Inferring Trees.

Molecular evolution can reveal the relationship between sets of homologous sequences and the patterns of change that occur during their evolution. An important aspect of these studies is the inference of a phylogenetic tree, which explicitly describes evolutionary relationships between homologous sequences. This chapter provides an introduction to evolutionary trees and how to infer them from sequence data using some commonly used inferential methodology. It focuses on statistical methods for inferring trees and how to assess the confidence one should have in any resulting tree, with a particular emphasis on the underlying assumptions of the methods and how they might affect the tree estimate. There is also some discussion of the underlying algorithms used to perform tree search and recommendations regarding the performance of different algorithms. Finally, there are a few practical guidelines, including how to combine multiple software packages to improve inference, and a comparison between Bayesian and Maximum likelihood phylogenetics.

Osteochondrosis, but not lameness, is more frequent among free-range pigs than confined herd-mates.

BACKGROUND: Organic pig production is expanding and amongst the objectives of organic farming are enhancing animal health and welfare. However, some studies have reported a higher prevalence of lameness and joint condemnation at slaughter in free-range/organic pigs than in conventionally raised pigs. Organic slaughter pigs have free-range housing in which indoor and outdoor access is compulsory, while in conventional farming the pigs are commonly confined to indoor pens. The present study evaluated the effects of free-range and confined housing on lameness prevalence in a herd of 106 finisher pigs, and whether osteochondrosis and Erysipelothrix rhusiopathiae associated arthritis influences these effects. We also evaluated the association between clinical lameness during the rearing period and joint condemnations at slaughter. RESULTS: Seventy free-range and 36 confined housed fattener pigs were scored for their gait twice during the rearing period and 848 joints were evaluated post mortem. Osteochondrosis was more frequent among free-range than confined pigs (P < 0.05), and when present it was also more severe (P < 0.001). Pigs with more numerous and more severe osteochondral lesions had their gait affected more than did pigs with fewer such lesions (P < 0.05). Hence it was a paradox that we did not detect more lameness among the free-range pigs than the confined pigs. E. rhusiopathiae associated arthritis was not diagnosed. The association between gait remarks/clinical lameness and joint condemnations at slaughter was not significant. CONCLUSIONS: The results indicate that free-range housing may have both positive and negative effects on locomotory traits. Free-range pigs may be less clinically affected by osteochondrosis than are confined pigs. One explanation for this effect may be strengthening of joint supportive tissue and pain relief promoted by exercise. Visual gait scoring missed serious joint lesions that probably were harmful to the pigs, and should therefore not be used as a sole indicator of joint/leg health in welfare inspection of pigs. The association between gait scores and joint condemnation appeared to be poor. This study was limited to one herd, and so more and larger studies on the effects of free-range housing on lameness severity and osteochondrosis development in pigs are recommended.

Transmission patterns of Fasciola hepatica to ruminants in Sweden.

Transmission patterns of Fasciola hepatica were investigated on beef cattle (n=3) and sheep (n=3) farms in Sweden between 2011 and 2012. The dynamics of fluke infection, particularly estimated time of infection, were screened each grazing season by ELISA detection of antibodies in lambs (n=94) and first grazing season calves (n=61). Colostral transfer of F. hepatica antibodies from seropositive ewes was detected in sheep up to 11 weeks of age. In sheep, the estimated time of infection differed significantly between herds and years. Typical 'winter infection' was observed on two sheep farms in 2012, but the most prevalent transmission pattern was found to be 'summer infection', characterised by infection of animals in late summer by F. hepatica originating from overwintered and/or spring-excreted eggs. In contrast, beef calves were infected mainly in September-October ('summer infection'). Furthermore, lymnaeid and succineid snails were collected on the pastures used by these animals both in spring and in the autumn each year. In total, 1726, 588, 138, 130, 93 and 42 specimens of Galba truncatula, Lymnaea palustris, Lymnaea glabra, Lymnaea fuscus, Radix peregra and Succinea putris, respectively, were collected and identified. These were subsequently examined for the presence of F. hepatica DNA by species-specific PCR and the findings compared against mean monthly rainfall and temperature data for each farm. The main intermediate host of the liver fluke was G. truncatula, with a prevalence range of F. hepatica infection from 0% to 82%. Only 1 out of 42 terrestrial S. putris tested positive for F. hepatica, casting doubt on the role of this species in transmission of F. hepatica in Sweden. In conclusion, two main peak periods of infection were observed: May-June (from overwintered infected snails='winter infection') and August-September (from metacercariae developed and produced by snails during summer='summer infection'). The occurrence and frequency of 'winter infection' were dependent on local environmental factors such as snail habitat availability or grazing behaviour of animals, rather than on climatic factors.

Metabolomics reveals differences in postprandial responses to breads and fasting metabolic characteristics associated with postprandial insulin demand in postmenopausal women.

Changes in serum metabolic profile after the intake of different food products (e.g., bread) can provide insight into their interaction with human metabolism. Postprandial metabolic responses were compared after the intake of refined wheat (RWB), whole-meal rye (WRB), and refined rye (RRB) breads. In addition, associations between the metabolic profile in fasting serum and the postprandial concentration of insulin in response to different breads were investigated. Nineteen postmenopausal women with normal fasting glucose and normal glucose tolerance participated in a randomized, controlled, crossover meal study. The test breads, RWB (control), RRB, and WRB, providing 50 g of available carbohydrate, were each served as a single meal. The postprandial metabolic profile was measured using nuclear magnetic resonance and targeted LC-mass spectrometry and was compared between different breads using ANOVA and multivariate models. Eight amino acids had a significant treatment effect (P < 0.01) and a significant treatment × time effect (P < 0.05). RWB produced higher postprandial concentrations of leucine (geometric mean: 224; 95% CI: 196, 257) and isoleucine (mean ± SD: 111 ± 31.5) compared with RRB (geometric mean: 165; 95% CI: 147, 186; mean ± SD: 84.2 ± 22.9) and WRB (geometric mean: 190; 95% CI: 174, 207; mean ± SD: 95.8 ± 17.3) at 60 min respectively (P < 0.001). In addition, 2 metabolic subgroups were identified using multivariate models based on the association between fasting metabolic profile and the postprandial concentration of insulin. Women with higher fasting concentrations of leucine and isoleucine and lower fasting concentrations of sphingomyelins and phosphatidylcholines had higher insulin responses despite similar glucose concentration after all kinds of bread (cross-validated ANOVA, P = 0.048). High blood concentration of branched-chain amino acids, i.e., leucine and isoleucine, has been associated with the increased risk of diabetes, which suggests that additional consideration should be given to bread proteins in understanding the beneficial health effects of different kinds of breads. The present study suggests that the fasting metabolic profile can be used to characterize the postprandial insulin demand in individuals with normal glucose metabolism that can be used for establishing strategies for the stratification of individuals in personalized nutrition.

Locomotor behavior in zebrafish (Danio rerio) larvae exposed to perfluoroalkyl acids.

Perfluoroalkyl acids (PFAAs) are persistent organic contaminants that have been detected in wildlife, humans and the environment. Studies have shown that the toxicity of PFAAs is determined by the carbon chain length as well as the attached functional group. The locomotor activity of zebrafish larvae has become widely used for evaluation of chemicals with neurotoxic properties. In the present study the behavioral effects of seven structurally different PFAAs (i.e. TFAA, PFBA, PFOA, PFNA, PFDA, PFBS and PFOS) were evaluated in zebrafish larvae. Exposure to high concentrations of TFAA, PFNA, PFBS and PFOS resulted in distinct changes in behavioral patterns. Based on redundancy analysis, our results demonstrate three main factors affecting zebrafish larval locomotor behavior. The strongest effect on behavior was determined by the carbon chain length and the attached functional group. PFAAs with longer carbon chain length as well as PFAAs with attached sulfonic groups showed larger potential to affect locomotor behavior in zebrafish larvae. Also the concentration of the PFAAs determined the behavior responses. The results of the present study are in agreement with previous studies showing correlations between the chemical structure of PFAAs and the toxicological effects.

Molecular identification of Sarcocystis aucheniae as the macrocyst-forming parasite of llamas.

The domestic South American camelids (SACs), llama (Lama glama) and alpaca (Lama paco), are frequently found to be infected with Sarcocystis parasites. Infections give rise in skeletal muscle to macroscopic cysts (1-5mm long) that resemble rice seeds, each containing several million living bradyzoites. The finding of cysts prevents commercialization of SAC meat, an important source of income for rural families in the Andean flatlands. Thus, development of diagnostic methods to facilitate the control of these infections is highly desirable, and the first step to this end is the unequivocal species identification of the causative agent. Based on the cyst form and size, the infecting parasite has been described as Sarcocystis aucheniae; however, this traditional approach is not reliable as similar cysts may contain different species. To date, molecular identification has been done for a single isolate of S. aucheniae from an alpaca in Australia. In order to verify the identity of the species present in SACs of South America, the complete 18S rRNA gene was PCR-amplified and sequenced from macrocyst DNA obtained from three llamas of the Andean flatlands. A phylogenetic Bayesian analysis was carried out using the analyzed and available 18S rRNA sequences of Sarcocystis spp. In the constructed tree, all of the new 18S rRNA gene sequences segregated in a single clade together with the 18S rRNA gene sequence reported from an alpaca in Australia, demonstrating that the isolated parasite is S. aucheniae, and that this parasite indiscriminately infects both domestic SACs. This work represents the first molecular identification of the causative agent of SAC sarcocystiosis in South America, and can contribute to the development of control methods for this neglected parasitosis.

Genomic analysis and mRNA expression of equine type I interferon genes.

This study aimed at identifying all of the type I interferon (IFN) genes of the horse and at monitoring their expression in equine cells on in vitro induction. We identified 32 putative type I IFN loci on horse chromosome 23 and an unplaced genomic scaffold. A phylogentic analysis characterized these into 8 different type I IFN classes, that is, putative functional genes for 6 IFN-α, 4 IFN-ß, 8 IFN-ω (plus 4 pseudogenes), 3 IFN-δ (plus 1 pseudogene), 1 IFN-κ and 1 IFN-ε, plus 1 IFN-ν pseudogene, and 3 loci belonging to what has previously been called IFN-αω. Our analyses indicate that the IFN-αω genes are quite distinct from both IFN-α and IFN-ω, and we refer to this type I IFN as IFN-µ. Results from cell cultures showed that leukocytes readily expressed IFN-α, IFN-ß, IFN-δ, IFN-µ, and IFN-ω mRNA on induction with, for example, live virus; while fibroblasts only expressed IFN-ß mRNA on stimulation. IFN-κ or IFN-ε expression was not consistently induced in these cell cultures. Thus, the equine type I IFN family comprised 8 classes, 7 of which had putative functional genes, and mRNA expression of 5 was induced in vitro. Moreover, a relatively low number of IFN-α subtypes was found in the horse compared with other eutherian mammals.

Networks: expanding evolutionary thinking.

Networks allow the investigation of evolutionary relationships that do not fit a tree model. They are becoming a leading tool for describing the evolutionary relationships between organisms, given the comparative complexities among genomes.

Babesia: a world emerging.

Babesia are tick-transmitted hemoprotozooans that infect mammals and birds, and which are acknowledged for their major impact on farm and pet animal health and associated economic costs worldwide. Additionally, Babesia infections of wildlife can be fatal if associated with stressful management practices; and human babesiosis, also transmitted by blood transfusion, is an increasing public-health concern. Due to the huge diversity of species reported to serve as Babesia hosts, all vertebrates might be potential carriers, as long as they are adequate hosts for Babesia-vector ticks. We here provide a comprehensive overview of the most relevant Babesia species, and a discussion of the classical taxonomic criteria. Babesia, Cytauxzoon and Theileria parasites are closely related and collectively referred to as piroplasmids. A possible scenario for the history of piroplasmids is presented in the context of recent findings, and its implications for future research avenues are outlined. Phylogenetic trees of all available 18S rRNA and hsp70 genes were generated, based on which we present a thoroughly revised molecular classification, comprising five monophyletic Babesia lineages, one Cytauxzoon clade, and one Theileria clade. Updated 18S rRNA and beta-tubulin gene trees of the B. microti isolates agree with those previously reported. To reconcile estimates of the origin of piroplasmids and ticks (~300 Ma, respectively), and mammalian radiation (60 Ma), we hypothesize that the dixenous piroplasmid life cycle evolved with the origin of ticks. Thus, the observed time gap between tick origin and mammalian radiation indicates the existence of hitherto unknown piroplasmid lineages and/or species in extant vertebrate taxa, including reptiles and possibly amphibians. The development and current status of the molecular taxonomy of Babesia, with emphasis on human-infecting species, is discussed. Finally, recent results from population genetic studies of Babesia parasites, and their implications for the development of pathogenicity, drug resistance and vaccines, are summarized.

Phylogeny of fish-infecting Calyptospora species (Apicomplexa: Eimeriorina).

There are numerous species of apicomplexans that infect poikilothermic vertebrates, such as fishes, and possess unique morphological features that provide insight into the evolution of this important phylum of parasites. Here, the relationship of the fish-infecting Calyptospora species to other coccidians was investigated based on DNA sequence analysis. Genetic data from the small subunit ribosomal DNA region of the genome were obtained for three of the five nominal species in the genus Calyptospora. Phylogenetic analyses supported a monophyletic lineage sister to a group composed of mostly Eimeria species. The monophyly of Calyptospora species supports the validity of the family Calyptosporidae, but the sister relationship to Eimeria species might also suggest the Eimeriidae be expanded to encompass Calyptospora. The validity of the family Calyptosporidae has been questioned because it is delineated from the Eimeriidae largely based on life cycle characteristics and sporocyst morphology. In general, Eimeria species have a homoxenous life cycle, whereas the type species of Calyptospora is heteroxenous. In the absence of experimental transmission studies, it may be difficult to demonstrate whether all Calyptospora species are heteroxenous. Other distinct morphological characteristics of Calyptospora such as an incomplete sporocyst suture, an apical opening for sporozoite release, a thin veil surrounding sporocysts supported by sporopodia, and a lack of Stieda and sub-Stieda bodies suggest there may be adequate features to delineate these taxa. Even without life cycle data for all species, the morphology and genetic data provide a means to reliably classify Calyptospora species. Placement in either the Calyptosporidae or Eimeriidae is discussed, along with issues relating to the phylogeny of the genus Goussia.

Population genetic structure of Ascaridia galli re-emerging in non-caged laying hens.

BACKGROUND: The poultry roundworm Ascaridia galli has reappeared in hens kept for egg production in Sweden after having been almost absent a decade ago. Today this is a frequent intestinal nematode parasite in non-caged laying hens. The aim of this study was to investigate the genetic diversity (Fst) in A. galli collected from different poultry production sites in southern Sweden, to identify possible common routes of colonization. METHODS: Adult parasites (n = 153) from 10 farms, including both broiler breeder parents and laying hens, were investigated by amplified restriction fragment length polymorphism analysis (AFLP). Worms from a Danish laying hen farm were also included for comparison. Most of the farms were represented by worms from a single host, but on two farms multiple samples from different hosts were assessed in order to study flock variation. RESULTS: A total of 97 fragments (loci) were amplified among which 81% were variable alleles. The average genetic diversity was 0.13 (range = 0.09-0.38), which is comparable to other AFLP studies on nematodes of human and veterinary importance. Within-farm variation showed that worms harboured by a single hen in a flock covered most of the A. galli genetic variation within the same flock (Fst = 0.01 and 0.03 for two farms). Between-farm analysis showed a moderate population genetic structure (Fst = 0.13), along with a low mutational rate but high gene flow between different farms, and absence of strong genetic selection. Network analysis showed repeated genetic patterns among the farms, with most worms on each farm clustering together as supported by high re-allocation rates. CONCLUSIONS: The investigated A. galli populations were not strongly differentiated, indicating that they have undergone a genetic bottlenecking and subsequent drift. This supports the view that the investigated farms have been recently colonized, and that new flocks are reinfected upon arrival with a stationary infection.

Using data-display networks for exploratory data analysis in phylogenetic studies.

Exploratory data analysis (EDA) is a frequently undervalued part of data analysis in biology. It involves evaluating the characteristics of the data "before" proceeding to the definitive analysis in relation to the scientific question at hand. For phylogenetic analyses, a useful tool for EDA is a data-display network. This type of network is designed to display any character (or tree) conflict in a data set, without prior assumptions about the causes of those conflicts. The conflicts might be caused by 1) methodological issues in data collection or analysis, 2) homoplasy, or 3) horizontal gene flow of some sort. Here, I explore 13 published data sets using splits networks, as examples of using data-display networks for EDA. In each case, I performed an original EDA on the data provided, to highlight the aspects of the resulting network that will be important for an interpretation of the phylogeny. In each case, there is at least one important point (possibly missed by the original authors) that might affect the phylogenetic analysis. I conclude that EDA should play a greater role in phylogenetic analyses than it has done.

Evolution of the Apicomplexa: where are we now?

The Apicomplexa is the only large taxonomic group whose members are entirely parasitic and is, therefore, presumably of major interest to parasitologists. We might, for example, expect that we know a great deal about the biology of the group by now and that we have a clear phylogenetic framework within which to organize that knowledge. It might thus come as a surprise to learn that in terms of biodiversity, the Apicomplexa is actually the least-known group of all. Furthermore, the taxonomic framework for the Apicomplexa is rather tenuous in many respects. This situation is unlikely to change in the short term.

Assessing the feasibility of targeted selective treatments for gastrointestinal nematodes in first-season grazing cattle based on mid-season daily weight gains.

A retrospective study was carried out to assess the possibility of using daily weight gain in first-season grazing cattle (FSG) as a marker for treatment decisions to prevent parasite-induced losses caused by gastrointestinal (GI) nematodes. This is intended as a proof of concept for using targeted selective treatments (TSTs) in the control of veterinary parasites. Historical data were combined from three independent grazing trials in Sweden, each of which was repeated over 2-3 years, in order to investigate the influences of parasites on the performance of FSG cattle subjected to different levels of parasite control. In general, the different trials and years produced congruent results. There was a good positive linear relationship between daily weight gains (Dwgt) registered around housing and those recorded in the middle of the grazing season (r(2)=0.54) but not between early-season Dwgt and housing Dwgt. The latter observation emphasizes that factors other than nematode infection influence the final weight of the cattle. However, significant differences in Dwgt ( approximately 0.2 kg/day) were also observed depending on the nematode-control level achieved. At selected time points, the mean number of trichostrongylid eggs, serum pepsinogen concentration and Ostertagia antibody levels were significantly higher in animals with poor performance. ROC analyses showed that anthelmintic treatment of animals with a Dwgt of <0.75 kg/day by mid-season had a sensitivity of approximately 70% and a specificity of approximately 50%. It thus seems feasible to base a targeted selective treatment for FSG cattle on Dwgt recorded approximately 4-8 weeks after turn-out, provided that it is accepted that some animals will be dewormed without indication. This now needs to be tested in controlled field trials.

Limited sequence variation in the major sperm protein 1 (MSP) gene within populations and species of the genus Dictyocaulus (Nematoda).

Populations of the bovine lungworm, Dictyocaulus viviparus, are genetically structured based on variation in mtDNA and AFLP data. Our aim was to investigate if this genetic variability also is reflected in a protein recognized by the host immune system. We focused on the major sperm protein (MSP), a small and abundant protein used in diagnostic immunoassays, which has been shown to be variable in some nematodes but not others. MSP was sequenced using worm DNA from eight adult worms from each of nine populations whose genetic structure previously had been quantified. For comparison, we also analyzed MSP sequences of the closely related Dictyocaulus eckerti and Dictyocaulus capreolus and from nematodes with sequences deposited in GenBank. In contrast to previous results, this study shows that the MSP ofD. viviparus is similar to that of other nematodes. Almost no sequence variation, and thus no antigenic diversity, was detected in MSP between worms from different sub-populations or in the other Dictyocaulus species investigated. A functional test of a recombinant variant of the MSP showed that the expressed protein was recognized by antibodies in sera from infected cattle. This has practical implications for the development of species-specific markers, recombinant vaccines, and immunodiagnostics.

How to summarize estimates of ancestral divergence times.

The use of molecular sequence data has increased interest in trying to date evolutionary events, with researchers wanting both an estimate of the divergence time and a confidence interval for that estimate. However, two methodological issues have recently been raised with respect to precision of the estimates: (i) the time of the ancestral event is over-estimated; and (ii) the confidence interval is asymmetrical. I argue that if the estimates of divergence time are considered to be samples from a lognormal probability distribution, then this would explain both of these problems. This implies that divergence times should be presented using geometric means rather than arithmetic means, both for estimates and for their confidence intervals. I present analyses based on both computer simulations and empirical data to show that this approach is effective for both single-gene and multiple-gene data sets. Treating divergence time as a lognormal variable thus provides a simple unifying framework for dealing with many of the problems associated with the estimation of divergence (and possibly coalescence) times. Use of this approach (based on geometric means) can, unfortunately, lead to very different biological conclusions compared to the currently used calculation methods (based on arithmetic means).