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Understanding the causes and consequences of population phenotypic divergence is a central goal in ecology and evolution. Phenotypic divergence among populations can result from genetic divergence, phenotypic plasticity or a combination of the two. However, few studies have deciphered these mechanisms for populations geographically close and connected by gene flow, especially in the case of personality traits. In this study, we used a common garden experiment to explore the genetic basis of the phenotypic divergence observed between two blue tit (Cyanistes caeruleus) populations inhabiting contrasting habitats separated by 25 km, for two personality traits (exploration speed and handling aggression), one physiological trait (heart rate during restraint) and two morphological traits (tarsus length and body mass). Blue tit nestlings were removed from their population and raised in a common garden for up to five years. We then compared adult phenotypes between the two populations, as well as trait-specific Qst and Fst . Our results revealed differences between populations similar to those found in the wild, suggesting a genetic divergence for all traits. Qst - Fst comparisons revealed that the traits divergences likely result from dissimilar selection patterns rather than from genetic drift. Our study is one of the first to report a Qst - Fst comparison for personality traits and adds to the growing body of evidence that population genetic divergence is possible at a small scale for a variety of traits including behavioural traits. Data filesArchive.zip

Changes in ocean ventilation driven by climate change result in loss of oxygen in the open ocean that, in turn, affects coastal areas in upwelling zones such as the northeast Pacific. Saanich Inlet, on the west coast of Canada, is a natural seasonally hypoxic fjord where certain continental shelf species occur in extreme hypoxia. One study site on the VENUS cabled subsea network is located in the hypoxic zone at 104 m depth. Photographs of the same 5 m2 area were taken with a remotely-controlled still camera every 2/3 days between October 6th 2009 and October 18th 2010 and examined for community composition, species behaviour and microbial mat features. Instruments located on a near-by platform provided high-resolution measurements of environmental variables. We applied multivariate ordination methods and a principal coordinate analysis of neighbour matrices to determine temporal structures in our dataset. Responses to seasonal hypoxia (0.1–1.27 ml/l) and its high variability on short time-scale (hours) varied among species, and their life stages. During extreme hypoxia, microbial mats developed then disappeared as a hippolytid shrimp, Spirontocaris sica, appeared in high densities (200 m22) despite oxygen below 0.2 ml/l. The slender sole Lyopsetta exilis was abundant in severe hypoxia and diminished as oxygen increased in the summer. This planktivore may be responding to changes in the depth of the diurnal migration of zooplankton. While the squat lobster Munida quadrispina was common at all times, juveniles disappeared in fluctuating conditions. Despite low oxygen conditions, animal densities were high indicating that the risk from hypoxia is balanced by factors such as food availability and escape from less tolerant predators. As hypoxia increases on the continental shelf, we expect benthic communities to become dominated by low diversity, hypoxia-tolerant species of low commercial significance. CHONe_MB08_Matabos_data_year

Darwin’s theory of sexual selection by female choice has become a standard explanation for exaggerated sexually dimorphic traits, such as the peacock’s (Pavo cristatus) long tail. Eyespot beauty-based female choice requires genetic variation in female preference and the number of eyespots, as well as a genetic correlation between the two. However, little genetic variation has been documented in either of these traits in natural and feral peacock populations. We examined the anatomical plan underlying feather development and discovered that eyespot feather follicles originate in alternating rows of 10/11, which uniquely determines the train’s feather complexity, bilateral symmetry, and eyespot arrangement and beauty. This pattern precludes intrinsic variation in eyespot number, resulting in a fixed number of total eyespots in fully mature individuals. Since number of eyespots and tail length are independent traits and function of the age of the animal, the only variation available in these trats is also function of age. We propose an alternate, male drive, hypothesis in which females choose males based on their overall dominance (size, vigour, call, courting), and beauty of the train may (or may not) be a factor in female choice but it cannot affect the train length. This hypothesis can explain all known results. Missing data values (indicated by "-" sign) are due to poor quality of the specimen. Collected from museum specimens of peacock's tail.

Seed dispersal is a key process driving the structure, composition, and regeneration of tropical forests. Larger frugivores play a crucial role in community structuring by dispersing large seeds not dispersed by smaller frugivores. We assessed the hypothesis that brown howler monkeys (Alouatta guariba clamitans) provide seed dispersal services for a wide assemblage of plant species in both small and large Atlantic forest fragments. Although fruit availability often decreases in small fragments compared with large ones, we predicted that brown howlers are efficient seed dispersers in quantitative and qualitative terms in both forest types given their high dietary flexibility. After a 36-month study period and 2,962 sampling hours, we found that howlers swallowed and defecated intact the vast majority of seeds (96%-100%) they handled in all study sites. Overall, they defecated ca. 315,600 seeds belonging to 98 species distributed in eight growth forms. We estimated that each individual howler dispersed an average of 143 (SD = 49) seeds >2 mm per day or 52,052 (SD = 17,782) seeds per year. They dispersed seeds of 58% to 93% of the local assemblages of fleshy-fruit trees. In most cases, the richness and abundance of seed species dispersed was similar between small and large fragments. However, groups inhabiting small fragments tended to disperse a higher diversity of seeds from rarely consumed fruits than those living in large fragments. We conclude that brown howlers are legitimate seed dispersers for most fleshy-fruit species of the angiosperm assemblages of their habitats, and that they might favor the regeneration of Atlantic forest fragments with the plentiful amount of intact seeds that they disperse each year. Dataset_seeds_dispersedHere we provided data on seed dispersal by six wild groups of brown howler monkeys (Alouatta guariba clamitans). This research was conducted during a 36-month period in three small (<10 ha: S1, S2, and S3) and three large (>90 ha: L1,L2, and L3) Atlantic forest fragments in Rio Grande do Sul State, southern Brazil.Dataset_seed_handlingHere we provided data on seed/fruit handling by six wild groups of brown howler monkeys (Alouatta guariba clamitans). This research was conducted during a 36-month period in three small (<10 ha: S1, S2, and S3) and three large (>90 ha: L1,L2, and L3) Atlantic forest fragments in Rio Grande do Sul State, southern Brazil.

Study area The study area included 40 farms distributed along a gradient of agricultural intensification covering approximately 10,200 km2 in southern Québec, Canada. Three land cover types dominated the study system: low-intensity agricultural fields (i.e. hay, alfalfa (Medicago sativa), clover (Trifolium spp.), and pastures, henceforth referred to as “forage crops”), intensive agricultural fields (i.e., annual row crops mainly composed of corn (Zea mays), soybean (Glycine max), and wheat (Triticum spp.)) and forest. Each farm included 10 identical nest boxes mostly arranged in a row along field margins and separated by at least 50 meters to limit intra and interspecific competition (see Ghilain and Bélisle 2008 for further details on the study system). A Thermochron iButton device was fixed on the outside of one nest box on each farm to record hourly ambient temperature (model DS1922L; Embedded Data Systems, Lawrenceburg, Kentucky, USA). A pluviometer collected precipitation data (millimeters of rainfall) on each farm. We used the mean daily temperature and mean daily rainfall between May 1 and May 15 to characterize spring climate. Nest monitoring We monitored nest boxes every other day from 2009 to 2018 starting in the first week of May. We recorded the occurrence of nest materials, the laying date (first egg), and the number of eggs, hatchlings and fledglings. Monitoring ended when all nestlings had fledged on a given farm, which occurred between June 15 and August 5 during the study. Nest boxes were cleared of any nest material and/or dead nestlings every year in October. Preference Preference for each nest box was estimated for each year according to the occurrence of a laying event (at least one egg laid) and settlement date (Julian date at which nesting material was first observed). Because some early settlement dates were left-censored given that some boxes already contained nest material at the first visit (45% of all boxes), settlement dates were classified as either “early” or “late” with respect to the annual median settlement date. The category “early” included boxes with settlement dates preceding or equal to the annual median, which comprised nearly all (91.3%) left-censored dates. Overall, the average difference between the annual mean settlement dates categorized as “early” and “late” was 10.4 ± 2.9 days (mean ± SD). Nest boxes occupied by other species were excluded from analyses (N = 964 boxes between 2009 and 2018). Such exclusions were made possible, even in the absence of a laying event, because the material and shape of nests are very species specific. We are thus confident that the vast majority of nests included in the study were initiated by tree swallows. The ordinal preference variable featured three categories: 1: No laying event 2: Laying event and late settlement 3: Laying event and early settlement Habitat quality We used two proxies of reproductive success: (1) the number of hatchlings produced in a nest box and (2) the proportion of hatchlings that successfully fledged in a nestbox (i.e., fledging success). Landscape context We characterized landscape habitat composition by measuring the relative cover of forest, perennial forage crops, as well as of water bodies and wetlands, within radii of respectively 100 m, 5 km and 10 km. We assessed landscape habitat composition up to the 500-m scale on a yearly basis in the field by visually identifying cultures and marginal habitats and delineating them using orthophotos (1:40,000). Characterization beyond the 500-m scale was based on a mosaic of yearly georeferenced classified optical and radar satellite images taken between 2011 and 2018 (pixel resolution 30 m × 30 m; Agriculture and Agri-Food Canada (AAFC) 2018). Only the year 2018 was used to assess water cover at the above range of scales because it showed better accuracy than the data of previous years (AAFC, 2020), and because the cover of large water bodies, as those covered by the data we used, did not vary significantly across years (e.g., median between-year correlation of yearly water cover between 2011 and 2018 was 0.90 at the 10-km scale). Food availability Two passive insect traps were installed on each farm around the first and second third of the nest box transect. Traps consisted of ~4-L yellow buckets placed 1.5 m above ground. They were filled with ~2 L of salty detergent solution to reduce surface tension and slow the growth of bacteria and fungi. Two transparent plexiglass screens were mounted perpendicularly to one another above each bucket to intercept flying insects (see Bellavance et al. 2018 and Garrett et al. 2021a for details). We collected the content of each trap on every visit to a farm (i.e., every other day) and conserved arthropods in 70% ethanol until processing. We sorted samples by removing arthropods unlikely to be preyed upon by tree swallows (i.e., bumble bees (Bombus spp.: Hymenoptera), June bugs (Phyllophaga spp.: Coleoptera), large spiders (Araneae, > 0.5 cm body width), and caterpillars (Lepidoptera); Bellavance et al. 2018). The rest of the sample was dried at 50ºC for at least 48 hours before being weighed (Adam Equipment, model AAA250L, ± 0.0001 g). The mean daily dry biomass of arthropods collected between May 1 and May 15 was used as a proxy of yearly food availability on a given farm at the time of nest site selection. Heterospecific social information House sparrows (Passer domesticus) are tree swallow’s main nest-site competitors in our system and they initiate breeding before swallows return from their wintering grounds (Robillard, Garant and Bélisle, 2013). We evaluated the use of heterospecific social information through the number of nest boxes occupied by house sparrows on each farm in the current year. Nest boxes and house sparrow nests were visited every other day concurrently to tree swallow monitoring. Occupancy was determined by the presence of at least one egg, and only first clutches observed in each box were included since a nest box is rarely used by another species once house sparrows have built a nest therein. Conspecific social information We defined two sources of social information regarding the future breeding success that an individual could expect to experience on a given farm: the density of tree swallows that bred on a farm during the previous year and the mean number of fledglings obtained by those breeders. Animals are expected to select a breeding habitat using cues that should reflect, directly or not, the fitness outcome of the different habitat options. However, human-induced environmental changes can alter the relationships between habitat characteristics and their fitness consequences, leading to maladaptive habitat choices. The most severe case of such nonideal habitat selection is the ecological trap, which occurs when individuals prefer to settle in poor-quality habitats while better ones are available. Here we studied the adaptiveness of nest box selection in a tree swallow (Tachycineta bicolor) population breeding over a 10-year period in a network of 400 nest boxes distributed along a gradient of agricultural intensification in southern Québec, Canada. We first examined the effects of multiple environmental and social habitat characteristics on nest box preference to identify potential settlement cues. We then assessed the links between those cues and habitat quality as defined by the reproductive performance of individuals that settled early or late in nest boxes. We found that tree swallows preferred nesting in open habitats with high cover of perennial forage crops, high spring insect biomass, and high density of house sparrows (Passer domesticus), their main competitors for nest sites. They also preferred nesting where the density of breeders and their mean number of fledglings during the previous year were high. However, we detected mismatches between preference and habitat quality for several environmental variables. The density of competitors and conspecific social information showed severe mismatches, as their relationships to preference and breeding success went in opposite direction under certain circumstances. Spring food availability and agricultural landscape context, while related to preferences, were not related to breeding success. Overall, our study emphasizes the complexity of habitat selection behavior and provides evidence that multiple mechanisms may potentially lead to an ecological trap in farmlands. 

Whole genome sequencing is helping generate robust phylogenetic hypotheses for a range of taxonomic groups that were previously recalcitrant to classical molecular phylogenetic approaches. As a case study, we performed a shallow shotgun sequencing of eight species in the tropical tree family Chrysobalanaceae to retrieve large fragments of high-copy number DNA regions and test the potential of these regions for phylogeny reconstruction. We were able to assemble the nuclear ribosomal cluster (nrDNA), the complete plastid genome (ptDNA) and a large fraction of the mitochondrial genome (mtDNA) with approximately 1000x, 450x and 120x sequencing depth respectively. The phylogenetic tree obtained with ptDNA resolved five of the seven internal nodes. In contrast, the tree obtained with mtDNA and nrDNA data were largely unresolved. This study demonstrates that genome skimming is a cost-effective approach and shows potential in plant molecular systematics within Chrysobalanaceae and other understudied groups. script_chloroUNIX script used for plastid reconstruction. The following tools must be installed: VELVET, PLAST, COPE, OBITOOLSscript_plastid.txtalignmentsPlastid DNA, mitochondrial DNA and nuclear ribosomic regions alignments, including the complete sequences or the non-intronic transcribed sequences only. Alignments were performed using MAFFT and cleaned using Gblocks. Files are in fasta format.treesTrees obtained with plastid DNA, mitochondrial DNA and nuclear ribosomic regions alignments, including the complete sequences or the non-intronic transcribed sequences only, using RAxML and MrBayes. Files are in NEXUS format.chrysobalanaceae_phylogenomic_trees(1).rar

Isodar theory can be used to evaluate fitness consequences of density-dependent habitat selection by animals. A typical habitat isodar is a regression curve plotting competitor densities in two adjacent habitats when individual fitness is equal. Despite the increasing use of habitat isodars, their application remains largely limited to areas composed of pairs of adjacent habitats that are defined a priori. We developed a resampling method that uses data from wildlife surveys to build isodars in heterogeneous landscapes without having to predefine habitat types. The method consists in randomly placing blocks over the survey area and dividing those blocks in two adjacent sub-blocks of the same size. Animal abundance is then estimated within the two sub-blocks. This process is done 100 times. Different functional forms of isodars can be investigated by relating animal abundance and differences in habitat features between sub-blocks. We applied this method to abundance data of raccoons and striped skunks, two of the main hosts of rabies virus in North America. Habitat selection by raccoons and striped skunks depended on both conspecific abundance and the difference in landscape composition and structure between sub-blocks. When conspecific abundance was low, raccoons and striped skunks favored areas with relatively high proportions of forests and anthropogenic features, respectively. Under high conspecific abundance, however, both species preferred areas with rather large corn-forest edge densities and corn field proportions. Based on random sampling techniques, we provide a robust method that is applicable to a broad range of species, including medium- to large-sized mammals with high mobility. The method is sufficiently flexible to incorporate multiple environmental covariates that can reflect key requirements of the focal species. We thus illustrate how isodar theory can be used with wildlife surveys to assess density-dependent habitat selection over large geographic extents. Capture data of raccoons and striped skunks in Montérégie and Estrie regionsCapture data of raccoons and striped skunks during wildlife surveys in Montérégie and Estrie regions, Québec, Canada. These data were used to illustrate the resampling method in the case study. The columns “X_METER” and “Y_METER” are X and Y projected coordinates (in meters) of live-trap locations. The locations were projected into UTM Zone 18N coordinates with NAD 1983 datum.Capture_data_Tardy_et_al.xlsx

Behavioural lateralization – the preferential use of one side of the body or either of the bilateral organs or limbs – has been well documented in many species, in a number of contexts. While the benefits reported are numerous, existing latent variability in the degree of lateralization within and across populations, species and taxa indicates that existing costs may modulate its expression. Few studies have reported changes in the degree of lateralization at the individual level, in response to long-term changes in environmental conditions, but not in response to short-term changes in environmental conditions. Predation is highly variable both temporally and spatially and hence is a good candidate for testing lateralization effects based on short-term changes in environmental conditions. Here, we tested the hypothesis that the degree of behavioural lateralization changes following short-term exposure to different levels of risk. We tested whether wild-caught juvenile damselfish exposed to a high or low background level of risk for 4 days would subsequently differ in their turning bias, a trait that has been linked to predator escape behaviour in fishes. We found that 4 days is enough to induce a difference in the absolute lateralization scores of the fish, with high-risk fish being more strongly lateralized than low-risk fish. Practically, this difference stemmed from decreasing lateralization scores for newly recruiting coral reef fishes that were kept in low-risk environments, with the concurrent maintenance of higher lateralization scores for fish maintained under high-risk conditions. Fish from the high-risk background had higher survival than those from the low-risk background upon release into mesocosms containing reef predators. Our study highlights how early exposure to differential predation risk affects the degree of behavioural lateralization. Given the profound effects of lateralization on many aspects of an animal's life from its ability to discriminate conspecifics to how it forages and interacts during agonistic interactions, predation risk may be a key driver of animal development. Lateralization ms dataFE lat data.xlsx

Cities are the planet’s newest ecosystem and thus provide the opportunity to study community formation directly following major permanent environmental change. The human social and built components of environments can vary widely in different cities, yet it is largely unknown how features of cities covary with the traits of colonizing species despite humans being the ultimate cause of environments and disturbances in cities. We constructed a dataset from open-source data comprised of 13,502 breeding season observations of 213 Passerine species observed in 551 Census-defined urban areas across the United States. We found that as a city became more compact with less sprawl it tended to support more migratory species and species with lower body mass, shorter lifespans, and larger clutches. We also found that species had lower body mass in cities with higher median income, and higher body mass in highly populated cities. Our results highlight the complexity of human-dominated urban ecosystems, where human socioeconomic actions and everyday activities intermix leading to structurally heterogeneous environments that support the colonization of some species over others. Kinnunen_etal_README.txt - Metadata. Citybirds_synthesized_dryad.xlsx - Raw data used for analyses and figures.

The ancient acquisition of the mitochondrion into the ancestor of modern-day eukaryotes is thought to have been pivotal in facilitating the evolution of complex life. Mitochondria retain their own diminutive genome, with mitochondrial genes encoding core subunits involved in oxidative phosphorylation. Traditionally, it was assumed that there was little scope for genetic variation to accumulate and be maintained within the mitochondrial genome. However, in the past decade, mitochondrial genetic variation has been routinely tied to the expression of life-history traits such as fertility, development and longevity. To examine whether these broad-scale effects on life-history trait expression might ultimately find their root in mitochondrially mediated effects on core bioenergetic function, we measured the effects of genetic variation across twelve different mitochondrial haplotypes on respiratory capacity and mitochondrial quantity in the fruit fly, Drosophila melanogaster. We used strains of flies that differed only in their mitochondrial haplotype, and tested each sex separately at two different adult ages. Mitochondrial haplotypes affected both respiratory capacity and mitochondrial quantity. However, these effects were highly context-dependent, with the genetic effects contingent on both the sex and the age of the flies. These sex- and age-specific genetic effects are likely to resonate across the entire organismal life-history, providing insights into how mitochondrial genetic variation may contribute to sex-specific trajectories of life-history evolution. Alstonville_DryadBarcelona_DryadBrownsville_DryadDahomey_DryadHawaii_DryadIsrael_DryadJapan_DryadMadang_DryadMysore_DryadOregon_DryadPuerto Montt_DryadSweden_Dryad