Global population genetic structure of Caenorhabditis remanei reveals incipient speciation

Abstract

Mating system transitions dramatically alter the evolutionary trajectories of genomes that can be revealed by contrasts of species with disparate modes of reproduction. For such transitions in Caenorhabditis nematodes, some major causes of genome variation in selfing species have been discerned. And yet, we have only limited understanding of species-wide population genetic processes for their outcrossing relatives, which represent the reproductive state of the progenitors of selfing species. Multilocus-multipopulation sequence polymorphism data provide a powerful means to uncover the historical demography and evolutionary processes that shape genomes. Here we survey nucleotide polymorphism across the X chromosome for three populations of the outcrossing nematode Caenorhabditis remanei and demonstrate its divergence from a fourth population describing a closely related new species from China, C. sp. 23. We find high genetic variation globally and within each local population sample. Despite geographic barriers and moderate genetic differentiation between Europe and North America, considerable gene flow connects C. remanei populations. We discovered C. sp. 23 while investigating C. remanei, observing strong genetic differentiation characteristic of reproductive isolation that was confirmed by substantial F2 hybrid breakdown in interspecific crosses. That C. sp. 23 represents a distinct biological species provides a cautionary example of how standard practice can fail for mating tests of species identity in this group. This species pair permits full application of divergence population genetic methods to obligately outcrossing species of Caenorhabditis and also presents a new focus for interrogation of the genetics and evolution of speciation with the Caenorhabditis model system.

Figure 1

Synonymous-site nucleotide diversity (π_syn-JC, Jukes–Cantor corrected for multiple hits) in local population samples of C. remanei and C. sp. 23. Boxplots indicate the median (thick gray bar) and interquartile range of values. Points beyond the whiskers represent potential outliers.

Figure 2

Tajima’s D measure of the site-frequency spectrum for synonymous sites in populations of C. remanei and C. sp. 23. Boxplots show the median (thick gray bar) and interquartile range of values, with points beyond the whiskers indicating potential outliers. Solid boxes indicate values of Tajima’s D that differ significantly from standard neutral expectations; open boxes represent nonsignificant values.

Figure 3

Population differentiation within C. remanei and between C. remanei and C. sp. 23. (A) Boxplots of N_ST (Jukes–Cantor corrected F_ST) for pairs of populations or species showing median (thick gray bar) and interquartile range of values, with values beyond the whiskers indicating potential outliers. (B) Cumulative proportions of fixed, unique, and shared polymorphisms indicate the disparity of population pairs within C. remanei relative to C. sp. 23.

Figure 4

Neighbor network for globally sampled C. remanei and C. sp. 23 based on concatenated sequence for 17 nuclear loci. Population samples of C. remanei (Ohio, Ontario, and Germany) and C. sp. 23 (Wuhan) are color coded. Strains labeled in gray represent geographically isolated samples. Nucleotide distances (Jukes–Cantor corrected) exclude gaps; reticulation indicates potential recombination in the ancestry of the strains.

Figure 5

Mean likelihood and ΔK plot for STRUCTURE runs based on (A) the combined data set of C. remanei and C. sp. 23 and (B) the data set containing only C. remanei strains. Boxplots of the estimated mean likelihood of the data (left axis), given K genetic clusters, indicating the median and interquartile range. Solid circles connected by dashed lines indicate ΔK (right axis).

Figure 6

Clustering analysis from STRUCTURE for the combined data set including strains of C. remanei and C. sp. 23 (A and B) and for the data set restricted to C. remanei strains only (C and D). Cumulative bar plots indicate the percentage ancestry of each strain from each inferred genetic cluster for a given value of K genetic clusters. Each genetic cluster is distinguished by a distinct color; colors are not necessarily equivalent among panels. The panels depict the STRUCTURE run with the highest likelihood for the given K value in the corresponding data partition.

Figure 7

Hybrid breakdown of F₂ progeny between C. remanei and C. sp. 23. Boxplots indicate the median (thick gray bar) and interquartile range of (A) total lifetime F₁ progeny and (B) total lifetime F₂ progeny derived from intrapopulation crosses of C. remanei and C. sp. 23 and crosses between the two species. Points beyond the whiskers indicate potential outliers. Significantly fewer F₂ progeny result from the hybrid cross between C. remanei and C. sp. 23 than from the intraspecies crosses (P < 0.001).