DOI: 10.5061/dryad.3bk3j9km1
title: Hybridisation boosts dispersal of two contrasted ecotypes in a grass species

description: Genetic exchanges between closely related groups of organisms with
 different adaptations have well-documented beneficial and detrimental
 consequences. In plants, pollen-mediated exchanges affect the sorting of
 alleles across physical landscapes, and influence rates of hybridisation.
 How these dynamics affect the emergence and spread of novel ecological
 strategies remains only partially understood. Here, we use phylogenomics
 and population genomics to retrace the origin and spread of two
 geographically overlapping ecotypes of the African grass Alloteropsis
 angusta. Besides an ecotype inhabiting wetlands, we report the existence
 of a previously undescribed ecotype inhabiting miombo woodlands and
 grasslands. The two ecotypes are consistently associated with different
 nuclear groups, which represent an advanced stage of divergence with
 secondary low-level gene flow. However, the seed-transported chloroplast
 genomes are consistently shared by distinct ecotypes inhabiting the same
 region. These patterns suggest that the nuclear genome of one ecotype can
 reach the seeds of the other via occasional pollen movements with sorting
 of nuclear groups in subsequent generations. The contrasting ecotypes of
 A. angusta can thus use each other as a gateway to new locations across a
 large part of Africa, showing that hybridisation can facilitate the
 geographical dispersal of distinct ecotypes of the same grass species.
description: Samples of <i>Alloteropsis angusta</i> were obtained
 from herbaria, or from fieldwork conducted in Uganda, Tanzania and
 Zambia. When <i>A. angusta</i> and <i>A.
 semialata</i> grew together, both were sampled. Whole genomes of
 <i>A. angusta</i> were sequenced here as 150-bp or 250-bp
 paired-end Illumina reads or retrieved from previous studies together with
 those of <i>A. semialata</i> and <i>A.
 cimicina</i> (Table S1). Raw reads obtained from fresh samples were
 cleaned using NGS QC Toolkit v.2.3.3 [30] to remove reads with more than
 20% of bases with a quality score below Q20, and those which had ambiguous
 bases. Bases with quality score below Q20 were further trimmed from the 3’
 end of reads. Adaptors were removed using NxTrim. New sequences can be
 found on the NCBI SRA under project number PRJNA715711. Cleaned reads were
 aligned to the <em>A. semialata </em>reference using bowtie2
 with default settings for paired end reads. and read processing scripts
 can be found
 at https://github.com/evcurran/Angusta-Pop-Genomics.
 The genomes of population-level samples were scanned using
 restriction site associated DNA (RAD) sequencing. In brief, the DNA of up
 to five individuals of each population (more in ZAM1930 where the two
 morphs occurred) were double digested and then pooled before sequencing 72
 – 96 individuals per lane of Illumina HiSeq 2500. Our final dataset
 included 196 <i>A. angusta </i>individuals. Raw RAD-sequencing
 reads were trimmed with Trimmomatic [40] to remove adaptor and other
 Illumina-specific sequences and bases with a low quality score (Q &lt;
 3) from the 5’ and 3’ ends. Reads were further clipped when the average
 quality within a sliding window of four bases dropped below 15. Reads were
 de-multiplexed using the module ‘process_radtags’ of STACKS [41], and they
 were mapped to the <i>A. semialata </i>reference<i>
 </i>genome using Bowtie2 with default settings for paired-end
 reads.
description: The alignment files are provided in the BAM format, the sample
 name is in the filename, and the relevant individual sample information
 can be found in Table S1.