Phylogenetic signal in floral temperature patterns

OBJECTIVES

Floral structures may be warmer than their environment, and can show thermal patterning, where individual floral structures show different temperatures across their surface. Pollinators can differentiate between artificial flowers that mimic both naturally warmed and thermally patterned ones, but it has yet to be demonstrated that these patterns are biologically meaningful. To explore the relationship between pollinators and temperature patterning, we need to know whether there is diversity in patterning, and that these patterns are not simply a by-product of floral architecture constrained by ancestry. We analysed a dataset of 97 species to explore whether intrafloral temperature differences were correlated within clades (phylogenetic signal), or whether the variation seen was diverse enough to suggest that floral temperature patterns are influenced by the abiotic or pollinator-related niches to which plant species are adapted.

RESULTS

Some phylogenetic signal was observed, with both the Asteraceae and species of Pelargonium being more similar than expected by chance, but with other species surveyed not showing signal. The Asteraceae tend to have large temperature differences across the floral surface, which may be due to floral architecture constraints within the family. Other families show no correlation, suggesting that patterning is influenced by pollinators and the environment.

Models in parasite and pathogen evolution: Genomic analysis reveals predominant clonality and progressive evolution at all evolutionary scales in parasitic protozoa, yeasts and bacteria

The predominant clonal evolution (PCE) model of pathogenic microorganisms postulates that the impact of genetic recombination in those pathogens' natural populations is not enough to erase a persistent phylogenetic signal at all evolutionary scales from microevolution till geological times in the whole ecogeographical range of the species considered. We have tested this model with a set of representative parasitic protozoa, yeasts and bacteria in the light of the most recent genomic data. All surveyed species, including those that were considered as highly recombining, exhibit similar PCE patterns above and under the species level, from macro- to micro-evolutionary scales (Russian doll pattern), suggesting gradual evolution. To our knowledge, it is the first time that such a strong common evolutionary feature among very diverse pathogens has been evidenced. The implications of this model for basic biology and applied research are exposed. These implications include our knowledge on the pathogens' reproductive mode, their population structure, the possibility to type strain and to follow up epidemics (molecular epidemiology) and to revisit pathogens' taxonomy through a flexible use of the phylogenetic species concept (Cracraft, 1983).

The evolution of fruit scent: phylogenetic and developmental constraints

BACKGROUND

Fruit scent is increasingly recognized as an evolved signal whose function is to attract animal seed dispersers and facilitate plant reproduction. However, like all traits, fruit scent is likely to evolve in response to conflicting selective pressures and various constraints. Two major constraints are (i) phylogenetic constraints, in which traits are inherited from ancestors rather than adapted to current conditions and (ii) developmental constraints, if phenotypes are limited by the expression of other traits within the individual. We tested whether phylogenetic constraints play a role in fruit scent evolution by calculating the phylogenetic signal in ripe fruits of 98 species from three study sites. We then estimated the importance of developmental constraints by examining whether ripe fruits tend to emit compounds that are chemically similar to, and share biosynthetic pathways with, compounds emitted by conspecific unripe fruits from which they develop.

RESULTS

We show that closely related taxa are not more similar to each other than to very distinct taxa, thus indicating that fruit scent shows little phylogenetic signal. At the same time, although ripe and unripe fruits of the same species tend to emit different chemicals, they tend to employ chemicals originating from similar biosynthetic pathways, thus indicating that some developmental constraints determine ripe fruit scent.

CONCLUSIONS

Our results highlight the complex landscape in which fruit scent has evolved. On one hand, fruit scent evolution is not limited by common ancestry. On the other hand, the range of chemicals that can be employed in ripe fruits is probably constrained by the needs of unripe fruits.

Conflicting phylogenetic signals in plastomes of the tribe Laureae (Lauraceae)

Background

Gene tree discordance is common in phylogenetic analyses. Many phylogenetic studies have excluded non-coding regions of the plastome without evaluating their impact on tree topology. In general, plastid loci have often been treated as a single unit, and tree discordance among these loci has seldom been examined. Using samples of Laureae (Lauraceae) plastomes, we explored plastome variation among the tribe, examined the influence of non-coding regions on tree topology, and quantified intra-plastome conflict.

Results

We found that the plastomes of Laureae have low inter-specific variation and are highly similar in structure, size, and gene content. Laureae was divided into three groups, subclades I, II and III. The inclusion of non-coding regions changed the phylogenetic relationship among the three subclades. Topologies based on coding and non-coding regions were largely congruent except for the relationship among subclades I, II and III. By measuring the distribution of phylogenetic signal across loci that supported different topologies, we found that nine loci (two coding regions, two introns and five intergenic spacers) played a critical role at the contentious node.

Conclusions

Our results suggest that subclade III and subclade II are successively sister to subclade I. Conflicting phylogenetic signals exist between coding and non-coding regions of Laureae plastomes. Our study highlights the importance of evaluating the influence of non-coding regions on tree topology and emphasizes the necessity of examining discordance among different plastid loci in phylogenetic studies.

Impact of industrial production system parameters on chicken microbiomes: mechanisms to improve performance and reduce Campylobacter

BACKGROUND

The factors affecting host-pathogen ecology in terms of the microbiome remain poorly studied. Chickens are a key source of protein with gut health heavily dependent on the complex microbiome which has key roles in nutrient assimilation and vitamin and amino acid biosynthesis. The chicken gut microbiome may be influenced by extrinsic production system parameters such as Placement Birds/m2 (stocking density), feed type and additives. Such parameters, in addition to on-farm biosecurity may influence performance and also pathogenic bacterial numbers such as Campylobacter. In this study, three different production systems 'Normal' (N), 'Higher Welfare' (HW) and 'Omega-3 Higher Welfare' (O) were investigated in an industrial farm environment at day 7 and day 30 with a range of extrinsic parameters correlating performance with microbial dynamics and Campylobacter presence.

RESULTS

Our data identified production system N as significantly dissimilar from production systems HW and O when comparing the prevalence of genera. An increase in Placement Birds/m2 density led to a decrease in environmental pressure influencing the microbial community structure. Prevalence of genera, such as Eisenbergiella within HW and O, and likewise Alistipes within N were representative. These genera have roles directly relating to energy metabolism, amino acid, nucleotide and short chain fatty acid (SCFA) utilisation. Thus, an association exists between consistent and differentiating parameters of the production systems that affect feed utilisation, leading to competitive exclusion of genera based on competition for nutrients and other factors. Campylobacter was identified within specific production system and presence was linked with the increased diversity and increased environmental pressure on microbial community structure. Addition of Omega-3 though did alter prevalence of specific genera, in our analysis did not differentiate itself from HW production system. However, Omega-3 was linked with a positive impact on weight gain.

CONCLUSIONS

Overall, our results show that microbial communities in different industrial production systems are deterministic in elucidating the underlying biological confounders, and these recommendations are transferable to farm practices and diet manipulation leading to improved performance and better intervention strategies against Campylobacter within the food chain. Video Abstract.

Behavioral, morphological, and ecological trait evolution in two clades of New World Sparrows (Aimophila and Peucaea, Passerellidae)

The New World sparrows (Passerellidae) are a large, diverse group of songbirds that vary in morphology, behavior, and ecology. Thus, they are excellent for studying trait evolution in a phylogenetic framework. We examined lability versus conservatism in morphological and behavioral traits in two related clades of sparrows (Aimophila, Peucaea), and assessed whether habitat has played an important role in trait evolution. We first inferred a multi-locus phylogeny which we used to reconstruct ancestral states, and then quantified phylogenetic signal among morphological and behavioral traits in these clades and in New World sparrows more broadly. Behavioral traits have a stronger phylogenetic signal than morphological traits. Specifically, vocal duets and song structure are the most highly conserved traits, and nesting behavior appears to be maintained within clades. Furthermore, we found a strong correlation between open habitat and unpatterned plumage, complex song, and ground nesting. However, even within lineages that share the same habitat type, species vary in nesting, plumage pattern, song complexity, and duetting. Our findings highlight trade-offs between behavior, morphology, and ecology in sparrow diversification.

Phylogenetic signals in pest abundance and distribution range of spider mites

Background

Attributes of pest species like host range are frequently reported as being evolutionarily constrained and showing phylogenetic signal. Because these attributes in turn could influence the abundance and impact of species, phylogenetic information could be useful in predicting the likely status of pests. In this study, we used regional (China) and global datasets to investigate phylogenetic patterns in occurrence patterns and host ranges of spider mites, which constitute a pest group of many cropping systems worldwide.

Results

We found significant phylogenetic signal in relative abundance and distribution range both at the regional and global scales. Relative abundance and range size of spider mites were positively correlated with host range, although these correlations became weaker after controlling for phylogeny.

Conclusions

The results suggest that pest impacts are evolutionarily constrained. Information that is easily obtainable – including the number of known hosts and phylogenetic position of the mites – could therefore be useful in predicting future pest risk of species.

Leaf vascular architecture in temperate dicotyledons: correlations and link to functional traits

Using 227 dicotyledonous species in temperate region, we found the relationships among densities of different-order veins, creating diversity of leaf vascular architectures. Dicotyledonous angiosperms commonly possess a hierarchical leaf vascular system, wherein veins of different orders have different functions. Minor vein spacing determines leaf hydraulic efficiency, whereas the major veins provide mechanical support. However, there is limited information on the coordination between these vein orders across species, limiting our understanding of how diversity in vein architecture is arrayed. We aimed to examine the (1) relationships between vein densities at two spatial scales (lower- vs. higher-order veins and among minor veins) and (2) relationships of vein densities with plant functional traits. We studied ten traits related to vein densities and three functional traits (leaf dry mass per area [LMA], leaf longevity [LL], and adult plant height [H_adult]) for 227 phylogenetically diverse plant species that occur in temperate regions and examined the vein-vein and vein-functional traits relationships across species. The densities of lower- and higher-order veins were positively correlated across species. The minor vein density was positively correlated with the densities of both areoles and free-ending veins, and vascular networks with higher minor vein density tended to have a lower ratio of free-ending veins to areoles across species. Neither densities of lower- nor higher-order veins were related to LMA and LL. On the other hand, the densities of veins and areoles tended to be positively correlated with H_adult. These results suggest that densities of different-order veins are developmentally coordinated across dicotyledonous angiosperms and form the independent axis in resource use strategies based on the leaf economics spectrum.

The use of wing shape for characterising macroevolution in mosquitoes (Diptera: Culicidae)

The wing form of culicid mosquitoes shows considerable variation among groups: this phenomenon has been addressed by several studies through space-time analyses in mosquito populations, species, and genera. The observed variation results from a combination of two distinct factors: heredity and phenotypic plasticity. The first is usually related to wing shape, a complex character that may serve as a taxonomic marker in specific cases. We hypothesized that wing shape might be phylogenetically meaningful in Culicidae. In this study, we applied a geometric morphometrical approach based on 18 landmarks in 81 species of mosquitoes, representing 19 different genera, to investigate whether wing shape can help retrieve macroevolutionary patterns or identify any phylogenetic signals. We observed that wing shape differed considerably among groups, especially between Anophelinae and Culicinae subfamilies; thus, some wing shape elements may be synapomorphic. Comparisons among wing consensus after Procrustes superimposition revealed that landmark #1, located between the veins RS and R1, was the most variable. Sabethini tribe was distinguished from other taxa owing to a strong phylogenetic signal of its wings, whereas other culicids presented weaker signals and were not that distinguishable. Evolutionary forces such as natural selection, evolutionary limitation/constraint, or canalization mechanisms might drive the evolution of wing phenotype. These findings suggest that the wing undergoes evolution over long periods, but is not neutral enough to reconstruct the phylogenetic history of these insects. Gene-based studies should be performed to understand the driving forces in wing evolution.

Realistic scenarios of missing taxa in phylogenetic comparative methods and their effects on model selection and parameter estimation

Model-based analyses of continuous trait evolution enable rich evolutionary insight. These analyses require a phylogenetic tree and a vector of trait values for the tree's terminal taxa, but rarely do a tree and dataset include all taxa within a clade. Because the probability that a taxon is included in a dataset depends on ecological traits that have phylogenetic signal, missing taxa in real datasets should be expected to be phylogenetically clumped or correlated to the modelled trait. I examined whether those types of missing taxa represent a problem for model selection and parameter estimation. I simulated univariate traits under a suite of Brownian Motion and Ornstein-Uhlenbeck models, and assessed the performance of model selection and parameter estimation under absent, random, clumped or correlated missing taxa. I found that those analyses perform well under almost all scenarios, including situations with very sparsely sampled phylogenies. The only notable biases I detected were in parameter estimation under a very high percentage (90%) of correlated missing taxa. My results offer a degree of reassurance for studies of continuous trait evolution with missing taxa, but the problem of missing taxa in phylogenetic comparative methods still demands much further investigation. The framework I have described here might provide a starting point for future work.

Genome assembly and phylogenomic data analyses using plastid data: Contrasting species tree estimation methods

Phylogenomics has become increasingly popular in recent years mostly due to the increased affordability of next generation sequencing techniques. Phylogenomics has sparked interest in multiple fields of research, including systematics, ecology, epidemiology, and even personalized medicine, agriculture and pharmacy. Despite this trend, it is usually difficult to learn and understand how the analyses were done, how the results were obtained, and most importantly, how to replicate the study. Here we present the data and all of the code utilized to perform phylogenomic inferences using plastome data: from raw data to extensive phylogenetic inference and accuracy assessment. The data presented here utilizes plastome sequences available on GenBank (accession numbers of 94 species are available below) and the code is also available at https://github.com/deisejpg/rosids. Gonçalves et al. is the research article associated with the data analyses presented here.

Evolution of phytochemical diversity in Pilocarpus (Rutaceae)

The evolution of phytochemical diversity and biosynthetic pathways in plants can be evaluated from a phylogenetic and environmental perspective. Pilocarpus Vahl (Rutaceae), an economically important medicinal plant in the family Rutaceae, has a great diversity of imidazole alkaloids and coumarins. In this study, we used phylogenetic comparative methods to determine whether there is a phylogenetic signal for chemical traits across the genus Pilocarpus; this included ancestral reconstructions of continuous and discrete chemical traits. Bioclimatic variables found to be associated with the distribution of this genus were used to perform OLS regressions between chemical traits and bioclimatic variables. Next, these regression models were evaluated to test whether bioclimatic traits could significantly predict compound concentrations. Our study found that in terms of compound concentration, variation is most significantly associated with adaptive environmental convergence rather than phylogenetic relationships. The best predictive model of chemical traits was the OLS regression that modeled the relationship between coumarin and precipitation in the coldest quarter. However, we also found one chemical trait was dependent on phylogenetic history and bioclimatic factors. These findings emphasize that consideration of both environmental and phylogenetic factors is essential to tease out the intricate processes in the evolution of chemical diversity in plants. These methods can benefit fields such as conservation management, ecology, and evolutionary biology.

Drivers of sociality in Gobiodon fishes: An assessment of phylogeny, ecology and life-history

What drives the evolution of sociality in animals? Many robust studies in terrestrial organisms have pointed toward various kinship-based, ecological and life-history traits or phylogenetic constraint which have played a role in the evolution of sociality. These traits are not mutually exclusive and the exact combination of traits is likely taxon-specific. Phylogenetic comparative analyses have been instrumental in identifying social lineages and comparing various traits with non-social lineages to give broad evolutionary perspectives on the development of sociality. Few studies have attempted this approach in marine vertebrate systems. Social marine fishes are particularly interesting because many have a pelagic larval phase and non-conventional life-history strategies (e.g. bi-directional sex-change) not often observed in terrestrial animals. Such strategies provide novel insights into terrestrially-derived theories of social evolution. Here, we assess the strength of the phylogenetic signal of sociality in the Gobiodon genus with Pagel's lambda and Blomberg's K parameters. We found some evidence of a phylogenetic signal of sociality, but factors other than phylogenetic constraint also have a strong influence on the extant social state of each species. We then use phylogenetic generalized least squares analyses to examine several ecological and life-history traits that may have influenced the evolution of sociality in the genus. We found an interaction of habitat size and fish length was the strongest predictor of sociality. Sociality in larger species was more dependent on coral size than in smaller species, but smaller species were more social overall, regardless of coral size. Finally, we comment on findings regarding the validity of the species G. spilophthalmus which arose during the course of our research. These findings in a group of marine fishes add a unique perspective on the evolution of sociality to the excellent terrestrial work conducted in this field.

The synergistic effect of concatenation in phylogenomics: the case in Pantoea

With the increased availability of genome sequences for bacteria, it has become routine practice to construct genome-based phylogenies. These phylogenies have formed the basis for various taxonomic decisions, especially for resolving problematic relationships between taxa. Despite the popularity of concatenating shared genes to obtain well-supported phylogenies, various issues regarding this combined-evidence approach have been raised. These include the introduction of phylogenetic error into datasets, as well as incongruence due to organism-level evolutionary processes, particularly horizontal gene transfer and incomplete lineage sorting. Because of the huge effect that this could have on phylogenies, we evaluated the impact of phylogenetic conflict caused by organism-level evolutionary processes on the established species phylogeny for Pantoea, a member of the Enterobacterales. We explored the presence and distribution of phylogenetic conflict at the gene partition and nucleotide levels, by identifying putative inter-lineage recombination events that might have contributed to such conflict. Furthermore, we determined whether smaller, randomly constructed datasets had sufficient signal to reconstruct the current species tree hypothesis or if they would be overshadowed by phylogenetic incongruence. We found that no individual gene tree was fully congruent with the species phylogeny of Pantoea, although many of the expected nodes were supported by various individual genes across the genome. Evidence of recombination was found across all lineages within Pantoea, and provides support for organism-level evolutionary processes as a potential source of phylogenetic conflict. The phylogenetic signal from at least 70 random genes recovered robust, well-supported phylogenies for the backbone and most species relationships of Pantoea, and was unaffected by phylogenetic conflict within the dataset. Furthermore, despite providing limited resolution among taxa at the level of single gene trees, concatenated analyses of genes that were identified as having no signal resulted in a phylogeny that resembled the species phylogeny of Pantoea. This distribution of signal and noise across the genome presents the ideal situation for phylogenetic inference, as the topology from a ≥70-gene concatenated species phylogeny is not driven by single genes, and our data suggests that this finding may also hold true for smaller datasets. We thus argue that, by using a concatenation-based approach in phylogenomics, one can obtain robust phylogenies due to the synergistic effect of the combined signal obtained from multiple genes.

Looking beyond the flowers: associations of stingless bees with sap-sucking insects

The main sources of food for stingless bees are the nectar and pollen harvested from flowers, whereas one important kind of nesting material (i.e. wax) is produced by their own abdominal glands. Stingless bees can, nonetheless, obtain alternative resources of food and wax from exudates released by sap-sucking insects as honeydew and waxy cover, respectively. To date, there are no comprehensive studies investigating how diversified and structured the network interactions between stingless bees and sap-sucking insects are. Here, we conducted a survey of the data on relationship between stingless bees and sap-sucking insects to evaluate: (1) which resources are collected by which stingless bee species; (2) how diverse the interaction network is, using species degree and specialisation index as a proxy; and if (3) there would be any phylogenetic signal in the species degree and specialisation indices. Our findings demonstrate that approximately 21 stingless bee species like Trigona spp. and Oxytrigona spp. have been observed interacting with 11 sap-sucking species, among which Aethalion reticulatum is the main partner. From ca. 50 records, Brazil is the country with most observations (n = 38) of this type of ecological interaction. We found also that stingless bees harvest fivefold more honeydew than waxy covers on sap-sucking insects. However, we did not find any phylogenetic signal for the occurrence of this interaction, considering species degree and specialisation indices, suggesting that both traits apparently evolved independently among stingless bee species. We suggest that specific ecological demands may drive this opportunistic behaviour exhibited by stingless bees, because major sources of food are obtained from flowers and these bees produce their own wax.

Phylogenetic signal analysis in the basicranium of Ursidae (Carnivora, Mammalia)

Ursidae is a monophyletic group comprised of three subfamilies: Tremarctinae, Ursinae and Ailuropodinae, all of which have a rich geographical distribution. The phylogenetic relationships within the Ursidae group have been underexamined, especially regarding morphological traits such as the basicranium. Importantly, the basicranium is a highly complex region that covers a small portion of the skull, combining both structural and functional aspects that determine its morphology. Phylogenetic hypotheses of the Ursidae (including Tremarctinae) have been made based on morphological characters that considers skull, mandible and teeth features, while specific characters of the auditory region and basicranium have not been taken into account. To do this, we analyse the shape and size macroevolution of the basicranium of Ursidae, testing its morphological disparity in a phylogenetic context, which is quantified by means of the phylogenetic signal. We investigated phylogenetical autocorrelation by shape (depicted by Principal Components Analysis scores from previous published analyses) and basicranium size (depicted by centroid size, CS) using an orthonormal decomposition analysis and Abouheif C mean. The main advantages of these methods are that they rely exclusively on cladogram topology and do not require branch-length estimates. Also, an optimisation of the ancestral nodes was performed using TNT 1.5 software. In relation to the phylogenetic signal, both methods showed similar results: the presence of autocorrelation was detected in PC1 and PC2, while in PC3, PC4 and PC5 and in the size of the basicranium (CS), the absence of autocorrelation occurred. The most significant nodes (where there is autocorrelation) are the basal nodes 'Ursidae' and 'Ursinae-Tremarctinae'. Within this last group, distinctive basicranium morphology is observed, being more conservative in Tremarctinae than in Ursinae. The differences between these subfamilies could be related to historical events involving varying food and environmental preferences. The high phylogenetic signal in the node Tremarctinae probably indicates that the basicranium configuration of these bears was obtained early in their evolutionary history. Finally, our results of the basicranium and skull length ratios indicate that in Tremarctinae, the basicranium size was not determined by phylogeny but instead by other factors, such as adaptive responses to climatic changes and competition with other carnivores.

Comparative reproductive dormancy differentiation in European black scavenger flies (Diptera: Sepsidae)

Seasonality is a key environmental factor that regularly promotes life history adaptation. Insects invading cold-temperate climates need to overwinter in a dormant state. We compared the role of temperature and photoperiod in dormancy induction in the laboratory, as well as winter survival and reproduction in the field and the laboratory, of 5 widespread European dung fly species (Diptera: Sepsidae) to investigate their extent of ecological differentiation and thermal adaptation. Unexpectedly, cold temperature is the primary environmental factor inducing winter dormancy, with short photoperiod playing an additional role mainly in species common at high altitudes and latitudes (Sepsis cynipsea, neocynipsea, fulgens), but not in those species also thriving in southern Europe (thoracica, punctum). All species hibernate as adults rather than juveniles. S. thoracica had very low adult winter survivorship under both (benign) laboratory and (harsh) field conditions, suggesting flexible quiescence rather than genetically fixed winter diapause, restricting their distribution towards the pole. All other species appear well suited for surviving cold, Nordic winters. Females born early in the season reproduce before winter while late-born females reproduce after winter, fulgens transitioning earliest before winter and thoracica and punctum latest; a bet-hedging strategy of reproduction during both seasons occurs rarely but is possible physiologically. Fertility patterns indicate that females can store sperm over winter. Winter dormancy induction mechanisms of European sepsids are congruent with their geographic distribution, co-defining their thermal niches. Flexible adult winter quiescence appears the easiest route for insects spreading towards the poles to evolve the necessary overwinter survival.

Climatic niche evolution in the viviparous Sceloporus torquatus group (Squamata: Phrynosomatidae)

The cold-climate hypothesis maintains that viviparity arose as a means to prevent increased egg mortality in nests owing to low temperatures, and this hypothesis represents the primary and most strongly supported explanation for the evolution of viviparity in reptiles. In this regard, certain authors have stated that viviparous species will exhibit speciation via climatic niche conservatism, with similar climatic niches being observed in allopatric sister species. However, this prediction remains to be tested with bioclimatic variables relevant to each viviparous group. In the present study, we examined climatic niche evolution in a group of North American viviparous lizards to determine whether their diversification is linked to phylogenetic niche conservatism (PNC). We evaluated the phylogenetic signal and trait evolution of individual bioclimatic variables and principal component (PC) scores of a PC analysis, along with reconstructions of ancestral climate tolerances. The results suggest that diversification of the Sceloporus torquatus group species is associated with both niche differentiation and PNC. Furthermore, we did not observe PNC across nearly all bioclimatic variables and in PC2 and PC3. However, in Precipitation Seasonality (Bio15), in Precipitation of Coldest Quarter (Bio19) and in PC1 (weakly associated with variability of temperature), we did observe PNC. Additionally, variation of the scores along the phylogeny and Pagel's delta (δ) >1 of PC3 suggests a fast, recent evolution to dry conditions in the clade that sustains S. serrifer.

Comparative effects of the parasiticide ivermectin on survival and reproduction of adult sepsid flies

Ivermectin is a veterinary pharmaceutical widely applied against parasites of livestock. Being effective against pests, it is also known to have lethal and sublethal effects on non-target organisms. While considerable research demonstrates the impact of ivermectin residues in livestock dung on the development and survival of dung feeding insect larvae, surprisingly little is known about its fitness effects on adults. We tested the impact of ivermectin on the survival of adult sepsid dung fly species (Diptera: Sepsidae) in the laboratory, using an ecologically relevant and realistic range of 69-1978 µg ivermectin/kg wet dung, and compared the sensitivities of larvae and adults in a phylogenetic framework. For one representative, relatively insensitive species, Sepsis punctum, we further investigated effects of ivermectin on female fecundity and male fertility. Moreover, we tested whether females can differentiate between ivermectin-spiked and non-contaminated dung in the wild. Adult sepsid flies exposed to ivermectin suffered increased mortality, whereby closely related species varied strongly in their sensitivity. Adult susceptibility to the drug correlated with larval susceptibility, showing a phylogenetic signal and demonstrating systemic variation in ivermectin sensitivity. Exposure of S. punctum females to even low concentrations of ivermectin lowered the number of eggs laid, while treatment of males reduced egg-to-adult offspring survival, presumably via impairment of sperm quality or quantity. The fitness impact was amplified when both parents were exposed. Lastly, sepsid flies did not discriminate against ivermectin-spiked dung in the field. Treatment of livestock with avermectins may thus have even more far-reaching sublethal ecological consequences than currently assumed via effects on adult dung-feeding insects.

Molecular genetic and biochemical evidence for adaptive evolution of leaf abaxial epicuticular wax crystals in the genus Lithocarpus (Fagaceae)

BACKGROUND

Leaf epicuticular wax is an important functional trait for physiological regulation and pathogen defense. This study tests how selective pressure may have forced the trait of leaf abaxial epicuticular wax crystals (LAEWC) and whether the presence/absence of LAEWC is associated with other ecophysiological traits. Scanning Electron Microscopy was conducted to check for LAEWC in different Lithocarpus species. Four wax biosynthesis related genes, including two wax backbone genes ECERIFERUM 1 (CER1) and CER3, one regulatory gene CER7 and one transport gene CER5, were cloned and sequenced. Ecophysiological measurements of secondary metabolites, photosynthesis, water usage efficiency, and nutrition indices were also determined. Evolutionary hypotheses of leaf wax character transition associated with the evolution of those ecophysiological traits as well as species evolution were tested by maximum likelihood.

RESULTS

Eight of 14 studied Lithocarpus species have obvious LAEWC appearing with various types of trichomes. Measurements of ecophysiological traits show no direct correlations with the presence/absence of LAEWC. However, the content of phenolic acids is significantly associated with the gene evolution of the wax biosynthetic backbone gene CER1, which was detected to be positively selected when LAEWC was gained during the late-Miocene-to-Pliocene period.

CONCLUSIONS

Changes of landmass and vegetation type accelerated the diversification of tropical and subtropical forest trees and certain herbivores during the late Miocene. As phenolic acids were long thought to be associated with defense against herbivories, co-occurrence of LAEWC and phenolic acids may suggest that LAEWC might be an adaptive defensive mechanism in Lithocarpus.

Filtering nucleotide sites by phylogenetic signal to noise ratio increases confidence in the Neoaves phylogeny generated from ultraconserved elements

Despite genome scale analyses, high-level relationships among Neoaves birds remain contentious. The placements of the Neoaves superorders are notoriously difficult to resolve because they involve deep splits followed by short internodes. Using our approach, we investigate whether filtering UCE loci on their phylogenetic signal to noise ratio helps to resolve key nodes in the Neoaves tree of life. We find that our analysis of data sets filtered for high signal to noise ratio results in topologies that are inconsistent with unfiltered results but that are congruent with whole-genome analyses. These relationships include the Columbea + Passerea sister relationship and the Phaethontimorphae + Aequornithia sister relationship. We also find increased statistical support for more recent nodes (i.e. the Pelecanidae + Ardeidae sister relationship, the Eucavitaves clade, and the Otidiformes + Musophagiformes sister relationship). We also find instances where support is reduced for well-established clades, possibly due to the removal of sites with moderate signal-to-noise ratio. Our results suggest that filtering on the basis of signal to noise ratio is a useful tool for resolving problematic splits in phylogenomic data sets.

Skin microbiome of coral reef fish is highly variable and driven by host phylogeny and diet

BACKGROUND

The surface of marine animals is covered by abundant and diversified microbial communities, which have major roles for the health of their host. While such microbiomes have been deeply examined in marine invertebrates such as corals and sponges, the microbiomes living on marine vertebrates have received less attention. Specifically, the diversity of these microbiomes, their variability among species, and their drivers are still mostly unknown, especially among the fish species living on coral reefs that contribute to key ecosystem services while they are increasingly affected by human activities. Here, we investigated these knowledge gaps analyzing the skin microbiome of 138 fish individuals belonging to 44 coral reef fish species living in the same area.

RESULTS

Prokaryotic communities living on the skin of coral reef fishes are highly diverse, with on average more than 600 OTUs per fish, and differ from planktonic microbes. Skin microbiomes varied between fish individual and species, and interspecific differences were slightly coupled to the phylogenetic affiliation of the host and its ecological traits.

CONCLUSIONS

These results highlight that coral reef biodiversity is greater than previously appreciated, since the high diversity of macro-organisms supports a highly diversified microbial community. This suggest that beyond the loss of coral reefs-associated macroscopic species, anthropic activities on coral reefs could also lead to a loss of still unexplored host-associated microbial diversity, which urgently needs to be assessed.

Host specificity of avian haemosporidian parasites is unrelated among sister lineages but shows phylogenetic signal across larger clades

Parasites can vary in the number of host species they infect, a trait known as "host specificity". Here we quantify phylogenetic signal-the tendency for closely related species to resemble each other more than distantly related species-in host specificity of avian haemosporidian parasites (genera Plasmodium, Haemoproteus and Leucocytozoon) using data from MalAvi, the global avian haemosporidian database. We used the genetic data (479 base pairs of cytochrome b) that define parasite lineages to produce genus level phylogenies. Combining host specificity data with those phylogenies revealed significant levels of phylogenetic signal while controlling for sampling effects; phylogenetic signal was higher when the phylogenetic diversity of hosts was taken into account. We then tested for correlations in the host specificity of pairs of sister lineages. Correlations were generally close to zero for all three parasite genera. These results suggest that while the host specificity of parasite sister lineages differ, larger clades may be relatively specialised or generalised.

Leaf stable isotopes suggest shared ancestry is an important driver of functional diversity

Plant physiological strategies of carbon (C) and nitrogen (N) uptake and metabolism are often regarded as outcomes of environmental selection. This is likely true, but the role of evolutionary history may also be important in shaping patterns of functional diversity. Here, we used leaf C and N stable isotope ratios (δ¹³C, δ¹⁵N) as integrators of physiological processes to assess the relative roles of phylogenetic history and environment in a diverse group of Ericaceae species native to North America. We found strong phylogenetic signal in both leaf δ¹³C and δ¹⁵N, suggesting that close relatives have similar physiological strategies. The signal of phylogeny was generally stronger than that of the local environment. However, within some specialized environments (e.g., wetlands, sandy soils), we found environmental effects and/or niche conservatism. Phylogenetic signal in δ¹³C appears to be most closely related to the constraints on metabolic demand and supply of C, and δ¹⁵N appears to be most strongly related to mycorrhizal associations within the family.

Topological support and data quality can only be assessed through multiple tests in reviewing Blattodea phylogeny

Assessing support for molecular phylogenies is difficult because the data is heterogeneous in quality and overwhelming in quantity. Traditionally, node support values (bootstrap frequency, Bayesian posterior probability) are used to assess confidence in tree topologies. Other analyses to assess the quality of phylogenetic data (e.g. Lento plots, saturation plots, trait consistency) and the resulting phylogenetic trees (e.g. internode certainty, parameter permutation tests, topological tests) exist but are rarely applied. Here we argue that a single qualitative analysis is insufficient to assess support of a phylogenetic hypothesis and relate data quality to tree quality. We use six molecular markers to infer the phylogeny of Blattodea and apply various tests to assess relationship support, locus quality, and the relationship between the two. We use internode-certainty calculations in conjunction with bootstrap scores, alignment permutations, and an approximately unbiased (AU) test to assess if the molecular data unambiguously support the phylogenetic relationships found. Our results show higher support for the position of Lamproblattidae, high support for the termite phylogeny, and low support for the position of Anaplectidae, Corydioidea and phylogeny of Blaberoidea. We use Lento plots in conjunction with mutation-saturation plots, calculations of locus homoplasy to assess locus quality, identify long branch attraction, and decide if the tree's relationships are the result of data biases. We conclude that multiple tests and metrics need to be taken into account to assess tree support and data robustness.