Progeny array analysis to estimate outcrossing rates, inbreeding coefficients, and inbreeding depression among native, naturalized, and invasive populations of (Phrymaceae).

The mating system of non-native plant populations plays a role in determining the colonizing success following introduction into locations outside of the native distribution. For plant species capable of mixed-mating, both selfing and outcrossing can be advantageous and promote the establishment, persistence, and spread of newly arrived populations. To investigate how mating systems may contribute to the invasion process we estimated mating system parameters in perennial populations of the model plant species, from its native range (West coast USA), non-native populations that are established but have not become invasive (East coast USA, >50 years), and populations in invasive regions (UK >200 years).

Population genomics of the Isoetes appalachiana (Isoetaceae) complex supports a 'diploids-first' approach to conservation.

Background And Aims: Allopolyploidy is an important driver of diversification and a key contributor to genetic novelty across the tree of life. However, many studies have questioned the importance of extant polyploid lineages, suggesting that the vast majority may constitute evolutionary 'dead ends'. This has important implications for conservation efforts where polyploids and diploid progenitors often compete for wildlife management resources.

Phylogenomic analyses using a new 1013-gene Vitaceae bait-set support major groups of North American Vitis.

A set of newly designed Vitaceae baits targeting 1013 genes was employed to explore phylogenetic relationships among North American Vitis. Eurasian Vitis taxa including Vitis vinifera were found to be nested within North American Vitis subgenus Vitis. North American Vitis subgenus Vitis can be placed into nine main groups: the Monticola group, the Occidentales group, the Californica group, the Vinifera group (introduced from Eurasia), the Mustangensis group, the Palmata group, the Aestivalis group, the Labrusca group, and the Cinerea group.

Genetic diversity and population structure among native, naturalized, and invasive populations of the common yellow monkeyflower, (Phrymaceae).

An ongoing controversy in invasion biology is the prevalence of colonizing plant populations that are able to establish and spread, while maintaining limited amounts of genetic variation. Invasive populations can be established through several routes including from a single source or from multiple introductions. The aim of this study was to examine genetic diversity in populations of in the United Kingdom, where the species is considered invasive, and compare this diversity to that in native populations on the west coast of North America.

Climate-influenced boreotropical survival and rampant introgressions explain the thriving of New World grapes in the north temperate zone.

The north temperate region was characterized by a warm climate and a rich thermophilic flora before the Eocene, but early diversifications of the temperate biome under global climate change and biome shift remain uncertain. Moreover, it is becoming clear that hybridization/introgression is an important driving force of speciation in plant diversity. Here, we applied analyses from biogeography and phylogenetic networks to account for both introgression and incomplete lineage sorting based on genomic data from the New World Vitis, a charismatic component of the temperate North American flora with known and suspected gene flow among species.

Synthesis of Nuclear and Chloroplast Data Combined With Network Analyses Supports the Polyploid Origin of the Apple Tribe and the Hybrid Origin of the Maleae-Gillenieae Clade.

Plant biologists have debated the evolutionary origin of the apple tribe (Maleae; Rosaceae) for over a century. The "wide-hybridization hypothesis" posits that the pome-bearing members of Maleae (base chromosome number = 17) resulted from a hybridization and/or allopolyploid event between progenitors of other tribes in the subfamily Amygdaloideae with = 8 and = 9, respectively. An alternative "spiraeoid hypothesis" proposed that the = 17 of Maleae arose via the genome doubling of = 9 ancestors to = 18, and subsequent aneuploidy resulting in = 17.

Homoploid hybrids, allopolyploids, and high ploidy levels characterize the evolutionary history of a western North American quillwort (Isoëtes) complex.

Polyploidy and hybridization are important processes in seed-free plant evolution. However, a major gap lies in our understanding of how these processes affect the evolutionary history of high-ploidy systems. The heterosporous lycophyte genus Isoëtes is a lineage with many putative hybrids and high-level polyploid taxa (ranging from tetraploid to dodecaploid).

A phylogenomic approach resolves the backbone of Prunus (Rosaceae) and identifies signals of hybridization and allopolyploidy.

The genus Prunus, which contains 250-400 species, has ample genomic resources for the economically important taxa in the group including cherries, peaches, and almonds. However, the backbone of Prunus, specifically the position of the racemose group relative to the solitary and corymbose groups, remains phylogenetically uncertain. Surprisingly, phylogenomic analyses to resolve relationships in the genus are lacking.

Phylogenomic relationships and character evolution of the grape family (Vitaceae).

The grape family consists of 16 genera and ca. 950 species. It is best known for the economically important fruit crop - the grape Vitis vinifera.

Nuclear and Chloroplast Sequences Resolve the Enigmatic Origin of the Concord Grape.

Despite the commercial importance of the Concord grape, its origin has remained unresolved for over 150 years without a comprehensive phylogenetic analysis. In this study we aimed to reconstruct the evolutionary history of the Concord grape using sequence data from four nuclear markers (, , , and ), six plastid markers (, , , , , and ), and the plastid genome. We sampled extensively the species native to northeastern North America as well as representative species from Europe and Asia, including the commercially important (wine grape), a native European species with hermaphroditic flowers, and its wild progenitor, .

Variable and sexually conflicting selection on Silene stellata floral traits by a putative moth pollinator selective agent.

Conflicting selection is an important evolutionary mechanism because it impedes directional evolution and helps to maintain phenotypic variation. It can arise when mutualistic and antagonistic selective agents exert opposing selection on the same trait and when distinct phenotypic optima are favored by different fitness components. In this study, we test for conflicting selection through different sexual functions of the hermaphroditic plant, Silene stellata during its early and late flowering season.

Transcriptome analysis of the curry tree (Bergera koenigii L., Rutaceae) during leaf development.

The curry tree (Bergera koenigii L.) is a widely cultivated plant used in South Asian cooking. Next-generation sequencing was used to generate the transcriptome of the curry leaf to detect changes in gene expression during leaf development, such as those genes involved in the production of oils which lend the leaf its characteristic taste, aroma, and medicinal properties.

Characterization of the mating system of a native perennial tetraploid herb, Silene stellata.

Premise Of The Study: Nursery pollination systems can range from obligate to facultative. In a system where generalists provide substantial pollination service, an important question is whether the cost of seed predation outweighs the benefit provided by the nursery pollinator to cause the plant to evolve toward more generalized pollination. Using a facultative system native to North America, we tested whether nursery pollinator vs.

Low-copy nuclear markers in (Isoëtaceae) identified with transcriptomes.

Premise Of The Study: Few genetic markers provide phylogenetic information in closely related species of (Isoëtaceae). We describe the development of primers for several putative low-copy nuclear markers to resolve the phylogeny of , particularly in the southeastern United States.

Methods And Results: We identified regions of interest in transcriptomes based on low-copy genes in other plants.

Comparison of population genetic structures of the plant Silene stellata and its obligate pollinating seed predator moth Hadena ectypa.

Background And Aims: Population genetic structures and patterns of gene flow of interacting species provide important insights into the spatial scale of their interactions and the potential for local co-adaptation. We analysed the genetic structures of the plant Silene stellata and the nocturnal moth Hadena ectypa. Hadena ectypa acts as one of the important pollinators of S.

Phylogeography and conservation genetics of the rare and relict Bretschneidera sinensis (Akaniaceae).

Bretschneidera sinensis, a class-I protected wild plant in China, is a relic of the ancient Tertiary tropical flora endemic to Asia. However, little is known about its genetics and phylogeography. To elucidate the current phylogeographic patterns and infer the historical population dynamics of B.

Herbarium collection-based phylogenetics of the ragweeds (Ambrosia, Asteraceae).

Ambrosia (Asteraceae) is a taxonomically difficult genus of weedy, wind-pollinated plants with an apparent center of diversity in the Sonoran Desert of North America. Determining Ambrosia's evolutionary relationships has been the subject of much interest, with numerous studies using morphological characters, cytology, comparative phytochemistry, and chloroplast restriction site variation to produce conflicting accounts the relationships between Ambrosia species, as well as the classification of their close relatives in Franseria and Hymenoclea. To resolve undetermined intra-generic relationships within Ambrosia, we used DNA extracted from tissues obtained from seed banks and herbarium collections to generate multi-locus genetic data representing nearly all putative species, including four from South America.

Evaluation and comparison of FTA card and CTAB DNA extraction methods for non-agricultural taxa.

Premise Of The Study: An efficient, effective DNA extraction method is necessary for comprehensive analysis of plant genomes. This study analyzed the quality of DNA obtained using paper FTA cards prepared directly in the field when compared to the more traditional cetyltrimethylammonium bromide (CTAB)-based extraction methods from silica-dried samples.

Methods: DNA was extracted using FTA cards according to the manufacturer's protocol.

Development of highly variable microsatellite markers for the tetraploid (Caryophyllaceae).

Premise Of The Study: We designed and tested microsatellite markers for the North American native species (Caryophyllaceae) to investigate its population genetic structure and identify selection on floral design through male reproductive success.

Methods And Results: A total of 153 candidate microsatellite loci were isolated based on next-generation sequencing. We identified 18 polymorphic microsatellite loci in three populations of , with di- or trinucleotide repeats.

Analysis of whole chloroplast genomes from the genera of the Clauseneae, the curry tribe (Rutaceae, Citrus family).

The Clauseneae (Aurantioideae, Rutaceae) is a tribe in the Citrus family that, although economically important as it contains the culinary and medicinally-useful curry tree (Bergera koenigii), has been relatively understudied. Due to the recent significant taxonomic changes made to this tribe, a closer inspection of the genetic relationships among its genera has been warranted. Whole genome skimming was used to generate chloroplast genomes from six species, representing each of the four genera (Bergera, Clausena, Glycosmis, Micromelum) in the Clauseneae tribe plus one closely related outgroup (Merrillia), using the published plastome sequence of Citrus sinensis as a reference.

The population genomic basis of geographic differentiation in North American common ragweed ( L.).

Common ragweed ( L.) is an invasive, wind-pollinated plant nearly ubiquitous in disturbed sites in its eastern North American native range and present across growing portions of Europe, Africa, Asia, and Australia. Phenotypic divergence between European and native-range populations has been described as rapid evolution.

Another look at the phylogenetic position of the grape order Vitales: Chloroplast phylogenomics with an expanded sampling of key lineages.

Vitales is well-known for including the economically important fruit crop, the wine grape (Vitis vinifera). However, the position of the Vitales in the higher eudicots has been a subject of much debate. It has been variously reported to be sister to the Saxifragales and together as sister to the rest of rosids, or sister to the fabids-malvids clade, or sister to the Santalales, or sister to the fabids-malvids-Saxifragales clade.

Congruent Deep Relationships in the Grape Family (Vitaceae) Based on Sequences of Chloroplast Genomes and Mitochondrial Genes via Genome Skimming.

Vitaceae is well-known for having one of the most economically important fruits, i.e., the grape (Vitis vinifera).