Search birdRS Box

Search birdRS blog posts

Browse the Blog Posts

Or scan through the blog archive below for items of interest as only the latest post is shown below, thanks.

Wednesday, 26 February 2014

Great Tit genetic analysis of UK and The Netherlands populations reveals subtle patterns of species level evolution

Title
Replicated high-density genetic maps of two great tit populations reveal fine-scale genomic departures from sex-equal recombination rates

Citation
Heredity (2014) 112, 307–316; doi:10.1038/hdy.2013.107; published online 23 October 2013
Link

Authors
K van Oers 1,6
AW Santure 2,6
I De Cauwer 2,3,6
NEM van Bers 1,4
RPMA Crooijmans 4
BC Sheldon 5
ME Visser 1
J Slate 2
MAM Groenen 4

Affiliations
1 Department of Animal Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands
2 Department of Animal and Plant Sciences, University of Sheffield, Sheffield, UK
3 Laboratoire de Genetique et Evolution des Populations Vege ́tales, UMR CNRS 8198, Batiment SN2, Universite des Sciences et Technologies de Lille - Lille 1, Villeneuve d’Ascq Cedex, France
4 Animal Breeding and Genomics Centre, Wageningen University, De Elst 1, Wageningen, The Netherlands
5 Edward Grey Institute, Department of Zoology, University of Oxford, Oxford, UK
6 These authors contributed equally to this work.
Correspondence: Dr K van Oers, Department of Animal Ecology, Netherlands Institute of Ecology (NIOO-KNAW), P.O. Box 50, 6700 AB Wageningen, The Netherlands. E-mail: k.vanoers@nioo.knaw.nl

Abstract
Linking variation in quantitative traits to variation in the genome is an important, but challenging task in the study of life- history evolution. Linkage maps provide a valuable tool for the unravelling of such trait - gene associations. Moreover, they give insight into recombination landscapes and between-species karyotype evolution. Here we used genotype data, generated from a 10k single-nucleotide polymorphism (SNP) chip, of over 2000 individuals to produce high-density linkage maps of the Great Tit (Parus major), a passerine bird that serves as a model species for ecological and evolutionary questions. We created independent maps from two distinct populations: a captive F2-cross from The Netherlands (NL) and a wild population from the United Kingdom (UK). The two maps contained 6554 SNPs in 32 linkage groups, spanning 2010 cM and 1917 cM for the NL and UK populations, respectively, and were similar in size and marker order. Subtle levels of heterochiasmy within and between chromosomes were remarkably consistent between the populations, suggesting that the local departures from sex-equal recombination rates have evolved. This key and surprising result would have been impossible to detect if only one population was mapped. A comparison with zebra finch (Taeniopygia guttata), chicken (Gallus gallus) and the green anole lizard (Anolis carolinensis) genomes provided further insight into the evolution of avian karyotypes.
-------------------------------------------

Comments
In this study, the authors describe two high-density whole-genome linkage maps of the Great Tit (Parus major), constructed using a set of SNP markers originating from a 9193 SNP Illumina iSelect BeadChip. They genotyped a captive F2 inter-cross population from the Netherlands Institute of Ecology (NIOO-KNAW; n=398), and birds from a wild study population (Wytham Woods; n=1656) near Oxford, UK. 
Studying replicate genetic maps for two independent populations was extremely beneficial and led to the following conclusions:
 Linkage maps produced by two different methods showed that there were no marker inconsistencies at linkage group level (that is, no marker was present on a specific linkage group on one map and present on another linkage group on the other map), and that within the linkage groups there was high consistency between the marker orders in the two populations.
 As linkage group sizes were similar between the wild and captive populations it was suggested that there was no population specific variation in recombination rates across chromosomes.
 The heterogametic sex (females in birds) is hypothesised to have a shorter genetic map due to less recombination however this was not found to be case in these Great Tits. Surprisingly though evidence was found for small differences in recombination rates between sexes (heterochiasmy) that was consistent within and between chromosomes, and across the two populations (see article Figure 3 below).
 Numerous intrachromosomal rearrangements were found when comparing the Great Tit genome to that of the Chicken suggesting that these were genuine evolutionary differences.

Figure 3 (representative cropped section)
Size Dimorphism Index (SDI, y-axis) calculated for windows of 20 SNP markers (marker order, x-axis) on the NL (orange) and UK (blue) framework maps. Positive SDI indicates that female recombination rates within the 20 SNP window was higher; negative values indicate greater recombination rates in males.



Authors Conclusions
"In conclusion, we have constructed high-density linkage maps of two independent great tit populations. The maps will be valuable resources to aid with quantitative trait loci mapping, genome-wide association studies and chromosome partitioning of quantitative genetic variation. More fundamentally, we show that replicated maps constructed using the same SNPs reveal new insight into bird karyotype evolution; in particular a hitherto undetected degree of fine scale heterochiasmy that opens up an exciting new opportunity to study the evolution and fitness consequences of heterochiasmy."

No comments:

Post a Comment