ABSTRACT
Identifying sex-linked markers in genomic datasets is important because their presence in supposedly neutral autosomal datasets can result in incorrect estimates of genetic diversity, population structure and parentage. However, detecting sex-linked loci can be challenging, and available scripts neglect some categories of sex-linked variation. Here, we present new R functions to (1) identify and separate sex-linked loci in ZW and XY sex determination systems and (2) infer the genetic sex of individuals based on these loci. We tested these functions on genomic data for two bird and one mammal species and compared the biological inferences made before and after removing sex-linked loci using our function. We found that our function identified autosomal loci with ≥98.8% accuracy and sex-linked loci with an average accuracy of 87.8%. We showed that standard filters, such as low read depth and call rate, failed to remove up to 54.7% of sex-linked loci. This led to (i) overestimation of population FIS by up to 24%, and the number of private alleles by up to 8%; (ii) wrongly inferring significant sex differences in heterozygosity; (iii) obscuring genetic population structure and (iv) inferring ~11% fewer correct parentages. We discuss how failure to remove sex-linked markers can lead to incorrect biological inferences (e.g. sex-biased dispersal and cryptic population structure) and misleading management recommendations. For reduced-representation datasets with at least 15 known-sex individuals of each sex, our functions offer convenient resources to remove sex-linked loci and to sex the remaining individuals (freely available at https://github.com/drobledoruiz/conservation_genomics).
ABSTRACT
In this work, we present a theoretical study of the angular dynamics of small nanoparticles induced by fast non-vortex electron beams. General expressions for the torque and the angular momentum transferred from an electron to an arbitrary-but small-nanoparticle are obtained using a full-retarded classical electrodynamics approach, within the small particle limit. We applied this methodology to study a particular case of interest: the angular dynamics of spherical nanoparticles with homogeneous and isotropic electromagnetic responses. We analytically calculate the total angular momentum transferred from a swift electron to such nanoparticles, finding that it is electric in nature and it is always in a direction determined by the electron trajectory relative to the center of the nanoparticle. We realize that it is possible to represent the angular momentum transferred as the product of two functions: the extinction cross-section of the nanoparticle and a function that only contains information about the swift electron. We present numerical results for the total angular momentum transferred from a swift electron to an aluminum and a gold nanoparticle. We also present an analysis of the temporal behavior of the torque and the electric dipole moment induced within the nanoparticle by the swift electron. We compare the angular momentum transfer calculated in this work with a previously reported case of vortex beams, finding that, for both aluminum and gold nanoparticles, our results are two orders of magnitude smaller. Finally, we consider a particular case of a frictionless gold spherical nanoparticle of radius a=5nm, obtaining that it can spin with an angular frequency up to 29.3Hz.
