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HybPiper: Extracting coding sequence and introns for phylogenetics from high-throughput sequencing reads using target enrichment1
TLDR
HybPiper is developed as a user-friendly platform for assembly of gene regions, extraction of exon and intron sequences, and identification of paralogous gene copies in Artocarpus. Expand
Out of Borneo: biogeography, phylogeny and divergence date estimates of Artocarpus (Moraceae)
TLDR
Borneo was central in the diversification of the genus Artocarpus and probably served as the centre from which species dispersed and diversified in several directions, and supports Borneo as an evolutionary biodiversity hotspot. Expand
Allele phasing has minimal impact on phylogenetic reconstruction from targeted nuclear gene sequences in a case study of Artocarpus.
TLDR
It is shown here that it is possible to infer phased alleles from target-enriched Illumina libraries and that highly heterozygous sequences do not contribute disproportionately to poor phylogeneticresolution and that the use of allele sequences for phylogeny reconstruction does not have a clear effect on phylogenetic resolution or topological consistency. Expand
Strategies for reducing per‐sample costs in target capture sequencing for phylogenomics and population genomics in plants
TLDR
The minimal equipment and consumable requirements for targeted sequencing are reviewed while comparing several alternatives to reduce bulk costs in DNA extraction, library preparation, target enrichment, and sequencing. Expand
Phylogeny and biogeography of Maclura (Moraceae) and the origin of an anachronistic fruit.
TLDR
This study reconstructs the phylogeny, estimates divergence dates, and infer ancestral ranges of Maclura in order to test the monophyly of subgeneric classifications and to understand evolution and dispersal patterns in this globally distributed group. Expand
Bridging the micro- and macroevolutionary levels in phylogenomics: Hyb-Seq solves relationships from populations to species and above.
TLDR
It is shown that probes designed using genomic resources from taxa not directly related to the focal group are effective in providing phylogenetic resolution at deep and shallow evolutionary levels. Expand
Chloroplast microsatellite markers for Artocarpus (Moraceae) developed from transcriptome sequences1
TLDR
These chloroplast microsatellite loci will complement existing nuclear markers by enabling confident identification of maternal and clone lines, which are often important in vegetatively propagated crops such as breadfruit. Expand
Low-coverage, whole-genome sequencing of Artocarpus camansi (Moraceae) for phylogenetic marker development and gene discovery1
TLDR
This study substantially increases the genomic resources available for Artocarpus and Moraceae and demonstrates the value of low-coverage de novo assemblies for nonmodel organisms with moderately large genomes. Expand
Land bridges in the Pleistocene contributed to flora assembly on the continental islands of South China: Insights from the evolutionary history of Quercus championii.
TLDR
This study used restriction site-associated DNA sequencing to identify the demographic dynamics and local adaptation of Quercus championii, a dominant forests tree distributed in SCM and Hainan/Taiwan Islands, and found a strong correlation between genetic variation and isothermality through a gradient forest analysis. Expand
A Flower in Fruit’s Clothing: Pollination of Jackfruit (Artocarpus heterophyllus, Moraceae) by a New Species of Gall Midge, Clinodiplosis ultracrepidata sp. nov. (Diptera: Cecidomyiidae)
TLDR
The results support the existence of insect pollination in jackfruit but do not negate the possibility of wind pollination, which warrants further study. Expand
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