Linkage Map ofLissotritonNewts Provides Insight into the Genetic Basis of Reproductive Isolation

Abstract

Linkage maps are widely used to investigate structure, function, and evolution of genomes. In speciation research, maps facilitate the study of the genetic architecture of reproductive isolation by allowing identification of genomic regions underlying reduced fitness of hybrids. Here we present a linkage map for European newts of the Lissotriton vulgaris species complex, constructed using two families of F2 L. montandoni × L. vulgaris hybrids. The map consists of 1146 protein-coding genes on 12 linkage groups, equal to the haploid chromosome number, with a total length of 1484 cM (1.29 cM per marker). It is notably shorter than two other maps available for salamanders, but the differences in map length are consistent with cytogenetic estimates of the number of chiasmata per chromosomal arm. Thus, large salamander genomes do not necessarily translate into long linkage maps, as previously suggested. Consequently, salamanders are an excellent model to study evolutionary consequences of recombination rate variation in taxa with large genomes and a similar number of chromosomes. A complex pattern of transmission ratio distortion (TRD) was detected: TRD occurred mostly in one family, in one breeding season, and was clustered in two genomic segments. This is consistent with environment-dependent mortality of individuals carrying L. montandoni alleles in these two segments and suggests a role of TRD blocks in reproductive isolation. The reported linkage map will empower studies on the genomic architecture of divergence and interactions between the genomes of hybridizing newts.

Differential introgression across newt hybrid zones: Evidence from replicated transects

“…Although a tendency in the expected direction was found in some cases, in general the differences were subtle and could not establish consistent differences between candidates and the remaining genes. We found a significant geographical cline shift towards Lm in HDM genes, which is in agreement with the direction of segregation distortion in F 2 hybrids (Niedzicka et al, ). In laboratory F 2 hybrids with HDM, Lm alleles showed increased, probably environment‐dependent mortality, so introgression of Lv alleles into the Lm part of the zone could be expected.…”

“…For all nuclear markers, Mendelian segregation within families and a lack of departures from Hardy–Weinberg (HW) expectations in pure populations of each species were confirmed. Most of the genes (92%) were placed on the linkage map (Niedzicka et al, ). Single nucleotide polymorphism (SNP) calling was performed with GATK (details in Appendix ).…”

“…Forty‐one F ST genes and 33 d xy genes were identified from transcriptome resequencing of six Lm and six Lv individuals sampled to encompass the genetic diversity of the species (Stuglik & Babik, ). HDM genes identified in an F 2 hybrid family clustered in two blocks on linkage groups (LG) 4 and 10 (Niedzicka et al, ). The pattern of distortion was consistent with environment‐dependent mortality of F 2 carrying Lm alleles, suggesting a role of these blocks in reproductive isolation.…”

Massive introgression of major histocompatibility complex (MHC) genes in newt hybrid zones

“…To determine MHC class II haplotypes we used the same individuals: parents and offspring from two families of interspecific L. montandoni × L. v. vulgaris crosses (11 and 13 F1 offspring). To estimate linkage between the two MHC classes we compared class I and II genotypes in one of the families (parents and 112 offspring) used previously for the construction of a linkage map (Niedzicka, Dudek, Fijarczyk, Zieliński, & Babik, ).…”

Nonhost wild lettuce as a donor for resistance to downy mildew in cultivated lettuce

“…Many studies on the genetics of speciation have focused on Drosophila (Castillo and Barbash 2017), but studies have also been conducted on other organisms including yeast, nematodes, salamander, African clawed frog and plant species such as Arabidopsis, rice, wheat and Mimulus (Hermsen 1963;Harushima et al 2001;Leppälä et al 2013;Snoek et al 2014;Hou et al 2015;Case et al 2016;Niedzicka et al 2017;Gibeaux et al 2018). BDM genes that cause hybrid lethality or sterility have been reviewed by Presgraves (2010), Rieseberg and Blackman (2010) and Maheshwari and Barbash (2011).…”