models: nearest-neighbor with two dichotomic observables per site; nearest- and next-to-nearest neighbor with two dichotomic observables per site, and nearest-neighbor with three dichotomic observables per site. For the first scenario, we give strong evidence that it cannot exhibit contextuality, not even in non-signaling physical theories beyond quantum mechanics. For the second one, we identify several low-dimensional models that reach the ultimate quantum limits, paving the way for self-testing ground states of quantum many-body systems. For the last scenario, which generalizes the Heisenberg model, we give strong evidence that, in order to exhibit contextuality, the dimension of the local quantum system must be at least 3. [ABSTRACT FROM AUTHOR]

Resurrection studies are a useful tool to measure how phenotypic traits have changed in populations through time. If these trait modifications correlate with the environmental changes that occurred during the time period, it suggests that the phenotypic changes could be a response to selection. Selfing, through its reduction of effective size, could challenge the ability of a population to adapt to environmental changes. Here, we used a resurrection study to test for adaptation in a selfing population of Medicago truncatula, by comparing the genetic composition and flowering times across 22 generations. We found evidence for evolution toward earlier flowering times by about two days and a peculiar genetic structure, typical of highly selfing populations, where some multilocus genotypes (MLGs) are persistent through time. We used the change in frequency of the MLGs through time as a multilocus fitness measure and built a selection gradient that suggests evolution toward earlier flowering times. Yet, a simulation model revealed that the observed change in flowering time could be explained by drift alone, provided the effective size of the population is small enough (<150). These analyses suffer from the difficulty to estimate the effective size in a highly selfing population, where effective recombination is severely reduced. [ABSTRACT FROM AUTHOR]

Although complex numbers are essential in mathematics, they are not needed to describe physical experiments, as those are expressed in terms of probabilities, hence real numbers. Physics, however, aims to explain, rather than describe, experiments through theories. Although most theories of physics are based on real numbers, quantum theory was the first to be formulated in terms of operators acting on complex Hilbert spaces1,2. This has puzzled countless physicists, including the fathers of the theory, for whom a real version of quantum theory, in terms of real operators, seemed much more natural3. In fact, previous studies have shown that such a ‘real quantum theory’ can reproduce the outcomes of any multipartite experiment, as long as the parts share arbitrary real quantum states4. Here we investigate whether complex numbers are actually needed in the quantum formalism. We show this to be case by proving that real and complex Hilbert-space formulations of quantum theory make different predictions in network scenarios comprising independent states and measurements. This allows us to devise a Bell-like experiment, the successful realization of which would disprove real quantum theory, in the same way as standard Bell experiments disproved local physics.A Bell-like experiment that discriminates between real-number and complex-number multipartite quantum systems could disprove real quantum theory. [ABSTRACT FROM AUTHOR]

In the context of epidemiology, policies for disease control are often devised through a mixture of intuition and brute-force, whereby the set of logically conceivable policies is narrowed down to a small family described by a few parameters, following which linearization or grid search is used to identify the optimal policy within the set. This scheme runs the risk of leaving out more complex (and perhaps counter-intuitive) policies for disease control that could tackle the disease more efficiently. In this article, we use techniques from convex optimization theory and machine learning to conduct optimizations over disease policies described by hundreds of parameters. In contrast to past approaches for policy optimization based on control theory, our framework can deal with arbitrary uncertainties on the initial conditions and model parameters controlling the spread of the disease, and stochastic models. In addition, our methods allow for optimization over policies which remain constant over weekly periods, specified by either continuous or discrete (e.g.: lockdown on/off) government measures. We illustrate our approach by minimizing the total time required to eradicate COVID-19 within the Susceptible-Exposed-Infected-Recovered (SEIR) model proposed by Kissler et al. (March, 2020). [ABSTRACT FROM AUTHOR]

Aim: Coastal plants are terrestrial organisms for which ocean surface currents often act as long‐distance dispersal vectors (thalassochorous species) favouring broad distributions and connecting distant populations. However, few studies have statistically assessed the role of currents in modulating gene flow and species distributions of terrestrial organisms. Here we evaluate the hypothesis that some thalassochorous plants exhibit population connectivity, presumably due to effective seed dispersal driven by sea currents. Location: Galápagos Islands (Ecuador). Taxon: Salt bush (Cryptocarpus pyriformis Kunth), a Galápagos native and locally widespread coastal angiosperm. Methods: Using 1806 SNPs obtained by ddRADseq, we evaluated the genetic structure and differentiation of the Galápagos salt bush. To assess the role of sea currents in modulating inter‐population gene flow, four explicit hypotheses were tested using reciprocal causal modelling and spatial eigenvector analysis: (a) isolation by sea resistance, considering that only sea dispersal is possible; (b) isolation by sea and inland resistance, considering that inland dispersal is also possible; (c) isolation by barrier, considering the sea as an obstacle to seed dispersal; and (d) isolation by geographical distance. Results: Low differentiation and little genetic structure were detected among populations of C. pyriformis. Pairwise genetic distances between populations from different islands were significantly correlated with cost distances calculated from sea‐current direction and speed. Nonetheless, inland dispersal also accounted for some gene flow within each island. Main conclusion: Extensive and frequent seed dispersal by sea has apparently favoured strong inter‐island genetic connectivity within Galápagos. A combination of methods developed for terrestrial and marine domains (landscape and seascape genetics) aids in understanding how landscape features modulate gene flow of coastal plant species, as these terrestrial organisms are highly dependent on the sea for seed dispersal. [ABSTRACT FROM AUTHOR]

We propose a funding scheme for theoretical research that does not rely on project proposals, but on recent past scientific productivity. Given a quantitative figure of merit on the latter and the total research budget, we introduce a number of policies to decide the allocation of funds in each grant call. Under some assumptions on scientific productivity, some of such policies are shown to converge, in the limit of many grant calls, to a funding configuration that is close to the maximum total productivity of the whole scientific community. We present numerical simulations showing evidence that these schemes would also perform well in the presence of statistical noise in the scientific productivity and/or its evaluation. Finally, we prove that one of our policies cannot be cheated by individual research units. Our work must be understood as a first step towards a mathematical theory of the research activity. [ABSTRACT FROM AUTHOR]

We studied the Pleistocene diversification of a relatively endemic Mediterranean insect (Ephippiger diurnus ; Orthoptera: Tettigoniidae) to understand how species with restricted range may nonetheless exhibit the complex phylogeography normally associated with broad distribution. A time-calibrated molecular phylogeny based on two mitochondrial genes showed that E. diurnus diverged into two major clades, distinguished largely by male song, before or early during the Pleistocene. Several subclades also diverged before the most recent glacial period. Data from 20 microsatellite loci indicated higher genetic diversity in populations along the Mediterranean coast in France, consistent with the hypothesis that glacial refuges were located there. 'Isolation by distance' accounts for much genetic differentiation between populations, but some adjacent populations are highly differentiated. A Bayesian approach defined genetically distinct clusters and assigned individuals to their most probable cluster. Clusters corresponded to clades in the phylogenetic tree, and we used cluster assignments to estimate interclade gene flow in areas of potential secondary contact. Gene flow is negligible in potential contact areas in the Pyrenees, but a narrow hybrid zone featuring a steep cline exists on the coast. This hybrid zone suggests that the major clades represent distinct species that diverged within a restricted area during the Pleistocene. [ABSTRACT FROM AUTHOR]

History and environment shape crop biodiversity, particularly in areas with vulnerable human communities and ecosystems. Tracing crop biodiversity over time helps understand how rural societies cope with anthropogenic or climatic changes. Exceptionally well preserved ancient DNA of quinoa (Chenopodium quinoa Willd.) from the cold and arid Andes of Argentina has allowed us to track changes and continuities in quinoa diversity over 18 centuries, by coupling genotyping of 157 ancient and modern seeds by 24 SSR markers with cluster and coalescence analyses. Cluster analyses revealed clear population patterns separating modern and ancient quinoas. Coalescence-based analyses revealed that genetic drift within a single population cannot explain genetic differentiation among ancient and modern quinoas. The hypothesis of a genetic bottleneck related to the Spanish Conquest also does not seem to apply at a local scale. Instead, the most likely scenario is the replacement of preexisting quinoa gene pools with new ones of lower genetic diversity. This process occurred at least twice in the last 18 centuries: first, between the 6th and 12th centuries—a time of agricultural intensification well before the Inka and Spanish conquests—and then between the 13th century and today—a period marked by farming marginalization in the late 19th century likely due to a severe multidecadal drought. While these processes of local gene pool replacement do not imply losses of genetic diversity at the metapopulation scale, they support the view that gene pool replacement linked to social and environmental changes can result from opposite agricultural trajectories. [ABSTRACT FROM AUTHOR]

We study the properties of the set of marginal distributions of infinite translation-invariant systems in the two-dimensional square lattice. In cases where the local variables can only take a small number d of possible values, we completely solve the marginal or membership problem for nearestneighbours distributions (d=2, 3) and nearest and next-to-nearest neighbours distributions (d=2). Remarkably, all these sets form convex polytopes in probability space. This allows us to devise an algorithm to compute the minimum energy per site of any TI Hamiltonian in these scenarios exactly. We also devise a simple algorithm to approximate the minimum energy per site up to arbitrary accuracy for the cases not covered above. For variables of a higher (but finite) dimensionality, we prove two no-go results. To begin, the exact computation of the energy per site of arbitrary TI Hamiltonians with only nearest-neighbour interactions is an undecidable problem. In addition, in scenarios with d .2947, the boundary of the set of nearest-neighbour marginal distributions contains both flat and smoothly curved surfaces and the set itself is not semi-algebraic. This implies, in particular, that it cannot be characterized via semidefinite programming, even if we allow the input of the programme to include polynomials of nearest-neighbour probabilities. [ABSTRACT FROM AUTHOR]

* Background and Aims The recurrence of wildfires is predicted to increase due to global climate change, resulting in severe impacts on biodiversity and ecosystem functioning. Recurrent fires can drive plant adaptation and reduce genetic diversity; however, the underlying population genetic processes have not been studied in detail. In this study, the neutral and adaptive evolutionary effects of contrasting fire regimes were examined in the keystone tree species Pinus halepensis Mill. (Aleppo pine), a fire-adapted conifer. The genetic diversity, demographic history and spatial genetic structure were assessed at local (within-population) and regional scales for populations exposed to different crown fire frequencies. * Methods Eight natural P. halepensis stands were sampled in the east of the Iberian Peninsula, five of them in a region exposed to frequent crown fires (HiFi) and three of them in an adjacent region with a low frequency of crown fires (LoFi). Samples were genotyped at nine neutral simple sequence repeats (SSRs) and at 251 single nucleotide polymorphisms (SNPs) from coding regions, some of them potentially important for fire adaptation. * Key Results Fire regime had no effects on genetic diversity or demographic history. Three high-differentiation outlier SNPs were identified between HiFi and LoFi stands, suggesting fire-related selection at the regional scale. At the local scale, fine-scale spatial genetic structure (SGS) was overall weak as expected for a wind-pollinated and wind-dispersed tree species. HiFi stands displayed a stronger SGS than LoFi stands at SNPs, which probably reflected the simultaneous post-fire recruitment of co-dispersed related seeds. SNPs with exceptionally strong SGS, a proxy for microenvironmental selection, were only reliably identified under the HiFi regime. * Conclusions An increasing fire frequency as predicted due to global change can promote increased SGS with stronger family structures and alter natural selection in P. halepensis and in plants with similar life history traits. [ABSTRACT FROM AUTHOR]

Human population migrations, as well as long-distance trade activities, have been responsible for the spread of many invasive organisms. The black rat, Rattus rattus, has colonized most of the world following ship-mediated trade. Owing to its tight association with human infrastructures, this species has been able to survive in unfavourable environments, such as Sahelian Africa. In this work, we combined interview-based and population genetic surveys to investigate the processes underlying the ongoing invasion of south-western Niger by black rats, with special emphasis on the capital city, Niamey. Our trapping and interview data are quite congruent, and all together point towards a patchy, but rather widespread, current distribution of R. rattus. Genetic data strongly suggest that road network development for truck-based commercial flow from/to international harbours located in neighbouring countries (Benin, Togo, and Nigeria) facilitates the passive dispersal of black rats over a long distance through unfavourable landscapes. Another potentially, more ancient, invasion route may be associated with boat transport along the Niger River. Human-mediated dispersal thus probably allows the foundation of persisting populations within highly anthropized areas while population dynamics may be more unstable in remote areas and mostly depends on propagule pressure. [ABSTRACT FROM AUTHOR]

Songbirds with recently (i.e., early Holocene) founded populations are suitable models for studying incipient differentiation in oceanic islands. On such systems each colonization event represents a different evolutionary episode that can be studied by addressing sets of diverging phenotypic and genetic traits. We investigate the process of early differentiation in the spectacled warbler ( Sylvia conspicillata) in 14 populations separated by sea barriers from three Atlantic archipelagos and from continental regions spanning from tropical to temperate latitudes. Our approach involved the study of sexual acoustic signals, morphology, and genetic data. Mitochondrial DNA did not provide clear population structure. However, microsatellites analyses consistently identified two genetic groups, albeit without correspondence to subspecies classification and little correspondence to geography. Coalescent analyses showed significant evidence for gene flow between the two genetic groups. Discriminant analyses could not correctly assign morphological or acoustic traits to source populations. Therefore, although theory predicting that in isolated populations genetic, morphological, or acoustic traits can lead to radiation, we have strikingly failed to document differentiation on these attributes in a resident passerine throughout three oceanic archipelagos. [ABSTRACT FROM AUTHOR]

Background Determining the presence or absence of gene flow between populations is the target of some statistical methods in population genetics. Until recently, these methods either avoided the use of recombining genes, or treated recombination as a nuisance parameter. However, genes with recombination contribute additional information for the detection of gene flow (i.e. through linkage disequilibrium). Methods We present three summary statistics based on the spatial arrangement of fixed differences, and shared and exclusive polymorphisms that are sensitive to the presence and direction of gene flow. Power and false positive rate for tests based on these statistics are studied by simulation. Results The application of these tests to populations from the Drosophila simulans species complex yielded results consistent with migration between D. simulans and its two endemic sister species D. mauritiana and D. sechellia, and between populations D. mauritiana on the islands of the Mauritius and Rodrigues. Conclusions We demonstrate the sensitivity of the developed statistics to the presence and direction of gene flow, and characterize their power as a function of differentiation level and recombination rate. The properties of these statistics make them especially suitable for analyzing high-throughput sequencing data or for their integration within the approximate Bayesian computation framework. [ABSTRACT FROM AUTHOR]

Bipartite correlations generated by non-signalling physical systems that admit a finite-dimensional local quantum description cannot exceed the quantum limits, i.e., they can always be interpreted as distant measurements of a bipartite quantum state. Here we consider the effect of dropping the assumption of finite dimensionality. Remarkably, we find that the same result holds provided that we relax the tensor structure of space-like separated measurements to mere commutativity. We argue why an extension of this result to tensor representations seems unlikely. [ABSTRACT FROM AUTHOR]

What can we say about the spectra of a collection of microscopic variables when only their coarse-grained sums are experimentally accessible? In this paper, using the tools and methodology from the study of quantum nonlocality, we develop a mathematical theory of the macroscopic fluctuations generated by ensembles of independent microscopic discrete systems. We provide algorithms to decide which multivariate Gaussian distributions can be approximated by sums of finitely valued random vectors. We study non-trivial cases where the microscopic variables have an unbounded range, as well as asymptotic scenarios with infinitely many macroscopic variables. From a foundational point of view, our results imply that bipartite Gaussian states of light cannot be understood as beams of independent d-dimensional particle pairs. It is also shown that the classical description of certain macroscopic optical experiments, as opposed to the quantum one, requires variables with infinite cardinality spectra. [ABSTRACT FROM AUTHOR]

Background: Pearl millet landraces display an important variation in their cycle duration. This diversity contributes to the stability of crop production in the Sahel despite inter-annual rainfall fluctuation. Conservation of phenological diversity is important for the future of pearl millet improvement and sustainable use. Identification of genes contributing to flowering time variation is therefore relevant. In this study we focused on three flowering candidate genes, PgHd3a, PgDwarf8 and PgPHYC. We tested for signatures of past selective events within polymorphism patterns of these three genes that could have been associated with pearl millet domestication and/or landraces differentiation. In order to implement ad hoc neutrality tests, a plausible demographic history of pearl millet domestication was inferred through Approximate Bayesian Computation by using eight neutral STS loci. Results: Domesticated pearl millet exhibited 84% of the nucleotide diversity level found in the wild population. No specific polymorphisms were found either in the wild or in the domestic populations. The Bayesian approach and previous studies suggest that gene flow between wild relatives and domesticated pearl millets is a main factor explaining these results. Early and late landraces did not show significant genetic differentiation at both the neutral and the candidate loci. A positive selection was evidenced in PgHd3a and PgDwarf8 genes of domestic forms but not in the wild population. Conclusion: Our results strongly suggest that PgHd3a and PgDwarf8 were likely targeted by selection during domestication. However, a potential role of any of the three candidate genes in the phenological differentiation between early and late landraces was not supported by our data. Reasons why these results contrast with previous results that have shown a slight but significant association between PgPHYC polymorphisms and variation in flowering time in pearl millet are discussed. [ABSTRACT FROM AUTHOR]

We study the scenarios where a finite set of non-demolition von Neumann measurements is available. We note that, in some situations, the repeated application of such measurements allows estimation of an infinite number of parameters of the initial quantum state, and we illustrate the point with a physical example. We also study how the system under consideration is perturbed after several rounds of projective measurements. While in the finite dimensional case the effect of this perturbation always saturates, there are instances of infinite dimensional systems where such a perturbation is accumulative, and the act of retrieving information about the system increases its energy indefinitely (i.e. we have 'heat vision').We analyze this effect and discuss a specific physical system with two dichotomic von Neumann measurements where heat vision is expected to show. [ABSTRACT FROM AUTHOR]

Y-chromosome microsatellites (Y-STRs) are typically used for kinship analysis and forensic identification, as well as for inferences on population history and evolution. All applications would greatly benefit from reliable locus-specific mutation rates, to improve forensic probability calculations and interpretations of diversity data. However, estimates of mutation rate from father-son transmissions are available for few loci and have large confidence intervals, because of the small number of meiosis usually observed. By contrast, population data exist for many more Y-STRs, holding unused information about their mutation rates. To incorporate single locus diversity information into Y-STR mutation rate estimation, we performed a meta-analysis using pedigree data for 80 loci and individual haplotypes for 110 loci, from 29 and 93 published studies, respectively. By means of logistic regression we found that relative genetic diversity, motif size and repeat structure explain the variance of observed rates of mutations from meiosis. This model allowed us to predict locus-specific mutation rates (mean predicted mutation rate 2.12 × 10−3, SD=1.58 × 10−3), including estimates for 30 loci lacking meiosis observations and 41 with a previous estimate of zero. These estimates are more accurate than meiosis-based estimates when a small number of meiosis is available. We argue that our methodological approach, by taking into account locus diversity, could be also adapted to estimate population or lineage-specific mutation rates. Such adjusted estimates would represent valuable information for selecting the most reliable markers for a wide range of applications. [ABSTRACT FROM AUTHOR]

The analysis of ancient DNA in a population genetic or phylogeographical framework is an emerging field, as traditional analytical tools were largely developed for the purpose of analysing data sampled from a single time point. Markov chain Monte Carlo approaches have been successfully developed for the analysis of heterochronous sequence data from closed panmictic populations. However, attributing genetic differences between temporal samples to mutational events between time points requires the consideration of other factors that may also result in genetic differentiation. Geographical effects are an obvious factor for species exhibiting geographical structuring of genetic variation. The departure from a closed panmictic model require researchers to either exploit software developed for the analysis of isochronous data, take advantage of simulation approaches using algorithms developed for heterochronous data, or explore approximate Bayesian computation. Here, we review statistical approaches employed and available software for the joint analysis of ancient and modern DNA, and where appropriate we suggest how these may be further developed. [ABSTRACT FROM AUTHOR]

The increasing ability to extract and sequence DNA from noncontemporaneous tissue offers biologists the opportunity to analyse ancient DNA (aDNA) together with modern DNA (mDNA) to address the taxonomy of extinct species, evolutionary origins, historical phylogeography and biogeography. Perhaps more exciting are recent developments in coalescence-based Bayesian inference that offer the potential to use temporal information from aDNA and mDNA for the estimation of substitution rates and divergence dates as an alternative to fossil and geological calibration. This comes at a time of growing interest in the possibility of time dependency for molecular rate estimates. In this study, we provide a critical assessment of Bayesian Markov chain Monte Carlo (MCMC) analysis for the estimation of substitution rate using simulated samples of aDNA and mDNA. We conclude that the current models and priors employed in Bayesian MCMC analysis of heterochronous mtDNA are susceptible to an upward bias in the estimation of substitution rates because of model misspecification when the data come from populations with less than simple demographic histories, including sudden short-lived population bottlenecks or pronounced population structure. However, when model misspecification is only mild, then the 95% highest posterior density intervals provide adequate frequentist coverage of the true rates. [ABSTRACT FROM AUTHOR]

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Chloroplast microsatellites are becoming increasingly popular markers for population genetic studies in plants, but there has been little focus on their potential for demographic inference. In this work the utility of chloroplast microsatellites for the study of population expansions was explored. First, we investigated the power of mismatch distribution analysis and the FS test with coalescent simulations of different demographic scenarios. We then applied these methods to empirical data obtained for the Canary Island pine ( Pinus canariensis). The results of the simulations showed that chloroplast microsatellites are sensitive to sudden population growth. The power of the FS test and accuracy of demographic parameter estimates, such as the time of expansion, were reduced proportionally to the level of homoplasy within the data. The analysis of Canary Island pine chloroplast microsatellite data indicated population expansions for almost all sample localities. Demographic expansions at the island level can be explained by the colonization of the archipelago by the pine, while population expansions of different ages in different localities within an island could be the result of local extinctions and recolonization dynamics. Comparable mitochondrial DNA sequence data from a parasite of P. canariensis, the weevil Brachyderes rugatus, supports this scenario, suggesting a key role for volcanism in the evolution of pine forest communities in the Canary Islands. [ABSTRACT FROM AUTHOR]