Primers for Castilleja and their Utility Across Orobanchaceae: II. Single‐copy nuclear loci

Premise of the study: We developed primers targeting nuclear loci in Castilleja with the goal of reconstructing the evolutionary history of this challenging clade. These primers were tested across other major clades in Orobanchaceae to assess their broader utility.Methods and Results: We assembled low-coverage genomes for three taxa in Castilleja and developed primer combinations for the single-copy conserved ortholog set (COSII) and the pentatricopeptide repeat (PPR) gene family. These primer combinations were designed to take advantage of the Fluidigm microfluidic PCR platform and are well suited for high-throughput sequencing applications. Eighty-seven primers were designed for Castilleja, and 27 were found to have broader utility in Orobanchaceae.Conclusions: These results demonstrate the utility of these primers, not only across Castilleja, but for other lineages within Orobanchaceae as well. This expanded molecular toolkit will be an asset to future phylogenetic studies in Castilleja and throughout Orobanchaceae

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

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 important quantities such as allele frequencies. Here we describe a statistical model to estimate biallelic SNP frequencies in a population of autopolyploids using high throughput sequencing data in the form of read counts.We bridge the gap from data collection (using restriction enzyme based techniques [e.g., GBS, RADseq]) to allele frequency estimation in a unified inferential framework using a hierarchical Bayesian model to sum over genotype uncertainty. Simulated data sets were generated under various conditions for tetraploid, hexaploid and octoploid populations to evaluate the model's performance and to help guide the collection of empirical data. We also provide an implementation of our model in the R package POLYFREQS and demonstrate its use with two example analyses that investigate (i) levels of expected and observed heterozygosity and (ii) model adequacy. Our simulations show that the number of individuals sampled from a population has a greater impact on estimation error than sequencing coverage. The example analyses also show that our model and software can be used to make inferences beyond the estimation of allele frequencies for autopolyploids by providing assessments of model adequacy and estimates of heterozygosity.</jats:p

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

AbstractMotivation: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 (auto polyploids), inbreeding can result from mixed mating and/or double reduction. For WGDs that involve hybridization (allopolyploids), alleles are typically inherited through independently segregating subgenomes.Results:We present two new models for estimating genotypes and population genetic parameters from genotype likelihoods for auto- and allopolyploids. We then use simulations to compare these models to existing approaches at varying depths of sequencing coverage and ploidy levels. These simulations show that our models typically have lower levels of estimation error for genotype and parameter estimates, especially when sequencing coverage is low. Finally, we also apply these models to two empirical data sets from the literature. Overall, we show that the use of genotype likelihoods to model non-standard inheritance patterns is a promising approach for conducting population genomic inferences in polyploids.Availability:A C++ program, EBG, is provided to perform inference using the models we describe. It is available under the GNU GPLv3 on GitHub:https://github.com/pblischak/polyploid-genotyping.Contact: [email protected].</jats:sec

Bann_spdelim_scripts

All python scripts associated with the genomic analyses for this stud

Data from: Genomic signatures of sympatric speciation with historical and contemporary gene flow in a tropical anthozoan (Hexacorallia: Actiniaria)

Sympatric diversification is increasingly thought to have played an important role in the evolution of biodiversity around the globe. However, an in situ sympatric origin for co-distributed taxa is difficult to demonstrate empirically because different evolutionary processes can lead to similar biogeographic outcomes- especially in ecosystems that can readily facilitate secondary contact due to a lack of hard barriers to dispersal. Here we use a genomic (ddRADseq), model-based approach to delimit a species complex of tropical sea anemones that are co-distributed on coral reefs throughout the Tropical Western Atlantic. We use coalescent simulations in fastsimcoal2 to test competing diversification scenarios that span the allopatric-sympatric continuum. We recover support that the corkscrew sea anemone Bartholomea annulata (Le Sueur, 1817) is a cryptic species complex, co-distributed throughout its range. Simulation and model selection analyses suggest these lineages arose in the face of historical and contemporary gene flow, supporting a sympatric origin, but an alternative secondary contact model also receives appreciable model support. Leveraging the genome of Exaiptasia diaphana we identify five loci under divergent selection between cryptic B. annulata lineages that fall within mRNA transcripts or CDS regions. Our study provides a rare empirical, genomic example of sympatric speciation in a tropical anthozoan. Finally, these data represent the first range-wide molecular study of any tropical sea anemone, underscoring that anemone diversity is under described in the tropics, and highlighting the need for additional systematic studies into these ecologically and economically important species

Data from: Accounting for genotype uncertainty in the estimation of allele frequencies in autopolyploids

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 important quantities such as allele frequencies. Here, we describe a statistical model to estimate biallelic SNP frequencies in a population of autopolyploids using high-throughput sequencing data in the form of read counts. We bridge the gap from data collection (using restriction enzyme based techniques [e.g. GBS, RADseq]) to allele frequency estimation in a unified inferential framework using a hierarchical Bayesian model to sum over genotype uncertainty. Simulated data sets were generated under various conditions for tetraploid, hexaploid and octoploid populations to evaluate the model's performance and to help guide the collection of empirical data. We also provide an implementation of our model in the R package polyfreqs and demonstrate its use with two example analyses that investigate (i) levels of expected and observed heterozygosity and (ii) model adequacy. Our simulations show that the number of individuals sampled from a population has a greater impact on estimation error than sequencing coverage. The example analyses also show that our model and software can be used to make inferences beyond the estimation of allele frequencies for autopolyploids by providing assessments of model adequacy and estimates of heterozygosity

Bannulata_spdelim_FINAL_interspecific_Arlequin

Arlequin input file of interspecific ddRADseq data generated for Bartholomea annulata for species-level analyse

Bannulata_spdelim_FINAL_intraspecific_arlequin

Arlequin input file of Bartholomea annulata ddRADseq for intraspecific population genetic structure analyse

Phylogenetics of a Rapid, Continental Radiation: Diversification, Biogeography, and Circumscription of the Beardtongues (<i>Penstemon</i>; Plantaginaceae)

AbstractPenstemon (Plantaginaceae), the largest genus of plants native to North America, represents a recent continental evolutionary radiation. We investigated patterns of diversification, phylogenetic relationships, and biogeography, and determined the age of the lineage using 43 nuclear gene loci. We also assessed the current taxonomic circumscription of the ca. 285 species by developing a phylogenetic taxonomic bootstrap method. Penstemon originated during the Pliocene/Pleistocene transition. Patterns of diversification and biogeography are associated with glaciation cycles during the Pleistocene, with the bulk of diversification occurring from 1.0–0.5 mya. The radiation across the North American continent tracks the advance and retreat of major and minor glaciation cycles during the past 2.5 million years with founder-event speciation contributing the most to diversification of Penstemon. Our taxonomic bootstrap analyses suggest the current circumscription of the genus is in need of revision. We propose rearrangement of subgenera, sections, and subsections based on our phylogenetic results. Given the young age and broad distribution of Penstemon across North America, it offers an excellent system for studying a rapid evolutionary radiation in a continental setting.</jats:p