Fine-scale genetic structure in rhizosphere microbial communities associated with (Fabaceae).

Soil microbiota of the rhizosphere are an important extension of the plant phenotype because they impact the health and fitness of host plants. The composition of these communities is expected to differ among host plants due to influence by host genotype. Given that many plant populations exhibit fine-scale genetic structure (SGS), associated microbial communities may also exhibit SGS.

The challenges of growing orchids from seeds for conservation: An assessment of asymbiotic techniques.

Lewis Knudson first successfully germinated orchid seeds asymbiotically on artificial medium in 1922. While many orchid species have since been grown asymbiotically, the tremendous variation in how species respond to artificial medium and growth conditions ex situ has also become apparent in the past century. In this study, we reviewed published journal articles on asymbiotic orchid seed germination to provide a summary of techniques used and to evaluate if these differ between terrestrial and epiphytic species, to identify areas where additional research is needed, and to evaluate whether asymbiotic germination could be used more often in ex situ conservation.

Molecular phylogeny and ancestral biogeographic reconstruction of Platanthera subgenus Limnorchis (Orchidaceae) using target capture methods.

Platanthera is one of the largest genera of temperate orchids in the Holarctic and exemplifies a lineage that has adaptively radiated into diverse habitats within North America, Asia, Europe, North Africa, Borneo, and Sarawak. Major centers of diversity in this genus are North America and eastern Asia. Despite its diversity, a thorough phylogenetic hypothesis for the genus is lacking because no studies have yet sampled taxa exhaustively or developed a robust molecular toolkit.

Fine-Scale Patterns of Genetic Structure in the Host Plant (Fabaceae) and Its Nodulating Rhizobia Symbionts.

In natural plant populations, a fine-scale spatial genetic structure (SGS) can result from limited gene flow, selection pressures or spatial autocorrelation. However, limited gene flow is considered the predominant determinant in the establishment of SGS. With limited dispersal ability of bacterial cells in soil and host influence on their variety and abundance, spatial autocorrelation of bacterial communities associated with plants is expected.

Patterns of Genetic Diversity in Highly Invasive Species: Cogongrass () Expansion in the Invaded Range of the Southern United States (US).

The spatial expansions of invasive organisms in the novel range are generally expected to follow an isolation-by-distance relationship (IBD) if the invasion is biologically driven; however, many invasions are facilitated anthropogenically. This research focused on the extant expansion patterns of cogongrass (). Cogongrass is a widespread invasive species throughout the southern United States (US).

Phylogeography and genetic structure of endemic and (Fabaceae) across the California Channel Islands.

Premise Of The Study: Taxa inhabiting the California Channel Islands exhibit variation in their degree of isolation, but few studies have considered patterns across the entire archipelago. We studied phylogeography of insular and to determine whether infraspecific taxa are genetically divergent and to elucidate patterns of diversification across these islands.

Methods: DNA sequences were collected from nuclear (ADH) and plastid genomes (, , ) from >450 samples on the Channel Islands and California.

Digitization workflows for flat sheets and packets of plants, algae, and fungi.

Effective workflows are essential components in the digitization of biodiversity specimen collections. To date, no comprehensive, community-vetted workflows have been published for digitizing flat sheets and packets of plants, algae, and fungi, even though latest estimates suggest that only 33% of herbarium specimens have been digitally transcribed, 54% of herbaria use a specimen database, and 24% are imaging specimens. In 2012, iDigBio, the U.

A review of the prevalence, utility, and caveats of using chloroplast simple sequence repeats for studies of plant biology.

Microsatellites occur in all plant genomes and provide useful markers for studies of genetic diversity and structure. Chloroplast microsatellites (cpSSRs) are frequently targeted because they are more easily isolated than nuclear microsatellites. Here, we quantified the frequency and uses of cpSSRs based on a literature review of over 400 studies published 1995-2013.

Inferred vs realized patterns of gene flow: an analysis of population structure in the Andros Island Rock Iguana.

Ecological data, the primary source of information on patterns and rates of migration, can be integrated with genetic data to more accurately describe the realized connectivity between geographically isolated demes. In this paper we implement this approach and discuss its implications for managing populations of the endangered Andros Island Rock Iguana, Cyclura cychlura cychlura. This iguana is endemic to Andros, a highly fragmented landmass of large islands and smaller cays.

Variable length chloroplast markers for population genetic studies in Acmispon (Fabaceae).

Premise Of The Study: To estimate genetic structure, chloroplast loci containing length-variable regions were developed for two legumes, Acmispon argophyllus and A. dendroideus. •

Methods And Results: Primers for 14 chloroplast loci containing repeat regions were developed from the chloroplast genome sequence of the legume Lotus japonicus and tested in Acmispon.

Asymmetrical gene flow in a hybrid zone of Hawaiian Schiedea (Caryophyllaceae) species with contrasting mating systems.

Asymmetrical gene flow, which has frequently been documented in naturally occurring hybrid zones, can result from various genetic and demographic factors. Understanding these factors is important for determining the ecological conditions that permitted hybridization and the evolutionary potential inherent in hybrids. Here, we characterized morphological, nuclear, and chloroplast variation in a putative hybrid zone between Schiedea menziesii and S.

Estimating the species tree for Hawaiian Schiedea (Caryophyllaceae) from multiple loci in the presence of reticulate evolution.

Schiedea (Caryophyllaceae) is a monophyletic genus of 34 species, all endemic to the Hawaiian Islands, that arose from a single colonization, providing one of the best examples of adaptive radiation in Hawai'i. Species utilize a range of habitats and exhibit a variety of growth forms and transitions in breeding systems from hermaphroditism toward dimorphism or autogamy. Our study included the most thorough sampling to date: 2-5 individuals per species and 4 independent genetic partitions: eight plastid and three low-copy nuclear loci (9217bps), allowing a three-locus BEST species tree.

Phylogeographic patterns and demographic history of Schiedea globosa (Caryophyllaceae) on the Hawaiian Islands.

Geomorphological changes have been demonstrated to have had profound impacts on biodiversity, often leading to demographic expansions and contractions and allopatric divergence of taxa. We examined DNA sequence variation at two nuclear and one maternally inherited plastid locus among 10 populations of Schiedea globosa on the Hawaiian Islands to assess the primary factors shaping genetic structure, phylogeographic patterns, and the importance of geographic isolation to population divergence. Schiedea globosa has characteristics that may promote gene flow, including wind pollination and rafting of plants in ocean currents.

PERMANENT GENETIC RESOURCES: Isolation of microsatellite loci from the endangered plant Sibara filifolia (Brassicaceae).

Sibara filifolia (Brassicaceae) is a federally endangered annual herb found on two of the California Channel Islands. Previous studies based on allozymes revealed little genetic variability on San Clemente Island. Nine polymorphic microsatellite loci were isolated from individuals on San Clemente Island.

Spatial genetic structure and frequency of interspecific hybridization in Platanthera aquilonis and P. dilatata (Orchidaceae) occurring in sympatry.

Knowledge of genetic structure at different scales is necessary for evaluating the importance of interactions between the genome and environment and for inferring underlying processes that bring about evolutionary diversification. Here, genetic and morphological variation was assessed for 154 individuals of Platanthera aquilonis and P. dilatata in Maine, using RAPD and PCR-RFLP markers and measurements of five morphological traits to determine the prevalence of interspecific hybrids and underlying spatial genetic structure of the population.

Genetic divergence does not predict change in ornament expression among populations of stalk-eyed flies.

Stalk-eyed flies (Diptera: Diopsidae) possess eyes at the ends of elongated peduncles, and exhibit dramatic variation in eye span, relative to body length, among species. In some sexually dimorphic species, evidence indicates that eye span is under both intra- and intersexual selection. Theory predicts that isolated populations should evolve differences in sexually selected traits due to drift.

Bayesian approaches for the analysis of population genetic structure: an example from Platanthera leucophaea (Orchidaceae).

We describe four extensions to existing Bayesian methods for the analysis of genetic structure in populations: (i) use of beta distributions to approximate the posterior distribution of f and theta(B); (ii) use of an entropy statistic to describe the amount of information about a parameter derived from the data; (iii) use of the Deviance Information Criterion (DIC) as a model choice criterion for determining whether there is evidence for inbreeding within populations or genetic differentiation among populations; and (iv) use of samples from the posterior distributions for f and theta(B) derived from different data sets to determine whether the estimates are consistent with one another. We illustrate each of these extensions by applying them to data derived from previous allozyme and random amplified polymorphic DNA surveys of an endangered orchid, Platanthera leucophaea, and we conclude that differences in theta(B) from the two data sets may represent differences in the underlying mutational processes.

The cost of inbreeding in Platanthera leucophaea (Orchidaceae).

Fragmentation and isolation are expected to have a considerable impact on viability and recruitment in populations of rare species. Platanthera leucophaea (Orchidaceae), a rare orchid, currently exists in a fragmented landscape of its natural habitat. Floral morphology suggests this species is predominantly outcrossing, but surveys of allozyme diversity suggest high, variable levels of inbreeding in populations (F(IS) = -0.

A comparison of two methods of calculating GST, a genetic measure of population differentiation.

G(ST) is a genetic statistic describing differentiation of populations and has frequently been compared with Hamrick and Godt's (1989) review of the plant literature. We show here that some comparisons may be inappropriate if G(ST) was calculated in a different way than that used by Hamrick and Godt (HG). An alternative method advocated by Nei is mathematically different from the HG technique, occasionally resulting in different G(ST) values.