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The genomic variation of an invasive species may be affected by complex demographic histories and evolutionary changes during the invasion. Here, we describe the relative influence of bottlenecks, clonality, and population expansion in determining genomic variability of the widespread red macroalga Agarophyton vermiculophyllum. Its introduction from mainland Japan to the estuaries of North America and Europe coincided with shifts from predominantly sexual to partially clonal reproduction and rapid adaptive evolution. A survey of 62,285 SNPs for 351 individuals from 35 populations, aligned to 24 chromosome-length scaffolds indicate that linkage disequilibrium (LD), observed heterozygosity (H o ), Tajima's D, and nucleotide diversity (Pi) were greater among non-native than native populations. Evolutionary simulations indicate LD and Tajima's D were consistent with a severe population bottleneck. Also, the increased rate of clonal reproduction in the non-native range could not have produced the observed patterns by itself but may have magnified the bottleneck effect on LD. Elevated marker diversity in the genetic source populations could have contributed to the increased H o and Pi observed in the non-native range. We refined the previous invasion source region to a ~50 km section of northeastern Honshu Island. Outlier detection methods failed to reveal any consistently differentiated loci shared among invaded regions, probably because of the complex A. vermiculophyllum demographic history. Our results reinforce the importance of demographic history, specifically founder effects, in driving genomic variation of invasive populations, even when localized adaptive evolution and reproductive system shifts are observed., (© 2021 John Wiley & Sons Ltd.)

For many taxa, including isomorphic haplodiplontic macroalgae, determining sex and ploidy is challenging, thereby limiting the scope of some population demographic and genetic studies. Here, we used double-digest restriction site-associated DNA sequencing (ddRAD-seq) to identify sex-linked molecular markers in the widespread red alga Agarophyton vermiculophyllum. In the ddRAD-seq library, we included 10 female gametophytes, 10 male gametophytes, and 16 tetrasporophytes from one native and one non-native site (N = 40 gametophytes and N = 32 tetrasporophytes total). We identified seven putatively female-linked and 19 putatively male-linked sequences. Four female- and eight male-linked markers amplified in all three life cycle stages. Using one female- and one male-linked marker that were sex-specific, we developed a duplex PCR and tested the efficacy of this assay on a subset of thalli sampled at two sites in the non-native range. We confirmed ploidy based on the visual observation of reproductive structures and previous microsatellite genotyping at 10 polymorphic loci. For 32 vegetative thalli, we were able to assign sex and confirm ploidy in these previously genotyped thalli. These markers will be integral to ongoing studies of A. vermiculophyllum invasion. We discuss the utility of RAD-seq over other approaches previously used, such as RAPDs (random amplified polymorphic DNA), for future work designing sex-linked markers in other haplodiplontic macroalgae for which genomes are lacking., (© 2020 Phycological Society of America.)

Determining how genes are associated with traits in plants and other organisms is a major challenge in modern biology. The unPAK project - undergraduates phenotyping Arabidopsis knockouts - has generated phenotype data for thousands of non-lethal insertion mutation lines within a single Arabidopsis thaliana genomic background. The focal phenotypes examined by unPAK are complex macroscopic fitness-related traits, which have ecological, evolutionary and agricultural importance. These phenotypes are placed in the context of the wild-type and also natural accessions (phytometers), and standardized for environmental differences between assays. Data from the unPAK project are used to describe broad patterns in the phenotypic consequences of insertion mutation, and to identify individual mutant lines with distinct phenotypes as candidates for further study. Inclusion of undergraduate researchers is at the core of unPAK activities, and an important broader impact of the project is providing students an opportunity to obtain research experience., (© 2019 The Authors The Plant Journal © 2019 John Wiley & Sons Ltd.)

We present a curriculum description, an initial student outcome investigation, and sample scientific results for a representative Course-Based Undergraduate Research Experience (CURE) that is part of the "Undergraduates Phenotyping Arabidopsis Knockouts" (unPAK) network. CUREs in the unPAK network characterize quantitative phenotypes of the model plant Arabidopsis from across environments to uncover connections between genotype and phenotype. Students in unPAK CUREs grow plants in a replicated block design and make quantitative measurements throughout the semester. This CURE enables students to answer plant science questions that draw from fields such as environmental science, genetics, ecology, and evolution. Findings indicate that this experience provides students with opportunities to make relevant scientific discoveries. Eighty percent of student datasets produced from the CURE met criteria for inclusion in the project database, indicative of student learning in data collection and analysis of quantitative plant traits. Student datasets uncovered novel effects of mutation on plant form. In addition, students' science self-efficacy increased as a result of course participation, and faculty feedback on course implementation was positive. We present unPAK as a new network that supports CUREs and research experiences focused on collecting biological data made publicly available to the scientific community. The unPAK CUREs can be tailored to address instructor interests or pedagogical needs while involving students in research investigating quantitative plant phenotypes.

Ecological theory suggests that coexistence of many species within communities requires negative frequency-dependent feedbacks to prevent exclusion of the least fit species. For plant communities, empirical evidence of negative frequency dependence driving species coexistence and diversity patterns is rapidly accumulating, but connecting these findings to theory has been difficult as corresponding theoretical frameworks only consider small numbers of species. Here, we show how frequency-dependent feedback constrains community coexistence, regardless of the number of species and inherent fitness inequalities between them. Any interaction network can be characterized by a single community interaction coefficient, I C , which determines whether community-level feedback is positive or negative. Negative feedback is a necessary (but not sufficient) condition for persistence of the entire community. Even in cases where the coexistence equilibrium state cannot recover from perturbations, I C  < 0 can enable species persistence via cyclic succession. The number of coexisting species is predicted to increase with the average strength of negative feedback. This prediction is supported by patterns of tree species diversity in more than 200,000 deciduous forest plots in the eastern United States, which can be reproduced in simulations that span the observed range of community feedback. By providing a quantitative metric for the strength of negative feedback needed for coexistence, we can now integrate theory and empirical data to test whether observed feedback-diversity correlations are strong enough to infer causality.

The rapid evolution of non-native species can facilitate invasion success, but recent reviews indicate that such microevolution rarely yields expansion of the climatic niche in the introduced habitats. However, because some invasions originate from a geographically restricted portion of the native species range and its climatic niche, it is possible that the frequency, direction, and magnitude of phenotypic evolution during invasion have been underestimated. We explored the utility of niche shift analyses in the red seaweed Gracilaria vermiculophylla , which expanded its range from the northeastern coastline of Japan to North America, Europe, and northwestern Africa within the last 100 years. A genetically informed climatic niche shift analysis indicates that native source populations occur in colder and highly seasonal habitats, while most non-native populations typically occur in warmer, less seasonal habitats. This climatic niche expansion predicts that non-native populations evolved greater tolerance for elevated heat conditions relative to native source populations. We assayed 935 field-collected and 325 common-garden thalli from 40 locations, and as predicted, non-native populations had greater tolerance for ecologically relevant extreme heat (40°C) than did Japanese source populations. Non-native populations also had greater tolerance for cold and low-salinity stresses relative to source populations. The importance of local adaptation to warm temperatures during invasion was reinforced by evolution of parallel clines: Populations from warmer, lower-latitude estuaries had greater heat tolerance than did populations from colder, higher-latitude estuaries in both Japan and eastern North America. We conclude that rapid evolution plays an important role in facilitating the invasion success of this and perhaps other non-native marine species. Genetically informed ecological niche analyses readily generate clear predictions of phenotypic shifts during invasions and may help to resolve debate over the frequency of niche conservatism versus rapid adaptation during invasion.

Screens of organisms with disruptive mutations in a single gene often fail to detect phenotypic consequences for the majority of mutants. One explanation for this phenomenon is that the presence of paralogous loci provides genetic redundancy. However, it is also possible that the assayed traits are affected by few loci, that effects could be subtle or that phenotypic effects are restricted to certain environments. We assayed a set of T-DNA insertion mutant lines of Arabidopsis thaliana to determine the frequency with which mutation affected fitness-related phenotypes. We found that between 8% and 42% of the assayed lines had altered fitness from the wild type. Furthermore, many of these lines exhibited fitness greater than the wild type. In a second experiment, we grew a subset of the lines in multiple environments and found whether a T-DNA insert increased or decreased fitness traits depended on the assay environment. Overall, our evidence contradicts the hypothesis that genetic redundancy is a common phenomenon in A. thaliana for fitness traits. Evidence for redundancy from prior screens of knockout mutants may often be an artefact of the design of the phenotypic assays which have focused on less complex phenotypes than fitness and have used single environments. Finally, our study adds to evidence that beneficial mutations may represent a significant component of the mutational spectrum of A. thaliana., (© 2017 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2017 European Society For Evolutionary Biology.)

The identification of native sources and vectors of introduced species informs their ecological and evolutionary history and may guide policies that seek to prevent future introductions. Population genetics provides a powerful set of tools to identify origins and vectors. However, these tools can mislead when the native range is poorly sampled or few molecular markers are used. Here, we traced the introduction of the Asian seaweed Gracilaria vermiculophylla (Rhodophyta) into estuaries in coastal western North America, the eastern United States, Europe, and northwestern Africa by genotyping more than 2,500 thalli from 37 native and 53 non-native sites at mitochondrial cox 1 and 10 nuclear microsatellite loci. Overall, greater than 90% of introduced thalli had a genetic signature similar to thalli sampled from the coastline of northeastern Japan, strongly indicating this region served as the principal source of the invasion. Notably, northeastern Japan exported the vast majority of the oyster Crassostrea gigas during the 20th century. The preponderance of evidence suggests G. vermiculophylla may have been inadvertently introduced with C. gigas shipments and that northeastern Japan is a common source region for estuarine invaders. Each invaded coastline reflected a complex mix of direct introductions from Japan and secondary introductions from other invaded coastlines. The spread of G. vermiculophylla along each coastline was likely facilitated by aquaculture, fishing, and boating activities. Our ability to document a source region was enabled by a robust sampling of locations and loci that previous studies lacked and strong phylogeographic structure along native coastlines.

Simulations are a key tool in molecular ecology for inference and forecasting, as well as for evaluating new methods. Due to growing computational power and a diversity of software with different capabilities, simulations are becoming increasingly powerful and useful. However, the widespread use of simulations by geneticists and ecologists is hindered by difficulties in understanding these softwares' complex capabilities, composing code and input files, a daunting bioinformatics barrier and a steep conceptual learning curve. skelesim (an R package) guides users in choosing appropriate simulations, setting parameters, calculating genetic summary statistics and organizing data output, in a reproducible pipeline within the R environment. skelesim is designed to be an extensible framework that can 'wrap' around any simulation software (inside or outside the R environment) and be extended to calculate and graph any genetic summary statistics. Currently, skelesim implements coalescent and forward-time models available in the fastsimcoal2 and rmetasim simulation engines to produce null distributions for multiple population genetic statistics and marker types, under a variety of demographic conditions. skelesim is intended to make simulations easier while still allowing full model complexity to ensure that simulations play a fundamental role in molecular ecology investigations. skelesim can also serve as a teaching tool: demonstrating the outcomes of stochastic population genetic processes; teaching general concepts of simulations; and providing an introduction to the R environment with a user-friendly graphical user interface (using shiny)., (© 2016 John Wiley & Sons Ltd.)

Baker's Law predicts uniparental reproduction will facilitate colonization success in novel habitats. While evidence supports this prediction among colonizing plants and animals, few studies have investigated shifts in reproductive mode in haplo-diplontic species in which both prolonged haploid and diploid stages separate meiosis and fertilization in time and space. Due to this separation, asexual reproduction can yield the dominance of one of the ploidy stages in colonizing populations. We tested for shifts in ploidy and reproductive mode across native and introduced populations of the red seaweed Gracilaria vermiculophylla. Native populations in the northwest Pacific Ocean were nearly always attached by holdfasts to hard substrata and, as is characteristic of the genus, haploid-diploid ratios were slightly diploid-biased. In contrast, along North American and European coastlines, introduced populations nearly always floated atop soft-sediment mudflats and were overwhelmingly dominated by diploid thalli without holdfasts. Introduced populations exhibited population genetic signals consistent with extensive vegetative fragmentation, while native populations did not. Thus, the ecological shift from attached to unattached thalli, ostensibly necessitated by the invasion of soft-sediment habitats, correlated with shifts from sexual to asexual reproduction and slight to strong diploid bias. We extend Baker's Law by predicting other colonizing haplo-diplontic species will show similar increases in asexuality that correlate with the dominance of one ploidy stage. Labile mating systems likely facilitate colonization success and subsequent range expansion, but for haplo-diplontic species, the long-term eco-evolutionary impacts will depend on which ploidy stage is lost and the degree to which asexual reproduction is canalized., (© 2016 John Wiley & Sons Ltd.)

Microsatellite loci are popular molecular markers due to their resolution in distinguishing individual genotypes. However, they have rarely been used to explore the population dynamics in species with biphasic life cycles in which both haploid and diploid stages develop into independent, functional organisms. We developed microsatellite loci for the haploid-diploid red seaweed Gracilaria vermiculophylla, a widespread non-native species in coastal estuaries of the Northern hemisphere. Forty-two loci were screened for amplification and polymorphism. Nine of these loci were polymorphic across four populations of the extant range with two to eleven alleles observed. Mean observed and expected heterozygosities ranged from 0.265 to 0.527 and 0.317 to 0.387, respectively. Overall, these markers will aid in the study of the invasive history of this seaweed and further studies on the population dynamics of this important haploid-diploid primary producer.

Predicting the response of fine roots to increased atmospheric CO₂ concentration has important implications for carbon (C) and nutrient cycling in forest ecosystems. Root architecture is known to play an important role in how trees acquire soil resources in changing environments. However, the effects of elevated CO₂ on the fine-root architecture of trees remain unclear. We investigated the architectural response of fine roots exposed to 14 yr of CO₂ enrichment and 6 yr of nitrogen (N) fertilization in a Pinus taeda (loblolly pine) forest. Root traits reflecting geometry, topology and uptake function were measured on intact fine-root branches removed from soil monoliths and the litter layer. CO₂ enrichment resulted in the development of a fine-root pool that was less dichotomous and more exploratory under N-limited conditions. The per cent mycorrhizal colonization did not differ among treatments, suggesting that root growth and acclimation to elevated CO₂ were quantitatively more important than increased mycorrhizal associations. Our findings emphasize the importance of architectural plasticity in response to environmental change and suggest that changes in root architecture may allow trees to effectively exploit larger volumes of soil, thereby pre-empting progressive nutrient limitations., (© 2014 The Authors. New Phytologist © 2014 New Phytologist Trust.)

Root systems serve important roles in carbon (C) storage and resource acquisition required for the increased photosynthesis expected in CO2-enriched atmospheres. For these reasons, understanding the changes in size, distribution and tissue chemistry of roots is central to predicting the ability of forests to capture anthropogenic CO2. We sampled 8000 cm(3) soil monoliths in a pine forest exposed to 14 years of free-air-CO2-enrichment and 6 years of nitrogen (N) fertilization to determine changes in root length, biomass, tissue C : N and mycorrhizal colonization. CO2 fumigation led to greater root length (98%) in unfertilized plots, but root biomass increases under elevated CO2 were only found for roots <1 mm in diameter in unfertilized plots (59%). Neither fine root [C] nor [N] was significantly affected by increased CO2. There was significantly less root biomass in N-fertilized plots (19%), but fine root [N] and [C] both increased under N fertilization (29 and 2%, respectively). Mycorrhizal root tip biomass responded positively to CO2 fumigation in unfertilized plots, but was unaffected by CO2 under N fertilization. Changes in fine root [N] and [C] call for further study of the effects of N fertilization on fine root function. Here, we show that the stimulation of pine roots by elevated CO2 persisted after 14 years of fumigation, and that trees did not rely exclusively on increased mycorrhizal associations to acquire greater amounts of required N in CO2-enriched plots. Stimulation of root systems by CO2 enrichment was seen primarily for fine root length rather than biomass. This observation indicates that studies measuring only biomass might overlook shifts in root systems that better reflect treatment effects on the potential for soil resource uptake. These results suggest an increase in fine root exploration as a primary means for acquiring additional soil resources under elevated CO2., (© The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.)

Since the 1970s, water temperatures along the Atlantic seaboard of the United States have risen by an average of 0.5 °C in summer months and 2.2 °C in winter months. In response, the distribution and abundance of several nearshore species have changed dramatically, but no study has attempted to document whether estuarine populations have evolved greater thermal tolerance. Here, we re-examine the classic latitudinal cline at lactate dehydrogenase (LDH) in the killifish Fundulus heteroclitus that was originally described by Dennis Powers and associates from samples collected between 1970 and 1972. Laboratory and field evidences indicated that northern and southern isozymes at muscle LDH are locally adapted to cold and warm temperatures, respectively. Despite the potential for evolutionary response at this adaptive locus, we detected no significant shift of the LDH cline from 20 to 30 F. heteroclitus collected at each of 13 locations between the early 1970s and 2010. We conclude that the microevolution of LDH-mediated thermal tolerance has not occurred, that shifts in alleles are too incremental to be distinguished from random processes, or that F. heteroclitus uses phenotypic and genetic mechanisms besides LDH to respond to warmer waters., (© The American Genetic Association 2014. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.)

Large-scale, long-term FACE (Free-Air CO2 enrichment) experiments indicate that increases in atmospheric CO2 concentrations will influence forest C cycling in unpredictable ways. It has been recently suggested that responses of mycorrhizal fungi could determine whether forest net primary productivity (NPP) is increased by elevated CO2 over long time periods and if forests soils will function as sources or sinks of C in the future. We studied the dynamic responses of ectomycorrhizae to N fertilization and atmospheric CO2 enrichment at the Duke FACE experiment using minirhizotrons over a 6 year period (2005-2010). Stimulation of mycorrhizal production by elevated CO2 was observed during only 1 (2007) of 6 years. This increased the standing crop of mycorrhizal tips during 2007 and 2008; during 2008, significantly higher mortality returned standing crop to ambient levels for the remainder of the experiment. It is therefore unlikely that increased production of mycorrhizal tips can explain the lack of progressive nitrogen limitations and associated increases in N uptake observed in CO2 -enriched plots at this site. Fertilization generally decreased tree reliance on mycorrhizae as tip production declined with the addition of nitrogen as has been shown in many other studies. Annual NPP of mycorrhizal tips was greatest during years with warm January temperatures and during years with cool spring temperatures. A 2 °C increase in average late spring temperatures (May and June) decreased annual production of mycorrhizal root tip length by 50%. This has important implications for ecosystem function in a warmer world in addition to potential for forest soils to sequester atmospheric C., (© 2013 John Wiley & Sons Ltd.)

Root systems are important for global models of below-ground carbon and nutrient cycling. Notoriously difficult sampling methods and the fractal distribution of root diameters in the soil make data being used in these models especially susceptible to error resulting from under-sampling. We applied the concept of species accumulation curves to root data to quantify the extent of under-sampling inherent to minirhizotron and soil coring sampling for both root uptake and carbon content studies. Based on differences in sample size alone, minirhizotron sampling missed approximately one third of the root diameters observed by soil core sampling. Sample volumes needed to encounter 90% of root diameters averaged 2481 cm(3) for uptake studies and 5878 cm(3) for root carbon content studies. These results show that small sample volumes encounter a non-representative sample of the overall root pool, and provide future guidelines for determining optimal sample volumes in root studies., (© 2013 John Wiley & Sons Ltd/CNRS.)

Molting in crustaceans is an important endocrine-controlled biological process that plays a critical role in growth and reproduction. Many factors can affect this physiological cycle in crustaceans including environmental stressors and disease agents. For example the pathology of Taura Syndrome Virus (TSV) of shrimp is closely related to molting cycle. Similarly, endosulfan, a commonly used pesticide is a potential endocrine disruptor. This study explores interrelationships between pesticide exposure, virus infection and their interactions with physiology and susceptibility of the shrimp. Litopenaeus vannamei (Pacific white shrimp) were challenged with increasing doses of endosulfan and TSV (TSV-C, a Belize reference strain) to determine the respective median lethal concentrations (LC(50)s). The 96-h endosulfan LC(50) was 5.32 μg L(-1), while the 7-d TSV LC(50) was 54.74 mg L(-1). Subsequently, based on their respective LC(50) values, a 20-d interaction experiment with sublethal concentrations of endosulfan (2 μg L(-1)) and TSV (30 mg L(-1)) confirmed a significant interaction (p<0.05, χ(2)=5.29), and thereby the susceptibility of the shrimp. Concurrently, molt-stage of animals, both at the time of exposure and death, was compared with mortality. For animals challenged with TSV, no strong correlation between molt-stage and mortality was observed (p>0.05). For animals exposed to endosulfan, animals in the postmolt stage were shown to be more susceptible to acute toxicity (p<0.05). For animals exposed to both TSV and endosulfan, interference of endosulfan-associated stress lead to increasingly higher susceptibility at postmolt (p<0.05) during the acute phase of the TSV disease cycle., (Copyright © 2011 Elsevier Ltd. All rights reserved.)

A common geographical pattern of genetic variation is the one-dimensional cline. Clines may be maintained by diversifying selection across a geographical gradient but can also reflect historical processes such as allopatry followed by secondary contact. To identify loci that may be undergoing diversifying selection, we examined the distribution of geographical variation patterns across the range of the killifish (Fundulus heteroclitus) in 310 loci, including microsatellites, allozymes, and single nucleotide polymorphisms. We employed two approaches to detect loci under strong diversifying selection. First, we developed an automated method to identify clinal variation on a per-locus basis and examined the distribution of clines to detect those that exhibited signifcantly steeper slopes. Second, we employed a classic [Formula: see text]-outlier method as a complementary approach. We also assessed performance of these techniques using simulations. Overall, latitudinal clines were detected in nearly half of all loci genotyped (i.e., all eight microsatellite loci, 12 of 16 allozyme loci and 44% of the 285 SNPs). With the exception of few outlier loci (notably mtDNA and malate dehydrogenase), the positions and slopes of Fundulus clines were statistically indistinguishable. The high frequency of latitudinal clines across the genome indicates that secondary contact plays a central role in the historical demography of this species. Our simulation results indicate that accurately detecting diversifying selection using genome scans is extremely difficult in species with a strong signal of secondary contact; neutral evolution under this history produces clines as steep as those expected under selection. Based on these results, we propose that demographic history can explain all clinal patterns observed in F. heteroclitus without invoking natural selection to either establish or maintain the pattern we observe today.

The usefulness of the polymerase chain reaction with restriction fragment length polymorphism (PCR-RFLP) and partial sequencing of the cytochrome oxidase I (COI) gene was tested regarding the utility of these techniques in unraveling philometrid life cycles and, in particular, to determine putative paratenic host species. Our focus was to study three species of philometrids commonly found in the estuaries of South Carolina: Philometroides paralichthydis and Philometra overstreeti from the southern flounder, Paralichthys lethostigma and Philometra carolinensis from the spotted seatrout, Cynoscion nebulosus. A total of 473 fish in 19 species known to be potential prey of the spotted seatrout and the southern flounder were dissected. Of all nematode larvae found in the mesenteries of 53 fish of 10 species, 21 specimens were determined to be philometrids using PCR. The use of PCR-RFLP allowed the identification of larvae of P. carolinensis and P. overstreeti in the freshwater goby, Ctenogobius shufeldti, and P. overstreeti in mummichog, Fundulus heteroclitus. However, 12 RFLP profiles could not be matched to control species, thus demonstrating the limitation of this technique in areas where diversity of philometrids is not well known and higher than anticipated. Similarly, COI procedures provided unknown sequences that did not match those of nine philometrid species used as controls. We concluded that although both techniques showed some usefulness and promise, at this point, however, they demonstrate the need of increasing our knowledge of marine and estuarine philometrid biodiversity.

tossm (Testing of Spatial Structure Methods) is a package for testing the performance of genetic analytical methods in a management context. In the tossm package, any method developed to detect population genetic structure can be combined with a mechanism for creating management units (MUs) based on the genetic analysis. The resulting Boundary-Setting Algorithm (BSA) dictates harvest boundaries with a genetic basis. These BSAs can be evaluated with respect to how well the MUs they define meet management objectives., (Published 2009. This article is a US Government work and is in the public domain in the USA.)

The residence time of fine-root carbon in soil is one of the least understood aspects of the global carbon cycle, and fine-root dynamics are one of the least understood aspects of plant function. Most recent studies of these belowground dynamics have used one of two methodological strategies. In one approach, based on analysis of carbon isotopes, the persistence of carbon is inferred; in the other, based on direct observations of roots with cameras, the longevity of individual roots is measured. We show that the contribution of fine roots to the global carbon cycle has been overstated because observations of root lifetimes systematically overestimate the turnover of fine-root biomass. On the other hand, isotopic techniques systematically underestimate the turnover of individual roots. These differences, by virtue of the separate processes or pools measured, are irreconcilable.

Seabeach amaranth (Amaranthus pumilus Raf.), a threatened annual marine plant, is a primary colonizer of the windward side of Atlantic coastal dunes. It serves an important ecological role in dune accumulation and stabilization. Because Hurricane Floyd eliminated all native seabeach amaranth in South Carolina in 1999, experimental reestablishment plantings have been attempted. In August 2000, seabeach amaranth on Dewees and Cape Island in Charleston County, Huntington Beach in Georgetown County, and Otter Island in Colleton County, South Carolina were stunted and senesced prematurely. Leaves on affected plants were only one-half of the normal size and internodes were shortened. Most plants (>90%) at each location were affected. Diseased leaves had small, pale green-to-tan spots above hypophyllous pustules that contained numerous, dry, hyaline, subglobose conidia. Conidia measured 13.5 (10 to 17) × 15.0 (11 to 18) μm. Based on morphological characters and the host, the pathogen was identified as Albugo bliti (Biv.-Bern.) Kuntze (1,2). No oospores were observed. Diseased plants were collected from Dewees and Otter Islands and kept frozen for use as a source of inoculum. Six A. pumilus plants each of six Plant Introductions (PI), 553080 through 553085, that had been grown from seed were sprayed with a suspension of 4.7 × 10 5 conidia per ml. One plant of each PI was sprayed with sterile distilled water as a noninoculated control. All plants were placed in a humidity chamber for 48 h and then moved to a greenhouse bench. Thirteen days after inoculation, all inoculated plants had pustules of white rust. Diseased plants had a mean of 42 pustules per plant and PI's did not differ in susceptibility. Five of six noninoculated plants also had white rust pustules, but only a mean of 2.3 (range 1 to 5) pustules each. White rust likely appeared on noninoculated plants because plants were spaced closely together in the chamber. Pustules and conidia on inoculated plants were identical to those on plants collected originally. Albugo bliti has been reported on 19 other Amaranthus species (1), but to our knowledge, this is the first report of white rust on seabeach amaranth in the United States. White rust reduced the biomass of infected plants and, hence, their ability to trap sand. White rust was not observed on subsequent plantings in 2001 and 2002 at any location. References: (1) D. F. Farr et al. Fungal Databases. Systematic Botany and Mycology Laboratory, On-line publication. ARS USDA, 2002. (2) G. W. Wilson. Bull. Torrey Bot. Club 34:61, 1907.

Long-distance seed dispersal influences many key aspects of the biology of plants, including spread of invasive species, metapopulation dynamics, and diversity and dynamics in plant communities. However, because long-distance seed dispersal is inherently hard to measure, there are few data sets that characterize the tails of seed dispersal curves. This paper is structured around two lines of argument. First, we argue that long-distance seed dispersal is of critical importance and, hence, that we must collect better data from the tails of seed dispersal curves. To make the case for the importance of long-distance seed dispersal, we review existing data and models of long-distance seed dispersal, focusing on situations in which seeds that travel long distances have a critical impact (colonization of islands, Holocene migrations, response to global change, metapopulation biology). Second, we argue that genetic methods provide a broadly applicable way to monitor long-distance seed dispersal; to place this argument in context, we review genetic estimates of plant migration rates. At present, several promising genetic approaches for estimating long-distance seed dispersal are under active development, including assignment methods, likelihood methods, genealogical methods, and genealogical/demographic methods. We close the paper by discussing important but as yet largely unexplored areas for future research.

While DNA-based markers can provide a wealth of information for the study of plant evolutionary biology, progress is limited by the lack of primers available for PCR. To overcome this limitation, we outline a protocol for developing oligonucleotide primers targeting regions of low copy-number nuclear genes. This protocol is intended to lead to universally useful primer sets. To test our approach, we designed eight primer sets and tested their abilities to amplify targets from representatives of each dicot and one monocot subclass. Five of the eight primer sets amplified targets from at least five of the seven taxa and thus exhibited broad taxonomic usefulness; the remaining primers were rather specific, however, and amplified targets from at most three taxa. In only one primer-taxon combination was a complex multiple-banded amplification produced. Overall, the protocol outlined proved quite useful at identifying broadly applicable primers targeted to low copy-number nuclear genes. Wider application of this approach should be effective at greatly increasing the amount of genetic information available for a diversity of plant nuclear genomes.

The degree to which conspecific populations are interconnected via ongoing gene flow remains an important focus of evolutionary biology. One major difficulty in distinguishing ongoing gene flow from historical subdivision is that either process can generate similar estimates of apparent gene flow. Thus, gene flow estimates themselves are insufficient to distinguish between these alternatives. However, genetic data coupled with additional information about demography and distribution do allow a distinction to be made. Here we address the specific question, does gene flow link populations of Aquilegia? In a survey of a 525 B.P. chloroplast DNA fragment sampled from 251 individual plants from 18 populations of three taxa, five haplotypes were identified. No significant relationship between geographic distance and apparent gene flow between population pairs existed. Further, the estimated level of gene flow was entirely compatible with a historical subdivision of Aquilegia populations during the late Pleistocene or early Holocene. Therefore, these patterns of variation are due not to ongoing gene flow, but rather to historical association among populations. Thus Aquilegia populations may be considered as distinct evolutionary entities with regard to seed-mediated processes. As a result, comparative analysis of ecological traits undergoing potentially rapid evolution (e.g., life histories, mating systems, inbreeding depression) should be possible in these taxa., (© 1996 The Society for the Study of Evolution.)