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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. [ABSTRACT FROM AUTHOR]

Transcription factors containing the Myb-homologous DNA-binding domain are widely found in eukaryotes. In plants, R2R3 Myb-domain proteins are involved in the control of form and metabolism. The Arabidopsis genome harbors > 100 R2R3 Myb genes, but few have been found in monocots, animals, and fungi. Using RT-PCR from different maize organs, we cloned 480 fragments corresponding to a 42-44 residue-long sequence spanning the region between the conserved DNA-recognition helices ([Myb.sup.BRH]) of R2R3 Myb domains. We determined that maize expresses >80 different R2R3 Myb genes, and evolutionary distances among maize [Myb.sup.BRH] sequences indicate that most of the amplification of the R2R3 Myb gene family occurred after the origin of land plants but prior to the separation of monocots and dicots. In addition, evidence is provided for the very recent duplication of particular classes of R2R3 Myb genes in the grasses. Together, these findings render a novel line of evidence for the amplification of the R2R3 Myb gene family in the early history of land plants and suggest that maize provides a possible model system to examine the hypothesis that the expansion of Myb genes is associated with the regulation of novel plato cellular functions.

Penstemon subg. Dasanthera is the basal subgenus of Penstemon (tribe Cheloneae; Scrophulariaceae) and is characterized by wooly anthers, a woody subshrub habit and epistaminal nectaries. The subgenus occurs throughout northwestern North America and hybridization is common in nature wherever two (or more) species are sympatric. Within the subgenus, two taxa are of purported hybrid origin (P. davidsonii var. praeterius and P. fruticosus var. serratus) based on morphology and flavonoids. In addition, there are two different hypotheses on the biogeographic relationships of the Dasanthera penstemons. First, an origin of Penstemon in the Northern rocky mountains followed by a rapid radiation and divergence from two centers, one in the Cascade/Sierra mountains and in the northern Rocky Mountains. However, recent evidence suggests an origin of Penstemon in the Siskiyou mountains of Northern California and Southern Oregon, followed by a rapid radiation and divergence in the Northern rocky mountains. The internal transcribed spacers of the nuclear ribosomal DNA (ITS-1&2) are currently being sequenced for all species within subgenus Dasanthera, selected subgeneric representatives of other lineages within Penstemon, and outgroup representatives from tribe Cheloneae in order to examine the biogeographic patterns within Penstemon and purported hybrid speciation. Preliminary analysis of ITS-1 reveals the presence of a synapomorphy uniting the Rocky mountain taxa (P. ellipticus, P. lyallii, and P. montanus) which is shared with other subgenera of Penstemon, supporting a diversification of Penstemon from the northern Rocky Mountains. This suggests that ITS sequences may provide a useful tool for examing the phylogenetic and biogeographic relationships among the Dasanthera penstemons and for distinguishing between these alternative biogeographic hypotheses of Penstemon.

The tropical dade of Orobanchaceae contains approximately forty genera, typically with fewer than ten species each, and contributes significantly to the variation in floral morphology found within the family. Despite the economic importance of this dade, which contains three of four most important genera of crop parasites within the family, it has been under-sampled in previous phylogenies. We tested the monophyly of the tropical dade and its major genera using DNA sequences from the nuclear (internal transcribed spacer) and plastid (rpll6, trnT-L) genomes. The tropical dade was strongly supported as mono-phyletic in all analyses, and four main clades were recovered. The earliest diverging lineage from the remainder of the tropical dade is comprised of the shrubby genera Asepalum and Cyclocheilon, previously placed within Cyclocheilaceae. The atypical holoparasitic Alectra alba was shown to belong within the primarily holoparasitic Harveya, and the hemiparasitic Harveya obtusifolia was shown to belong to an otherwise holoparasitic lineage within Harveya. Both New World Melasma species were included here for the first time, and these were shown to be more closely related to the Neotropical hem iparasitic Escobedia than the African Melasma lineage. These results support a previous study recognizing Nesogenes within the tropical dade of Orobanchaceae rather than the separate family Nesogenaceae. [ABSTRACT FROM AUTHOR]

Focuses on the relationship among the asteraceae andlactuceace based upon the analyses on inter simple sequence repeat(ISSR) markers. Usage of DNA sequence data to reconstructphylogeny; Potential patterns of dispersal within the genus;Importance of the ISSR.

The analysis of hybridization and gene flow among closely related taxa is a common goal for researchers studying speciation and phylogeography. Many methods for hybridization detection use simple site pattern frequencies from observed genomic data and compare them to null models that predict an absence of gene flow. The theory underlying the detection of hybridization using these site pattern probabilities exploits the relationship between the coalescent process for gene trees within population trees and the process of mutation along the branches of the gene trees. For certain models, site patterns are predicted to occur in equal frequency (i.e. their difference is 0), producing a set of functions called phylogenetic invariants. In this article, we introduce HyDe, a software package for detecting hybridization using phylogenetic invariants arising under the coalescent model with hybridization. HyDe is written in Python and can be used interactively or through the command line using pre-packaged scripts. We demonstrate the use of HyDe on simulated data, as well as on two empirical data sets from the literature. We focus in particular on identifying individual hybrids within population samples and on distinguishing between hybrid speciation and gene flow. HyDe is freely available as an open source Python package under the GNU GPL v3 on both GitHub (https://github.com/pblischak/HyDe) and the Python Package Index (PyPI: https://pypi.python.org/pypi/phyde). [ABSTRACT FROM AUTHOR]

Studies the phylogenetic relationships within Zaluzianskya, a diverse genus of 55 species of annual and perennial herbs, endemic to southern Africa. DNA sequence data from nrDNA ITS regions, rpl16 and trnL-trnF to produce the first broad phylogenetic hypothesis for Zaluzianskyal; First tests of the monophyly of the genus and its sections; Examination of character evolution and biogeography.

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 ornithophiles are scattered throughout the traditional taxonomy and across phylogenies estimated from nuclear (internal transcribed spacer (ITS)) and chloroplast DNA (trnCD/TL) sequence data. Here, the number of separate origins of ornithophily is estimated, using bootstrap phylogenies and constrained parsimony searches. Analyses suggest 21 separate origins, with overwhelming support for 10 of these. Because species sampling was incomplete, this is probably an underestimate. Penstemons therefore show great evolutionary lability with respect to acquiring hummingbird pollination; this syndrome acts as an attractor to which species with large sympetalous nectar-rich flowers have frequently been drawn. By contrast, penstemons have not undergone evolutionary shifts backwards or to other pollination syndromes. Thus, they are an example of both striking evolutionary lability and constrained evolution.

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 reconstruct the phylogeny of Penstemon. Trees generated from nuclear and chloroplast DNA sequences are incongruent, which is probably the result of hybridization, and not fully resolved, which is likely due to a rapid evolutionary radiation. Penstemon represents a recent continental radiation where speciation has resulted primarily from evolutionary adaptations to ecological niches such as pollinator specialization. The results from these analyses show that the current circumscription of subgenera and sections needs revision to reflect more closely the evolutionary relationships of species. Specifically, species in subgenera Saccanthera, Habroanthus, and Penstemon are polyphyletic. These results also confirm the independent origin of hummingbird floral morphology in 10 clades.

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. An open reading frame in all but a single species of Harveya is maintained by purifying selection and is expressed. However, the function of Rubisco in this putative holoparasite is unknown. Conversely, Hyobanche has undergone rbcL pseudogene formation, and comparison of synonymous and nonsynonymous rates of evolution indicates that selection has not played a role in its evolution. This is complicated by the following findings: multiple pseudogene copies of rbcL exist in tissues of Hyobanche, rbcL transcripts also encode pseudogenes, and the large subunit is present in some tissues of Hyobanche. We hypothesize that the rbcL operon is in a state of degradation as may be expected in a holoparasite and is not endogenously expressed. Rather, the large subunit may be taken up from the host plants, and accumulate in tissues as a result of transpiration.

Despite apparent ethological isolation based on specialized pollination systems, hybridization between day-flowering Zaluzianskya microsiphon and night-flowering Z. natalensis has been proposed due to intermediate individuals found in sympatric populations of these species. The extent of this putative hybridization was investigated using inter-simple sequence repeat (ISSR) markers and principal components analysis (PCA) of morphological traits. The species are genetically similar, but show some intra- and interspecific variation in band frequencies. Neighbor-joining analyses of the ISSR data demonstrated that although the species largely formed distinct groups, several individuals from the sympatric populations of each species and the "hybrids" clustered together rather than with members of their own species. These results are consistent with hybridization, although they could also indicate historical similarity. Nine loci were present only in individuals of Z. microsiphon, the "hybrids," and sometimes the sympatric individuals of Z. natalensis. In contrast, only one locus showed the reverse pattern. This suggests unidirectional gene flow from Z. microsiphon to Z. natalensis, which is also supported by population-level examinations of four loci. Ordination revealed separate phenotype clusters for each species, with hybrid individuals located in between but often closer to the Z. natalensis cluster. One hypothesis is that hybrids are backcrossing with Z. natalensis, leading to introgression of Z. microsiphon genetic material.