TY - JOUR
T1 - Patterns of population structure and complex haplotype sharing among field isolates of the green alga Chlamydomonas reinhardtii
AU - Craig, Rory J.
AU - Böndel, Katharina B.
AU - Arakawa, Kazuharu
AU - Nakada, Takashi
AU - Ito, Takuro
AU - Bell, Graham
AU - Colegrave, Nick
AU - Keightley, Peter D.
AU - Ness, Rob W.
N1 - Funding Information:
We thank Ahmed Hasan for useful discussions and comments on the manuscript and Yuki Takai for technical assistance in sequencing. We thank three anonymous reviewers for their insightful comments on an earlier version of this manuscript. This project was funded by a grant from the UK Biotechnology and Biological Sciences Research Council (BBSRC) and has received funding from the European Research Council under the European Union's Horizon 2020 research and innovation programme (grant agreement no. 694212). This work was also supported in part by research funds from the Yamagata Prefectural Government and Tsuruoka City, Japan. Rory Craig is supported by a BBSRC EASTBIO Doctoral Training Partnership grant, and Rob Ness is supported by a Natural Sciences and Engineering Research Council discovery grant and Canada Foundation for Innovation JELF.
Publisher Copyright:
© 2019 John Wiley & Sons Ltd
PY - 2019/9/1
Y1 - 2019/9/1
N2 - The nature of population structure in microbial eukaryotes has long been debated. Competing models have argued that microbial species are either ubiquitous, with high dispersal and low rates of speciation, or that for many species gene flow between populations is limited, resulting in evolutionary histories similar to those of macroorganisms. However, population genomic approaches have seldom been applied to this question. Here, we analyse whole-genome resequencing data for all 36 confirmed field isolates of the green alga Chlamydomonas reinhardtii. At a continental scale, we report evidence for putative allopatric divergence, between both North American and Japanese isolates, and two highly differentiated lineages within N. America. Conversely, at a local scale within the most densely sampled lineage, we find little evidence for either spatial or temporal structure. Taken together with evidence for ongoing admixture between the two N. American lineages, this lack of structure supports a role for substantial dispersal in C. reinhardtii and implies that between-lineage differentiation may be maintained by reproductive isolation and/or local adaptation. Our results therefore support a role for allopatric divergence in microbial eukaryotes, while also indicating that species may be ubiquitous at local scales. Despite the high genetic diversity observed within the most well-sampled lineage, we find that pairs of isolates share on average ~9% of their genomes in long haplotypes, even when isolates were sampled decades apart and from different locations. This proportion is several orders of magnitude higher than the Wright–Fisher expectation, raising many further questions concerning the evolutionary genetics of C. reinhardtii and microbial eukaryotes generally.
AB - The nature of population structure in microbial eukaryotes has long been debated. Competing models have argued that microbial species are either ubiquitous, with high dispersal and low rates of speciation, or that for many species gene flow between populations is limited, resulting in evolutionary histories similar to those of macroorganisms. However, population genomic approaches have seldom been applied to this question. Here, we analyse whole-genome resequencing data for all 36 confirmed field isolates of the green alga Chlamydomonas reinhardtii. At a continental scale, we report evidence for putative allopatric divergence, between both North American and Japanese isolates, and two highly differentiated lineages within N. America. Conversely, at a local scale within the most densely sampled lineage, we find little evidence for either spatial or temporal structure. Taken together with evidence for ongoing admixture between the two N. American lineages, this lack of structure supports a role for substantial dispersal in C. reinhardtii and implies that between-lineage differentiation may be maintained by reproductive isolation and/or local adaptation. Our results therefore support a role for allopatric divergence in microbial eukaryotes, while also indicating that species may be ubiquitous at local scales. Despite the high genetic diversity observed within the most well-sampled lineage, we find that pairs of isolates share on average ~9% of their genomes in long haplotypes, even when isolates were sampled decades apart and from different locations. This proportion is several orders of magnitude higher than the Wright–Fisher expectation, raising many further questions concerning the evolutionary genetics of C. reinhardtii and microbial eukaryotes generally.
KW - Chlamydomonas reinhardtii
KW - admixture
KW - genetic differentiation
KW - identity by descent
KW - microbial eukaryotes
KW - population structure
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U2 - 10.1111/mec.15193
DO - 10.1111/mec.15193
M3 - Article
C2 - 31338894
AN - SCOPUS:85072508942
VL - 28
SP - 3977
EP - 3993
JO - Molecular Ecology
JF - Molecular Ecology
SN - 0962-1083
IS - 17
ER -