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1. SNP genotyping and parameter estimation in polyploids using low-coverage sequencing data

Author:
Wolfe, Andrea D,   et al.   ; Blischak, Paul D; Kubatko, Laura S; Berger, Bonnie;     Show all 4 Authors
Source:
Bioinformatics 2018 v.34 no.3 pp. 407-415
ISSN:
1460-2059
Subject:
alleles; allopolyploidy; autopolyploidy; bioinformatics; data collection; diploidy; genomics; genotype; genotyping; high-throughput nucleotide sequencing; hybridization; inbreeding; inheritance (genetics); models; single nucleotide polymorphism
Abstract:
... Genotyping and parameter estimation using high throughput sequencing data are everyday tasks for population geneticists, but methods developed for diploids are typically not applicable to polyploid taxa. This is due to their duplicated chromosomes, as well as the complex patterns of allelic exchange that often accompany whole genome duplication (WGD) events. For WGDs within a single lineage (autop ...
DOI:
10.1093/bioinformatics/btx587

2. Investigating the genetic diversity and differentiation patterns in the Penstemon scariosus species complex under different sample sizes using AFLPs and SSRs

Author:
Wolfe, Andrea D.,   et al.   ; Rodríguez-Peña, Rosa A.; Johnson, Robert L.; Johnson, Leigh A.; Anderson, Chris D.; Ricks, Nathan J.; Farley, Kevin M.; Robbins, Matthew D.; Stevens, Mikel R.;     Show all 9 Authors
Source:
Conservation genetics 2018 v.19 no.6 pp. 1335-1348
ISSN:
1566-0621
Subject:
Bayesian theory; Penstemon; amplified fragment length polymorphism; anthropogenic activities; biodiversity; conservation genetics; data collection; endangered species; genetic variation; habitat destruction; habitat fragmentation; habitats; industrialization; loci; microsatellite repeats; population structure; taxonomy
Abstract:
... Habitat fragmentation due to anthropogenic activities is the major cause of biodiversity loss. Endemic and narrowly distributed species are the most susceptible to habitat degradation. Penstemon scariosus is one of many species whose natural habitat is vulnerable to industrialization. All varieties of P. scariosus (P. scariosus var. albifluvis, P. scariosus var. cyanomontanus, P. scariosus var. ga ...
DOI:
10.1007/s10592-018-1103-6

3. Accounting for genotype uncertainty in the estimation of allele frequencies in autopolyploids

Author:
Wolfe, Andrea D.,   et al.   ; Blischak, Paul D.; Kubatko, Laura S.;     Show all 3 Authors
Source:
Molecular ecology resources 2016 v.16 no.3 pp. 742-754
ISSN:
1755-098X
Subject:
alleles; autopolyploidy; computer software; data collection; gene frequency; heterozygosity; hexaploidy; high-throughput nucleotide sequencing; restriction endonucleases; single nucleotide polymorphism; statistical models; tetraploidy; uncertainty
Abstract:
... Despite the increasing opportunity to collect large‐scale data sets for population genomic analyses, the use of high‐throughput sequencing to study populations of polyploids has seen little application. This is due in large part to problems associated with determining allele copy number in the genotypes of polyploid individuals (allelic dosage uncertainty–ADU), which complicates the calculation of ...
DOI:
10.1111/1755-0998.12493

4. Sequence-Related Amplified Polymorphism (SRAP) Markers: A Potential Resource for Studies in Plant Molecular Biology

Author:
Wolfe, Andrea D.,   et al.   ; Robarts, Daniel W. H.;     Show all 2 Author
Source:
Applications in plant sciences 2014 v.2 no.7
ISSN:
2168-0450
Subject:
DNA; DNA primers; amplified fragment length polymorphism; biogeography; case studies; ecology; genetic variation; germplasm conservation; horticulture; hybrids; microsatellite repeats; molecular biology; open reading frames; plant biology; plant taxonomy; publications; quantitative trait loci; random amplified polymorphic DNA technique; statistics
Abstract:
... In the past few decades, many investigations in the field of plant biology have employed selectively neutral, multilocus, dominant markers such as inter-simple sequence repeat (ISSR), random-amplified polymorphic DNA (RAPD), and amplified fragment length polymorphism (AFLP) to address hypotheses at lower taxonomic levels. More recently, sequence-related amplified polymorphism (SRAP) markers have b ...
DOI:
10.3732/apps.1400017
PubMed:
25202637
PubMed Central:
PMC4103474

5. Population genetics of Penstemon albomarginatus (Plantaginaceae), a rare Mojave Desert species of conservation concern

Author:
Wolfe, Andrea D.,   et al.   ; Necamp, Timothy; Fassnacht, Susan; Blischak, Paul; Kubatko, Laura;     Show all 5 Authors
Source:
Conservation genetics 2016 v.17 no.6 pp. 1245-1255
ISSN:
1566-0621
Subject:
Penstemon; dunes; genetic variation; habitats; heterozygosity; inbreeding; latitude; microsatellite repeats; rare species; sand; Arizona; California; Mojave Desert; Nevada
Abstract:
... Penstemon albomarginatus is a psammophytic endemic of the Mojave Desert, found only in deep sand and dune habitats of San Bernardino County, California, Mohave County, Arizona, and Clark and Nye Counties in Nevada. We used six microsatellite loci to assess genetic differentiation and diversity for 228 individuals across the 12 known populations of this rare species. A slight heterozygote deficienc ...
DOI:
10.1007/s10592-016-0857-y

6. Gene Prediction and Annotation in Penstemon (Plantaginaceae): A Workflow for Marker Development from Extremely Low-Coverage Genome Sequencing

Author:
Wolfe, Andrea D.,   et al.   ; Blischak, Paul D.; Wenzel, Aaron J.;     Show all 3 Authors
Source:
Applications in plant sciences 2014 v.2 no.12
ISSN:
2168-0450
Subject:
Penstemon; sequence analysis; loci; genomic libraries; bioinformatics; data collection; phylogeny; exons; chloroplasts; prediction; North America
Abstract:
... Premise of the study: Penstemon (Plantaginaceae) is a large and diverse genus endemic to North America. However, determining the phylogenetic relationships among its 280 species has been difficult due to its recent evolutionary radiation. The development of a large, multilocus data set can help to resolve this challenge. Methods: Using both previously sequenced genomic libraries and our own low-co ...
DOI:
10.3732/apps.1400044
PubMed:
25506519
PubMed Central:
PMC4259454

7. Taxonomic Revision of the Alectra sessiliflora Complex (Orobanchaceae)

Author:
Wolfe, Andrea D.,   et al.   ; Morawetz, Jeffery J.;     Show all 2 Author
Source:
Systematic botany 2011 v.36 no.1 pp. 141-152
ISSN:
0363-6445
Subject:
Alectra; biogeography; calyx; geographical distribution; herbaria; phenotype; plant collections; plant morphology; sampling; stamens; statistical analysis; taxonomic revisions; trichomes; China; India; Philippines; Sub-Saharan Africa
Abstract:
... Alectra sessiliflora (Orobanchaceae) is the most widespread species within the genus, occurring throughout sub-Saharan Africa, and into India, China and the Philippines. Three varieties are currently recognized (A. sessiliflora var. monticola, A. sessiliflora var. senegalensis, and A. sessiliflora var. sessiliflora) and are distinguished by geographic range, calyx pubescence and stamen filament pu ...
DOI:
10.1600/036364411X553234

8. Conservation genetics and breeding system of Penstemon debilis (Plantaginaceae), a rare beardtongue endemic to oil shale talus in western Colorado, USA

Author:
WOLFE, Andrea D.,   et al.   ; MCMULLEN‐SIBUL, Amy; TEPEDINO, V. J.; KUBATKO, Laura; NECAMP, Timothy; FASSNACHT, Susan;     Show all 6 Authors
Source:
Journal of systematics and evolution 2014 v.52 no.5 pp. 598-611
ISSN:
1674-4918
Subject:
Penstemon; collaborative management; extinction; gene flow; genetic variation; government agencies; habitats; inbreeding; inbreeding depression; indigenous species; landowners; natural gas; nongovernmental organizations; oil shale; outcrossing; pollen; pollination; rare species; threatened species; Colorado
Abstract:
... Rare species of plants are especially vulnerable to extinction when populations are few, have small numbers of individuals, and are fragmented. Such conditions lead to a reduction in gene flow and genetic diversity, and encourage inbreeding depression. We conducted a study of the reproductive biology and population genetics of Penstemon debilis (Plantaginaceae), a Federally Threatened species ende ...
DOI:
10.1111/jse.12100

9. Phylogeny and origins of holoparasitism in Orobanchaceae

Author:
Wolfe, Andrea D,   et al.   ; McNeal, Joel R.; Bennett, Jonathan R.; Mathews, Sarah;     Show all 4 Authors
Source:
American journal of botany 2013 v.100 no.5 pp. 971-983
ISSN:
0002-9122
Subject:
Orobanchaceae; biogeochemical cycles; biomass; hosts; internal transcribed spacers; loci; parasitism; phylogeny; weeds
Abstract:
... • Premise: Orobanchaceae are a family of angiosperms that range from fully autotrophic and free-living to completely heterotrophic and dependent on their hosts (holoparasites). Most of the ca. 2060 species are hemiparasites that photosynthesize throughout all or part of their life cycles. Certain family members are ecologically important due to direct impacts on community biomass and diversity, pl ...
DOI:
10.3732/ajb.1200448
PubMed:
23608647

10. The evolution and expression of RBCL in holoparasitic sister-genera Harveya and Hyobanche (Orobanchaceae)

Author:
Wolfe, Andrea D.,   et al.   ; Randle, Christopher P.;     Show all 2 Author
Source:
American journal of botany 2005 v.92 no.9 pp. 1575-1585
ISSN:
0002-9122
Subject:
ribulose-bisphosphate carboxylase; plastid DNA; pseudogenes; messenger RNA; open reading frames; Harveya; transpiration; gene expression; operon; natural selection; photosynthesis; plant taxonomy; parasitic plants
Abstract:
... The evolution of holoparasitism decreases the adaptive value of genes maintaining the photosynthetic apparatus. These may become pseudogenes through insertion or deletion events resulting in frameshift mutations, or by the evolution of premature stop codons. The holoparasitic sister genera Harveya and Hyobanche have undergone alternate pathways of evolution and expression at the plastid locus rbcL ...
DOI:
10.3732/ajb.92.9.1575
PubMed:
21646175

11. Constrained lability in floral evolution: counting convergent origins of hummingbird pollination in Penstemon and Keckiella

Author:
Wolfe, Andrea D.,   et al.   ; Wilson, Paul; Armbruster, W. Scott; Thomson, James D.;     Show all 4 Authors
Source:
New phytologist 2007 v.176 no.4 pp. 883-890
ISSN:
0028-646X
Subject:
Hymenoptera; Penstemon; chloroplast DNA; flowers; hummingbirds; insects; internal transcribed spacers; phylogeny; pollination; taxonomy
Abstract:
... In the clade of Penstemon and segregate genera, pollination syndromes are well defined among the 284 species. Most display combinations of floral characters associated with pollination by Hymenoptera, the ancestral mode of pollination for this clade. Forty-one species present characters associated with hummingbird pollination, although some of these ornithophiles are also visited by insects. The o ...
DOI:
10.1111/j.1469-8137.2007.02219.x
PubMed:
17897322

12. Phylogeny, taxonomic affinities, and biogeography of Penstemon (Plantaginaceae) based on ITS and cpDNA sequence data

Author:
Wolfe, Andrea D.,   et al.   ; Randle, Christopher P.; Datwyler, Shannon L.; Morawetz, Jeffery J.; Arguedas, Nidia; Diaz, Jose;     Show all 6 Authors
Source:
American journal of botany 2006 v.93 no.11 pp. 1699-1713
ISSN:
0002-9122
Subject:
Penstemon; sequence analysis; taxonomic revisions; chloroplast DNA; pollinators; phylogeny; phytogeography; internal transcribed spacers; molecular systematics; interspecific hybridization
Abstract:
... The large and diverse genus Penstemon (ca. 271 species) is endemic to North America and has been divided into six subgenera primarily based on anther dehiscence patterns. Species of Penstemon are known to be pollinated by a variety of insects (hymenopterans, lepidopterans, dipterans) and hummingbirds. Nucleotide sequence data from ITS and two noncoding regions of chloroplast DNA were used to recon ...
DOI:
10.3732/ajb.93.11.1699
PubMed:
21642115