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opencc-zeroNov 2020View details →

Contrasting effects of Miocene and Anthropocene levels of atmospheric CO2 on silicon accumulation in a model grass

Grasses are hyper-accumulators of silicon (Si) which they acquire from the soil and deposit in tissues to resist environmental stresses. Moreover, given the high metabolic costs of herbivore defensive chemicals and structural constituents (e.g. cellulose), grasses may substitute Si for these components when carbon (C) is limited. Indeed, high Si uptake grasses evolved in the Miocene when atmospheric CO2 concentration was much lower than present levels. It is; however, unknown how pre-industrial CO2 concentrations affect Si accumulation in grasses. Using Brachypodium distachyon, we hydroponically manipulated Si-supply (0.0, 0.5, 1, 1.5, 2 mM) and grew plants under Miocene (200 ppm) and Anthropocene levels of CO2 comprising ambient (410 ppm) and elevated (640 ppm) CO2 concentrations. We showed that regardless of Si-treatments, the Miocene CO2 levels increased foliar Si concentrations by 47% and 56% relative to plants grown under ambient and elevated CO2, respectively. This is due to higher accumulation overall, but also the reallocation of Si from the roots into the shoots. Our results suggest that grasses may accumulate high Si concentrations in foliage when carbon is less available (i.e. pre-industrial CO2 levels) but this is likely to decline under future climate change scenarios, potentially leaving grasses more susceptible to environmental stresses

opencc-zeroNov 2020View details →

RAD-seq reveals patterns of diversification, hybridization, and the accumulation of reproductive isolation in a clade of partially sympatric, tropical island trees

A common pattern observed in temperate tree clades is that species are often morphologically distinct and partially interfertile but maintain species cohesion despite ongoing hybridization where ranges overlap. Although closely related species commonly occur in sympatry in tropical ecosystems, little is known about patterns of hybridization within a clade over time, and the implications of this hybridization for the maintenance of species boundaries. In this study, we focused on a clade of sympatric trees in the genus Diospyros in the Mascarene islands and investigated whether species are genetically distinct, whether they hybridize, and how patterns of hybridization are related to the time since divergence among species. We sampled multiple populations from each of 12 Mascarene Diospyros species, generated genome-wide SNP data using 2bRADseq, and conducted population genomic and phylogenomic analyses. We found that Mascarene Diospyros species diverged millions of years ago and are largely genetically distinct from one another. Although hybridization was observed between closely related species belonging to the same subclade, more distantly related species showed little evidence of interspecific hybridization. Phylogenomic analyses also suggested that introgression occurred during the evolutionary history of the clade. This suggests that, as diversification progressed, interspecific hybridization also occurred among species, but became infrequent as lineages diverged from one another and evolved reproductive barriers. Species now co-exist in partial sympatry, and experience limited hybridization between close relatives. Additional research is needed to better understand the role introgression may have played in adaptation and diversification of Mascarene Diospyros, and its relevance for conservation.

opencc-zeroDec 2020View details →

French (F) and Swedish (S) Founder (P) and Mutation Accumulation Line (MA) performance in France and Sweden

Little is empirically known about the contribution of mutations to fitness in natural environments. However, Fisher's Geometric Model (FGM) provides a conceptual foundation to consider the influence of the environment on mutational effects. To quantify mutational properties in the field, we established eight sets of MA lines (7-10 generations) derived from eight founders collected from natural populations of Arabidopsis thaliana from French and Swedish sites, representing the range margins of the species in Europe. We reciprocally planted the MA lines and their founders at French and Swedish sites, allowing us to test predictions of FGM under naturally occurring environmental conditions. The performance of the MA lines relative to each other and to their respective founders confirmed some and contradicted other predictions of the FGM: the contribution of mutation to fitness variance increased when the genotype was in an environment where its fitness was low, i.e., in the away environment, but mutations were more likely to be beneficial when the genotype was in its home environment. Consequently, environmental context plays a large role in the contribution of mutations to evolutionary process and local adaptation does not guarantee that a genotype is at or close to its optimum.

opencc-zeroDec 2014View details →

Data from: Indirect effects of global change accumulate to alter plant diversity but not ecosystem function in alpine tundra

1. Environmental change can affect species directly by altering their physical environment and indirectly by altering the abundance of interacting species. A key challenge at the interface of community ecology and conservation biology is to predict how direct and indirect effects combine to influence response in a changing environment. In particular, little is known about how direct and indirect effects on biodiversity develop over time or their potential to influence ecosystem function. 2. We studied how nitrogen (N), winter precipitation (snow), and warming influenced diversity and ecosystem function over six years in alpine tundra. We used path analyses to partition direct effects of environmental manipulations from indirect effects due to changes in the abundance of two dominant plants. We hypothesize that 1) indirect effects will develop more slowly but will become stronger than direct effects over time, and 2) after six years, indirect effects will more strongly influence diversity while direct effects will influence ecosystem function. 3. Indirect effects of N on diversity were consistently stronger than direct effects and actually developed quickly, prior to direct effects. Direct effects of snow on diversity were detected in year two but then subsequently were reversed, while indirect effects were detected in year four and grew stronger over time. Overall in year six, indirect effects were much stronger than direct effects. 4. Direct effects predominated for three of four ecosystem functions we measured (productivity, N mineralization, winter N availability). The only indirect effects we found were that N and snow indirectly affected microbial biomass N by influencing Geum abundance. Across all four ecosystem measures, indirect effects were infrequent and weaker than direct effects. 5. Synthesis. Increasing indirect effects on diversity over time indicate that short-term experiments or monitoring of natural systems may underestimate the full magnitude of global change effects on plant communities. Explicitly accounting for changes in dominant plant abundance may be necessary for forecasting plant community response to environmental change. Conversely, weak indirect effects for ecosystem processes suggest that predicting ecosystem function without knowledge of plant responses to global change may be possible.

opencc-zeroDec 2013View details →

Data from: Balancing sample accumulation and DNA degradation rates to optimize noninvasive genetic sampling of sympatric carnivores

Noninvasive genetic sampling, or noninvasive DNA sampling (NDS), can be an effective monitoring approach for elusive, wide-ranging species at low densities. However, few studies have attempted to maximize sampling efficiency. We present a model for combining sample accumulation and DNA degradation to identify the most efficient (i.e. minimal cost per successful sample) NDS temporal design for capture–recapture analyses. We use scat accumulation and faecal DNA degradation rates for two sympatric carnivores, kit fox (Vulpes macrotis) and coyote (Canis latrans) across two seasons (summer and winter) in Utah, USA, to demonstrate implementation of this approach. We estimated scat accumulation rates by clearing and surveying transects for scats. We evaluated mitochondrial (mtDNA) and nuclear (nDNA) DNA amplification success for faecal DNA samples under natural field conditions for 20 fresh scats/species/season from <1–112 days. Mean accumulation rates were nearly three times greater for coyotes (0.076 scats/km/day) than foxes (0.029 scats/km/day) across seasons. Across species and seasons, mtDNA amplification success was ≥95% through day 21. Fox nDNA amplification success was ≥70% through day 21 across seasons. Coyote nDNA success was ≥70% through day 21 in winter, but declined to <50% by day 7 in summer. We identified a common temporal sampling frame of approximately 14 days that allowed species to be monitored simultaneously, further reducing time, survey effort and costs. Our results suggest that when conducting repeated surveys for capture–recapture analyses, overall cost-efficiency for NDS may be improved with a temporal design that balances field and laboratory costs along with deposition and degradation rates.

opencc-zeroMay 2020View details →

Nitrogen isotope fractionation during archaeal ammonia oxidation: coupled estimates from measurements of residual ammonium and accumulated nitrite

The naturally occurring nitrogen (N) isotopes, 15N and 14N, exhibit different reaction rates during many microbial N transformation processes, which results in N isotope fractionation. Such isotope effects are critical parameters for interpreting natural stable isotope abundances as proxies for biological process rates in the environment across scales. The kinetic isotope effect of ammonia oxidation (AO) to nitrite (NO2-), performed by ammonia-oxidizing archaea (AOA) and bacteria (AOB), is generally ascribed to the enzyme ammonia monooxygenase (AMO), which catalyzes the first step in this process. However, the kinetic isotope effect of AMO, or εAMO , has been typically determined based on isotope kinetics during product formation (cumulative product, NO2-) alone, which may have overestimated εAMO due to possible accumulation of chemical intermediates and alternative sinks of ammonia/ammonium (NH3/NH4+). Here, we analyzed 15N isotope fractionation during archaeal ammonia oxidation based on both isotopic changes in residual substrate (RS, NH4+) and cumulative product (CP, NO2-) pools in pure cultures of the soil strain Nitrososphaera viennensis EN76, and in highly enriched cultures of the marine strain Nitrosopumilus adriaticus NF5, under non-limiting substrate conditions. We obtained εAMO values of 31.9-33.1‰ for both strains based on RS (δ15NH4+), and show that estimates based on CP (δ15NO2-) give larger isotope fractionation factors by 6-8‰. Complementary analyses showed that, at the end of the growth period, microbial biomass was 15N-enriched (10.1‰), whereas nitrous oxide (N2O) was highly 15N depleted (-38.1‰) relative to the initial substrate. Although we did not determine the isotope effect of NH4+ assimilation (biomass formation) and N2O production by AOA, our results nevertheless show that the discrepancy between εAMO estimates based on RS and CP might have derived from incorporation of 15N-enriched residual NH4+ after AMO reaction into microbial biomass, and that N2O production did not affect isotope fractionation estimates significantly.

opencc-zeroDec 2014View details →

Data from: The accumulation of deleterious mutations as a consequence of domestication and improvement in sunflowers and other Compositae crops

For populations to maintain optimal fitness, harmful mutations must be efficiently purged from the genome. Yet, under circumstances that diminish the effectiveness of natural selection, such as the process of plant and animal domestication, deleterious mutations are predicted to accumulate. Here, we compared the load of deleterious mutations in 21 accessions from natural populations and 19 domesticated accessions of the common sunflower using whole-transcriptome single nucleotide polymorphism data. Although we find that genetic diversity has been greatly reduced during domestication, the remaining mutations were disproportionally biased toward nonsynonymous substitutions. Bioinformatically predicted deleterious mutations affecting protein function were especially strongly over-represented. We also identify similar patterns in two other domesticated species of the sunflower family (globe artichoke and cardoon), indicating that this phenomenon is not due to idiosyncrasies of sunflower domestication or the sunflower genome. Finally, we provide unequivocal evidence that deleterious mutations accumulate in low recombining regions of the genome, due to the reduced efficacy of purifying selection. These results represent a conundrum for crop improvement efforts. Although the elimination of harmful mutations should be a long-term goal of plant and animal breeding programs, it will be difficult to weed them out because of limited recombination.

opencc-zeroDec 2016View details →

Data from: Do genetic drift and accumulation of deleterious mutations preclude adaptation? Empirical investigation using RADseq in a northern lacustrine fish

Understanding genomic signatures of divergent selection underlying long-term adaptation in populations located in heterogeneous environments is a key goal in evolutionary biology. In this study, we investigated neutral, adaptive and deleterious genetic variation using 7,192 SNPs in 31 Lake Trout (Salvelinus namaycush) populations (n = 673) from Québec, Canada. Average genetic diversity was low, weakly shared among lakes, and positively correlated to lake size, indicating a major role for genetic drift subsequent to lake isolation. Putatively deleterious mutations were on average at lower frequencies than the other SNPs, and their abundance relative to the entire polymorphism in each population was positively correlated to inbreeding, suggesting that the effectiveness of purifying selection was negatively correlated to inbreeding, as predicted from theory. Despite evidence for pronounced genetic drift and inbreeding, several outlier loci were associated with temperature and found in or close to genes with biologically relevant functions notably related to heat-stress and immune responses. Outcomes of gene-temperature associations were influenced by the inclusion of the most inbred populations, in which allele frequencies deviated the most from model predictions. This result illustrates challenge in identifying gene-environment associations in cases of high genetic drift and restricted gene flow and suggests limited adaptation in populations experiencing higher inbreeding. We discuss the relevance of these findings for the conservation and management, notably regarding stocking and genetic rescue, of Lake Trout populations and other species inhabiting highly fragmented habitats.

opencc-zeroDec 2018View details →

Data from: Assemblage Accumulation Curves: A framework for resolving species accumulation in biological communities using chloroplast genome sequences

The timing and tempo of the processes involved in community assembly are of substantial concern to community ecologists and conservation managers. The fossil record is a valuable source of data for studying past changes in community composition, but it is not always detailed enough to allow the process of community assembly to be resolved at regional or site scales while tracing the trajectories of known species with associated known traits. We present a three‐step framework for studying present‐day species accumulation through time: DNA sampling from multiple individuals from multiple species within a community; estimates of coalescence times for each species using molecular dating methods; and plotting the accumulation of present‐day species through time using the inferred population ages. Our approach is illustrated using whole chloroplast genomes from plants from three rainforest communities in eastern Australia. Expected times to coalescence for multiple species in each community were inferred from pooled high‐throughput sequence libraries. Local assemblage accumulation curves for each community were constructed. We also explored the variation in assemblage accumulation curves of species with different functional traits. Models of equilibrium species richness informed our null hypothesis and largely explained the shape of the assemblage accumulation curves and indicated that the complexities of the accumulation process should be explored with additional parameters, for example allowing species classes with different extinction rates. The assemblage accumulation curves for the study sites showed evidence of recent population expansions within each of the communities. This signal of recent accumulation is consistent with the increase in suitable rainforest habitat that followed the Last Glacial Maximum. Our method of constructing assemblage accumulation curves provides a simple approach for visualizing species‐accumulation data. It can be used to test hypotheses such as the relative survival potential of species‐specific ecological attributes. Although our example used single‐nucleotide polymorphisms derived from whole‐chloroplast sequencing, this framework can be applied to mitochondrial genomes and to communities of other organisms.

opencc-zeroDec 2015View details →

Data from: Coastal landforms and accumulation of mangrove peat increase carbon sequestration and storage

Given their relatively small area, mangroves and their organic sediments are of disproportionate importance to global carbon sequestration and carbon storage. Peat deposition and preservation allows some mangroves to accrete vertically and keep pace with sea-level rise by growing on their own root remains. In this study we show that mangroves in desert inlets in the coasts of the Baja California have been accumulating root peat for nearly 2,000 y and harbor a belowground carbon content of 900–34,00 Mg C/ha, with an average value of 1,130 (± 128) Mg C/ha, and a belowground carbon accumulation similar to that found under some of the tallest tropical mangroves in the Mexican Pacific coast. The depth–age curve for the mangrove sediments of Baja California indicates that sea level in the peninsula has been rising at a mean rate of 0.70 mm/y (± 0.07) during the last 17 centuries, a value similar to the rates of sea-level rise estimated for the Caribbean during a comparable period. By accreting on their own accumulated peat, these desert mangroves store large amounts of carbon in their sediments. We estimate that mangroves and halophyte scrubs in Mexico's arid northwest, with less than 1% of the terrestrial area, store in their belowground sediments around 28% of the total belowground carbon pool of the whole region.

opencc-zeroApr 2020View details →

Accumulation of deleterious mutations in landlocked threespine stickleback populations

Colonization of new habitats often reduces population sizes and may result in the accumulation of deleterious mutations by genetic drift. Compared to the genomic basis for adaptation to new environments, genome-wide analysis of deleterious mutations in isolated populations remains limited. In the present study, we investigated the accumulation of deleterious mutations in five endangered freshwater populations of threespine stickleback (Gasterosteus aculeatus) in the central part of the mainland of Japan. Using whole genome resequencing data, we first conducted phylogenomic analysis and confirmed at least two independent freshwater colonization events in the central mainland from ancestral marine ecotypes. Next, analyses of single nucleotide polymorphisms (SNPs) showed a substantial reduction of heterozygosity in freshwater populations compared to marine populations. Reduction in heterozygosity was more apparent at the center of each chromosome than the peripheries and on X-chromosomes compared to autosomes. Third, bioinformatic analysis of deleterious mutations showed increased accumulation of putatively deleterious mutations in the landlocked freshwater populations compared to marine populations. For the majority of populations examined, the frequencies of putatively deleterious mutations were higher on X-chromosomes than on autosomes. The inter-population comparison indicated that the majority of putatively deleterious mutations may have accumulated independently. Thus, whole genome resequencing of endangered populations can help to estimate the accumulation of deleterious mutations and inform us of which populations are the most severely endangered. Furthermore, analysis of variation among chromosomes can give insights into whether any particular chromosomes are likely to accumulate deleterious mutations.

opencc-zeroDec 2014View details →

Data from: Lianas reduce carbon accumulation and storage in tropical forests

Tropical forests store nearly 30% of global terrestrial carbon and contribute to 40% of the global terrestrial carbon sink. By affecting tree growth and survival, lianas impact the carbon balance of these forests. Here we demonstrate with a 3-y experiment that lianas substantially reduce forest-level carbon uptake and storage. This study is, to our knowledge, the first direct demonstration of liana effects at the ecosystem scale and illustrates the important role of lianas in tropical forests, particularly with respect to carbon budgets. Lianas are increasing in biomass and productivity throughout the tropics, and thus our findings have even greater relevance in terms of the fate of the tropical carbon balance, as well as for global atmospheric CO2 levels, in a changing climate.

opennotspecifiedDec 2007View details →

FIGURE 2. Smoothed species accumulation curves for Paraguayan ants, generated over 50 in A catalogue of the ants of Paraguay (Hymenoptera: Formicidae)

FIGURE 2. Smoothed species accumulation curves for Paraguayan ants, generated over 50 sampling iterations on 3,912 randomized species records.

Fig. 6 in Improved fallow: growth and nitrogen accumulation of five native tree species in Brazil

Fig. 6 Nitrogen content (kg ha-1) in the wood and leaf compartments, respectively, of planted trees in a mixed-culture slash-and-mulch agroforestry system in eastern Amazonia of Brazil at Year 6 after planting in 2005. Capital letters indicate significant differences in the main-plot treatment with P + K fertilization (PK+), or without (PK-). Lower case letters indicate significant differences between treatments. Error bars represent ±1SE (N = 4)

Fig. 5 in Improved fallow: growth and nitrogen accumulation of five native tree species in Brazil

Fig. 5 Soil organic carbon stocks (g kg-1) of soils at 0–10 and 10–20 cm depths in a mixed-culture slash-and-mulch agroforestry system in eastern Amaznonia of Brazil at Year 6 after planting in 2005. No significant differences (p> 0.3) were detected between treatments. Error bars represent ±1SE (N = 4)

Fig. 3 in Improved fallow: growth and nitrogen accumulation of five native tree species in Brazil

Fig. 3 Volume (m -3 ha -1) of five species of native trees planted in a mixed-culture slash-and-mulch agroforestry system in Eastern Amazonia of Brazil at Year 6 after planting in 2005. Letters indicate significant differences within species by treatment (N = 4)

Fig. 2 in Improved fallow: growth and nitrogen accumulation of five native tree species in Brazil

Fig. 2 Height (cm) response at Year 6 after planting in 2005 of a slash-and-mulch, improved fallow, mixed-culture agroforestry system in Igarapé Açu, Pará, Brazil. Error bars represent ±1SE (N = 4)

Fig. 4 in Improved fallow: growth and nitrogen accumulation of five native tree species in Brazil

Fig. 4 Above-ground biomass carbon (kg ha-1) of five (5) species of native trees planted in a mixed-culture slash-andmulch agroforestry system in the Eastern Amazon of Brazil at Year 6 after planting in 2005. Capital letters indicate significant differences among the main-plot treatment with P + K fertilization (PK+) or without (PK-). Lower case letters indicate significant differences between treatments (N = 4)

Fig. 1 in Improved fallow: growth and nitrogen accumulation of five native tree species in Brazil

Fig. 1 Ground line diameter (mm) response through Year 6 after planting in 2005 of a slash-and-mulch, improved fallow, mixedculture agroforestry system in Igarapé Açu, Pará, Brazil. Error bars represent ±1SE (N = 4)