The genomic origin of early maize in eastern North America
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PROVIDER: PRJEB73480 | ENA |
REPOSITORIES: ENA
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Project description:BackgroundThis paper describes 11 of 18 new species recognised in the recent book, "Field Guide to the Flower Flies of Northeastern North America". Four species are omitted as they need to be described in the context of a revision (three Cheilosia and a Palpada species) and three other species (one Neoascia and two Xylota) will be described by F. Christian Thompson in a planned publication. Six of the new species have been recognised for decades and were treated by J. Richard Vockeroth in unpublished notes or by Thompson in his unpublished but widely distributed "A conspectus of the flower flies (Diptera: Syrphidae) of the Nearctic Region". Five of the 11 species were discovered during the preparation of the Field Guide. Eight of the 11 have DNA barcodes available that support the morphology.New informationNew species treated in this paper include: Anasimyia diffusa Locke, Skevington and Vockeroth (Smooth-legged Swamp Fly), Anasimyia matutina Locke, Skevington and Vockeroth (Small-spotted Swamp Fly), Brachyopa caesariata Moran and Skevington (Plain-winged Sapeater), Brachyopa cummingi Moran and Skevington (Somber Sapeater), Hammerschmidtia sedmani Vockeroth, Moran and Skevington (Pale-bristled Logsitter), Microdon (Microdon) scauros Skevington and Locke (Big-footed Ant Fly), Mixogaster fattigi Locke, Skevington and Greene (Fattig's Ant Fly), Neoascia guttata Skevington and Moran (Spotted Fen Fly), Orthonevra feei Moran and Skevington (Fee's Mucksucker), Psilota klymkoi Locke, Young and Skevington (Black Haireye) and Trichopsomyia litoralis Vockeroth and Young (Coastal Psyllid-killer). Common names follow the "Field Guide to the Flower Flies of Northeastern North America" (Skevington et al. 2019).
| S-EPMC6736894 | biostudies-literature
Project description:Heterosis (hybrid vigor) refers to the superior performance of hybrid progeny relative to their parents. Although widely exploited in agriculture, the mechanisms responsible for heterosis are not well understood. As a monoecious organism, a given maize plant can be used as both male and female parents of crosses. Regardless of the cross direction, the maize inbred lines B73 and Mo17 produce hybrids that substantially out-perform their parents. These reciprocal hybrids differ phenotypically from each other despite having identical nuclear genomes. Consistent with these phenotypic observations, 30-50% of genes were differentially expressed between these reciprocal hybrids. An eQTL experiment conducted to better understand the regulation of gene expression in inbred and hybrid lines detected ~4,000 eQTL associations. The majority of these eQTL act in trans to regulate expression of genes on other chromosomes. Surprisingly, many of the trans-eQTL, when heterozygous, differentially regulated transcript accumulation in a manner consistent with gene expression in the hybrid being regulated exclusively by the paternally transmitted allele. The design of the eQTL experiment controlled for cytoplasmic and maternal effects, suggesting that widespread paternal genomic imprinting contributes to the regulation of gene expression in maize hybrids. Keywords: eQTL, parent-of-origin
2009-11-20 | GSE16136 | GEO
Project description:We analyzed the geographic distribution of the Ixodes ricinus-like ticks in eastern North America by comparing the mitochondrial 16S rDNA sequences of specimens sampled directly from the field during the 1990s. Two distinct lineages are evident. The southern clade includes ticks from the southeastern and middle-eastern regions of the United States. The range of the northern clade, which appears to have been restricted to the northeastern region until the mid-1900s, now extends throughout the northeastern and middle-eastern regions. These phyletic units correspond to northern and southern taxa that have previously been assigned specific status as Ixodes dammini and Ixodes scapularis, respectively. The expanding range of I. dammini appears to drive the present outbreaks of zoonotic disease in eastern North America that include Lyme disease and human babesiosis.
| S-EPMC41502 | biostudies-other
Project description:We perform Q Lg tomography for the northeastern part of North America. Vertical broadband seismograms of 473 crustal earthquakes recorded by 302 stations are processed to extract the Lg amplitude spectra. Tomographic inversions are independently conducted at 58 discrete frequencies distributed evenly in log space between 0.1 and 20.0 Hz. This relatively large dataset with good ray coverage allows us to image lateral variation of the crustal attenuation over the region. Obtained Q Lg maps at broadband and individual frequencies provide new insights into the crustal attenuation of the region and its relationship to geological structures and past tectonic activity in the area. The Q Lg shows more uniform values over the older, colder, and drier Canadian Shield, in contrast to higher variations in the younger margins. Results confirm the correlation of large-scale variations with crustal geological features in the area. Existence of low-velocity anomalies, thick sediments, volcanic rocks, and thin oceanic crust are potential sources of observed anomalies. The mean Q values are inversely correlated with average heat flow/generation for main geological provinces.
| S-EPMC5940689 | biostudies-literature
Project description:We report de novo genome assemblies, transcriptomes, annotations, and methylomes for the 26 maize inbreds that serve as the founders for the maize nested association mapping population. The data indicate that the number of pan-genes in maize exceeds 103,000 and that the ancient tetraploid character of maize continues to degrade by fractionation to the present day. Excellent contiguity over repeat arrays and complete annotation of centromeres further revealed the locations and internal structures of major cytological landmarks. We show that combining structural variation with SNPs can improve the power of quantitative mapping studies. Finally, we document variation at the level of DNA methylation, and demonstrate that unmethylated regions are enriched for cis-regulatory elements that correlate with known QTLs and changes in gene expression.
2021-02-01 | GSE165787 | GEO
Project description:Phylogenetic analyses of genes with demonstrated involvement in evolutionary transitions can be an important means of resolving conflicting hypotheses about evolutionary history or process. In sunflower, two genes have previously been shown to have experienced selective sweeps during its early domestication. In the present study, we identified a third candidate early domestication gene and conducted haplotype analyses of all three genes to address a recent, controversial hypothesis about the origin of cultivated sunflower. Although the scientific consensus had long been that sunflower was domesticated once in eastern North America, the discovery of pre-Columbian sunflower remains at archaeological sites in Mexico led to the proposal of a second domestication center in southern Mexico. Previous molecular studies with neutral markers were consistent with the former hypothesis. However, only two indigenous Mexican cultivars were included in these studies, and their provenance and genetic purity have been questioned. Therefore, we sequenced regions of the three candidate domestication genes containing SNPs diagnostic for domestication from large, newly collected samples of Mexican sunflower landraces and Mexican wild populations from a broad geographic range. The new germplasm also was genotyped for 12 microsatellite loci. Our evidence from multiple evolutionarily important loci and from neutral markers supports a single domestication event for extant cultivated sunflower in eastern North America.
| S-EPMC3161615 | biostudies-literature
Project description:A new species of Hydnum subgenus Rufescentia is described based on collections made in Canada (New Brunswick, Newfoundland and Labrador) and the USA (New York). The new species is found in conifer dominated forests (e.g. Abies, Picea) and occurs in bryophyte-covered (Sphagnum, Bazzania) soil. It differs from the ecologically similar H. quebecense in the duller brown colors of the basidiomes, the smaller basidiospores and the basidia predominantly with three or four sterigmata. Phylogenetic analysis of the ITS region place H. subconnatum and H. oregonense as the closest relatives of H. atlanticum, but these taxa differ in the larger basidiospores, number of sterigmata per basidium, caespitose growth and/or geographic distribution. Citation: Justo A, Hood AW, Swenie RA, Matheny PB (2023). Hydnum atlanticum, a new species from Eastern North America. Fungal Systematics and Evolution 11: 63-70. doi: 10.3114/fuse.2023.11.05.
| S-EPMC10956580 | biostudies-literature
Project description:Sambaqui (shellmound) societies are among the most intriguing archaeological phenomena in pre-colonial South America, extending from approximately 8,000 to 1,000 years before present (yr BP) across 3,000 km on the Atlantic coast. However, little is known about their connection to early Holocene hunter-gatherers, how this may have contributed to different historical pathways and the processes through which late Holocene ceramists came to rule the coast shortly before European contact. To contribute to our understanding of the population history of indigenous societies on the eastern coast of South America, we produced genome-wide data from 34 ancient individuals as early as 10,000 yr BP from four different regions in Brazil. Early Holocene hunter-gatherers were found to lack shared genetic drift among themselves and with later populations from eastern South America, suggesting that they derived from a common radiation and did not contribute substantially to later coastal groups. Our analyses show genetic heterogeneity among contemporaneous Sambaqui groups from the southeastern and southern Brazilian coast, contrary to the similarity expressed in the archaeological record. The complex history of intercultural contact between inland horticulturists and coastal populations becomes genetically evident during the final horizon of Sambaqui societies, from around 2,200 yr BP, corroborating evidence of cultural change.
| S-EPMC10406606 | biostudies-literature
Project description:The underlying causes of biodiversity disparities among geographic regions have long been a fundamental theme in ecology and evolution. However, the patterns of phylogenetic diversity (PD) and phylogenetic beta diversity (PBD) of congeners that are disjunctly distributed between eastern Asia-eastern North America (EA-ENA disjuncts) and their associated factors remain unknown. Here we investigated the standardized effect size of PD (SES-PD), PBD, and potentially associated factors in 11 natural mixed forest sites (five in EA and six in ENA) where abundant EA-ENA disjuncts occur. We found that the disjuncts in ENA possessed higher SES-PD than those in EA at the continental scale (1.96 vs -1.12), even though the number of disjunct species in ENA is much lower than in EA (128 vs 263). SES-PD of the EA-ENA disjuncts tended to decrease with increasing latitude in 11 sites. The latitudinal diversity gradient of SES-PD was stronger in EA sites than in ENA sites. Based on the unweighted unique fraction metric (UniFrac) distance and the phylogenetic community dissimilarity, PBD showed that the two northern sites in EA were more similar to the six-site ENA group than to the remaining southern EA sites. Based on the standardized effect size of mean pairwise distances (SES-MPD), nine of eleven studied sites showed a neutral community structure (-1.96 ≤ SES-MPD ≤ 1.96). Both Pearson's r and structural equation modeling suggested that SES-PD of the EA-ENA disjuncts was mostly associated with mean divergence time. Moreover, SES-PD of the EA-ENA disjuncts was positively correlated with temperature-related climatic factors, although negatively correlated with mean diversification rate and community structure. By applying approaches from phylogenetics and community ecology, our work sheds light on historical patterns of the EA-ENA disjunction and paves the way for further research.
| S-EPMC9975473 | biostudies-literature
Project description:Invasive species may rapidly spread throughout new areas once introduced, which may potentially lead to serious damage to local fauna and flora. Information on geographical origins, introduction routes, and biology in native regions of such invasive species is of critical importance in identifying means of transport, preventing reintroduction, and establishing control/eradication methods. The plataspid stinkbug Megacopta cribraria, known as kudzu bug, recently invaded North America and now has become not only an agricultural pest of soybean but also a nuisance pest. Here we investigate the geographical origin of the invasive M. cribraria populations. Phylogeographical analyses based on 8.7 kb mitochondrial DNA sequences of the introduced and East Asian native Megacopta populations identified a well-supported clade consisting of the introduced populations and M. punctatissima populations in the Kyushu region of Japan, which strongly suggests that the invading M. cribraria populations are derived from a M. punctatissima population in the Kyushu region. Therefore, the region is proposed as a promising source of natural enemies for biological control of the invasive pest. Based on the phylogenetic information, relationship and treatment of the two Megacopta species are discussed.
| S-EPMC3923857 | biostudies-literature