Multicollinearity in spatial genetics: separating the wheat from the chaff using commonality analyses.

Direct gradient analyses in spatial genetics provide unique opportunities to describe the inherent complexity of genetic variation in wildlife species and are the object of many methodological developments. However, multicollinearity among explanatory variables is a systemic issue in multivariate regression analyses and is likely to cause serious difficulties in properly interpreting results of direct gradient analyses, with the risk of erroneous conclusions, misdirected research and inefficient or counterproductive conservation measures. Using simulated data sets along with linear and logistic regressions on distance matrices, we illustrate how commonality analysis (CA), a detailed variance-partitioning procedure that was recently introduced in the field of ecology, can be used to deal with nonindependence among spatial predictors. By decomposing model fit indices into unique and common (or shared) variance components, CA allows identifying the location and magnitude of multicollinearity, revealing spurious correlations and thus thoroughly improving the interpretation of multivariate regressions. Despite a few inherent limitations, especially in the case of resistance model optimization, this review highlights the great potential of CA to account for complex multicollinearity patterns in spatial genetics and identifies future applications and lines of research. We strongly urge spatial geneticists to systematically investigate commonalities when performing direct gradient analyses.

Comparative landscape genetic analyses show a Belgian motorway to be a gene flow barrier for red deer (Cervus elaphus), but not wild boars (Sus scrofa).

While motorways are often assumed to influence the movement behaviour of large mammals, there are surprisingly few studies that show an influence of these linear structures on the genetic make-up of wild ungulate populations. Here, we analyse the spatial genetic structure of red deer (Cervus elaphus) and wild boars (Sus scrofa) along a stretch of motorway in the Walloon part of Belgium. Altogether, 876 red deer were genotyped at 13 microsatellite loci, and 325 wild boars at 14 loci. In the case of the red deer, different genetic clustering tools identified two genetic subpopulations whose borders matched the motorway well. Conversely, no genetic structure was identified in the case of the wild boar. Analysis of isolation-by-distance patterns of pairs of individuals on the same side and on different sides of the motorway also suggested that the road was a barrier to red deer, but not to wild boar movement. While telemetry studies seem to confirm that red deer are more affected by motorways than wild boar, the red deer sample size was also much larger than that of the wild boars. We therefore repeated the analysis of genetic structure in the red deer with randomly sub-sampled data sets of decreasing size. The power to detect the genetic structure using clustering methods decreased with decreasing sample size.

Genetic structure and assignment tests demonstrate illegal translocation of red deer (Cervus elaphus) into a continuous population.

Molecular forensic methods are being increasingly used to help enforce wildlife conservation laws. Using multilocus genotyping, illegal translocation of an animal can be demonstrated by excluding all potential source populations as an individual's population of origin. Here, we illustrate how this approach can be applied to a large continuous population by defining the population genetic structure and excluding suspect animals from each identified cluster. We aimed to test the hypothesis that recreational hunters had illegally introduced a group of red deer into a hunting area in Luxembourg. Reference samples were collected over a large area in order to test the possibility that the suspect individuals might be recent immigrants. Due to isolation-by-distance relationships in the data set, inferring the number of genetic clusters using Bayesian methods was not straightforward. Biologically meaningful clusters were only obtained by simultaneously analysing spatial and genetic information using the program baps 4.1. We inferred the presence of three genetic clusters in the study region. Using partial Mantel tests, we detected barriers to gene flow other than distance, probably created by a combination of urban areas, motorways and a river valley used for viticulture. The four focal animals could be excluded with a high certainty from the three genetic subpopulations and it was therefore likely that they had been released illegally.

Structure of fuscopeptins, phytotoxic metabolites of Pseudomonas fuscovaginae.

The structure of the fuscopeptins, bioactive lipodepsipeptides produced in culture by the gramineae pathogen Pseudomonas fuscovaginae, has been determined. The combined use of FAB mass spectroscopy NMR spectroscopy and chemical and enzymatic procedures allowed one to define a peptide moiety corresponding to Z-Dhb-D-Pro-L-Leu-D-Ala-D-Ala-D-Ala-D-Ala-D-Val-Gly-D-Ala-D-Val-D-Ala-D- Val-Z-Dhb-Da-Thr-L-Ala-L-Dab-D-Dab-L-Phe with the terminal carboxyl group closing a macrocyclic ring on the hydroxyl group of the allothreonine residue. The N-terminus is in turn acylated by 3-hydroxyoctanoate in fuscopeptin A and 3-hydroxydecanoate in fuscopeptin B. Some preliminary data on the biological activity of fuscopeptins are also reported.

Variant mitochondrial plasmids of broad bean arose by recombination and are controlled by the nuclear genome.

Various cytoplasms of broad bean contain three mitochondrial plasmids (mtp1, 2 and 3), previously described. In cytoplasm 350 we have observed several additional mitochondrial plasmids, varying in number and in identity according to the nuclear background. Replacement of the nucleus by backcrossing led to the appearance or disappearance of additional plasmids, indicating that the nuclear genome controls either the creation or the copy level of mitochondrial plasmids. Analysis of eight variant additional plasmids (mtp4-11) suggests that they all result from a double recombination event between mtp1 and mtp2. In all cases, one recombination point was located within a 276-bp sequence, identical in both plasmids. For 7 plasmids, the region in which the second recombination event occurred could be narrowed down to a short stretch containing imperfect tandem repeats of a 31-bp motif. The largest sequence shared by the recombination regions was hexanucleotide GCGACG.

Sequence and transcription analysis of mitochondrial plasmids isolated from cytoplasmic male-sterile lines of Vicia faba.

Three mitochondrial plasmids (1704, 1695 and 1478 bp) were isolated from sterile cytoplasms of Vicia faba L. and cloned into a bacterial plasmid vector. Their nucleotide sequence was found to be 99 to 100% homologous to their counterparts isolated from a fertile cytoplasm (J.A. Wahleithner and D.R. Wolstenholme, Curr Genet 12 (1987) 55-76). Several overlapping transcripts were localized in the region which is unique to each of the three plasmids. S1 nuclease mapping indicated for all of them several 3' termini but a unique 5' boundary which was located downstream of the consensus sequence CNTAAGTGANNNNNGAA also found at the transcript 5' boundary of other plant mitochondrial plasmids. Southern blot hybridization with nuclear DNA indicated the presence of nuclear sequences homologous to each plasmid.

Nucleotide sequence and transcriptional analysis of a mitochondrial plasmid from a cytoplasmic male-sterile line of sunflower.

A mitochondrial plasmid of 1,939 bp (P2) from a cytoplasmic male-sterile line of sunflower has been cloned and sequenced. It presents 437 bp of near-perfect homology to the 1.4-kb mitochondrial plasmid P1 from sunflower. Sequences homologous to P2 were found in nuclear DNA. P2 was transcribed into a major 980-nucleotide (nt) RNA molecule and two minor transcripts of 570 and 520 nt. They were all transcribed from the same strand and within the region nonhomologous to P1. A single 5' boundary and three 3' termini were determined for P2 transcripts. The 5' end is similar to a consensus sequence for plant mitochondrial genes. No evidence of translation products can be provided.