phyr: An r package for phylogenetic species‐distribution modelling in ecological communities

Seed size and dispersal mode select mast seeding in perennial plants

Reproduction by perennial plants varies from being relatively constant over years to the production of massive and synchronous seed crops at irregular intervals, a reproductive strategy called mast seeding. The sources of interspecific differences in the extent of interannual variation in seed production are largely unknown. We conducted a global meta-analysis of animal-dispersed species to quantify how the interannual variability in seed crops produced by plants can be explained by the seed mass, dispersal mode, phylogeny, and climate. Phylogenetic analysis indicated that the interannual variations in seed production and seed mass tended to be similar in related species due to their shared evolution. The interannual variation in seed production was 1.22 times higher in synzoochorous species dispersed by scatter-hoarders compared with endozoochorous species dispersed by frugivores. Furthermore, the production of small seeds was associated with higher interannual variation in seed production, although synzoochorous species produced larger seeds than endozoochorous species. Precipitation rather than temperature had a significant positive effect on the interannual variation in seed production. The seed mass and dispersal mode contributed more to the interannual variation in seed production than phylogeny, climate, and fruit type. Our findings support a long-standing hypothesis that interspecific variation in the masting intensity is largely shaped by interactions between plants and animals.

Mechanistic insights into plant community responses to environmental variables: genome size, cellular nutrient investments, and metabolic tradeoffs

Affecting biodiversity, plants with larger genome sizes (GS) may be restricted in nutrient-poor conditions. This pattern has been attributed to their greater cellular nitrogen (N) and phosphorus (P) investments and hypothesized nutrient-investment tradeoffs between cell synthesis and physiological attributes associated with growth. However, the influence of GS on cell size and functioning may also contribute to GS-dependent growth responses to nutrients. To test whether and how GS is associated with cellular nutrient, stomata, and/or physiological attributes, we examined > 500 forbs and grasses from seven grassland sites conducting a long-term N and P fertilization experiment. Larger GS plants had increased cellular nutrient contents and larger, but fewer stomata than smaller GS plants. Larger GS grasses (but not forbs) also had lower photosynthetic rates and water-use efficiencies. However, nutrients had no direct effect on GS-dependent physiological attributes and GS-dependent physiological changes likely arise from how GS influences cells. At the driest sites, large GS grasses displayed high water-use efficiency mostly because transpiration was reduced relative to photosynthesis in these conditions. We suggest that climatic conditions and GS-associated cell traits that modify physiological responses, rather than resource-investment tradeoffs, largely explain GS-dependent growth responses to nutrients (especially for grasses).

Plasticity cannot fully compensate evolutionary differences in heat tolerance across fish species

Understanding how evolution and phenotypic plasticity contribute to variation in heat tolerance is crucial to predicting responses to warming. Here, we analyze 272 thermal death time curves of 53 fish species acclimated to different temperatures and quantify their relative contributions. Analyses show that evolution and plasticity account, respectively, for 80.5% and 12.4% of the variation in elevation across curves, whereas their slope remained invariant. Evolutionary and plastic adaptive responses differ in magnitude, with heat tolerance increasing to 0.54 °C between species and 0.32 °C within species for every 1 °C increase in environmental temperatures. After successfully predicting critical temperatures under ramping conditions to validate these estimates, we show that fish populations can only partly ameliorate the impact of warming waters via thermal acclimation, and this deficit in plasticity could increase as the warming accelerates.

Shorebirds Are Shrinking and Shape-Shifting: Declining Body Size and Lengthening Bills in the Past Half-Century

Animals are predicted to shrink and shape-shift as the climate warms, declining in size, while their appendages lengthen. Determining which types of species are undergoing these morphological changes, and why, is critical to understanding species responses to global change, including potential adaptation to climate warming. We examine body size and bill length changes in 25 shorebird species using extensive field data (> 200,000 observations) collected over 46 years (1975-2021) by community scientists. We show widespread body size declines over time, and after short-term exposure to warmer summers. Meanwhile, shorebird bills are lengthening over time but shorten after hot summers. Shrinking and shape-shifting patterns are consistent across ecologically diverse shorebirds from tropical and temperate Australia, are more pronounced in smaller species and vary according to migration behaviour. These widespread morphological changes could be explained by multiple drivers, including adaptive and maladaptive responses to nutritional stress, or by thermal adaptation to climate warming.

The global diet diversity spectrum in avian apex predators

Some predators depend heavily on one or a few prey types, and others have exceptionally broad diets. It is unclear how this diet variation arises. Here, we demonstrate a strong link between diet species richness and Shannon entropy of prey frequencies (a diet diversity spectrum) for a globally distributed group of apex predators-raptors. For many raptors, diet entropy is consistent with random sampling expectations given a lognormal distribution of abundances among prey species. Yet most species-rich diets often approach the maximum possible diet entropy, indicating an unexpected level of diet evenness that is not predicted by theory. Positioning along this diet diversity spectrum is linked to evolutionary history, the types of prey that are acceptable and the role of raptors as food web integrators through cross-habitat sampling. These results suggest that raptors may have a highly stabilizing effect on terrestrial food webs and play an important role in maintaining biodiversity.

A trade-off between investment in molecular defense repertoires and growth in plants

Given the negative fitness effects that pathogens impose on their hosts, the benefits of resistance should be universal. However, there is marked variation across plant species in the number of nucleotide-binding leucine-rich repeat receptors, which form a cornerstone of defense. The growth-defense trade-off hypothesis predicts costs associated with defense investment to generate variation in these traits. Our analysis comparing features of the intracellular immune-receptor repertoires with trait data of 187 species shows that in wild plants, the size of the molecular defense repertoire correlates negatively with growth. By contrast, we do not find evidence for a growth-defense trade-off in agricultural plants. Our cross-species approach highlights the central role of defense investment in shaping ecological trait variation and its sensitivity to domestication.

Distinct Escherichia coli transcriptional profiles in the guts of recurrent UTI sufferers revealed by pangenome hybrid selection

Low-abundance members of microbial communities are difficult to study in their native habitats, including Escherichia coli, a minor but common inhabitant of the gastrointestinal tract, and key opportunistic pathogen of the urinary tract. While multi-omic analyses have detailed interactions between uropathogenic Escherichia coli (UPEC) and the bladder mediating urinary tract infection (UTI), little is known about UPEC in its pre-infection reservoir, the gastrointestinal tract, partly due to its low relative abundance (<1%). To sensitively explore the genomes and transcriptomes of diverse gut E. coli, we develop E. coli PanSelect, which uses probes designed to specifically capture E. coli's broad pangenome. We demonstrate its ability to enrich diverse E. coli by orders of magnitude, in a mock community and in human stool from a study investigating recurrent UTI (rUTI). Comparisons of transcriptomes between gut E. coli of women with and without history of rUTI suggest rUTI gut E. coli are responding to increased oxygen and nitrate, suggestive of mucosal inflammation, which may have implications for recurrent disease. E. coli PanSelect is well suited for investigations of in vivo E. coli biology in other low-abundance environments, and the framework described here has broad applicability to other diverse, low-abundance organisms.

Global analysis of acoustic frequency characteristics in birds

Animal communication plays a crucial role in biology, yet the wide variability in vocalizations is not fully understood. Previous studies in birds have been limited in taxonomic and analytical breadth. Here, we analyse an extensive dataset of >140 000 recordings of vocalizations from 8450 bird species, representing nearly every avian order and family, under a structural causal model framework, to explore the influence of eco-evolutionary traits on acoustic frequency characteristics. We find that body mass, beak size, habitat associations and geography influence acoustic frequency characteristics, with varying degrees of interaction with song acquisition type. We find no evidence for the influence of vegetation density, sexual dimorphism, range size and competition on our measures of acoustic frequency characteristics. Our results, built on decades of researchers' empirical observations collected across the globe, provide a new breadth of evidence about how eco-evolutionary processes shape bird communication.

Color polymorphic carnivores have faster speciation rates

Variation in coat color is a prominent feature in carnivores, thought to be shaped by environmental factors. As new traits could allow populations to occupy novel niches and habitats, color polymorphism may be maintained by balancing selection. Consequently, color polymorphic species may speciate more rapidly and can give rise to monomorphic daughter species. We thus predicted that, within the Carnivora, (i) speciation rate is higher in polymorphic lineages, (ii) divergence between color polymorphic lineages is more recent, and (iii) within closely related groups, polymorphic lineages are ancestral and monomorphic lineages derived. We also tested whether accelerated speciation rates relate to niche breadth, measured by the number of occupied habitats and range size. We collected data of 48 polymorphic and 192 monomorphic carnivore species, and assessed speciation rates using phylogenetic comparative methods. We found that polymorphic carnivores had higher speciation rates (λ1 = 0.29, SD = 0.13) than monomorphic species (λ0 = 0.053, SD = 0.044). Hidden and quantitative state speciation and extinction models inferred that color polymorphism was the main contributing factor, and that niche breadth was not of influence. Therefore, other selective forces than spatial niche segregation, such as predator-prey coevolution, may contribute to color polymorphism in wild carnivores.

Bird Leg Skin Lesions and Urbanization in a Neotropical Savanna City

Urban sprawl threatens biodiversity and is responsible for significant changes in the species that live in these environments. Given the high cost of comprehensive surveillance, monitoring disease indirectly, such as detecting skin lesions in birds, may help us better understand the prevalence of diseases affecting wild populations. We assessed the frequency of leg skin lesions, as a proxy of disease presence, in 1,565 individuals of 25 species, along the urban matrix of a large Neotropical city, Brasília, Federal District, Brazil. We tested the hypothesis that there is an increase in the frequency of skin lesions in birds due to urban intensification. We observed an increasing trend in some bird species between the frequency of occurrence of lesions and the intensity of urbanization. Species with a higher number of captures had an increase in the percentage of lesions, indicating that the occurrence of lesions may be linked to higher population density or that detection of the effect occurs only when sample sizes are high and controlled among urbanization categories. Our study highlights how the intensity of urbanization may increase the risk of disease transmission for these species. Unfortunately, studies on this topic are scarce in Neotropical regions, despite the region's high biodiversity and urban expansion.

Longevity of hymenopteran parasitoids in natural versus agricultural habitats and implications for biological control

Agricultural habitats are frequently disturbed, and disturbances could have major effects on species in upper trophic levels such as hymenopteran parasitoids that are important for biological control. A strategy for conservation biological control is to provide a diversified agricultural landscape which increases the availability of resources such as sugar required by parasitoid biological control agents. Here, we ask whether parasitoids occurring in agriculture benefit from sugar resources more or less than parasitoids occurring in natural habitats surrounding agricultural fields. We collected parasitoids from agricultural alfalfa fields, field margins, and natural prairies, and in the lab we randomly divided them into two treatments: half were given a constant supply of a sugar source to test their residual lifespan, and half were given neither sugar nor water to test their hardiness. Collected individuals were monitored daily and their day of death recorded. Parasitoids receiving a sugar source lived substantially longer than those without. Parasitoids collected in prairies lived longer than those from alfalfa fields in both the residual lifespan and hardiness treatments, with parasitoids from field margins being intermediate between them. Furthermore, the benefits of a sugar source to increase longevity was lower for parasitoids collected in agriculture than in natural habitats. This suggests that, even though parasitoid biological control agents benefit from sugar resources, their short lifespans make the benefit of sugar resources small compared to parasitoids that occur in natural habitats and have longer lifespans, and are adapted to consistent sugar sources.

Elemental and isotopic analysis of leaves predicts nitrogen-fixing phenotypes

Nitrogen (N)-fixing symbiosis is critical to terrestrial ecosystems, yet possession of this trait is known for few plant species. Broader presence of the symbiosis is often indirectly determined by phylogenetic relatedness to taxa investigated via manipulative experiments. This data gap may ultimately underestimate phylogenetic, spatial, and temporal variation in N-fixing symbiosis. Still needed are simpler field or collections-based approaches for inferring symbiotic status. N-fixing plants differ from non-N-fixing plants in elemental and isotopic composition, but previous investigations have not tested predictive accuracy using such proxies. Here we develop a regional field study and demonstrate a simple classification model for fixer status using nitrogen and carbon content measurements, and stable isotope ratios (δ15N and δ13C), from field-collected leaves. We used mixed models and classification approaches to demonstrate that N-fixing phenotypes can be used to predict symbiotic status; the best model required all predictors and was 80-94% accurate. Predictions were robust to environmental context variation, but we identified significant variation due to native vs. non-native (exotic) status and phylogenetic affinity. Surprisingly, N content-not δ15N-was the strongest predictor, suggesting that future efforts combine elemental and isotopic information. These results are valuable for understudied taxa and ecosystems, potentially allowing higher-throughput field-based N-fixer assessments.

Flexible oviposition behavior enabled the evolution of terrestrial reproduction

Among vertebrates, nearly all oviparous animals are considered to have either obligate aquatic or terrestrial oviposition, with eggs that are specialized for developing in those environments. The terrestrial environment has considerably more oxygen but is dry and thus presents both opportunities and challenges for developing embryos, particularly those adapted for aquatic development. Here, we present evidence from field experiments examining egg-laying behavior, egg size, and egg jelly function of 13 species of Central and South American treefrogs in the genus Dendropsophus, which demonstrates that flexible oviposition (individuals laying eggs both in and out of water) and eggs capable of both aquatic and terrestrial development are the likely factors which enable the transition from aquatic to terrestrial reproduction. Nearly half of the species we studied had previously undescribed degrees of flexible oviposition. Species with obligate terrestrial reproduction have larger eggs than species with aquatic reproduction, and species with flexible reproduction have eggs of intermediate sizes. Obligate terrestrial breeding frogs also have egg masses that absorb water more quickly than those with flexible oviposition. We also examined eight populations of a single species, Dendropsophus ebraccatus, and document substantial intraspecific variation in terrestrial oviposition; populations in rainy, stable climates lay fewer eggs in water than those in drier areas. However, no differences in egg size were found, supporting the idea that the behavioral component of oviposition evolves before other adaptations associated with obligate terrestrial reproduction. Collectively, these data demonstrate the key role that behavior can have in facilitating major evolutionary transitions.

Mast seeding is stronger in taller plants

Introduction

Two economies of scale, predator satiation and pollination efficiency, have been proposed to explain the evolutionary mechanisms of mast seeding adopted by some long-lived plants. Plant height is strongly selected by pollination vectors and may also provide economies of scale; however, it remains unknown whether there is a close relationship between adult plant height and mast seeding intensity.

Methods

Here, we analyzed mast seeding intensity of 158 plant species to test if adult plant height can select for mast seeding.

Results

We show that mast seeding intensities are higher in taller plant species irrespective of phylogeny, life form, pollination vector, and type of Spermatophytes. We also show that anemophily rather than entomophily selects for taller plant species and higher mast seeding intensities.

Discussion

The linear correlations and evolutionary links between adult plant height and mast seeding intensity provide evidence that mast seeding could have evolved as an adaptation to taller strategy of perennial plant species.

Latitudinal specificity of plant-avian frugivore interactions

Broad-scale assessments of plant-frugivore interactions indicate the existence of a latitudinal gradient in interaction specialization. The specificity (i.e. the similarity of the interacting partners) of plant-frugivore interactions could also change latitudinally given that differences in resource availability could favour species to become more or less specific in their interactions across latitudes. Species occurring in the tropics could be more taxonomically, phylogenetically and functionally specific in their interactions because of a wide range of resources that are constantly available in these regions that would allow these species to become more specialized in their resource usage. We used a data set on plant-avian frugivore interactions spanning a wide latitudinal range to examine these predictions, and we evaluated the relationship between latitude and taxonomic, phylogenetic and functional specificity of plant and frugivore interactions. These relationships were assessed using data on population interactions (population level), species means (species level) and community means (community level). We found that the specificity of plant-frugivore interactions is generally not different from null models. Although statistically significant relationships were often observed between latitude and the specificity of plant-frugivore interactions, the direction of these relationships was variable and they also were generally weak and had low explanatory power. These results were consistent across the three specificity measures and levels of organization, suggesting that there might be an interplay between different mechanisms driving the interactions between plants and frugivores across latitudes.

Reactions of wintering passerines to male calls of the European cuckoo Cuculus canorus

The reaction of birds to the nest parasite, the European cuckoo Cuculus canorus, has been the subject of extensive testing in various aspects. However, while the cuckoo is a long-distance migrant, some of its hosts are sedentary species. In this study, we aimed to investigate whether species, primarily hosts, react to the presence of the cuckoo also in the winter season. This behaviour may involve an attempt to drive the parasite away from locations that will subsequently become their breeding sites. During playback experiments conducted in the winter of 2021/2022 in Poland, we demonstrated that numerous bird species react to the male cuckoo calls in winter. These calls may be perceived as a source of danger, particularly by cuckoo hosts, who responded to this call more frequently than non-hosts and the control species (pigeon). Nonetheless, the birds' reactions were not strong, as they did not approach the source of the call. However, our results are constrained by the limited number of cuckoo host species wintering in Poland. To better evaluate the intensity of bird responses to the male cuckoo's call during the non-breeding season, further studies should be conducted in regions where a greater variety of species, especially those most susceptible to parasitism, overwinter.

Distinct Escherichia coli transcriptional profiles in the guts of recurrent UTI sufferers revealed by pangenome hybrid selection

Low-abundance members of microbial communities are difficult to study in their native habitats. This includes Escherichia coli, a minor, but common inhabitant of the gastrointestinal tract and opportunistic pathogen, including of the urinary tract, where it is the primary pathogen. While multi-omic analyses have detailed critical interactions between uropathogenic Escherichia coli (UPEC) and the bladder that mediate UTI outcome, comparatively little is known about UPEC in its pre-infection reservoir, partly due to its low abundance there (<1% relative abundance). To accurately and sensitively explore the genomes and transcriptomes of diverse E. coli in gastrointestinal communities, we developed E. coli PanSelect which uses a set of probes designed to specifically recognize and capture E. coli's broad pangenome from sequencing libraries. We demonstrated the ability of E. coli PanSelect to enrich, by orders of magnitude, sequencing data from diverse E. coli using a mock community and a set of human stool samples collected as part of a cohort study investigating drivers of recurrent urinary tract infections (rUTI). Comparisons of genomes and transcriptomes between E. coli residing in the gastrointestinal tracts of women with and without a history of rUTI suggest that rUTI gut E. coli are responding to increased levels of oxygen and nitrate, suggestive of mucosal inflammation, which may have implications for recurrent disease. E. coli PanSelect is well suited for investigations of native in vivo biology of E. coli in other environments where it is at low relative abundance, and the framework described here has broad applicability to other highly diverse, low abundance organisms.

Bacterial sepsis triggers stronger transcriptomic immune responses in larger primates

Empirical data relating body mass to immune defence against infections remain limited. Although the metabolic theory of ecology predicts that larger organisms would have weaker immune responses, recent studies have suggested that the opposite may be true. These discoveries have led to the safety factor hypothesis, which proposes that larger organisms have evolved stronger immune defences because they carry greater risks of exposure to pathogens and parasites. In this study, we simulated sepsis by exposing blood from nine primate species to a bacterial lipopolysaccharide (LPS), measured the relative expression of immune and other genes using RNAseq, and fitted phylogenetic models to determine how gene expression was related to body mass. In contrast to non-immune-annotated genes, we discovered hypermetric scaling in the LPS-induced expression of innate immune genes, such that large primates had a disproportionately greater increase in gene expression of immune genes compared to small primates. Hypermetric immune gene expression appears to support the safety factor hypothesis, though this pattern may represent a balanced evolutionary mechanism to compensate for lower per-transcript immunological effectiveness. This study contributes to the growing body of immune allometry research, highlighting its importance in understanding the complex interplay between body size and immunity over evolutionary timescales.

Functional similarity affects similarity in partner composition in flea-mammal networks

Functional signal in an interaction network is a phenomenon in which species resembling each other in their traits interact with similar partners. We tested the functional signal concept in realm-specific and regional flea-host networks from four biogeographic realms and asked whether the species composition of (a) host spectra and (b) flea assemblages is similar between functionally similar flea and host species, respectively. Analogously to testing for phylogenetic signal, we applied Mantel tests to investigate the correlation between flea or host functional distances calculated from functional dendrograms and dissimilarities in sets of interacting partners. In all realm-specific networks, functionally similar fleas tended to exploit similar hosts often belonging to the same genus, whereas functionally similar hosts tended to harbour similar fleas, again often belonging to the same genus. The strength of realm-specific functional signals and the frequency of detecting a significant functional signal in the regional networks differed between realms. The frequency of detecting a significant functional signal in the regional networks correlated positively with the network size for fleas and with the number of hosts in a network for hosts. A functional signal in the regional networks was more frequently found for hosts than for fleas. We discuss the mechanisms behind the functional signal in both fleas and their hosts, relate geographic functional signal patterns to the historic biogeography of fleas and conclude that functional signals in the species composition of host spectra for fleas and of flea assemblages for hosts result from the interplay of evolutionary and ecological processes.

Shared Features Underlying Compact Genomes and Extreme Habitat Use in Chironomid Midges

Nonbiting midges (family Chironomidae) are found throughout the world in a diverse array of aquatic and terrestrial habitats, can often tolerate harsh conditions such as hypoxia or desiccation, and have consistently compact genomes. Yet we know little about the shared molecular basis for these attributes and how they have evolved across the family. Here, we address these questions by first creating high-quality, annotated reference assemblies for Tanytarsus gracilentus (subfamily Chironominae, tribe Tanytarsini) and Parochlus steinenii (subfamily Podonominae). Using these and other publicly available assemblies, we created a time-calibrated phylogenomic tree for family Chironomidae with outgroups from order Diptera. We used this phylogeny to test for features associated with compact genomes, as well as examining patterns of gene family evolution and positive selection that may underlie chironomid habitat tolerances. Our results suggest that compact genomes evolved in the common ancestor of Chironomidae and Ceratopogonidae and that this occurred mainly through reductions in noncoding regions (introns, intergenic sequences, and repeat elements). Significantly expanded gene families in Chironomidae included biological processes that may relate to tolerance of stressful environments, such as temperature homeostasis, carbohydrate transport, melanization defense response, and trehalose transport. We identified several positively selected genes in Chironomidae, notably sulfonylurea receptor, CREB-binding protein, and protein kinase D. Our results improve our understanding of the evolution of small genomes and extreme habitat use in this widely distributed group.

Dorsal and Ventral Plumage Coloration Evolve as Distinct Modules with Different Environmental Correlations

AbstractMany animals exhibit contrast between their dorsal coloration and their ventral coloration. If selection acts differently on dorsal versus ventral coloration, ancestral covariance between these traits should break down, eventually leading to independent modules of trait evolution. Here, we compare the evolution of feather color across body regions for a clade of Australasian songbirds (Meliphagoidea). We find evidence for three modules of covarying color regions. Among these modules, ventral feathers evolve with high lability, evolving at three times the rate of dorsal plumage and 20 times the rate of flight feathers. While both dorsal plumage and ventral plumage are darker in areas with more precipitation and vegetation, we find that dorsal plumage is twice as similar to colors in satellite photos of background substrates. Overall, differential selection on ventral and dorsal colors likely maintains these as distinct modules over evolutionary timescales-a novel explanation for dorsoventral contrast in pigmentation.

Heat and desiccation tolerances predict bee abundance under climate change

Climate change could pose an urgent threat to pollinators, with critical ecological and economic consequences. However, for most insect pollinator species, we lack the long-term data and mechanistic evidence that are necessary to identify climate-driven declines and predict future trends. Here we document 16 years of abundance patterns for a hyper-diverse bee assemblage1 in a warming and drying region2, link bee declines with experimentally determined heat and desiccation tolerances, and use climate sensitivity models to project bee communities into the future. Aridity strongly predicted bee abundance for 71% of 665 bee populations (species × ecosystem combinations). Bee taxa that best tolerated heat and desiccation increased the most over time. Models forecasted declines for 46% of species and predicted more homogeneous communities dominated by drought-tolerant taxa, even while total bee abundance may remain unchanged. Such community reordering could reduce pollination services, because diverse bee assemblages typically maximize pollination for plant communities3. Larger-bodied bees also dominated under intermediate to high aridity, identifying body size as a valuable trait for understanding how climate-driven shifts in bee communities influence pollination4. We provide evidence that climate change directly threatens bee diversity, indicating that bee conservation efforts should account for the stress of aridity on bee physiology.

Convergent genomic signatures associated with vertebrate viviparity

BACKGROUND

Viviparity-live birth-is a complex and innovative mode of reproduction that has evolved repeatedly across the vertebrate Tree of Life. Viviparous species exhibit remarkable levels of reproductive diversity, both in the amount of care provided by the parent during gestation, and the ways in which that care is delivered. The genetic basis of viviparity has garnered increasing interest over recent years; however, such studies are often undertaken on small evolutionary timelines, and thus are not able to address changes occurring on a broader scale. Using whole genome data, we investigated the molecular basis of this innovation across the diversity of vertebrates to answer a long held question in evolutionary biology: is the evolution of convergent traits driven by convergent genomic changes?

RESULTS

We reveal convergent changes in protein family sizes, protein-coding regions, introns, and untranslated regions (UTRs) in a number of distantly related viviparous lineages. Specifically, we identify 15 protein families showing evidence of contraction or expansion associated with viviparity. We additionally identify elevated substitution rates in both coding and noncoding sequences in several viviparous lineages. However, we did not find any convergent changes-be it at the nucleotide or protein level-common to all viviparous lineages.

CONCLUSIONS

Our results highlight the value of macroevolutionary comparative genomics in determining the genomic basis of complex evolutionary transitions. While we identify a number of convergent genomic changes that may be associated with the evolution of viviparity in vertebrates, there does not appear to be a convergent molecular signature shared by all viviparous vertebrates. Ultimately, our findings indicate that a complex trait such as viviparity likely evolves with changes occurring in multiple different pathways.

Resource adaptation drives the size-complexity rule in termites

The size-complexity rule posits that the evolution of larger cooperative groups should favour more division of labour. Examples include more cell types in larger multicellular organisms, and more polymorphic castes in larger eusocial colonies. However, a correlation between division of labour and group size may reflect a shared response of both traits to resource availability and/or profitability. Here, this possibility was addressed by investigating the evolution of sterile caste number (worker and soldier morphotypes) in termites, a major clade of eusocial insects in which the drivers of caste polymorphism are poorly understood. A novel dataset on 90 termite species was compiled from the published literature. The analysis showed that sterile caste number did increase markedly with colony size. However, after controlling for resource adaptations and phylogeny, there was no evidence for this relationship. Rather, sterile caste number increased with increasing nest-food separation and decreased with soil-feeding, through changes in worker (but not soldier) morphotype number. Further, colony size increased with nest-food separation, thus driving the false correlation between sterile caste number and colony size. These findings support adaptation to higher energy acquisition as key to the rise of complex insect societies, with larger size being a by-product.

Seasonally increasing parasite load is associated with microbiome dysbiosis in wild bumblebees

The microbiome is increasingly recognized for its complex relationship with host fitness. Bumblebees are host to a characteristic gut microbiome community that is derived and reinforced through social contact between individuals. The bumblebee microbiome is species-poor, and primarily composed from a small number of core taxa that are associated with the greater tribe of corbiculate bees. Experimental findings support a role for the core bumblebee microbiome in resistance to severe infections by a common trypanosomal parasite, Crithidia bombi. However, most studies have been small in scale, often considering just one or two bumblebee species, or making use of commercially-reared bees. To better understand the microbiome diversity of wild populations, we have deeply sampled field populations of ten sympatric species found throughout central and down east Maine in a three-year microbiome field survey. We have used 16S amplicon sequencing to produce microbiome community profiles, and qPCR to screen samples for infections by Crithidia bombi. The breadth of our dataset has enabled us to test for seasonal and interspecific trends in the microbiome community. Controlling for these external sources of variation, we have identified microbial factors associated with infection and parasite load that support the role of the core microbiome in resistance to severe infection.

Phylogeny more than plant height and leaf area explains variance in seed mass

Although variation in seed mass can be attributed to other plant functional traits such as plant height, leaf size, genome size, growth form, leaf N and phylogeny, until now, there has been little information on the relative contributions of these factors to variation in seed mass. We compiled data consisting of 1071 vascular plant species from the literature to quantify the relationships between seed mass, explanatory variables and phylogeny. Strong phylogenetic signals of these explanatory variables reflected inherited ancestral traits of the plant species. Without controlling phylogeny, growth form and leaf N are associated with seed mass. However, this association disappeared when accounting for phylogeny. Plant height, leaf area, and genome size showed consistent positive relationship with seed mass irrespective of phylogeny. Using phylogenetic partial R2s model, phylogeny explained 50.89% of the variance in seed mass, much more than plant height, leaf area, genome size, leaf N, and growth form explaining only 7.39%, 0.58%, 1.85%, 0.06% and 0.09%, respectively. Therefore, future ecological work investigating the evolution of seed size should be cautious given that phylogeny is the best overall predictor for seed mass. Our study provides a novel avenue for clarifying variation in functional traits across plant species, improving our better understanding of global patterns in plant traits.

Squamate metabolic rates decrease in winter beyond the effect of temperature

The reptilian form of hibernation (brumation) is much less studied than its mammalian and insect equivalents. Hibernation and brumation share some basic features but may differ in others. Evidence for hypometabolism in brumating reptiles beyond the effect of temperature is sporadic and often ignored. We calculated the standard metabolic rates (SMR, oxygen uptake during inactivity), in winter and/or summer, of 156 individuals representing 59 species of Israeli squamates across all 17 local families. For 32 species, we measured the same individuals during both seasons. We measured gas exchange continuously in a dark metabolic chamber, under the average January high and low temperatures (20°C and 12°C), during daytime and nighttime. We examined how SMR changes with season, biome, body size, temperature and time of day, using phylogenetic mixed models. Metabolic rates increased at sunrise in the diurnal species, despite no light or other external cues, while in nocturnal species the metabolic rates did not increase. Cathemeral species shifted from a diurnal-like diel pattern in winter to a nocturnal-like pattern in summer. Regardless of season, Mediterranean species SMRs were 30% higher than similar-sized desert species. Summer SMR of all species together scaled with body size with an exponent of 0.84 but dropped to 0.71 during brumation. Individuals measured during both seasons decreased their SMR between summer and winter by a 47%, on average, at 20°C and by 70% at 12°C. Q10 was 1.75 times higher in winter than in summer, possibly indicating an active suppression of metabolic processes under cold temperatures. Our results challenge the commonly held perception that squamate physiology is mainly shaped by temperature, with little role for intrinsic metabolic regulation. The patterns we describe indicate that seasonal, diel and geographic factors can trigger remarkable shifts in metabolism across squamate species.

Linking physiology and climate to infer species distributions in Australian skinks

Climate has a key impact on animal physiology, which in turn can have a profound influence on geographic distributions. Yet, the mechanisms linking climate, physiology and distribution are not fully resolved. Using an integrative framework, we tested the predictions of the climatic variability hypothesis (CVH), which states that species with broader distributions have broader physiological tolerance than range-restricted species, in a group of Lampropholis skinks (8 species, 196 individuals) along a latitudinal gradient in eastern Australia. We investigated several physiological aspects including metabolism, water balance, thermal physiology, thermoregulatory behaviour and ecological performance. Additionally, to test whether organismal information (e.g. behaviour and physiology) can enhance distribution models, hence providing evidence that physiology and climate interact to shape range sizes, we tested whether species distribution models incorporating physiology better predict the range sizes than models using solely climatic layers. In agreement with the CVH, our results confirm that widespread species can tolerate and perform better at broader temperature ranges than range-restricted species. We also found differences in field body temperatures, but not thermal preference, between widespread and range-restricted species. However, metabolism and water balance did not correlate with range size. Biophysical modelling revealed that the incorporation of physiological and behavioural data improves predictions of Lampropholis distributions compared with models based solely on macroclimatic inputs, but mainly for range-restricted species. By integrating several aspects of the physiology and niche modelling of a group of ectothermic animals, our study provides evidence that physiology correlates with species distributions. Physiological responses to climate are central in establishing geographic ranges of skinks, and the incorporation of processes occurring at local scales (e.g. behaviour) can improve species distribution models.

Trade-offs in non-native plant herbivore defences enhance performance

Non-native plants are typically released from specialist enemies but continue to be attacked by generalists, albeit at lower intensities. This reduced herbivory may lead to less investment in constitutive defences and greater investment in induced defences, potentially reducing defence costs. We compared herbivory on 27 non-native and 59 native species in the field and conducted bioassays and chemical analyses on 12 pairs of non-native and native congeners. Non-natives suffered less damage and had weaker constitutive defences, but stronger induced defences than natives. For non-natives, the strength of constitutive defences was correlated with the intensity of herbivory experienced, whereas induced defences showed the reverse. Investment in induced defences correlated positively with growth, suggesting a novel mechanism for the evolution of increased competitive ability. To our knowledge, these are the first linkages reported among trade-offs in plant defences related to the intensity of herbivory, allocation to constitutive versus induced defences, and growth.

Weather anomalies more important than climate means in driving insect phenology

Studies of long-term trends in phenology often rely on climatic averages or accumulated heat, overlooking climate variability. Here we test the hypothesis that unusual weather conditions are critical in driving adult insect phenology. First, we generate phenological estimates for Lepidoptera (moths and butterflies) across the Eastern USA, and over a 70 year period, using natural history collections data. Next, we assemble a set of predictors, including the number of unusually warm and cold days prior to, and during, the adult flight period. We then use phylogenetically informed linear mixed effects models to evaluate effects of unusual weather events, climate context, species traits, and their interactions on flight onset, offset and duration. We find increasing numbers of both warm and cold days were strong effects, dramatically increasing flight duration. This strong effect on duration is likely driven by differential onset and termination dynamics. For flight onset, impact of unusual climate conditions is dependent on climatic context, but for flight cessation, more unusually cold days always lead to later termination particularly for multivoltine species. These results show that understanding phenological responses under global change must account for unusual weather events, especially given they are predicted to increase in frequency and severity.

Vulnerability to climate change increases with trophic level in terrestrial organisms

The resilience of ecosystem function under global climate change is governed by individual species vulnerabilities and the functional groups they contribute to (e.g. decomposition, primary production, pollination, primary, secondary and tertiary consumption). Yet it remains unclear whether species that contribute to different functional groups, which underpin ecosystem function, differ in their vulnerability to climate change. We used existing upper thermal limit data across a range of terrestrial species (N = 1701) to calculate species warming margins (degrees distance between a species upper thermal limit and the maximum environmental temperature they inhabit), as a metric of climate change vulnerability. We examined whether species that comprise different functional groups exhibit differential vulnerability to climate change, and if vulnerability trends change across geographic space while considering evolutionary history. Primary producers had the broadest warming margins across the globe (μ = 18.72 °C) and tertiary consumers had the narrowest warming margins (μ = 9.64 °C), where vulnerability tended to increase with trophic level. Warming margins had a nonlinear relationship (second-degree polynomial) with absolute latitude, where warming margins were narrowest at about 33°, and were broader at lower and higher absolute latitudes. Evolutionary history explained significant variation in species warming margins, as did the methodology used to estimate species upper thermal limits. We investigated if variation in body mass across the trophic levels could explain why higher trophic level organisms had narrower warming margins than lower trophic level organisms, however, we did not find support for this hypothesis. This study provides a critical first step in linking individual species vulnerabilities with whole ecosystem responses to climate change.

Can sociality facilitate learning of complex tasks? Lessons from bees and flowers

The emergence of animal societies is a major evolutionary transition, but its implications for learning-dependent innovations are insufficiently understood. Bees, with lifestyles ranging from solitary to eusocial, are ideal models for exploring social evolution. Here, we ask how and why bees may acquire a new 'technology', foraging on morphologically complex flowers, and whether eusociality facilitates this technological shift. We consider 'complex' flowers that produce high food rewards but are difficult to access, versus 'simple' flowers offering easily accessible yet lower rewards. Complex flowers are less profitable than simple flowers to naive bees but become more rewarding after a learning period. We model how social bees optimally choose between simple and complex flowers over time, to maximize their colony's food balance. The model predicts no effect of colony size on the bees' flower choices. More foraging on complex flowers is predicted as colony longevity, its proportion of foragers, individual longevity and learning ability increase. Of these traits, only long-lived colonies and abundant foragers characterize eusocial bees. Thus, we predict that eusociality supports, but is not mandatory for, learning to exploit complex flowers. A re-analysis of a large published dataset of bee-flower interactions supports these conclusions. We discuss parallels between the evolution of insect sociality and other major transitions that provide scaffolds for learning innovations. This article is part of the theme issue 'Human socio-cultural evolution in light of evolutionary transitions'.

Susceptibility to Predation Varies with Body Mass, Foraging Niche, and Anti-Predator Responses among Bird Species

Predation is a major source of mortality for many avian species. Species that face more predators, and those with less effective anti-predator responses, are presumably more likely to die from predation over time. Predation rate, as a measure of susceptibility to predation, is difficult to measure in the field. Radio-tracking studies, however, allow researchers to determine the time and cause of death of marked individuals, making it possible to estimate predation rate. I used estimates of predation rates from a large number of published radio-tracking studies in birds to assess in a phylogenetic framework the effect of several potential determinants. I obtained 393 estimates of predation rates from 129 species. Predation rates were lower in areas with fewer predators, such as islands and aquatic habitats, and for species with fewer potential predators, such as larger species. The predation rate was also lower for prey species with effective anti-predator responses, such as those that forage in flocks. Radio-tracking studies provide a unique opportunity to estimate overall predation rate in the field. Broadening the range of species and the range of habitats involved in such studies will help to further elucidate the factors that affect susceptibility to predation.

Tree mycorrhizal association types control biodiversity-productivity relationship in a subtropical forest

Mycorrhizae are symbiotic associations between terrestrial plants and fungi in which fungi obtain nutrients in exchange for plant photosynthates. However, it remains unclear how different types of mycorrhizae affect their host interactions and productivity. Using a long-term experiment with a diversity gradient of arbuscular (AM) and ectomycorrhizal (EcM) tree species, we show that the type of mycorrhizae critically controls the effect of diversity on productivity. With increasing diversity, the net primary production of AM trees increased, but EcM trees decreased, largely because AM trees are more effective in acquiring nitrogen and phosphorus. Specifically, with diversity increase, AM trees enhance both nutrient resorption and litter decomposition, while there was a trade-off between litter decomposability and nutrient resorption in EcM trees. These results provide a mechanistic understanding of why AM trees using a different nutrient acquisition strategy from EcM trees can dominate in subtropical forests and at the same time their diversity enhances productivity.

Phylogenetic diversity of eastern Asia-eastern North America disjunct plants is mainly associated with divergence time

The underlying causes of biodiversity disparities among geographic regions have long been a fundamental theme in ecology and evolution. However, the patterns of phylogenetic diversity (PD) and phylogenetic beta diversity (PBD) of congeners that are disjunctly distributed between eastern Asia-eastern North America (EA-ENA disjuncts) and their associated factors remain unknown. Here we investigated the standardized effect size of PD (SES-PD), PBD, and potentially associated factors in 11 natural mixed forest sites (five in EA and six in ENA) where abundant EA-ENA disjuncts occur. We found that the disjuncts in ENA possessed higher SES-PD than those in EA at the continental scale (1.96 vs -1.12), even though the number of disjunct species in ENA is much lower than in EA (128 vs 263). SES-PD of the EA-ENA disjuncts tended to decrease with increasing latitude in 11 sites. The latitudinal diversity gradient of SES-PD was stronger in EA sites than in ENA sites. Based on the unweighted unique fraction metric (UniFrac) distance and the phylogenetic community dissimilarity, PBD showed that the two northern sites in EA were more similar to the six-site ENA group than to the remaining southern EA sites. Based on the standardized effect size of mean pairwise distances (SES-MPD), nine of eleven studied sites showed a neutral community structure (-1.96 ≤ SES-MPD ≤ 1.96). Both Pearson's r and structural equation modeling suggested that SES-PD of the EA-ENA disjuncts was mostly associated with mean divergence time. Moreover, SES-PD of the EA-ENA disjuncts was positively correlated with temperature-related climatic factors, although negatively correlated with mean diversification rate and community structure. By applying approaches from phylogenetics and community ecology, our work sheds light on historical patterns of the EA-ENA disjunction and paves the way for further research.

Functional traits mediate individualistic species-environment distributions at broad spatial scales while fine-scale species associations remain unpredictable

PREMISE

Numerous processes influence plant distributions and co-occurrence patterns, including ecological sorting, limiting similarity, and stochastic effects. To discriminate among these processes and determine the spatial scales at which they operate, we investigated how functional traits and phylogenetic relatedness influence the distribution of temperate forest herbs.

METHODS

We surveyed understory plant communities across 257 forest stands in Wisconsin and Michigan (USA) and applied Bayesian phylogenetic linear mixed-effects models (PGLMMs) to quantify how functional traits and phylogenetic relatedness influence the environmental distribution of 139 herbaceous plant species along broad edaphic, climatic, and light gradients. These models also allowed us to test how functional and phylogenetic similarity affect species co-occurrence within microsites.

RESULTS

Leaf height, specific leaf area, and seed mass all influenced individualistic plant distributions along landscape-scale gradients in soil texture, soil fertility, light availability, and climate. In contrast, phylogenetic relationships did not consistently predict species-environment relationships. Neither functionally similar nor phylogenetically related herbs segregated among microsites within forest stands.

CONCLUSIONS

Trait-mediated ecological sorting appears to drive temperate-forest community assembly, generating individualistic plant distributions along regional environmental gradients. This finding links classic studies in plant ecology and prior research in plant physiological ecology to current trait-based approaches in community ecology. However, our results fail to support the common assumption that limiting similarity governs local plant co-occurrences. Strong ecological sorting among forest stands coupled with stochastic fine-scale interactions among species appear to weaken deterministic, niche-based assembly processes at local scales.

Thermal adaptation best explains Bergmann's and Allen's Rules across ecologically diverse shorebirds

Bergmann's and Allen's rules state that endotherms should be larger and have shorter appendages in cooler climates. However, the drivers of these rules are not clear. Both rules could be explained by adaptation for improved thermoregulation, including plastic responses to temperature in early life. Non-thermal explanations are also plausible as climate impacts other factors that influence size and shape, including starvation risk, predation risk, and foraging ecology. We assess the potential drivers of Bergmann's and Allen's rules in 30 shorebird species using extensive field data (>200,000 observations). We show birds in hot, tropical northern Australia have longer bills and smaller bodies than conspecifics in temperate, southern Australia, conforming with both ecogeographical rules. This pattern is consistent across ecologically diverse species, including migratory birds that spend early life in the Arctic. Our findings best support the hypothesis that thermoregulatory adaptation to warm climates drives latitudinal patterns in shorebird size and shape.

Testing Morphological Relationships Between Female and Male Copulatory Structures in Bats

The lower reproductive tract of female mammals has several competing functions including mating, tract health maintenance, and parturition. Diverse vaginal anatomy suggests interactions between natural and sexual selection, yet despite its importance, female copulatory morphology remains under-studied. We undertook a comparative study across the species-rich mammalian order Chiroptera (bats) with a focus on the suborder Yangochiroptera (Vespertilioniformes) to examine how female vaginal features may have coevolved with male penis morphology to minimize mechanical damage to their tissues during copulation. The penis morphology is diverse, presenting great potential for post-copulatory sexual selection and coevolution with the female morphology, but vaginas have not been carefully examined. Here we test the hypotheses that vaginal thickness and collagen density have coevolved with features of the male penis including the presence of spines and a baculum. We present histological data from females of 24 species from 7 families of bats, and corresponding data on male penis anatomy. We also examine the role of phylogenetic history in the morphological patterns we observe. We found evidence that female vaginal thickness has coevolved with the presence of penile spines, but not with baculum presence or width. Collagen density did not appear to covary with male penile features. Our findings highlight the importance of considering interactions between the sexes in influencing functional reproductive structures and examine how these structures have been under selection in bats.

Small brains predisposed Late Quaternary mammals to extinction

The Late Quaternary witnessed a dramatic wave of large mammal extinctions, that are usually attributed to either human hunting or climatic change. We hypothesized that the large mammals that survived the extinctions might have been endowed with larger brain sizes than their relatives, which could have conferred enhanced behavioral plasticity and the ability to cope with the rapidly changing Late Quaternary environmental conditions. We assembled data on brain sizes of 291 extant mammal species plus 50 more that went extinct during the Late Quaternary. Using logistic, and mixed effect models, and controlling for phylogeny and body mass, we found that large brains were associated with higher probability to survive the Late Quaternary extinctions, and that extant species have brains that are, on average, 53% larger when accounting for order as a random effect, and 83% when fitting a single regression line. Moreover, we found that models that used brain size in addition to body size predicted extinction status better than models that used only body size. We propose that possessing a large brain was an important, yet so far neglected characteristic of surviving megafauna species.

The drivers of avian-haemosporidian prevalence in tropical lowland forests of New Guinea in three dimensions

Haemosporidians are among the most common parasites of birds and often negatively impact host fitness. A multitude of biotic and abiotic factors influence these associations, but the magnitude of these factors can differ by spatial scales (i.e., local, regional and global). Consequently, to better understand global and regional drivers of avian-haemosporidian associations, it is key to investigate these associations at smaller (local) spatial scales. Thus, here, we explore the effect of abiotic variables (e.g., temperature, forest structure, and anthropogenic disturbances) on haemosporidian prevalence and host-parasite networks on a horizontal spatial scale, comparing four fragmented forests and five localities within a continuous forest in Papua New Guinea. Additionally, we investigate if prevalence and host-parasite networks differ between the canopy and the understory (vertical stratification) in one forest patch. We found that the majority of Haemosporidian infections were caused by the genus Haemoproteus and that avian-haemosporidian networks were more specialized in continuous forests. At the community level, only forest greenness was negatively associated with Haemoproteus infections, while the effects of abiotic variables on parasite prevalence differed between bird species. Haemoproteus prevalence levels were significantly higher in the canopy, and an opposite trend was observed for Plasmodium. This implies that birds experience distinct parasite pressures depending on the stratum they inhabit, likely driven by vector community differences. These three-dimensional spatial analyses of avian-haemosporidians at horizontal and vertical scales suggest that the effect of abiotic variables on haemosporidian infections are species specific, so that factors influencing community-level infections are primarily driven by host community composition.

Flower Color as Predictor for Nectar Reward Quantity in an Alpine Flower Community

Entomophilous plants have evolved colorful floral displays to attract flower visitors to achieve pollination. Although many insects possess innate preferences for certain colors, the underlying proximate and ultimate causes for this behavior are still not well understood. It has been hypothesized that the floral rewards, e.g., sugar content, of plants belonging to a particular color category correlate with the preference of the flower visitors. However, this hypothesis has been tested only for a subset of plant communities worldwide. Bumble bees are the most important pollinators in alpine environments and show a strong innate preference for (bee) “UV-blue” and “blue” colors. We surveyed plants visited by bumble bees in the subalpine and alpine zones (&gt;1,400 m a.s.l.) of the Austrian Alps and measured nectar reward and spectral reflectance of the flowers. We found that the majority of the 105 plant samples visited by bumble bees fall into the color categories “blue” and “blue-green” of a bee-specific color space. Our study shows that color category is only a weak indicator for nectar reward quantity; and due to the high reward variance within and between categories, we do not consider floral color as a reliable signal for bumble bees in the surveyed habitat. Nevertheless, since mean floral reward quantity differs between categories, naïve bumble bees may benefit from visiting flowers that fall into the innately preferred color category during their first foraging flights.

Face mask-wear did not affect large-scale patterns in escape and alertness of urban and rural birds during the COVID-19 pandemic

Actions taken against the COVID-19 pandemic have dramatically affected many aspects of human activity, giving us a unique opportunity to study how wildlife responds to the human-induced rapid environmental changes. The wearing of face masks, widely adopted to prevent pathogen transmission, represents a novel element in many parts of the world where wearing a face mask was rare before the COVID-19 outbreak. During September 2020-March 2021, we conducted large-scale multi-species field experiments to evaluate whether face mask-use in public places elicits a behavioural response in birds by comparing their escape and alert responses when approached by a researcher with or without a face mask in four European countries (Czech Republic, Finland, Hungary, and Poland) and Israel. We also tested whether these patterns differed between urban and rural sites. We employed Bayesian generalized linear mixed models (with phylogeny and site as random factors) controlling for a suite of covariates and found no association between the face mask-wear and flight initiation distance, alert distance, and fly-away distance, respectively, neither in urban nor in rural birds. However, we found that all three distances were strongly and consistently associated with habitat type and starting distance, with birds showing earlier escape and alert behaviour and longer distances fled when approached in rural than in urban habitats and from longer initial distances. Our results indicate that wearing face masks did not trigger observable changes in antipredator behaviour across the Western Palearctic birds, and our data did not support the role of habituation in explaining this pattern.

Climate drivers of adult insect activity are conditioned by life history traits

Insect phenological lability is key for determining which species will adapt under environmental change. However, little is known about when adult insect activity terminates and overall activity duration. We used community-science and museum specimen data to investigate the effects of climate and urbanisation on timing of adult insect activity for 101 species varying in life history traits. We found detritivores and species with aquatic larval stages extend activity periods most rapidly in response to increasing regional temperature. Conversely, species with subterranean larval stages have relatively constant durations regardless of regional temperature. Species extended their period of adult activity similarly in warmer conditions regardless of voltinism classification. Longer adult durations may represent a general response to warming, but voltinism data in subtropical environments are likely underreported. This effort provides a framework to address the drivers of adult insect phenology at continental scales and a basis for predicting species response to environmental change.