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131.
The analysis of genomic data can be an intimidating process, particularly for researchers who are not experienced programmers. Commonly used analyses are spread across many programs, each requiring their own specific input formats, and so data must often be repeatedly reorganized and transformed into new formats. Analyses often require splitting data according to metadata variables such as population or family, which can be challenging to manage in large data sets. Here, we introduce snpR, a user-friendly data analysis package in R for processing SNP genomic data. snpR is designed to automate data subsetting and analyses across categorical metadata while also streamlining repeated analyses by integrating approaches contained in many different packages in a single ecosystem. snpR facilitates iterative and efficient analyses centred on a single R object for an entire analysis pipeline. 相似文献
132.
Paul Savary Jean-Christophe Foltête Hervé Moal Gilles Vuidel Stéphane Garnier 《Molecular ecology resources》2023,23(7):1574-1588
In connectivity models, land cover types are assigned cost values characterizing their resistance to species movements. Landscape genetic methods infer these values from the relationship between genetic differentiation and cost distances. The spatial heterogeneity of population sizes, and consequently genetic drift, is rarely included in this inference although it influences genetic differentiation. Similarly, migration rates and population spatial distributions potentially influence this inference. Here, we assessed the reliability of cost value inference under several migration rates, population spatial patterns and degrees of population size heterogeneity. Additionally, we assessed whether considering intra-population variables, here using gravity models, improved the inference when drift is spatially heterogeneous. We simulated several gene flow intensities between populations with varying local sizes and spatial distributions. We then fit gravity models of genetic distances as a function of (i) the ‘true’ cost distances driving simulations or alternative cost distances, and (ii) intra-population variables (population sizes, patch areas). We determined the conditions making the identification of the ‘true’ costs possible and assessed the contribution of intra-population variables to this objective. Overall, the inference ranked cost scenarios reliably in terms of similarity with the ‘true’ scenario (cost distance Mantel correlations), but this ‘true’ scenario rarely provided the best model goodness of fit. Ranking inaccuracies and failures to identify the ‘true’ scenario were more pronounced when migration was very restricted (<4 dispersal events/generation), population sizes were most heterogeneous and some populations were spatially aggregated. In these situations, considering intra-population variables helps identify cost scenarios reliably, thereby improving cost value inference from genetic data. 相似文献
133.
Brian W. Bowen Anne B. Meylan J. Perran Ross Colin J. Limpus George H. Balazs John C. Avise 《Evolution; international journal of organic evolution》1992,46(4):865-881
To address aspects of the evolution and natural history of green turtles, we assayed mitochondrial (mt) DNA genotypes from 226 specimens representing 15 major rookeries around the world. Phylogenetic analyses of these data revealed (1) a comparatively low level of mtDNA variability and a slow mtDNA evolutionary rate (relative to estimates for many other vertebrates); (2) a fundamental phylogenetic split distinguishing all green turtles in the Atlantic-Mediterranean from those in the Indian-Pacific Oceans; (3) no evidence for matrilineal distinctiveness of a commonly recognized taxonomic form in the East Pacific (the black turtle C.m. agassizi or C. agassizi); (4) in opposition to published hypotheses, a recent origin for the Ascension Island rookery, and its close genetic relationship to a geographically proximate rookery in Brazil; and (5) a geographic population substructure within each ocean basin (typically involving fixed or nearly fixed genotypic differences between nesting populations) that suggests a strong propensity for natal homing by females. Overall, the global matriarchal phylogeny of Chelonia mydas appears to have been shaped by both geography (ocean basin separations) and behavior (natal homing on regional or rookery-specific scales). The shallow evolutionary population structure within ocean basins likely results from demographic turnover (extinction and colonization) of rookeries over time frames that are short by evolutionary standards but long by ecological standards. 相似文献
134.
JAMES MURRAY BRYAN CLARKE 《Biological journal of the Linnean Society. Linnean Society of London》1989,36(1-2):49-54
The pale brown colour morph in Cepaea nemoralis appears to be determined by an allele at the C (colour) locus ( C P B ). Pale brown is dominant to yellow, codominant with pink and recessive to dark brown. It is linked to the B locus (which controls the presence or absence of banding on the shell), but not to the U locus, which determines whether there is one band or five. In segregations of pale brown and yellow there is a significant deficiency of pale brown, suggesting that there are differences in viability between the morphs. 相似文献
135.
We examined population substructure of bottlenose dolphins ( Tursiops sp). in Shark Bay, Western Australia, using 10 highly polymorphic microsatellite loci, and mitochondrial DNA (mtDNA). For microsatellite analysis, 302 different animals were sampled from seven localities throughout the bay. Analysis of genetic differentiation between sampling localities showed a significant correlation between the number of migrants ( Nm ) calculated from F ST , R ST and private alleles, and distance between localities–a pattern of isolation-by-distance. For mtDNA, 220 individuals from all seven localities were sequenced for a 351 base pair fragment of the control region, resulting in eight haplotypes, with two distinct clusters of haplotypes. Values of F ST and (φ)ST for mtDNA yielded statistically significant differences, mostly between localities that were not adjacent to each other, suggesting female gene flow over a scale larger than the sampled localities. We also observed a significant correlation between the number of female migrants calculated from F ST and φST and the distance of sampling localities. Our results indicate that dispersal in female dolphins in Shark Bay is more restricted than that of males. 相似文献
136.
137.
Valérie Copié John A. Battles John M. Schwab Dennis A. Torchia 《Journal of biomolecular NMR》1996,7(4):335-340
Summary Nearly complete backbone 1H, 15N and 13C signal assignments are reported for -hydroxydecanoyl thiol ester dehydrase, a 39-kDa homodimer containing 342 amino acids. Although 15N relaxation data show that the protein has a rotational correlation time of 18 ns, assignments were derived from triple-resonance experiments recorded at 500 MHz and pH 6.8, without deuteration. The Chemical Shift Index, CSI, identified two long helices and numerous -strands in dehydrase. The CSI predictions are in close agreement with the secondary structure identified in the recently derived crystal structure, particularly when one takes account of the numerous bulges in the -strands. The assignment of dehydrase and a large deuterated protein [Yamazaki et al. (1994) J. Am. Chem. Soc., 116, 11655–11666] suggest that assignment of 40–60 kDa proteins is feasible. Hence, further progress in understanding the chemical shift/structure relationship could open the way to determine the structures of such large proteins.
Supplementary Material is available on request, comprising Table S1 listing the spectral parameters; Table S2 listing the assignments; Fig. S1 showing the 2D 1H–15N HSQC spectrum; Fig. S2 showing sequential NOEs, secondary shifts, H-exchange and 3JHN
data; and Fig. S3 showing plots of the H, C, CO and C Chemical Shift Indexes.To whom correspondence should be addressed. 相似文献
138.
Sjaak Peelen Sybren S. Wijmenga Paul J. A. Erbel Robert L. Robson Robert R. Eady Jacques Vervoort 《Journal of biomolecular NMR》1996,7(4):315-330
Summary The 1H, 15N and 13C backbone and 1H and 13C beta resonance assignments of the long-chain flavodoxin from Azotobacter chroococcum (the 20-kDa nifF product, flavodoxin-2) in its oxidized form were made at pH 6.5 and 30°C using heteronuclear multidimensional NMR spectroscopy. Analysis of the NOE connectivities, together with amide exchange rates, 3JHnH coupling constants and secondary chemical shifts, provided extensive solution secondary structure information. The secondary structure consists of a five-stranded parallel -sheet and five -helices. One of the outer regions of the -sheet shows no regular extended conformation, whereas the outer strand 4/6 is interrupted by a loop, which is typically observed in long-chain flavodoxins. Two of the five -helices are nonregular at the N-terminus of the helix. Loop regions close to the FMN are identified. Negatively charged amino acid residues are found to be mainly clustered around the FMN, whereas a cluster of positively charged residues is located in one of the -helices. Titration of the flavodoxin with the Fe protein of the A. chroococcum nitrogenase enzyme complex revealed that residues Asn11, Ser68 and Asn72 are involved in complex formation between the flavodoxin and Fe protein. The interaction between the flavodoxin and the Fe protein is influenced by MgADP and is of electrostatic nature.Abbreviations SQ
semiquinone
- FMN
riboflavin 5-monophosphate; nif, nitrogen fixation
- TSP
3-(trimethylsilyl)propionate sodium salt
- DSS
2,2-dimethyl-2-silapentane-5-sulfonate sodium salt
Supplementary Material is available on request, comprising a Materials and Methods section for the expression and purification of the A. chroococcum flavodoxin, a Table S1 containing the parameters of the titration of A. chroococcum flavodoxin with the Fe protein, and a Table S2 containing the 15N, HN, 13C, 1H, 13C, 1H and 13CO chemical shifts.To whom correspondence should be addressed. 相似文献
139.
Summary Sequence-specific 1H and 15N resonance assignments have been made for 137 of the 146 nonprolyl residues in oxidized Desulfovibrio desulfuricans [Essex 6] flavodoxin. Assignments were obtained by a concerted analysis of the heteronuclear three-dimensional 1H-15N NOESY-HMQC and TOCSY-HMQC data sets, recorded on uniformly 15N-enriched protein at 300 K. Numerous side-chain resonances have been partially or fully assigned. Residues with overlapping 1HN chemical shifts were resolved by a three-dimensional 1H-15N HMQC-NOESY-HMQC spectrum. Medium-and long-range NOEs, 3JNH
coupling constants, and 1HN exchange data indicate a secondary structure consisting of five parallel -strands and four -helices with a topology similar to that of Desulfovibrio vulgaris [Hidenborough] flavodoxin. Prolines at positions 106 and 134, which are not conserved in D. vulgaris flavodoxin, contort the two C-terminal -helices.Abbreviations CSI
chemical shift index
- DQF-COSY
double-quantum-filtered correlation spectroscopy
- DIPSI
decoupling in the presence of scalar interactions
- FMN
flavin mononucleotide
- GARP
globally optimized alternating phase rectangular pulse
- HMQC
heteronuclear multiple-quantum coherence
- HSQC
heteronuclear single-quantum coherence
- NOE
nuclear Overhauser effect
- NOESY
nuclear Overhauser enhancement spectroscopy
- TOCSY
total correlation spectroscopy
- TPPI
time-proportional phase increments
- TSP
3-(trimethylsilyl)propionic-2,2,3,3-d
4 acid, sodium salt 相似文献
140.
毛细管气相色谱/质谱/计算机联用仪器分析结果表明,在四川省成都市一人工种植的银木(Cinnamomumseptentrionale)种群中,其枝叶精油主要化学组成在各植株间存在很大差异,发现精油存在1,8-桉叶油素,樟脑,异丁香酚甲醇和9-氧代橙花叔醇等四个化学类型.除异丁香酚甲醚类型外,其余类型均为第一次报道.综观樟属其它种的化学类型研究可见,化学类型在樟属植物中普遍存在种内多型性和种间共性. 相似文献