Differentiation in parasitism among ecotypes of whitefish segregating along depth gradients

Parasitism is a potential mechanism initiating or facilitating ecotypic differentiation and speciation in freshwater fish. While recent studies have begun to explore this question, there are no empirical studies of parasitism in evolutionary replicates of ecotype‐pairs at variable stages of speciation. Such comparative studies of parasitism along continuums of host differentiation are needed as a first step towards testing the role of parasites in ecological speciation. We explored parasitism of whitefish Coregonus lavaretus in four pre‐alpine lakes in Switzerland that hold replicate species radiations of whitefish. We sampled shallow and deep‐spawning ecotypes on their breeding grounds. We found significant and consistent differences in infection between the ecotypes so that the shallow‐spawning fish had more trematode infections, whereas the deepspawning fish had more cestodes. The magnitude of these differences correlated positively with the degree of the genetic differentiation among the ecotypes and negatively with the extent of eutrophication of the lakes. Although the overall diversity of infections was low, some parasite species with potential effects on fish showed marked differences in infection between the ecotypes, suggesting that parasitism may have a role in maintaining ecotype differentiation in this system. Our results also indicate previously unknown habitat segregation of the better differentiated ecotypes, i.e. species, along the depth gradient outside the breeding season. Moreover, oligotrophic lakes tended to have higher parasite species richness and higher abundances of infection, than mesotrophic and eutrophic lakes, suggesting that the history of eutrophication affects parasite diversity.     

Improving Illumina assemblies with Hi‐C and long reads: An example with the North African dromedary

Researchers have assembled thousands of eukaryotic genomes using Illumina reads, but traditional mate‐pair libraries cannot span all repetitive elements, resulting in highly fragmented assemblies. However, both chromosome conformation capture techniques, such as Hi‐C and Dovetail Genomics Chicago libraries and long‐read sequencing, such as Pacific Biosciences and Oxford Nanopore, help span and resolve repetitive regions and therefore improve genome assemblies. One important livestock species of arid regions that does not have a high‐quality contiguous reference genome is the dromedary (Camelus dromedarius). Draft genomes exist but are highly fragmented, and a high‐quality reference genome is needed to understand adaptation to desert environments and artificial selection during domestication. Dromedaries are among the last livestock species to have been domesticated, and together with wild and domestic Bactrian camels, they are the only representatives of the Camelini tribe, which highlights their evolutionary significance. Here we describe our efforts to improve the North African dromedary genome. We used Chicago and Hi‐C sequencing libraries from Dovetail Genomics to resolve the order of previously assembled contigs, producing almost chromosome‐level scaffolds. Remaining gaps were filled with Pacific Biosciences long reads, and then scaffolds were comparatively mapped to chromosomes. Long reads added 99.32 Mbp to the total length of the new assembly. Dovetail Chicago and Hi‐C libraries increased the longest scaffold over 12‐fold, from 9.71 Mbp to 124.99 Mbp and the scaffold N50 over 50‐fold, from 1.48 Mbp to 75.02 Mbp. We demonstrate that Illumina de novo assemblies can be substantially upgraded by combining chromosome conformation capture and long‐read sequencing.     

Two-phase importance sampling for inference about transmission trees

There has been growing interest in the statistics community to develop methods for inferring transmission pathways of infectious pathogens from molecular sequence data. For many datasets, the computational challenge lies in the huge dimension of the missing data. Here, we introduce an importance sampling scheme in which the transmission trees and phylogenies of pathogens are both sampled from reasonable importance distributions, alleviating the inference. Using this approach, arbitrary models of transmission could be considered, contrary to many earlier proposed methods. We illustrate the scheme by analysing transmissions of Streptococcus pneumoniae from household to household within a refugee camp, using data in which only a fraction of hosts is observed, but which is still rich enough to unravel the within-household transmission dynamics and pairs of households between whom transmission is plausible. We observe that while probability of direct transmission is low even for the most prominent cases of transmission, still those pairs of households are geographically much closer to each other than expected under random proximity.     

Information collected during the post-breeding season guides future breeding decisions in a migratory bird

Breeding habitat choice and investment decisions are key contributors to fitness in animals. Density of individuals is a well-known cue of habitat quality     

The change of sediment composition during recovery of two Finnish lakes induced by waste water purification and lake oxygenation

Total oxygen deficit occurred regularly during stagnation periods in the deepest part of Lake Kallavesi in the period 1973–1986. The sediment was black and anaerobic during the first sampling in 1987. After beginning of artificial lake oxygenation and efficient purification of waste waters of a paper board mill in 1986 the oxygen deficit decreased gradually and a light brown oxidized uppermost sediment layer appeared and began to thicken. The following changes in the sediment composition were observed during 1987–1996: loss on ignition, total nitrogen and BOD₇ concentrations decreased in the uppermost sediment layer (0–2 cm) and BOD₇ concentration increased in the next sediment layer beneath (2–10 cm). There were no significant change in phosphorus and iron concentrations.Lake oxygen, total phosphorus and suspended solids concentrations fluctuated in a noticeable degree in Lake Huruslahti depending on waste water input and artificial oxygenation during the years 1980–1993. Oxygen condition was good at times of successful waste water elimination and lake oxygenation while deterioration of either resulted oxygen deficiency as well as increase of total phosphorus and suspended solids concentration. Most of the internal load entered with suspended solids during periods of total oxygen deficiency.An explanation for the findings in Lake Huruslahti could be microbiological. Gas formation inside sediment lift organic material towards top of the sediment and into the water, but after the lake recovery the material retain in the sediment. Also in Lake Kallavesi microbiological gas formation resuspended sediment particles with phosphorus into the overlaying water prior to oxygenation. During oxygenation microbiological processes in uppermost sediment utilize the anaerobic metabolic products, organic acids and methane, and block gas formation. Organic substances remain in the top sediment decomposing gradually in the uppermost layer.     

Meiofauna of the profundal zone of the northern part of Lake Ladoga as an indicator of pollution

Benthic meiofauna was sampled at 19 stations, mainly in the northern part of Lake Ladoga, from depths between 13 and 199 m and from types of environment ranging from sheltered areas near pollution sources to less polluted open areas. About 80 taxa were identified, of these 70 to the species level. The greatest numbers of species were oligochaetes (24 species) and harpacticoids (8 species). Certain quantitative ratios of meiofauna were shown to be correlated with environmental data. The species of the oligochaete families Lumbriculidae and Aeolosomatidae and the harpacticoids as a collective group, excluding Canthocamptus staphylinus, were most clearly confined to the less eutrophied environments. The oligochaete species Amphichaeta leydigii, Dero digitata and Tubifex tubifex, the resting stages of Cyclopinae, and Eucyclops serrulatus among the Eucyclopinae were most clearly concentrated in the eutrophicated or polluted environments. The groups of Naididae, Cladocera and Eucyclopinae did not have much value as indicators. Shannon diversity index correlated positively with the total phosphorus content of the water, and number of species decreased with increasing depth. In general, it seems that the pollution tolerance of the meiofauna in a very large lake such as Lake Ladoga is high, presumably due to the effective mixing of water masses.     

Phenotypic Correlation of Juvenile Growth Rate between Different Consecutive foraging Environments in a Salmonid fish: A Field Experiment

Many organisms occupy considerably different environments during individual's lifespan. We are interested in how the phenotypic characteristics that are favourable in the earlier environment predict fitness in the later environment. High predictability of fitness between the two consecutive environments suggests that the either the same traits are favored in both environments, or that the favourable traits are genetically correlated. In this study, we ask how similarity of consecutive foraging environments affects the phenotypic correlation of juvenile brown trout growth rate. More specifically, we used a genetically narrow stock of hatchery-bred fish to contrast individual growth rates between high and low density hatchery environments, and thereafter between hatchery and natural lake environment. As expected, growth rate was highly dependent on the environment, and the fish showed considerable phenotypic plasticity. Furthermore, we found a strong positive correlation in growth rate between similar foraging environments, for example, between high and low density hatchery stocks, and between hatchery and a lake with small fish as main prey. However, hatchery growth did not predict growth rate in lakes where fish had to forage on bottom-dwelling invertebrates. Our results suggest that when the consecutive environments differed dramatically with respect to traits that fish use for foraging, relative performance of individual fish changed, earlier performance not being an accurate predictor of performance in the new environment. In this case, fitness of the fish was determined by an environment-specific set of traits that were not the same between the two consecutive environments. The result indicates that assessment of individual performance may be highly environment specific in trout. This revised version was published online in July 2006 with corrections to the Cover Date.