Data from: A dedicated target capture approach reveals variable genetic markers across micro- and macro-evolutionary time scales in palms

Understanding the genetics of biological diversification across micro- and
macro-evolutionary time scales is a vibrant field of research for
molecular ecologists as rapid advances in sequencing technologies promise
to overcome former limitations. In palms, an emblematic, economically and
ecologically important plant family with high diversity in the tropics,
studies of diversification at the population and species levels are still
hampered by a lack of genomic markers suitable for the genotyping of large
numbers of recently diverged taxa. To fill this gap, we used a whole
genome sequencing approach to develop target sequencing for molecular
markers in 4,184 genome regions, including 4,051 genes and 133 non-genic
putatively neutral regions. These markers were chosen to cover a wide
range of evolutionary rates allowing future studies at the family, genus,
species and population levels. Special emphasis was given to the avoidance
of copy number variation during marker selection. In addition, a set of
149 well-known sequence regions previously used as phylogenetic markers by
the palm biological research community were included in the target
regions, to open the possibility to combine and jointly analyse already
available data sets with genomic data to be produced with this new
toolkit. The bait set was effective for species belonging to all three
palm subfamilies tested (Arecoideae, Ceroxyloideae and Coryphoideae), with
high mapping rates, specificity and efficiency. The number of high quality
Single Nucleotide Polymorphisms (SNPs) detected at both the subfamily and
population levels facilitates efficient analyses of genomic diversity
across micro- and macro-evolutionary time scales.