Deep sampling of HawaiianCaenorhabditis elegansreveals high genetic diversity and admixture with global populations

Abstract

37 Recent efforts to understand the natural niche of the keystone model organism Caenorhabditis elegans have 38 suggested that this species is cosmopolitan and associated with rotting vegetation and fruits. However, most 39 of the strains isolated from nature have low genetic diversity likely because recent chromosome-scale 40 selective sweeps contain alleles that increase fitness in human-associated habitats. Strains from the Hawaii 41 Islands are highly divergent from non-Hawaiian strains. This result suggests that Hawaiian strains might 42contain ancestral genetic diversity that was purged from most non-Hawaiian strains by the selective sweeps. 43To characterize the genetic diversity and niche of Hawaiian C. elegans, we sampled across the Hawaiian 44Islands and isolated 100 new C. elegans strains. We found that C. elegans strains are not associated with 45any one substrate but are found in cooler climates at high elevations. These Hawaiian strains are highly 46 Page 2 of 23 diverged compared to the rest of the global population. Admixture analysis identified 11 global populations, 47 four of which are from Hawaii. Surprisingly, one of the Hawaiian populations shares recent ancestry with non-48Hawaiian populations, including portions of globally swept haplotypes. This discovery provides the first 49 evidence of gene flow between Hawaiian and non-Hawaiian populations. Most importantly, the high levels of 50 diversity observed in Hawaiian strains might represent the complex patterns of ancestral genetic diversity in 51 the C. elegans species before human influence. 52 53Introduction 54Over the last 50 years, the nematode Caenorhabditis elegans has been central to many important 55 discoveries in the fields of developmental, cellular, and molecular biology. The vast majority of these insights 56 came from the study of a single laboratory-adapted strain collected in Bristol, England known as N2 (Brenner, 57

Balancing selection of the Intracellular Pathogen Response in natural Caenorhabditis elegans populations

“…Genetic analysis of 330 world-wide C. elegans strains reveals that genetic diversity within the IPR-related palsgenes can be categorized in a few haplotypes worldwide. Importantly, two key-IPR regulators, pals-22 and pals- 25, are in a genomic region carrying signatures of balancing selection. Therefore, distinct pals-22/pals-25 alleles have been maintained in C. elegans populations over time, which suggests different evolutionary strategies exist in IPR regulation.…”

“…In total, we found three major pals-22/pals-25 haplotypes (N2-like, CB4856-like, and WN2002-like) that occur globally ( Fig 2, Table S2). The highest local genetic diversity was found on the Hawaiian islands and pacific region where C. elegans could originate from [25]. The genetic variation in the region where pals-22 and pals-25 are located is estimated to have diverged 10 6 generations ago [26].…”

Balancing selection maintains hyper-divergent haplotypes inC. elegans

“…This remarkable genetic diversity sampled from the Hawaiian Islands suggests that C. elegans likely originated from the Pacific region 12,13 .…”

Dissecting the eQTL Micro-Architecture in Caenorhabditis elegans

“…For instance, polymorphic regulators in genes affecting thermo-sensation may be important for controlling locomotor behavior induced by thermal stress via control neural decision-making (Stegeman et al, 2019). C. elegans is ectothermal and inhabits ecological niches that are prone to rapid temperature fluctuations in Europa (N2), but stable temperatures in Hawaii (CB4856) (Crombie et al, 2019). Hence, in Europe it needs to cope with these sudden temperature changes.…”