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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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Apples are a nutritious food source with significant amounts of polyphenols that contribute to human health and wellbeing, primarily as dietary antioxidants. Although numerous pre- and post-harvest factors can affect the composition of polyphenols in apples, genetics is presumed to play a major role because polyphenol concentration varies dramatically among apple cultivars. Here we investigated the genetic architecture of apple polyphenols by combining high performance liquid chromatography (HPLC) data with ~100,000 single nucleotide polymorphisms (SNPs) from two diverse apple populations. We found that polyphenols can vary in concentration by up to two orders of magnitude across cultivars, and that this dramatic variation was often predictable using genetic markers and frequently controlled by a small number of large effect genetic loci. Using GWAS, we identified candidate genes for the production of quercitrin, epicatechin, catechin, chlorogenic acid, 4-O-caffeoylquinic acid and procyanidins B1, B2, and C1. Our observation that a relatively simple genetic architecture underlies the dramatic variation of key polyphenols in apples suggests that breeders may be able to improve the nutritional value of apples through marker-assisted breeding or gene editing.
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Insect flight is made possible by different morphological structures: wings produce the lift, the thorax drives the wings’ movements and the abdomen serves as a secondary control device. As such, the covariation of these structures could reflect functional constraints related to flight performances. This study examines evolutionary convergences in wasp body shapes to provide the first evidence for morphological integration between insect wings, thorax and abdomen. Shapes of the fore- and hindwings, thorax and petiole (connecting abdomen and thorax) of 22 Vespidae species were analyzed using computerized tomography and geometric morphometrics. Results show a clear relationship between petiole and wings or thorax shapes, but not between wings and thorax. Wasps with elongated bodies have pointed wings, both features thought to improve flight maneuverability. In contrast, stouter species have rounded wings, which may allow for higher flight speeds. These integration patterns suggest that multiple selective regimes on flight performance, some of them biased towards maneuverability or maximal speed, drove the morphological diversity in Vespidae. The results also suggest that wing shapes evolved under constraints related to the body type they have to lift. The abdomen morphology is thus another factor to take into account to understand the flight performance of insects.
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1. Metabarcoding extra-organismal DNA from environmental samples is now a key technique in aquatic biomonitoring and ecosystem health assessment. However, choice of genetic marker and primer set is a critical consideration when designing experiments, especially so when developing community standards and legislative frameworks. Mitochondrial cytochrome c oxidase subunit I (COI), the standard DNA barcode marker for animals, with its extensive reference library, taxonomic discriminatory power, and predictable sequence variation, is the natural choice for many metabarcoding applications such as the bulk sequencing of invertebrates. However, the overall utility of COI for environmental sequencing of targeted taxonomic groups has yet to be fully scrutinised. 2. Here, by using a case study of marine and freshwater fishes from the British Isles, we quantify the in silico performance of twelve mitochondrial primer pairs from COI, cytochrome b, 12S and 16S, in terms of reference library coverage, taxonomic discriminatory power, and primer universality. We subsequently test in vitro three COI primer pairs and one 12S pair for their specificity, reproducibility, and congruence with independent datasets derived from traditional survey methods at five estuarine and coastal sites in the English Channel and North Sea coast. 3. Our results show that for aqueous extra-organismal DNA at low template concentrations, both metazoan and fish-targeted COI primers perform poorly in comparison to 12S, exhibiting low levels of reproducibility due to non-specific amplification of prokaryotic and non-target eukaryotic DNAs. 4. An ideal metabarcode would have an extensive reference library for which custom primer sets can be designed for either broad assessments of biodiversity or taxon specific surveys, but unfortunately, low primer specificity hinders the use of COI, while the paucity of reference sequences is problematic for 12S. The latter, however, can be mitigated by expanding the concept of DNA barcodes to include whole mitochondrial genomes generated by genome-skimming existing tissue collections.
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Aim: Explore the spatial variation of the relationships between species richness (SR), phylogenetic diversity (PD) and environmental factors to infer the possible mechanisms underlying patterns of diversity in different regions of the globe. Location: Global. Time period: Present day. Major taxa studied: Terrestrial mammals. Methods: We used a hexagonal grid to map SR and PD of mammals and four environmental factors (temperature, productivity, elevation and climate-change velocity since the Last Glacial Maximum). We related those variables through direct and indirect pathways using a novel combination of Path Analysis and Geographically Weighted Regression to account for spatial non-stationarity of path coefficients. Results: SR, PD and environmental factors relate differently across the geographic space, with most relationships varying in both, magnitude and direction. Species richness is associated with lower phylogenetic diversity in much of the tropics and in the Americas, which reflects the tropical origin and the recent diversification of some mammalian clades in these regions. Environmental effects on PD are predominantly mediated by their effects on SR. But once richness is controlled for, the relationships between environmental factors and PD (i.e. PDSR) highlight environmentally driven changes in species composition. Environmental-PDSR relationships suggest that the relative importance of different mechanisms driving biodiversity shifts spatially. Across most of the globe, temperature and productivity are the strongest predictors of richness, while PDSR is best predicted by temperature. Main conclusions: Richness explains most spatial variation in PD, but both dimensions of biodiversity respond differently to environmental conditions across the globe, as indicated by the spatial mismatches in the relationships between environmental factors and these two types of diversity. We show that accounting for spatial non-stationarity and environmental effects on PD while controlling for richness uncovers a more complex scenario of drivers of biodiversity than previously observed.
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