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In large clonal populations, several clones generally compete which results in complex evolutionary and ecological dynamics: experiments show successive selective sweeps of favorable mutations as well as long-term coexistence of multiple clonal strains. The mechanisms underlying either coexistence or fixation of several competing strains have rarely been studied altogether. Conditions for coexistence has mostly been studied by population and community ecology, while rates of invasion and fixation have mostly been studied by population genetics. In order to provide a global understanding of the complexity of the dynamics observed in large clonal populations, we develop a stochastic model where three clones compete. Competitive interactions can be intransitive and we suppose that strains enter the population via mutations or rare immigrations. We first describe all possible final states of the population, including stable coexistence of two or three strains, or the fixation of a single strain. Second, we give estimate of the invasion and fixation times of a favorable mutant (or immigrants) entering the population in a single copy. We especially show that invasion and fixation can be slower or faster when considering complex competitive interactions. Third, we explore the parameter space assuming prior distributions of reproduction, death and competitive rates and we estimate the likeliness of the possible dynamics. We especially show that when mutations can affect competitive interactions, even slightly, stable coexistence is likely. We discuss our results in the context of the evolutionary dynamics of large clonal populations.
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We reassessed whether two parapatric non-sister Australian honeyeater species (Aves: Meliphagidae), varied and mangrove honeyeaters (Gavicalis versicolor and G. fasciogularis, respectively), that diverged from a common ancestor c. 2.5 Mya intergrade in the Townsville area of north-eastern Queensland. Consistent with a previous specimenbased study, by using genomics methods we show one-way gene flow for autosomal but not Z-linked markers from varied into mangrove honeyeaters. Introgression barely extends south of the area of parapatry in and around the city of Townsville. While demonstrating the long-term porosity of species boundaries over several million years, our data also suggest a clear role of sex chromosomes in maintaining reproductive isolation.
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The North Sea is one of the most extensively studied marine regions of the world. Hence, large amounts of molecular data for species identification are available in public repositories, and expectations to find numerous new species in this well-known region are rather low. However, molecular reference data for harpacticoid copepods from this area in particular but also for this group in general is scarce. By assessing COI barcodes and MALDI-TOF mass spectra for this group of small crustaceans, it was discovered that there is a huge unknown diversity in this area. In total, COI sequences for 548 specimens from 115 species of harpacticoid copepods are presented. Over 19% of these were new to science and ten MOTUs were found to be part of cryptic species complexes. MALDI-TOF mass spectra were assessed for 622 specimens from 75 species. Because results were in concordance with species delimitation by COI barcoding and also enabled recognition of possible cryptic species, the discriminative power of this technique for biodiversity assessments is highlighted. Findings imply, species diversity in this group may be largely underestimated and total species number can be expected to be much higher than previously assumed.
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The sugarcane borer moth, Diatraea saccharalis, is one of the most important pests of sugarcane and maize crops in the Western Hemisphere. The pest is widespread throughout South and Central America, the Caribbean region and the southern United States. One of the most intriguing features of D. saccharalis population dynamics is the high rate of range expansion reported in recent years. To shed light on the history of colonization of D. saccharalis, we investigated the genetic structure and diversity in American populations using single nucleotide polymorphism (SNPs) markers throughout the genome and sequences of the mitochondrial gene cytochrome oxidase (COI). Our primary goal was to propose possible dispersal routes from the putative center of origin that can explain the spatial pattern of genetic diversity. Our findings showed a clear correspondence between genetic structure and the geographical distributions of this pest insect on the American continents. The clustering analyses indicated three distinct groups: one composed of Brazilian populations, a second group composed of populations from El Salvador, Mexico, Texas and Louisiana and a third group composed of the Florida population. The predicted time of divergence predates the agriculture expansion period, but the pattern of distribution of haplotype diversity suggests that human-mediated movement was most likely the factor responsible for the widespread distribution in the Americas. The study of the early history of D. saccharalis promotes a better understanding of range expansion, the history of invasion, and demographic patterns of pest populations in the Americas.
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Increasing evidence suggests that conscious awareness is supported by critical or near-critical cortical dynamics, which exhibit scale-free cascades of spatiotemporal activity. These avalanches of neural origin have been detected at multiple scales, from in vitro and in vivo microcircuits to voltage imaging and brain-wide functional magnetic resonance imaging (fMRI) recordings. Criticality endows the cortex with information processing capacities postulated as necessary for consciousness, yet it remains unknown how reduced awareness impacts on the avalanche-like behaviour of large-scale human hemodynamic activity. We observed a scale-free hierarchy of co-activated connected clusters by applying a point-process transformation to fMRI data recorded during wakefulness and non-rapid eye movement (NREM) sleep. Maximum likelihood estimates revealed a significant effect of sleep stage on the scaling parameters of the cluster size power-law distributions. Post-hoc statistical tests showed that differences were maximal between wakefulness and N2 sleep. These results were robust against spatial coarse-graining and different point-process thresholds, and disappeared upon phase-shuffling the fMRI time series. The onset of evoked neural bistabilities that prevent arousals during N2 sleep do not suffice to explain these differences, which point towards changes in the intrinsic dynamics of the brain that are necessary to consolidate a state of deep sleep.
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Date palms (Phoenix dactylifera) are an important fruit crop of arid regions of the Middle East and North Africa. Despite its importance, few genomic resources exist for date palms, hampering evolutionary genomic studies of this perennial crop species. Here we report an improved long-read genome assembly for P. dactylifera that is 772.3 Mb in length, with contig N50 of 897.2 Kb, and use this to perform GWAS mapping of the sex determining region and 21 fruit traits. We find a fruit color GWAS at the R2R3-MYB transcription factor (VIRESCENS) gene and identify functional alleles that include a retrotransposon insertion and start codon mutation. We also find a GWAS peak for sugar composition spanning deletion polymorphisms in multiple linked invertase genes. MYB transcription factors and invertase are implicated in fruit color and sugar composition in other crop species, demonstrating the importance of parallel evolution in the evolutionary diversification of domesticated species.
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The latitudinal diversity gradient (LDG), in which the number of species increases from the poles to the Equator, is one of the best-established patterns of life on Earth. The pattern of species-rich Tropics relative to species-poor temperate areas has been recognized for well over a century, but mechanisms for its genesis are still debated vigorously. We use simulations to assess the possibility that spatio-temporal climatic changes could have generated large-scale patterns of biodiversity as a function of only three biological processes—speciation, extinction, and dispersal—omitting adaptive niche evolution, diversity-dependence and coexistence limits. In our simulations, speciation occurred in response to range disjunction, and only when populations had been isolated for a sufficient period of time, whereas extinction occurred when a species could no longer access suitable sites. Our simulations generated clear LDGs that closely match empirical LDGs for three major vertebrate groups. Higher tropical diversity resulted primarily from higher rates of low-latitude speciation. This speciation was driven by spatio-temporal variation in precipitation at low latitudes, rather than in temperature. We therefore propose that spatio-temporal heterogenous precipitation change may have driven high rates of low-latitude speciation, contributing to LDGs. Overall, simulations show that major global biodiversity patterns can derive from the interaction of species’ niches (fixed a priori in our simulations) with dynamic climate across complex, existing landscapes, without the need to invoke biotic interactions or niche-related adaptations.
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Plant sigma factors (SIGs) are key regulators of chloroplast gene expression and chloroplast differentiation. Despite their functional importance, the evolutionary history of these factors remains unclear. Using newly available genomic and transcriptomic data, we conducted a detailed and comprehensive phylogenetic analysis of SIG homologues from land plants and algae. Our results reveal that plants have acquired sigma factors from ancestor cyanobacteria via endosymbiotic gene transfers, forming four major clades, namely, super-SIG2 (SIG2/3/4/6/SIG2-like), SIG1, SIG5 and SIGX. The super-SIG2 clade was confirmed to have evolved from cyanobacterial SIGA factors, and a novel clade (SIGX) specific to non-angiosperms was revealed here. Gene duplications (mainly whole genome duplications) within lineages and species have contributed to the expansion of sigma factors in plants, especially flowering plants. We hypothesize that plant sigma factors originated from different endosymbiotic ancestors and evolved diverse functions. This not only sheds new light on the evolution of plant SIG genes but also paves the way for understanding the functional diversification of these genes.
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When postulating evolutionary hypotheses for diverse groups of taxa using molecular data, there is a tradeoff between sampling large numbers of taxa with a few Sanger sequenced genes or sampling fewer taxa with hundreds to thousands of next-generation sequenced genes. High taxon sampling enables the testing of evolutionary hypotheses that are sensitive to sampling bias (i.e. dating, biogeography, and diversification analyses), whereas high character sampling improves resolution of critical nodes. In a group of ant parasitoids (Hymenoptera: Eucharitidae: Oraseminae), we analyze both of these types of datasets independently (203 taxa with 5 Sanger loci; 92 taxa with 348 Anchored Hybrid Enrichment loci) and in combination (229 taxa, 353 loci) to explore divergence dating, biogeography, host relationships, and differential rates of diversification. Oraseminae specialize as parasitoids of the immature stages of ants in the subfamily Myrmicinae (Hymenoptera: Formicidae), with ants in the genus Pheidole being their most common and presumed ancestral host. A general assumption is that the distribution of the parasite must be limited by any range contraction or expansion of its host. Recent studies support a single New World to Old World dispersal pattern for Pheidole approximately 11–22 Ma. Using multiple phylogenetic inference methods (parsimony, maximum likelihood, dated Bayesian, and coalescent analyses), we provide a robust phylogeny showing that Oraseminae dispersed in the opposite direction, from Old World to New World, approximately 24–33 Ma, which implies that they existed in the Old World prior to their presumed ancestral hosts. Their dispersal into the New World appears to have promoted an increased diversification rate. Both the host and parasitoid show single unidirectional dispersals in accordance with the presence of the Beringian Land Bridge during the Oligocene, a time when the changing northern climate likely limited the dispersal ability of such tropically adapted groups.
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Recombination is an important driver of genetic diversity, though it is relatively uncommon in hepatitis C virus (HCV). Recent investigation of sequence data acquired from HCV clinical trials produced 21 full-genome recombinant viruses belonging to three putative inter-subtype forms 2b/1a, 2b/1b, and 2k/1b. The 2k/1b chimera is the only known HCV circulating recombinant form (CRF), provoking interest in its genetic structure and origin. Discovered in Russia in 1999, 2k/1b cases have since been detected throughout the former Soviet Union, Western Europe, and North America. Although 2k/1b prevalence is highest in the Caucasus mountain region (i.e., Armenia, Azerbaijan, and Georgia), the origin and migration patterns of CRF 2k/1b have remained obscure due to a paucity of available sequences. We assembled an alignment which spans the entire coding region of the HCV genome containing all available 2k/1b sequences (>500 nucleotides; n=109) sampled in 19 countries from public databases (102 individuals), additional newly sequenced genomic regions (from 48 of these 102 individuals), unpublished isolates with newly sequenced regions (5 additional individuals), and novel complete genomes (2 additional individuals) generated in this study. Analysis of this expanded dataset reconfirmed the monophyletic origin of 2k/1b with a recombination breakpoint at position 3,187 (95% confidence interval: 3,172–3,202; HCV GT1a reference strain H77). Phylogeography is a valuable tool used to reveal viral migration dynamics. Inference of the timed history of spread in a Bayesian framework identified Russia as the ancestral source of the CRF 2k/1b clade. Further, we found evidence for migration routes leading out of Russia to other former Soviet Republics or countries under the Soviet sphere of influence. These findings suggest an interplay between geopolitics and the historical spread of CRF 2k/1b.
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