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Fossil calibration of molecular divergence infers a moderate mutation rate and recent radiations for pinus.
- A. Willyard, J. Syring, D. Gernandt, A. Liston, R. Cronn
- Environmental Science, GeographyMolecular biology and evolution
- 22 September 2006
By extending the sampling to encompass the phylogenetic diversity of Pinus, it is predicted that most extant subsections diverged during the Miocene and that further refinements in age and mutation rate estimates will require a synthetic examination of pine fossil history.
Targeted enrichment strategies for next-generation plant biology.
While the benefits of targeted sequencing are greatest in plants with large genomes, nearly all comparative projects can benefit from the improved throughput offered by targeted multiplex DNA sequencing, particularly as the amount of data produced from a single instrument approaches a trillion bases per run.
Widespread genealogical nonmonophyly in species of Pinus subgenus Strobus.
It is felt that incomplete lineage sorting remains the best explanation for the polymorphisms shared among species, and taxa sharing similar life history traits with Pinus are likely to show species nonmonophyly using nuclear markers.
Evolutionary relationships among Pinus (Pinaceae) subsections inferred from multiple low-copy nuclear loci.
Combined analysis of low-copy nuclear loci produces a well-supported subsectional topology of two subgenera, each divided into two sections, congruent with prior hypotheses of deep divergence in Pinus.
Finding a (pine) needle in a haystack: chloroplast genome sequence divergence in rare and widespread pines
Critical to conservation efforts and other investigations at low taxonomic levels, DNA sequence data offer important insights into the distinctiveness, biogeographic partitioning and evolutionary…
Interspecific phylogenetic analysis enhances intraspecific phylogeographical inference: a case study in Pinus lambertiana
- A. Liston, Mariah Parker-Defeniks, J. Syring, A. Willyard, R. Cronn
- BiologyMolecular ecology
- 1 September 2007
Pinus lambertiana (sugar pine) is an economically and ecologically important conifer with a 1600‐km latitudinal range extending from Oregon, USA, to northern Baja California, Mexico. Like all North…
Evaluating allopolyploid origins in strawberries (Fragaria) using haplotypes generated from target capture sequencing
This study is one of the first in which target capture sequencing followed by computational deconvolution of individual haplotypes is used for tracing origins of polyploid taxa, and provides new perspectives on the evolutionary history of Fragaria.
The conifers (Pinophyta).
Estimates of ages and mutation rates in the group are expected to improve greatly as conceptual advances related to fossil interpretation converge with the enormous quantities of new sequence data being generated by genetic and phylogenetic studies of living species.
Multilocus analyses reveal little evidence for lineage‐wide adaptive evolution within major clades of soft pines (Pinus subgenus Strobus)
This work has estimated the distribution of deleterious fitness effects (DFE) and the fraction of adaptive nonsynonymous substitutions (α) for 11 species of soft pines using DNA sequence data from 167 orthologous nuclear gene fragments, illustrating a strong consistency with the expectations from the Nearly Neutral Theory of molecular evolution.
Targeted Capture Sequencing in Whitebark Pine Reveals Range-Wide Demographic and Adaptive Patterns Despite Challenges of a Large, Repetitive Genome
- J. Syring, J. Tennessen, T. Jennings, J. Wegrzyn, Camille Scelfo-Dalbey, R. Cronn
- Environmental ScienceFront. Plant Sci.
- 21 April 2016
The results show that even under non-optimal conditions (low enrichment efficiency; inclusion of repetitive elements in baits), targeted enrichment produces high quality, codominant genotypes from large genomes.