Lindsay V. Clark

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We present an R package to help remedy the lack of software for manipulating and analysing autopolyploid and allopolyploid microsatellite data. POLYSAT can handle genotype data of any ploidy, including populations of mixed ploidy, and assumes that allele copy number is always ambiguous in partial heterozygotes. It can import and export genotype data in(More)
In facultatively asexual invasive species, an understanding of the origins and diversity of clones can reveal introduction and invasion pathways and inform management efforts. In this study, we use microsatellite and chloroplast DNA markers to infer clonal diversity of the Rubus fruticosus agg. invasion in the Western United States, determine the(More)
BACKGROUND AND AIMS Miscanthus is a perennial C4 grass that is a leading potential feedstock crop for the emerging bioenergy industry in North America, Europe and China. However, only a single, sterile genotype of M. × giganteus (M×g), a nothospecies derived from diploid M. sinensis (Msi) and tetraploid M. sacchariflorus (Msa), is currently available to(More)
Unilateral introgression from diploids to tetraploids has been hypothesized to be an important evolutionary mechanism in plants. However, few examples have been definitively identified, perhaps because data of sufficient depth and breadth were difficult to obtain before the advent of affordable high-density genotyping. Throughout Japan, tetraploid(More)
Facultative asexual reproduction is a trait commonly found in invasive species. With a combination of sexual and asexual reproductive modes, such species may adapt to new environments via sexual recombination during range expansion, while at the same time having the benefits of asexuality such as the maintenance of fitness effects that depend upon(More)
The genus Miscanthus is a perennial C4 grass native to eastern Asia and is a promising candidate bioenergy crop for cool temperate areas. Flowering time is a crucial factor governing regional and seasonal adaptation; in addition, it is also a key target trait for extending the vegetative phase to improve biomass potential. Homologues of CONSTANS(More)
BACKGROUND AND AIMS Miscanthus is a genus of perennial C4 grasses native to East Asia. It includes the emerging ligno-cellulosic biomass crop M. ×giganteus, a hybrid between M. sinensis and M. sacchariflorus Biomass yield and cold tolerance are of particular interest in Miscanthus, given that this crop is more temperate adapted than its C4 relatives maize,(More)
In genotyping-by-sequencing (GBS) and restriction site-associated DNA sequencing (RAD-seq), read depth is important for assessing the quality of genotype calls and estimating allele dosage in polyploids. However, existing pipelines for GBS and RAD-seq do not provide read counts in formats that are both accurate and easy to access. Additionally, although(More)