Genomic Porosity between Invasive <i>Chondrostoma nasus</i> and Endangered Endemic <i>Parachondrostoma toxostoma</i> (Cyprinidae): The Evolution of MHC IIB Genes

<div><p>Two cyprinid species, <i>Parachondrostoma toxostom</i>a, an endemic threatened species, and <i>Chondrostoma nasus</i>, an invasive species, live in sympatry in southern France and form two sympatric zones where the presence of intergeneric hybrids is reported. To estimate the potential threat to endemic species linked to the introduction of invasive species, we focused on the DAB genes (functional MHC IIB genes) because of their adaptive significance and role in parasite resistance. More specifically, we investigated (1) the variability of MHC IIB genes, (2) the selection pattern shaping MHC polymorphism, and (3) the extent to which trans-species evolution and intergeneric hybridization affect MHC polymorphism.</p><p>In sympatric areas, the native species has more diversified MHC IIB genes when compared to the invasive species, probably resulting from the different origins and dispersal of both species. A similar level of MHC polymorphism was found at population level in both species, suggesting similar mechanisms generating MHC diversity. In contrast, a higher number of <i>DAB</i>-like alleles per specimen were found in invasive species. Invasive species tended to express the alleles of two <i>DAB</i> lineages, whilst native species tended to express the alleles of only the <i>DAB3</i> lineage. Hybrids have a pattern of MHC expression intermediate between both species. Whilst positive selection acting on peptide binding sites (PBS) was demonstrated in both species, a slightly higher number of positively selected sites were identified in <i>C. nasus</i>, which could result from parasite-mediated selection. Bayesian clustering analysis revealed a similar pattern of structuring for the genetic variation when using microsatellites or the MHC approach. We confirmed the importance of trans-species evolution for MHC polymorphism. In addition, we demonstrated bidirectional gene flow for MHC IIB genes in sympatric areas. The positive significant correlation between MHC and microsatellites suggests that demographic factors may contribute to MHC variation on a short time scale.</p></div

Distribution of <i>DAB</i>-like alleles in <i>P. toxostoma</i> (A), <i>C. nasus</i> (B), and hybrid (C) specimens.

<p>Distribution of <i>DAB</i>-like alleles in <i>P. toxostoma</i> (A), <i>C. nasus</i> (B), and hybrid (C) specimens.</p

Microsatellite diversity for <i>P. toxostoma</i> populations (PT), <i>C. nasus</i> populations (CN) and hybrid sample (H) including number of different alleles (N_a), number of private alleles, allelic richness per sample with sample size >8 (i.e. per population or hybrid sample).

<p>n. e. – not evaluated.</p

Frequency of the <i>DAB1</i> and <i>DAB3</i> expression patterns in <i>P. toxostoma</i> and <i>C. nasus</i> populations.

<p>Frequency of the <i>DAB1</i> and <i>DAB3</i> expression patterns in <i>P. toxostoma</i> and <i>C. nasus</i> populations.</p

Genetic structure of <i>P. toxostoma</i> and <i>C. nasus</i> populations in MHC IIB genes and microsatellites.

<p>Genetic structure of <i>P. toxostoma</i> and <i>C. nasus</i> populations in MHC IIB genes (A, B) and microsatellites (C) inferred from Structure analysis for K = 2. The squares, circles and triangles correspond to <i>C. nasus</i>, <i>P. toxostoma</i> and hybrids identification based on the cyt <i>b</i> and microsatellites. Assignment of populations and hybrid samples to <i>P. toxostoma</i> and <i>C. nasus</i> clusters using MHC IIB genes is shown on the map (A).</p

Log-likelihood values and parameter estimates under random-site models for <i>P. toxostoma</i> and <i>C. nasus</i>.

<p>The number following the model code given in parentheses represents the number of free parameters for the ω ratios. Parameters in parentheses are presented for clarity only but are not free parameters; for example, under M8 <i>p</i>1 = 1-<i>p</i>0; PSS are the positive selected sites identified using the BEB method at.</p>*<p>: P>95%;</p>**<p>: P>99%;</p><p>ω is the selection parameter; p_n is the proportion of sites that fall into the ω_n site class; p and q are the shape parameters of the β function (for M7 and M8 models).</p

The neighbour-joining tree including all <i>DAB</i>-like alleles identified in <i>P. toxostoma</i> and <i>C. nasus</i>.

<p>The alleles found in pure specimens of both species, i.e. <i>P. toxostoma</i> (<i>Pato-DAB</i> alleles) and <i>C. nasus</i> (<i>Chna-DAB</i> alleles), are shown in black. The alleles shared between two species are shown in red, and those identified exclusively in hybrids are shown in green; both of them are termed as <i>Pctn-DAB</i> alleles. All alleles found in hybrids (i.e. species-specific, common or exclusively hybrid) are shown with #. Bootstrap values >50% are shown.</p

The average rates of non-synonymous (d_N) and synonymous (d_S) substitutions (mean and standard errors obtained using 1000 bootstrap replicates), Z-test of positive selection with p-value included.

<p>The average rates of non-synonymous (d_N) and synonymous (d_S) substitutions (mean and standard errors obtained using 1000 bootstrap replicates), Z-test of positive selection with p-value included.</p

Populations of <i>P. toxostoma</i> (PT) and <i>C. nasus</i> (CN) studied plus sample sizes for hybrids (H) in sympatric zones.

<p>The total number of <i>DAB</i>-like alleles, number of <i>DAB1</i>-like alleles and number of <i>DAB3</i>-like alleles in a population, and number of alleles per specimen (min - max, mean with standard deviation) are included. n. e. - not evaluated because of low sample size.</p

Bayesian clustering analyses of microsatellites using Structure.

<p>Estimated population structure for population samples representative of <i>Telestes</i> genus (A) and <i>T. s. souffia</i> (B). “*” indicates K values retained from Δ<i>K </i><a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0034423#pone.0034423-Evanno1" target="_blank">[67]</a> and Δ<i>Fst </i><a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0034423#pone.0034423-Campana1" target="_blank">[64]</a> tests and when maximizing the posterior probability value <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0034423#pone.0034423-Pritchard1" target="_blank">[60]</a>. Between parentheses, the number of convergent runs associated to the structure displayed.</p