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46 results for “geographical origin”
Data from: Shared genetic diversity across the global invasive range of the Monk parakeet suggests a common restricted geographic origin and the possibility of convergent selection
While genetic diversity is hypothesized to be an important factor explaining invasion success, there is no consensus yet on how variation in source populations or demographic processes affects invasiveness. We used mitochondrial DNA haplotypic and microsatellite genotypic data to investigate levels of genetic variation and reconstruct the history of replicate invasions on three continents in a globally invasive bird, the monk parakeet (Myiopsitta monachus). We evaluated whether genetic diversity at invasive sites could be explained by (i) the native source populations from which they were derived and (ii) demographic bottlenecks during introduction. Genetic data indicated a localized source area for most sampled invasive populations, with limited evidence for admixing of native source populations. This pattern largely coincides with historical data on pet trade exports. However, the invasive populations are genetically more similar than predicted from the export data alone. The extent of bottleneck effects varied among invasive populations. The observed low genetic diversity, evidence of demographic contraction and restricted source area do not support the hypothesis that invasion is favoured by the mixing and recombining of genetic variation from multiple source populations. Instead, they suggest that reduced genetic variation through random processes may not inhibit successful establishment and invasion in this species. However, convergent selection across invasive sites could also explain the observed patterns of reduction and similarity in genetic variation and/or the restricted source area. In general, the alternative explanation of intraspecific variation in invasive potential among genotypes or geographic areas is neglected, but warrants more attention as it could inform comparative studies and management of biological invaders.
Data from: A hypervariable mitochondrial protein coding sequence associated with geographical origin in a cosmopolitan bloom-forming alga, Heterosigma akashiwo
Geographic distributions of phytoplankton species can be defined by events on both evolutionary time and shorter scales, e.g., recent climate changes. Additionally, modern industrial activity, including the transport of live fish and spat for aquaculture and aquatic microorganisms in ship ballast water, may aid the spread of phytoplankton. Obtaining a reliable marker is key to gaining insight into the phylogeographic history of a species. Here, we report a hypervariable mitochondrial gene in the cosmopolitan bloom-forming alga, Heterosigma akashiwo. We compared the entire mitochondrial genome sequences of seven H. akashiwo strains from Japanese and North American coastal waters and identified a hypervariable segment. The region codes for a hypothetical protein with no defined function, and its variations between Japanese and North American isolates, were prominent, while the sequences were more conserved among Japanese strains and North American isolates. Comparison of the sequence in isolates obtained from different geographical points in the Northern Hemisphere revealed that the sequence variations largely correlated with latitude and longitude (i.e. Pacific/Atlantic oceans). Our results demonstrate the usefulness of the sequence in determining the phylogeographic history of H. akashiwo.
Data from: Plant geographic origin and phylogeny as potential drivers of community structure in root-inhabiting fungi
1. Root-inhabiting fungal communities, including mutualists and antagonists, influence host plant performance, and can potentially shape plant community composition. However, there is uncertainty about how root-inhabiting fungal communities are structured, and if fungal community characteristics are significant predictors of host plant abundance. 2. In this study, we first assessed how root-inhabiting fungal communities were structured in relation to the phylogeny and geographic origins (native vs exotic) of their host plants in an old-field community. In addition, we took into consideration the spatial arrangements (i.e. physical locations) of the individual host plants. We then tested if the relative abundances of pathogenic and beneficial arbuscular mycorrhizal (AM) fungi could predict host plant abundances. 3. We found that host plant phylogeny was an important factor in structuring the whole fungal community, irrespective of host plant origin. Furthermore, the spatial arrangements of individual host plants were a strong predictor of AM fungal community structure. Host plant phylogeny and spatial arrangements appeared to similarly affect the structure of pathogenic fungal communities. No distinct differences were observed between native and exotic plant species in fungal community characteristics. The relative abundances of AM and pathogenic fungi were not significant predictors for observed abundances of their host plants. 4. Synthesis. Host plant phylogeny and spatial arrangements can structure naturally occurring root-inhabiting fungal communities. The absence of distinct differences in fungal community composition, including pathogens, in exotic and native plants suggests long residence times and the consequent naturalization of exotic species in the region, allowing for the establishment of similar plant-microbial interactions between native and exotic species.
Competing Technologies: Determining the Geographical Origin of Strawberries (Fragaria × ananassa) using laboratory based Near-Infrared Spectroscopy compared to a simple portable device
<p><span>The application and development of fast and simple screening methods for the authentication of foods has increased continuously in recent years. A widely used analytical technique is Fourier transform near-infrared spectroscopy (FT-NIR). Despite the simple application of FT-NIR analysis, the analyses are usually carried out on benchtop devices in the laboratory. However small, inexpensive and mobile NIR devices could be used on-site. Despite the simple use of FT-NIR analysis, the examinations are usually carried out on a stationary benchtop device in a laboratory. However, in order to be able to perform the application directly on site, the application of small, cost-effective and mobile NIR devices for food analysis is crucial. In this study, both, a benchtop NIR instrument and a handheld NIR device with a lower resolution and analyzed wavenumber range were applied for the differentiation of strawberries from different geographical origins. Distinguishing German and non-German strawberries using linear discriminant analysis (LDA) yielded an accuracy of 91.9 % and 84.0 % using the benchtop and the handheld devices, respec-tively. Relevant variables could be assigned to lipids, carbohydrates and proteins. Overall, our study demonstrated for the first time that analyzing the geographical origin of strawberries using NIR spectroscopy is also possible by means of a handheld device.</span></p>
Figure 2 in Insights into the geographical origin and phylogeographical patterns of Paradisaea birds-of-paradise
Figure 2. BEAST MCC tree of Paradisaea. Grey node bars (95% highest posterior densities) and support values (circles on branches: BS = RAxML bootstrap values, PP = MrBayes posterior probabilities, BPP = BEAST posterior probabilities) are only provided for major nodes/clades (node numbers N1–N13, Clades 1–3) discussed in the text and in Figure 3 and Table 2. Bird-of-paradise illustrations (from top to bottom: P. apoda, P. raggiana, P. minor, P. rubra, P. decora, P. guilielmi and P. rudolphi; Lynx Edicions, Barcelona, Spain). Individuals no. 113–115 were originally determined as P. apoda. However, a re-examination revealed that while it is difficult to correctly assign these subadult individuals, their overall body size is indicative of P. raggiana.
Data for: Combining stable isotopes, trace elements, and distribution models to assess the geographic origins of migratory bats
<p>The expansion of industrial-scale wind-energy facilities has increased the production of low-carbon emission energy but has also resulted in mortality of wildlife, including migratory bats. Management decisions can be limited by a lack of understanding of the geographic impact of bats killed at wind-energy facilities. Several studies have leveraged stable hydrogen isotope ratios (δ<sup>2</sup>H) of bat fur to illuminate this issue but are limited in the precision of conclusion because δ<sup>2</sup>H values vary primarily across latitudinal and elevational bands. One approach to increase the precision of geographic assignment is to combine independent inferences about spatial location from additional biomarkers and other related information. To test this possibility, we assigned known-origin individuals of three bat species commonly killed at on-shore wind-energy facilities in North America (<em>Lasiurus</em> <em>borealis</em>, <em>L</em>. <em>cinereus</em>, and <em>Lasionycteris</em> <em>noctivagans</em>) to probable origin using δ<sup>2</sup>H values, trace element concentrations, and species distribution models. We used cross-validation calibrated combined model tuning to determine the degree to which assignment probabilities improved when combining datasets. We found that combining markers typically performed better than single approaches. For <em>L. borealis</em> and <em>L. cinereus</em>, combining all three data sources outperformed any single or other combined approach. With an accuracy set at 80%, an average of 39.7% and 36.0% of each species' total geographic range was considered a potential origin, respectively; stable hydrogen alone included 51.8% and 50.6% of the total geographic area. In contrast, for <em>L. noctivagans</em>, including trace elements did not increase precision, and adding distribution data to δ<sup>2</sup>H values only improved precision by 0.6%. Thus, we found that a combination of multiple biomarkers typically, but not always, outperforms single marker approaches, and optimized combinations of different markers outperform equal weighting of each marker. From a practical perspective, δ<sup>2</sup>H values performed better than trace elements alone; in cases where cost is a limiting factor, the stable hydrogen should be the single biomarker used in conjunction with species distribution models. Overall, these results highlight the importance of validating methods for each species they are applied to and show that combining information from intrinsic biomarker approaches is a useful tool to document bat movements.</p>
Data from: Assessing the potential of genotyping-by-sequencing-derived single nucleotide polymorphisms to identify the geographic origins of intercepted gypsy moth (Lymantria dispar) specimens: a proof-of-concept study
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Data from: Understanding geographic origins and history of admixture among chimpanzees in European zoos, with implications for future breeding programmes
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Data for: Combining stable isotopes, trace elements, and distribution models to assess the geographic origins of migratory bats
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Data from: A hypervariable mitochondrial protein coding sequence associated with geographical origin in a cosmopolitan bloom-forming alga, Heterosigma akashiwo
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Data from: Plant geographic origin and phylogeny as potential drivers of community structure in root-inhabiting fungi
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Data from: Inferring the geographic origin of a range expansion: latitudinal and longitudinal coordinates inferred from genomic data in an ABC framework with the program X-ORIGIN
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Data from: Shared genetic diversity across the global invasive range of the Monk parakeet suggests a common restricted geographic origin and the possibility of convergent selection
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Data from: Where do wintering cormorants come from? Long-term changes in the geographical origin of a migratory bird on a continental scale
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Data from: Geographic origins and population genetics of bats killed at wind-energy facilities
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Data from: Domestication and geographic origin of Oryza sativa in China: insights from multilocus analyses of nucleotide variation of O. sativa and O. rufipogon
Previous studies have indicated that China is one of the domestication centres of Asian cultivated rice (Oryza sativa), and common wild rice (O. rufipogon) is the progenitor of O. sativa. However, the number of domestication times and the geographic origin of Asian cultivated rice in China are still under debate. In this study, 100 accessions of Asian cultivated rice and 111 accessions of common wild rice in China were selected to examine the relationship between O. sativa and O. rufipogon and thereby infer the domestication and evolution of O. sativa in China through sequence analyses of six gene regions, trnC-ycf6 in chloroplast genomes, cox3 in mitochondrial genomes and ITS, Ehd1, Waxy, Hd1 in nuclear genomes. The results indicated that the two subspecies of O. sativa (indica and japonica) were domesticated independently from different populations of O. rufipogon with gene flow occurring later from japonica to indica; Southern China was the genetic diversity centre of O. rufipogon, and the Pearl River basin near the Tropic of Cancer was the domestication centre of O. sativa in China.
Data from: Comparing genomic signatures of domestication in two Atlantic salmon (Salmo salar L.) populations with different geographical origins
Selective breeding and genetic improvement have left detectable signatures on the genomes of domestic species. The elucidation of such signatures is fundamental for detecting genomic regions of biological relevance to domestication and improving management practices. In aquaculture, domestication was carried out independently in different locations worldwide, which provides opportunities to study the parallel effects of domestication on the genome of individuals that have been selected for similar traits. In the present study, we aimed to detect potential genomic signatures of domestication in two independent pairs of wild/domesticated Atlantic salmon populations of Canadian and Scottish origins respectively. Putative genomic regions under divergent selection were investigated using a 200K SNP array by combining three different statistical methods based either on allele frequencies (LFMM, Bayescan) or haplotype differentiation (Rsb). We identified 337 and 270 SNPs potentially under divergent selection in wild and hatchery populations of Canadian and Scottish origins respectively. We observed little overlap between results obtained from different statistical methods, highlighting the need to test complementary approaches for detecting a broad range of genomic footprints of selection. The vast majority of the outliers detected were population-specific but we found four candidate genes that were shared between the populations. We propose that these candidate genes may play a role in the parallel process of domestication. Overall, our results suggest that genetic drift may have override the effect of artificial selection and/or point towards a different genetic basis underlying the expression of similar traits in different domesticated strains. Finally, it is likely that domestication may predominantly target polygenic traits (e.g., growth) such that its genomic impact might be more difficult to detect with methods assuming selective sweeps.
Food authentication goes green: Novel DART-MS approach for rapid and environmentally friendly determination of the geographical origin of hazelnuts (Corylus avellana L.)
<p>Dataset of 172 Hazelnut samples of 5 different origins measured using a DART-MS device.</p>
Data from: Comparing genomic signatures of domestication in two Atlantic salmon (Salmo salar L.) populations with different geographical origins
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Data from: Comparison of chemical composition in the buds of Aralia elata from different geographical origins of China
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