PRDM9 Diversity at Fine Geographical Scale Reveals Contrasting Evolutionary Patterns and Functional Constraints in Natural Populations of House Mice

Abstract

One of the major challenges in evolutionary biology is the identification of the genetic basis of postzygotic reproductive isolation. Given its pivotal role in this process, here we explore the drivers that may account for the evolutionary dynamics of the PRDM9 gene between continental and island systems of chromosomal variation in house mice. Using a data set of nearly 400 wild-caught mice of Robertsonian systems, we identify the extent of PRDM9 diversity in natural house mouse populations, determine the phylogeography of PRDM9 at a local and global scale based on a new measure of pairwise genetic divergence, and analyze selective constraints. We find 57 newly described PRDM9 variants, this diversity being especially high on Madeira Island, a result that is contrary to the expectations of reduced variation for island populations. Our analysis suggest that the PRDM9 allelic variability observed in Madeira mice might be influenced by the presence of distinct chromosomal fusions resulting from a complex pattern of introgression or multiple colonization events onto the island. Importantly, we detect a significant reduction in the proportion of PRDM9 heterozygotes in Robertsonian mice, which showed a high degree of similarity in the amino acids responsible for protein-DNA binding. Our results suggest that despite the rapid evolution of PRDM9 and the variability detected in natural populations, functional constraints could facilitate the accumulation of allelic combinations that maintain recombination hotspot symmetry. We anticipate that our study will provide the basis for examining the role of different PRDM9 genetic backgrounds in reproductive isolation in natural populations.

Keywords: Mus musculus domesticus; PRDM9; Robertsonian fusion; postzygotic reproductive isolation; recombination; selection.

Fig. 1.

Geographical distribution and chromosomal characteristics of the Mus musculus domesticus populations analyzed. (A) Localities sampled in the Barcelona Rb system. Standard populations (blue dots) correspond to mice with 40 acrocentric chromosomes (standard karyotype) whereas Rb populations (red dots) had diploid numbers ranging from 2n = 39 to 2n = 28 (see supplementary table 1, Supplementary Material online, for further details of chromosomes involved in Rb fusions). (B) Localities sampled in the Madeira archipelago. Porto Santo Island is displayed in the inset; it contains standard mice with 40 acrocentric chromosomes (standard karyotype). Six metacentric races have been sampled on the Madeira Island: PEDC, PADC, PLDB, PPOD, PSAN, and PSVI (see supplementary tables 2 and 3, Supplementary Material online, for further details on the chromosomal composition of the chromosomal races). Following previous studies (Britton-Davidian et al. 2000), the chromosomal race PEDC is distributed on both on the northern (PEDC N.) and southern (PEDC S.) coasts of the Madeira Island.

Fig. 2.

Natural PRDM9 allelic diversity found in the Barcelona Rb system and Madeira archipelago Mus musculus domesticus populations. (A) Representation of the mouse PRDM9^Dom2 protein (reference genome, C57/BL6 strain). It consists of four domains: KRAB-like, SSXRD, PR/SET, and ZnF array. The underlined ZnFs represent repeats from position ZnF3 to ZnF6 that bind to the DNA in the mouse (Baker et al. 2015; Paigen and Petkov 2018). (B) Representation of the ZnF alignments for all PRDM9 alleles found in the present study. Each ZnF is color coded based on amino acid sequence affinity found at the most variable sites (−1, +3, +6) responsible for DNA binding. Additional information on ZnF amino acid sequences is provided in supplementary table 5, Supplementary Material online. Purple boxes encompass the more variable ZnF among individuals. Red asterisks indicate previously described PRDM9 alleles (Buard et al. 2014; Capilla et al. 2014; Kono et al. 2014). Geographical labels: (b) PRDM9 alleles found only in the Barcelona Rb system, (b/m) PRDM9 alleles found in both the Barcelona Rb system and the Madeira archipelago. PRDM9 alleles without geographical label correspond to alleles found only in the Madeira archipelago.

Fig. 3.

Allelic frequencies, population structure and phylogeny of the ZnFs found in the Barcelona Rb system. (A) Representation of the PRDM9 allelic frequencies in each locality (see table 1 and supplementary table 1, Supplementary Material online, for further details on the chromosomal composition of each locality). Legend—N, number of specimens sequenced per locality. (B) PCA in a subset of 50 mice from 5 localities of the Barcelona Rb system (CAS, Castelldefels; OLO, Olost; BOI, Castellfollit del Boix; ANO, Sant Sadurní d’Anoia; and MOG, Sta. Perpètua de Mogoda). (C) Plots showing the proportion of inferred ancestry for K = 3 to K = 5 in a subset of 50 mice from 5 localities of the Barcelona system (CAS, Castelldefels; OLO, Olost; BOI, Castellfollit del Boix; ANO, Sant Sadurní d’Anoia; and MOG, Sta. Perpètua de Mogoda). (D) Phylogenetic tree including all mice sequenced from the Barcelona Rb system (see text for further details). PRDM9 alleles are color coded following the pattern used in panel (A). For each individual, both the karyotype (white: standard; red: Rb fusions) and the locality (see inserted color legend) are indicated.

Fig. 4.

Allelic frequencies and phylogeny of the ZnFs found in the Madeira archipelago. (A) Representation of the PRDM9 allelic frequencies found in each metacentric race from the Madeira Island and Porto Santo Island (see supplementary tables 2 and 3, Supplementary Material online, for further details on chromosomal composition of metacentric races). Number of specimens sequenced per locality on Madeira Island: Achadas da Cruz (N = 7), Arco da Calheta (N = 11), Chão da Ribeira (N = 16), Estreito da Calheta (N = 3), Faial (N = 2), Fajã da Ovelha (N = 2), Levada Grande (N = 2), Lombada dos Cedros (N = 1), Lombada dos Marinheiros (N = 4), Lombo da Velha (N = 3), Lombo das Laranjeiras (N = 3), Lombo do Doutor (N = 3), Lugar da Raposeira (N = 2), Madalena do Mar (N = 2), Maloeira (N = 18), Moledos (N = 2), Ponta Delgada (N = 8), Ponta do Pargo (N = 18), Ponta do Sol (N = 3), Porto da Cruz (N = 1), Porto Moniz (N = 3), Prazeres (N = 2), Ribeira da Janela (N = 6), Ribeira da Laje (N = 3), Ribeira da Vaca (N = 3), Ribeira Funda (N = 3), Santa (N = 1), Santana (N = 4), São Vicente (N = 3), Seixal (N = 1), Sítio da Fajã (N = 3), Socorro (N = 7), Solar da Maloeira (N = 1), Solar dos Prazeres (N = 1), and Porto Santo Island (N = 8). (B) Phylogenetic tree including all mice sequenced from the Madeira archipelago (see text for further details). PRDM9 alleles are color coded following the pattern used in panel (A). For each individual, both the diploid number (2n) and the geographical distribution are indicated (see inserted color legend).

Fig. 5.

Conservation in amino acid sequence of the ZnF repeats located in positions 3–6 (ZnF3–ZnF6) along the ZnF array in PRDM9 heterozygous combinations found in the study. (A) Bubble chart representing population frequency (size of the bubble) and the percentage of amino acid (Aa) sequence conservation of the highly variable positions (−1, +3, and +6) of the initial repeats along the array (from ZnF3 to ZnF6) (purple intensity). Data are shown for each heterozygous combination found in Standard and Rb mice in the Barcelona Rb system and the Madeira archipelago (see supplementary table 7, Supplementary Material online, for further details). (B, C) Examples of PRDM9 alleles in heterozygous combination and the predicted distribution of recombination hotspots. Yellow starts represent the location of recombination hotspots across homologous chromosomes (red and blue lines). (B) The ZnF repeats located in positions 3–6 (ZnF3–ZnF6) in the 10A/12E combination present 100% of Aa sequence conservation. This can result in symmetric distribution of recombination hotspot in homologous chromosomes. (C) The ZnF repeats located in positions 3–6 (ZnF3–ZnF6) in the 10B/11B combination present 33.3% of Aa sequence conservation. This can result in asymmetric distribution of recombination hotspot in homologous chromosomes.

Fig. 6.

Phylogeographic depiction of PRDM9 at a global scale. Phylogenetic reconstruction including mice sequenced from the Madeira archipelago, Barcelona Rb system and Eurasia (data extracted from Kono et al. [2014] and Buard et al. [2014]). For each individual, both the diploid number (2n) and the geographical distribution (Madeira, Barcelona, and Eurasia) are indicated (see inserted legends). The diploid number is not known for Eurasian samples so they are represented in gray.