Universal primers for a large cryptically simple cpDNA microsatellite region in Aristolochia (Aristolochiaceae)

We provide a new and valuable marker to study species relationships and population genetics in order to trace evolutionary, ecological, and conservational aspects in the genus Aristolochia. Universal primers for amplification and subsequent sequencing of a chloroplast microsatellite locus inside the trnK intron are presented. Utility of the primers has been tested in 32 species representing all clades of Aristolochia, including population studies within the A. pallida complex, A. clusii and A. rotunda. The microsatellite region is characterized as a (A_nT_m)_k repeat of 22–438 bp containing a combination of different repeats arranged as ‘cryptically simple’.     

Nitrogen deficiency increases the residence time of respiratory carbon in the respiratory substrate supply system of perennial ryegrass

Plant respiration draws on substrate pools of different functional/biochemical identity. Little is known about the effect of nitrogen deficiency on those pools' sizes, half-lives and relative contribution to respiration, and consequently, of carbon residence time in respiratory metabolism. Here we studied how nitrogen fertilization affects the respiratory carbon supply system of shoots and roots of Lolium perenne , a perennial grass. Plants grown at two nitrogen supply levels in continuous light were labelled with ¹³CO₂/¹²CO₂ for intervals ranging from 1 h to 1 month. The rate and isotopic composition of shoot, root and plant respiration were measured, and the time-courses of tracer incorporation into respired CO₂ were analysed by compartmental modelling. Nitrogen deficiency reduced specific respiration rate by 30%, but increased the size of the respiratory supply system by 30%. In consequence, mean residence time of respiratory carbon increased with nitrogen deficiency (4.6 d at high nitrogen and 9.2 d at low nitrogen supply). To a large extent, this was due to a greater involvement of stores with a long half-life in respiratory carbon metabolism of nitrogen-deficient plants. At both nitrogen supply levels, stores supplying root respiration were primarily located in the shoot, probably in the form of fructans.     

Morphological and molecular evidence for a new endemic freshwater crab, Sesarma ayatum sp. n., (Grapsidae, Sesarminae) from eastern Jamaica

Recent morphological studies have shown that the Jamaican mountain stream crab, Sesarma bidentatum Benedict, 1892 (Sensu Abele 1992), consists of several allopatric forms. Three new species have been described from western Jamaica (summarized in Reimer et al. 1998) restricting the range of S. bidentatum to central and eastern Jamaica. In this study we used morphology and genetic markers to further distinguish crab populations from different East Jamaican river systems. Morphological characters such as the shape of male gonopods, front, chelar carpus, and walking legs, as well as mtDNA sequence (16s rRNA gene) comparisons were consistent in the separation of populations of S. bidentatum into two distinct groups. A new species, Sesarma ayatum sp. n., is described with a distribution from easternmost Jamaica to the eastern Blue Mountains.     

Empirical and deterministic accuracies of across-population genomic prediction

Background

Differences in linkage disequilibrium and in allele substitution effects of QTL (quantitative trait loci) may hinder genomic prediction across populations. Our objective was to develop a deterministic formula to estimate the accuracy of across-population genomic prediction, for which reference individuals and selection candidates are from different populations, and to investigate the impact of differences in allele substitution effects across populations and of the number of QTL underlying a trait on the accuracy.

Methods

A deterministic formula to estimate the accuracy of across-population genomic prediction was derived based on selection index theory. Moreover, accuracies were deterministically predicted using a formula based on population parameters and empirically calculated using simulated phenotypes and a GBLUP (genomic best linear unbiased prediction) model. Phenotypes of 1033 Holstein-Friesian, 105 Groninger White Headed and 147 Meuse-Rhine-Yssel cows were simulated by sampling 3000, 300, 30 or 3 QTL from the available high-density SNP (single nucleotide polymorphism) information of three chromosomes, assuming a correlation of 1.0, 0.8, 0.6, 0.4, or 0.2 between allele substitution effects across breeds. The simulated heritability was set to 0.95 to resemble the heritability of deregressed proofs of bulls.

Results

Accuracies estimated with the deterministic formula based on selection index theory were similar to empirical accuracies for all scenarios, while accuracies predicted with the formula based on population parameters overestimated empirical accuracies by ~25 to 30%. When the between-breed genetic correlation differed from 1, i.e. allele substitution effects differed across breeds, empirical and deterministic accuracies decreased in proportion to the genetic correlation. Using a multi-trait model, it was possible to accurately estimate the genetic correlation between the breeds based on phenotypes and high-density genotypes. The number of QTL underlying the simulated trait did not affect the accuracy.

Conclusions

The deterministic formula based on selection index theory estimated the accuracy of across-population genomic predictions well. The deterministic formula using population parameters overestimated the across-population genomic accuracy, but may still be useful because of its simplicity. Both formulas could accommodate for genetic correlations between populations lower than 1. The number of QTL underlying a trait did not affect the accuracy of across-population genomic prediction using a GBLUP method.     

Site‐to‐site variability and temporal trends of DOC concentrations and fluxes in temperate forest soils

Here, we report site‐to‐site variability and 12–14 year trends of dissolved organic carbon (DOC) from organic layers and mineral soils of 22 forests in Bavaria, Germany. DOC concentrations in the organic layer were negatively correlated with mean annual precipitation and elevation whereas air temperature had a positive effect on DOC concentrations. DOC fluxes in subsoils increased by 3 kg ha^?1 yr^?1 per 100 mm precipitation or per 100 m elevation. The highest DOC concentrations were found under pine stands with mor humus. Average DOC concentrations in organic layer leachates followed the order: pine>oak>spruce>beech. However, the order was different for mean DOC fluxes (spruce>pine>oak>beech) because of varying precipitation regimes among the forest types. In 12 of 22 sites, DOC concentrations of organic layer leachates significantly increased by 0.5 to 3.1 mg C L^?1 yr^?1 during the sampling period. The increase in DOC concentration coincided with decreasing sulfate concentration, indicating that sulfate concentration is an important driver of DOC solubility in the organic layer of these forest sites. In contrast to the organic layer, DOC concentrations below 60 cm mineral soil depth decreased by <0.1–0.4 mg C L^?1 yr^?1 at eight sites. The negative DOC trends were attributed to (i) increasing adsorption of DOC by mineral surfaces resulting from desorption of sulfate and (ii) increasing decay of DOC resulting from decreasing stabilization of DOC by organo‐Al complexes. Trends of DOC fluxes from organic layers were consistent with those of DOC concentrations although trends were only significant at seven sites. DOC fluxes in the subsoil were with few exceptions small and trends were generally not significant. Our results suggest that enhanced mobilization of DOC in forest floors contributed to the increase of DOC in surface waters while mineral horizons did not contribute to increasing DOC export of forest soils.     

Long-term response to genomic selection: effects of estimation method and reference population structure for different genetic architectures

Background

Genomic selection has become an important tool in the genetic improvement of animals and plants. The objective of this study was to investigate the impacts of breeding value estimation method, reference population structure, and trait genetic architecture, on long-term response to genomic selection without updating marker effects.

Methods

Three methods were used to estimate genomic breeding values: a BLUP method with relationships estimated from genome-wide markers (GBLUP), a Bayesian method, and a partial least squares regression method (PLSR). A shallow (individuals from one generation) or deep reference population (individuals from five generations) was used with each method. The effects of the different selection approaches were compared under four different genetic architectures for the trait under selection. Selection was based on one of the three genomic breeding values, on pedigree BLUP breeding values, or performed at random. Selection continued for ten generations.

Results

Differences in long-term selection response were small. For a genetic architecture with a very small number of three to four quantitative trait loci (QTL), the Bayesian method achieved a response that was 0.05 to 0.1 genetic standard deviation higher than other methods in generation 10. For genetic architectures with approximately 30 to 300 QTL, PLSR (shallow reference) or GBLUP (deep reference) had an average advantage of 0.2 genetic standard deviation over the Bayesian method in generation 10. GBLUP resulted in 0.6% and 0.9% less inbreeding than PLSR and BM and on average a one third smaller reduction of genetic variance. Responses in early generations were greater with the shallow reference population while long-term response was not affected by reference population structure.

Conclusions

The ranking of estimation methods was different with than without selection. Under selection, applying GBLUP led to lower inbreeding and a smaller reduction of genetic variance while a similar response to selection was achieved. The reference population structure had a limited effect on long-term accuracy and response. Use of a shallow reference population, most closely related to the selection candidates, gave early benefits while in later generations, when marker effects were not updated, the estimation of marker effects based on a deeper reference population did not pay off.     

Habitat overlap between predatory benthic fish and their invertebrate prey in streams: the relative influence of spatial and temporal factors on predation risk

1. The spatial heterogeneity of ecosystems as well as temporal activity patterns of organisms can have far‐reaching effects on predator–prey relationships. We hypothesised that spatiotemporal constraints in mesohabitat use by benthic fish predators would reduce habitat overlap with benthic invertebrates and lead to mesohabitat‐specific predation risks. 2. We analysed the spatiotemporal activity patterns of two small‐bodied benthivorous fishes, gudgeon (Gobio gobio) and stone loach (Barbatula barbatula), and of benthic invertebrates in a small temperate stream during three 24‐h field experiments. By applying a novel method of field video observation, we monitored the spatiotemporal foraging behaviour of the fish in their natural environment. A parallel analysis of invertebrate mesohabitat use by means of small area Hess sampling allowed a direct estimation of habitat overlap at a pool–riffle scale. 3. Gudgeon showed a dominant spatial activity pattern preferring pools at all times of day, whereas stone loach used both mesohabitats but with a distinct temporal (nocturnal) activity pattern. The patterns of residence were not identical with those of active foraging. Invertebrate community composition differed significantly between mesohabitats but not between times of day. More than half of the total dissimilarity between pools and riffles was accounted for by six invertebrate taxa. Five of these were subject to higher fish predation in pools than in riffles. The total prey consumption of the two fish species together in pools was about three times as high as in riffles. Trophic niche breadth of stone loach and thus its predation range was broader than that of gudgeon. 4. These results indicate that the potential predation risk for stream invertebrates depends on the combination of spatial and temporal patterns of both predator and prey. Given the distinct differences in predation risk found between pools and riffles, we conclude that spatial heterogeneity at the mesohabitat scale can influence mechanisms and consequences of selective predation. We also suggest that the analysis of spatiotemporal predator–prey relationships should not be based on the premise that the main residence habitat and active foraging habitat of a predator are identical.     

Impacts of fine sediment addition to tussock, pasture, dairy and deer farming streams in New Zealand

1. Increased fine sediment input caused by agricultural development is expected to act as a stressor for stream ecosystems. In a large‐scale field experiment, we added fine river sand to 50‐m reaches of three second‐order streams in each of four categories of catchment development (ungrazed tussock grasslands, grazed pasture, dairying and deer farming) and measured the responses of macroinvertebrates and aquatic moss. 2. Before addition, fine sediment cover differed between land uses, being lowest in tussock (7%), intermediate in pasture (30%) and dairy (47%) and highest in deer streams (88%). Sediment addition increased cover by one land‐use category (e.g. augmented sediment cover in tussock streams was similar to pre‐existing cover in pasture streams), and cover remained high in impact reaches (compared with controls) throughout the 5‐week experiment. Sediment addition did not change concentrations of phosphate, nitrate and ammonium, which were generally highest in dairy streams and lowest in tussock streams. 3. Aquatic mosses (most common in tussock, absent in dairy and deer), invertebrate density (highest in deer, lowest in tussock), taxon richness (highest in pasture, lowest in deer) and diversity (highest in pasture and tussock, lowest in dairy and deer) all differed between land uses. Sediment addition resulted in reductions of moss cover, invertebrate taxon richness and richness of Ephemeroptera, Plecoptera and Trichoptera in impact relative to control reaches. 4. The impact of sediment addition was strongest in pasture streams where pre‐existing sediment cover was moderate and richness and diversity of the invertebrate community highest. However, even in the already sediment‐rich and species‐poor deer streams, density of one common taxon was reduced significantly by sediment addition, and another two were affected in the same way in dairy streams, the second‐most intense land use. 5. Our experiment has disentangled the impact of sediment addition from other concomitant land‐use effects that could not be reliably distinguished in previous research, which has mainly consisted of correlative studies or unrealistically small‐scale experiments.