Seed-setting by alpine gentian (Gentiana nivalis L.)

Summary

The seed content of individual capsules of alpine gentian (Gentiana nivalis L.), a rare annual of Scottish mountains, was compared amongst (a) single- and multi-flowered plants and (b) the years 1987–92 inclusive. Capsules contained two types of seeds, ‘live’ seeds that were terete and apparently viable, and ‘aborted’ seeds that were shrunken and clearly dead. The topmost capsule on plants with two-five flowers contained two-three times the number of live seeds found in capsules from plants with a single flower. The mean annual production of live seeds per plant ranged from 176 in single-flowered plants through 445, 580, 983 and 1145 in plants with two, three, four and five flowers respectively. The mean live seed content of capsules varied annually, depending on the numbers of seeds that aborted. Annual variation in the proportion of aborted seeds was negatively correlated with mean maximum temperature during July, when the plants began flowering. It is suggested that cold temperatures in July possibly inhibited the activity of pollinating insects and the growth of pollen tubes. The results are discussed in the context of possible future changes in the Scottish climate.     

Size and longevity of seed banks of alpine gentian (Gentiana nivalis L.)

Summary

The alpine gentian (Gentiana nivalis L.) is a mountain rarity found at only two localities in Britain. It is an annual, establishing anew from seed each year and so the size and persistence of its seed bank is important for survival. Seed bank size was measured in summer, before seeds were shed, by sampling from soils at two sites where the alpine gentian is common. As the seeds do not germinate readily in the laboratory, it was assumed that all apparently healthy seeds extracted from the soils were alive and viable. This assumption was corroborated when 95–97% of seeds buried experimentally for 9–12 years germinated after repeated applications of gibberellic acid solution over a period of 6 months.

Densities of naturally buried alpine gentian seeds at the two sites ranged from 1.3 to 6.8 × 10³ seeds m^-2 and they comprised a major component of the community seed bank, disproportionately greater than the abundance of parent plants in the vegetation. The half-life of experimentally buried seeds was estimated as 15 or 32 years, depending on depth of burial and soil type. The findings explain why alpine gentian numbers can recover quickly after a population crash and emphasise the importance of the seed bank to the species' long-term survival in the montane environment.     

Multiscale landscape genomic models to detect signatures of selection in the alpine plant Biscutella laevigata

Plant species are known to adapt locally to their environment, particularly in mountainous areas where conditions can vary drastically over short distances. The climate of such landscapes being largely influenced by topography, using fine‐scale models to evaluate environmental heterogeneity may help detecting adaptation to micro‐habitats. Here, we applied a multiscale landscape genomic approach to detect evidence of local adaptation in the alpine plant Biscutella laevigata. The two gene pools identified, experiencing limited gene flow along a 1‐km ridge, were different in regard to several habitat features derived from a very high resolution (VHR) digital elevation model (DEM). A correlative approach detected signatures of selection along environmental gradients such as altitude, wind exposure, and solar radiation, indicating adaptive pressures likely driven by fine‐scale topography. Using a large panel of DEM‐derived variables as ecologically relevant proxies, our results highlighted the critical role of spatial resolution. These high‐resolution multiscale variables indeed indicate that the robustness of associations between genetic loci and environmental features depends on spatial parameters that are poorly documented. We argue that the scale issue is critical in landscape genomics and that multiscale ecological variables are key to improve our understanding of local adaptation in highly heterogeneous landscapes.     

Identifying signatures of natural selection in cork oak (Quercus suber L.) genes through SNP analysis

Cork oak (Quercus suber L.) is an evergreen tree species endemic to the western Mediterranean Basin with a major economical, social and ecological relevance, associated with cork extraction and exploitation. In the last years, cork oak stands have been facing a significant decline, which may be aggravated by the climate changes that are predicted to occur within cork oak distribution range during this century. Under this scenario, the assessment of adaptive genetic variation is essential to understand how cork oak may cope with these threats and to delineate strategies for the management of its genetic resources. In this study, six candidate genes possibly significant for environmental adaptation were analysed in cork oak populations from its entire distribution range. Signatures of natural selection were investigated using population genetic statistics and environmental association tests under alternative scenarios of population genetic structure. Signals of balancing selection were detected in the putative non-expressor of pathogenesis-related gene 1 (NPR1), involved in plant defence response against pathogens, in auxin response factor 16 (ARF16), a gene implicated in root development, in RAN3, also involved in developmental processes, and in glutamine synthetase nodule isozyme (GS), involved in nitrogen fixation. Furthermore, for ARF16, a class I heat shock protein (sHSP) and GS, associations were found between SNP allele and haplotype frequencies and several spatial and climatic variables, suggesting that these genes may have a role on cork oak local adaptation. In this study, the first steps were taken into gathering information on cork oak adaptation to environmental conditions.     

Inference of hazel grouse population structure using multilocus data: a landscape genetic approach

In conservation and management of species it is important to make inferences about gene flow, dispersal and population structure. In this study, we used 613 georeferenced tissue samples from hazel grouse (Bonasa bonasia) where each individual was genotyped at 12 microsatellite loci to make inference on population genetic structure, gene flow and dispersal in northern Sweden. Observed levels of genetic diversity suggest that Swedish hazel grouse do not suffer loss of genetic diversity compared with other grouse species. We found significant F(IS) (deviation from Hardy-Weinberg expectations) over the entire sample using jack-knifed estimators over loci, which is most likely explained by a Wahlund effect. With the use of spatial autocorrelation methods, we detected significant isolation by distance among individuals. Neighbourhood size was estimated in the order of 62-158 individuals corresponding to a dispersal distance of 950-1500 m. Using a spatial statistical model for landscape genetics to infer the number of populations and the spatial location of genetic discontinuities between these populations we found indications that Swedish hazel grouse are divided into a northern and a southern population. We could not find a sharp border between these two populations and none of the observed borders appeared to coincide with any potential geographical barriers.These results imply that gene flow appears somewhat unrestricted in the boreal taiga forests of northern Sweden and that the two populations of hazel grouse in Sweden may be explained by the post-glacial reinvasion history of the Scandinavian Peninsula.     

The basis of food selection in some estuarine fishes. Eels, Anguilla anguilla (L.), whiting, Merlangius merlangus (L.), sprat, Sprattus sprattus (L.) and stickleback, Gasterosteus aculeatus L.

The factors influencing the selection of food by eels, Anguilla anguilla, whiting, Merlanglus merlangius, sprat, Sprattus sprattus, and stickleback, Gasterosteus aculeatus have been investigated by analysing collections made in the Severn Estuary for 1 year. Non–migratory (yellow) eels measuring from 19–5–56–5 cm in length fed mainly on either the decapod Crangon vulgaris or on the mysid Neomysis integer during the warmer months but ceased to feed in the winter. Whiting measuring between 2–5 and 15 cm fed almost exclusively on C. vulgaris, N. integer and the sand goby, Pomatoschistus minutus. Sprats fed chiefly on either the arnphipod Gammarus salinus or N. integer. Sticklebacks seldom contained any food in their stomachs despite the presence of large quantities of suitable prey and the high level of hunting efficiency. Gammarus salinus, although normally abundant in the environment, was usually ingested in disproportionately small quantities by all fishes except sprats reflecting its concealment among floating weeds and a selection against small (less than 1 cm) organisms. Because of the limitations of size and the unusually efficient escape reaction of larger animals, only young representatives of Crangon vulgaris were captured. The isopod Eurydice pulchra was rarely eaten by any of the fishes even though it was common in the environment. Burrowing polychaetes, mainly Nereis diversicolor, were never utilized possibly due to the difficulty involved in removing these organisms from the substrate. Neomysis integer was the most frequently consumed organism. Although the average length of prey ingested by the whitings increased with the size of fish, this was not the case for the other species. The proportion of non–feeding eels and the dry weight of stomach contents of this species depended on the temperature of the water but were not related to the availability of prey and tidal conditions whereas the feeding of whiting could not be related to any environmental parameter.     

Genetics of intrinsic postzygotic isolation in a circumpolar plant species, Draba nivalis (Brassicaceae)

Sterility barriers, ranging from incomplete to fully developed, were recently demonstrated within taxonomic species of the genus Draba, suggesting the existence of numerous, cryptic biological species. Because these taxa are predominately selfers and of Pleistocene origin, it was concluded that hybrid sterility evolved quickly and possibly by genetic drift. Here we used genetic mapping and QTL analyses to determine the genetic basis of hybrid sterility between geographically distant populations of one of these taxonomic species, Draba nivalis. Fifty microsatellite loci were mapped, and QTL analyses identified five loci underlying seed fertility and two underlying pollen fertility. Four of five seed fertility QTLs reduced fertility in heterozygotes, an observation most consistent with drift-based fixation of underdominant sterility loci. However, several nuclear-nuclear interactions were also found, including two that acted like reciprocal translocations with lowest fitness in double heterozygotes, and two that had a pattern of fitness consistent with Bateson-Dobzhansky-Muller incompatibilities. In contrast, pollen fertility QTLs exhibited additive inheritance, with lowest fertility associated with the paternal allele, a pattern of inheritance suggestive of cytonuclear incompatibilities. The results imply that multiple genetic mechanisms underlie the rapid evolution of reproductive barriers in Draba.     

Effects of species turnover on reserve site selection in a fragmented landscape

Changes in species composition is an important process in many ecosystems but rarely considered in systematic reserve site selection. To test the influence of temporal variability in species composition on the establishment of a reserve network, we compared network configurations based on species data of small mammals and frogs sampled during two consecutive years in a fragmented Atlantic Forest landscape (SE Brazil). Site selection with simulated annealing was carried out with the datasets of each single year and after merging the datasets of both years. Site selection resulted in remarkably divergent network configurations. Differences are reflected in both the identity of the selected fragments and in the amount of flexibility and irreplaceability in network configuration. Networks selected when data for both years were merged did not include all sites that were irreplaceable in one of the 2 years. Results of species number estimation revealed that significant changes in the composition of the species community occurred. Hence, temporal variability of community composition should be routinely tested and considered in systematic reserve site selection in dynamic systems.     

The basis of food selection in flounders, Platichthys flesus (L.), in the Severn Estuary

The factors influencing the selection of food by flounders, Platichthys flesus (L.), have been investigated by analysing collections made in the Severn Estuary for 1 year and the results of experiments. Flounders measuring between 6–0 and 35 cm fed heavily on the polychaete Nereis diversicolor in February and on the amphipod Gammarus salinus between February and April. Thereafter these species were replaced by the mysid Neomysis integer with the decapod Crangon vulgaris. Flounders shorter than 6.0 cm, fed mainly on Neomysis integer regardless of month. Numerous factors were involved in the choice of the food including (1) the maximum and minimum length of prey, (2) its spatial distribution in the water column, (3) its degree of concealment, (4) its motility and ability to escape predation, (5) conditioning of the flounders for certain foods, (6) the fish's swimming speed and (7) the turbidity and temperature of the water.
Although the average length of ingested prey remained unchanged as the fish grew in size, an increase in the maximum and minimum lengths was observed. The percentage of stomachs that contained no identifiable remains in flounders greater than 6–0 cm averaged 80–95 % during part of the winter and 60% in the summer and between January and March. These changes partly reflected the influence of low water temperature on the metabolic rate and availability of prey. The dry weight of the stomach contents in flounders longer than 6–0 cm was lowest in winter but high values were recorded in the spring. This latter feature was probably because the rate of feeding was greater than that of digestion. During the summer, under more normal feeding conditions, the weight of the stomach contents remained relatively low compared to other fish populations. Flounders shorter than 6–0 cm always contained more food in their stomachs on a unit weight basis than larger individuals, reflecting metabolic rate and hunting efficiency.     

Identifying population thresholds for flowering plant reproductive success: the marsh gentian (<Emphasis Type="Italic">Gentiana pneumonanthe</Emphasis>) as a flagship species of humid meadows and heathland

The threshold below which population declines impact the effectiveness of plant reproduction is essential for the identification of populations that can no longer spontaneously recover following habitat management or restoration, below the minimum viable population (MVP) size. We hypothesized that risk of reproductive limitation can be evaluated from combined analysis of pollen activity, ovule fertilization and germination in the context of population demographics and fragmentation. The marsh gentian (Gentiana pneumonanthe), a rare emblematic species of European heathland and fen, was investigated at the southern limit of its range in eighteen populations encompassing one to several hundred thousand individuals, spanning small fragments to extensive well-preserved areas. An index of habitat fragmentation was determined from GIS; field surveys determined the ratio of juvenile to reproductive age states; fluorescence microscopy of pistils determined, for each population, the proportion of flowers exhibiting active pollen tube growth. Analysis of seed lots determined the ovule fertilization rate and seed germination capacity. Some of the small populations occupying restricted habitat fragments showed high rates of pollination (100%) and ‘normal’ age state demographics. However, reproductive characters all exhibited exponential rise to maximum relationships with population size, indicating clear tipping points (for pollination, at a threshold of 7 reproductive adults, and for ovule fertilization rate and germination at 42 reproductive adults). Thus although small populations may set seed, exhibit a ‘normal’ age state structure, and may appear viable, reproductive effectiveness declines when population size falls below 42 generative individuals and < 7 is an indicator of strong limitation. Although many remnant populations of G. pneumonanthe are in the order of 50–150 individuals these should be not be considered as MVPs; they are on the brink of calamity.     

The diet and growth of 0-group dace, Leuciscus leuciscus (L.), and roach, Rutilus rutilus (L.), in a lowland river

The diets of 0-group dace and roach in the Lower Welsh Dee were studied by stomach contents analysis of seasonal and diel samples. During development, dace preyed on a sequence of food types, initially being mainly carnivorous then becoming nocturnally carnivorous and diurnally omnivorous. Roach showed a similar pattern, although after the first two months of life they were more herbivorous/detritivorous. From the variations in the diets, it is hypothesised that both species are limited by food. This receives circumstantial support from their poor observed growth. The food supply routes by which flow regulation of the River Dee could affect juvenile fish production are noted.     

Patterns of ancestry, signatures of natural selection, and genetic association with stature in Western African pygmies

African Pygmy groups show a distinctive pattern of phenotypic variation, including short stature, which is thought to reflect past adaptation to a tropical environment. Here, we analyze Illumina 1M SNP array data in three Western Pygmy populations from Cameroon and three neighboring Bantu-speaking agricultural populations with whom they have admixed. We infer genome-wide ancestry, scan for signals of positive selection, and perform targeted genetic association with measured height variation. We identify multiple regions throughout the genome that may have played a role in adaptive evolution, many of which contain loci with roles in growth hormone, insulin, and insulin-like growth factor signaling pathways, as well as immunity and neuroendocrine signaling involved in reproduction and metabolism. The most striking results are found on chromosome 3, which harbors a cluster of selection and association signals between approximately 45 and 60 Mb. This region also includes the positional candidate genes DOCK3, which is known to be associated with height variation in Europeans, and CISH, a negative regulator of cytokine signaling known to inhibit growth hormone-stimulated STAT5 signaling. Finally, pathway analysis for genes near the strongest signals of association with height indicates enrichment for loci involved in insulin and insulin-like growth factor signaling.     

Optimizing imputation of marker data from genotyping-by-sequencing (GBS) for genomic selection in non-model species: Rubber tree (Hevea brasiliensis) as a case study

Genotyping-by-sequencing (GBS) provides the marker density required for genomic predictions (GP). However, GBS gives a high proportion of missing SNP data which, for species without a chromosome-level genome assembly, must be imputed without knowing the SNP physical positions. Here, we compared GP accuracy with seven map-independent and two map-dependent imputation approaches, and when using all SNPs against the subset of genetically mapped SNPs. We used two rubber tree (Hevea brasiliensis) datasets with three traits. The results showed that the best imputation approaches were LinkImputeR, Beagle and FImpute. Using the genetically mapped SNPs increased GP accuracy by 4.3%. Using LinkImputeR on all the markers allowed avoiding genetic mapping, with a slight decrease in GP accuracy. LinkImputeR gave the highest level of correctly imputed genotypes and its performances were further improved by its ability to define a subset of SNPs imputed optimally. These results will contribute to the efficient implementation of genomic selection with GBS. For Hevea, GBS is promising for rubber yield improvement, with GP accuracies reaching 0.52.     

The genetic architecture of ecological speciation and the association with signatures of selection in natural lake whitefish (Coregonus sp. Salmonidae) species pairs

Adaptive evolutionary change is contingent on variation and selection; thus, understanding adaptive divergence and ultimately speciation requires information on both the genetic basis of adaptive traits as well as an understanding of the role of divergent natural selection on those traits. The lake whitefish (Coregonus clupeaformis) consists of several sympatric "dwarf" (limnetic) and normal (benthic) species pairs that co-inhabit northern postglacial lakes. These young species pairs have evolved independently and display parallelism in life history, behavioral, and morphological divergence associated with the use of distinct trophic resources. We identified phenotype-environment associations and determined the genetic architecture and the role of selection modulating population genetic divergence in sympatric dwarf and normal lake whitefish. The genetic architecture of 9 adaptive traits was analyzed in 2 hybrid backcrosses individually phenotyped throughout their life history. Significant quantitative trait loci (QTL) were associated with swimming behavior (habitat selection and predator avoidance), growth rate, morphology (condition factor and gill rakers), and life history (onset of maturity and fecundity). Genome scans among 4 natural sympatric pairs, using loci segregating in the map, revealed a signature of selection for 24 loci. Loci exhibiting a signature of selection were associated with QTL relative to other regions of the genome more often than expected by chance alone. Two parallel QTL outliers for growth and condition factor exhibited segregation distortion in both mapping families, supporting the hypothesis that adaptive divergence contributing to parallel reductions of gene flow among natural populations may cause genetic incompatibilities. Overall, these findings offer evidence that the genetic architecture of ecological speciation is associated with signatures of selection in nature, providing strong support for the hypothesis that divergent natural selection is currently maintaining adaptive differentiation and promoting ecological speciation in lake whitefish species pairs.     

Coupling of heart rate and locomotor activity in sole, Solea solea (L.), and bass, Dicentrarchus labrax (L.), in their natural environment by using ultrasonic telemetry

Field measurements of distance moved and heart rate in sole, Solea solea (L.) and bass, Dicentrarchus labrax (L.) using ultrasonic telemetry revealed two different strategies. Heart rate in the sole increases during activity, accurately reflecting fluctuation in metabolic rate and so can be used as a measure of metabolic rate in the field. In contrast, the relatively stable value of the heart rate in bass during the whole tracking period whatever the activity level suggests that in this species heart rate in the field cannot be associated with metabolic rate determination.