DOI: 10.5061/dryad.gqnk98sh8
title: Genetic assignment of individuals to source populations using network estimation tools

description: Dispersal, the movement of individuals between populations, is crucial in
 many ecological and genetic processes. However, direct identification of
 dispersing individuals is difficult or impossible in natural populations.
 By using genetic assignment methods, individuals with unknown genetic
 origin can be assigned to source populations. This knowledge is necessary
 in studying many key questions in ecology, evolution and conservation. We
 introduce a network-based tool BONE (Baseline Oriented Network Estimation)
 for genetic population assignment, which borrows concepts from undirected
 graph inference. In particular, we use sparse multinomial Least Absolute
 Shrinkage and Selection Operator (LASSO) regression to estimate
 probability of the origin of all mixture individuals and their mixture
 proportions without tedious selection of the LASSO tuning parameter. We
 compare BONE with three genetic assignment methods implemented in R
 packages radmixture, assignPOP and RUBIAS. Probability of the origin and
 mixture proportion estimates of both simulated and real data (an insular
 house sparrow metapopulation and Chinook salmon populations) given by BONE
 are competitive or superior compared to other assignment methods. Our
 examples illustrate how the network estimation method adapts to population
 assignment, combining the efficiency and attractive properties of sparse
 network representation and model selection properties of the L1
 regularization. As far as we know, this is the first approach showing how
 one can use network tools for genetic identification of individuals'
 source populations. BONE is aimed at any researcher performing genetic
 assignment and trying to infer the genetic population structure. Compared
 to other methods, our approach also identifies outlying mixture
 individuals that could originate outside of the baseline populations. BONE
 is a freely available R package under the GPL license and can be
 downloaded at GitHub. In addition to the R package, a tutorial for BONE is
 available at https://github.com/markkukuismin/BONE/.
description: The house sparrow study metapopulation consists of 18 islands
 located in an archipelago off the coast of Helgeland in northern Norway.
 Monitoring of the metapopulation, that covers more than 1600
 km<sup>2</sup> started in 1993 and is still ongoing.
 Population-level data on population sizes, and individual data on year and
 island of birth, information on individual survival, and blood samples for
 DNA were collected annually in the breeding season (May-August) and
 post-breeding season (September-November). Most nestlings, fledged
 juveniles and adults in the study metapopulation have been ringed with a
 numbered metal ring and a unique combination of plastic colour rings.
 This, in combination with intensive recapture and re-sighting efforts, has
 provided high recapture rates (mean: 0.75) and good ecological dispersal
 data, that can be used to, e.g., test the accuracy of genetic assignment
 methods. SNP-genotyping was carried out on house
 sparrows present on 8 islands that differ in microenvironments and habitat
 types depending on the occurrence of livestock and dairy farms (five farm
 islands, and three non-farm islands) and distance from the mainland. On
 the five farm islands, all ringed adult individuals present from 1998 to
 2013 were genotyped, whereas all ringed adult individuals present from
 2003 or 2004 to 2013 were genotyped on the three non-farm islands. A total
 of 3269 adults were genotyped on a custom 200K Affymetrix Axiom SNP array.
 These SNPs are evenly distributed throughout the genome. After rigorous
 quality control, 183,145 SNPs with minor allele frequency above 0.01, and
 3116 individuals with genotyping rate above 0.90 were found suitable. This
 is data of adults present in the year 2012. The data is
 anonymized.
description: The PED file is a white-space (space or tab) delimited file. The
 first six columns are: Family ID
 Individual ID (anonymized) Patternal ID
 (0=missing) Maternal ID (0=missing)
 Sex (0=missing) Phenotype
 Rest columns are genotypes. REF
 file contains the island information of each individual.
 The MAP file is a file, and one line per variant with the
 following fields: Chromosome
 code Variant identifier Position
 in morgans or centimorgans Base-pair
 coordinate