Seasonal and among‐site variation in the occurrence and abundance of fleas on California ground squirrels (Otospermophilus beecheyi)

An improved understanding of the ecology of fleas on California ground squirrels, Otospermophilus beecheyi, is warranted given the role of fleas in the transmission, and perhaps persistence, of the plague‐causing bacterium Yersinia pestis. We sampled O. beecheyi on a seasonal basis from three study sites, each representing a different land use type (preserve, pasture, and agriculture) in the San Joaquin Valley, CA. Overall, the abundance of fleas on squirrels was greatest in spring at the preserve site, in summer at the agriculture and pasture sites, and in winter at the pasture site. Hoplopsyllus anomalus, the species most frequently found on squirrels, was most abundant in spring at the preserve site and in summer at the agriculture and pasture sites. Oropsylla montana was most abundant in winter at the pasture site and on adult squirrels. Echidnophaga gallinacea was most abundant in fall on juvenile squirrels at the preserve site. All three flea species we encountered are known to be potential vectors of Y. pestis. Future efforts to predict flea species occurrence and abundance (and plague risk) at sites of concern should consider seasonal microclimatic conditions and the potential influence of human land use practices.     

Optimal germination timing in unpredictable environments: the importance of dormancy for both among‐ and within‐season variation

For organisms living in unpredictable environments, timing important life‐history events is challenging. One way to deal with uncertainty is to spread the emergence of offspring across multiple years via dormancy. However, timing of emergence is not only important among years, but also within each growing season. Here, we study the evolutionary interactions between germination strategies that deal with among‐ and within‐season uncertainty. We use a modelling approach that considers among‐season dormancy and within‐season germination phenology of annual plants as potentially independent traits and study their separate and joint evolution in a variable environment. We find that higher among‐season dormancy selects for earlier germination within the growing season. Furthermore, our results indicate that more unpredictable natural environments can counter‐intuitively select for less risk‐spreading within the season. Furthermore, strong priority effects select for earlier within‐season germination phenology which in turn increases the need for bet hedging through among‐season dormancy.     

Within‐ and among‐population variation in infectivity,latency and spore production in a host–pathogen system

In spatially structured populations, host–parasite coevolutionary potential depends on the distribution of genetic variation within and among populations. Inoculation experiments using the plant, Silene latifolia, and its fungal pathogen, Microbotryum violaceum, revealed little overall differentiation in infectivity/resistance, latency or spore production among host or pathogen populations. Within populations, fungal strains had similar means, but varied in performance across plant populations. Variation in resistance among seed families indicates the potential for parasite‐mediated selection, whereas there was little evidence for local pathogen genotype × plant genotype interactions assumed by most theoretical coevolution models. Lower spore production on sympatric than allopatric hosts confirmed local fungal maladaptation already observed for infectivity. Correlations between infectivity and latency or spore production suggest a common mechanism for variation in these traits. Our results suggest low variation available to this pathogen for tracking its coevolving host. This may be caused by random drift, breeding system or migration characteristic of metapopulation dynamics.     

Range position and climate sensitivity: The structure of among‐population demographic responses to climatic variation

Species’ distributions will respond to climate change based on the relationship between local demographic processes and climate and how this relationship varies based on range position. A rarely tested demographic prediction is that populations at the extremes of a species’ climate envelope (e.g., populations in areas with the highest mean annual temperature) will be most sensitive to local shifts in climate (i.e., warming). We tested this prediction using a dynamic species distribution model linking demographic rates to variation in temperature and precipitation for wood frogs (Lithobates sylvaticus) in North America. Using long‐term monitoring data from 746 populations in 27 study areas, we determined how climatic variation affected population growth rates and how these relationships varied with respect to long‐term climate. Some models supported the predicted pattern, with negative effects of extreme summer temperatures in hotter areas and positive effects on recruitment for summer water availability in drier areas. We also found evidence of interacting temperature and precipitation influencing population size, such as extreme heat having less of a negative effect in wetter areas. Other results were contrary to predictions, such as positive effects of summer water availability in wetter parts of the range and positive responses to winter warming especially in milder areas. In general, we found wood frogs were more sensitive to changes in temperature or temperature interacting with precipitation than to changes in precipitation alone. Our results suggest that sensitivity to changes in climate cannot be predicted simply by knowing locations within the species’ climate envelope. Many climate processes did not affect population growth rates in the predicted direction based on range position. Processes such as species‐interactions, local adaptation, and interactions with the physical landscape likely affect the responses we observed. Our work highlights the need to measure demographic responses to changing climate.     

Phenotypic integration in an extended phenotype: among‐individual variation in nest‐building traits of the alfalfa leafcutting bee (Megachile rotundata)

Structures such as nests and burrows are an essential component of many organisms’ life‐cycle and require a complex sequence of behaviours. Because behaviours can vary consistently among individuals and be correlated with one another, we hypothesized that these structures would (1) show evidence of among‐individual variation, (2) be organized into distinct functional modules and (3) show evidence of trade‐offs among functional modules due to limits on energy budgets. We tested these hypotheses using the alfalfa leafcutting bee, Megachile rotundata, a solitary bee and important crop pollinator. Megachile rotundata constructs complex nests by gathering leaf materials to form a linear series of cells in pre‐existing cavities. In this study, we examined variation in the following nest construction traits: reproduction (number of cells per nest and nest length), nest protection (cap length and number of leaves per cap), cell construction (cell size and number of leaves per cell) and cell provisioning (cell mass) from 60 nests. We found a general decline in investment in cell construction and provisioning with each new cell built. In addition, we found evidence for both repeatability and plasticity in cell provisioning with little evidence for trade‐offs among traits. Instead, most traits were positively, albeit weakly, correlated (r ~ 0.15), and traits were loosely organized into covarying modules. Our results show that individual differences in nest construction are detectable at a level similar to that of other behavioural traits and that these traits are only weakly integrated. This suggests that nest components are capable of independent evolutionary trajectories.     

c-mos variation in songbirds: molecular evolution, phylogenetic implications, and comparisons with mitochondrial differentiation

Nucleotide sequences from the c-mos proto-oncogene have previously been used to reconstruct the phylogenetic relationships between distantly related vertebrate taxa. To explore c-mos variation at shallower levels of avian divergence, we compared c-mos sequences from representative passerine taxa that span a range of evolutionary differentiation, from basal passerine lineages to closely allied genera. Phylogenetic reconstructions based on these c-mos sequences recovered topologies congruent with previous DNA-DNA hybridization-based reconstructions, with many nodes receiving high support, as indicated by bootstrap and reliability values. One exception was the relationship of Acanthisitta to the remaining passerines, where the c-mos-based searches indicated a three-way polytomy involving the Acanthisitta lineage and the suboscine and oscine passerine clades. We also compared levels of c-mos and mitochondrial differentiation across eight oscine passerine taxa and found that c-mos nucleotide substitutions accumulate at a rate similar to that of transversion substitutions in mitochondrial protein-coding genes. These comparisons suggest that nuclear-encoded loci such as c-mos provide a temporal window of phylogenetic resolution that overlaps the temporal range where mitochondrial protein-coding sequences have their greatest utility and that c-mos substitutions and mtDNA transversions can serve as complementary, informative, and independent phylogenetic markers for the study of avian relationships.     

The impact of anchored phylogenomics and taxon sampling on phylogenetic inference in narrow‐mouthed frogs (Anura,Microhylidae)

Despite considerable progress in unravelling the phylogenetic relationships of microhylid frogs, relationships among subfamilies remain largely unstable and many genera are not demonstrably monophyletic. Here, we used five alternative combinations of DNA sequence data (ranging from seven loci for 48 taxa to up to 73 loci for as many as 142 taxa) generated using the anchored phylogenomics sequencing method (66 loci, derived from conserved genome regions, for 48 taxa) and Sanger sequencing (seven loci for up to 142 taxa) to tackle this problem. We assess the effects of character sampling, taxon sampling, analytical methods and assumptions in phylogenetic inference of microhylid frogs. The phylogeny of microhylids shows high susceptibility to different analytical methods and datasets used for the analyses. Clades inferred from maximum‐likelihood are generally more stable across datasets than those inferred from parsimony. Parsimony trees inferred within a tree‐alignment framework are generally better resolved and better supported than those inferred within a similarity‐alignment framework, even under the same cost matrix (equally weighted) and same treatment of gaps (as a fifth nucleotide state). We discuss potential causes for these differences in resolution and clade stability among discovery operations. We also highlight the problem that commonly used algorithms for model‐based analyses do not explicitly model insertion and deletion events (i.e. gaps are treated as missing data). Our results corroborate the monophyly of Microhylidae and most currently recognized subfamilies but fail to provide support for relationships among subfamilies. Several taxonomic updates are provided, including naming of two new subfamilies, both monotypic.     

Within‐and among‐year germination in Sonoran Desert winter annuals: bet hedging and predictive germination in a variable environment

In variable environments, organisms must have strategies to ensure fitness as conditions change. For plants, germination can time emergence with favourable conditions for later growth and reproduction (predictive germination), spread the risk of unfavourable conditions (bet hedging) or both (integrated strategies). Here we explored the adaptive value of within‐ and among‐year germination timing for 12 species of Sonoran Desert winter annual plants. We parameterised models with long‐term demographic data to predict optimal germination fractions and compared them to observed germination. At both temporal scales we found that bet hedging is beneficial and that predicted optimal strategies corresponded well with observed germination. We also found substantial fitness benefits to varying germination timing, suggesting some degree of predictive germination in nature. However, predictive germination was imperfect, calling for some degree of bet hedging. Together, our results suggest that desert winter annuals have integrated strategies combining both predictive plasticity and bet hedging.     

Effects of sample size and intraspecific variation in phylogenetic comparative studies: a meta‐analytic review

Comparative analyses aim to explain interspecific variation in phenotype among taxa. In this context, phylogenetic approaches are generally applied to control for similarity due to common descent, because such phylogenetic relationships can produce spurious similarity in phenotypes (known as phylogenetic inertia or bias). On the other hand, these analyses largely ignore potential biases due to within‐species variation. Phylogenetic comparative studies inherently assume that species‐specific means from intraspecific samples of modest sample size are biologically meaningful. However, within‐species variation is often significant, because measurement errors, within‐ and between‐individual variation, seasonal fluctuations, and differences among populations can all reduce the repeatability of a trait. Although simulations revealed that low repeatability can increase the type I error in a phylogenetic study, researchers only exercise great care in accounting for similarity in phenotype due to common phylogenetic descent, while problems posed by intraspecific variation are usually neglected. A meta‐analysis of 194 comparative analyses all adjusting for similarity due to common phylogenetic descent revealed that only a few studies reported intraspecific repeatabilities, and hardly any considered or partially dealt with errors arising from intraspecific variation. This is intriguing, because the meta‐analytic data suggest that the effect of heterogeneous sampling can be as important as phylogenetic bias, and thus they should be equally controlled in comparative studies. We provide recommendations about how to handle such effects of heterogeneous sampling.     

Growth‐rate variation in brown trout in small neighbouring streams: evidence for density‐dependence?

The within- and among-population variation in individual growth rate of brown trout Salmo trutta L. was studied in five small neighbouring streams (seven isolated populations) within a distance of 70 km in east Norway. Observed growth rate was only weakly correlated with predicted maximum growth rate based on laboratory models, and there was a significant interaction with site. A generalized linear model showed that growth rate was positively correlated with temperature, but also that growth rate decreased as the summer season progressed. This might indicate either a seasonal decline in food availability or appetite, or a change in energy allocation strategy. Growth rate decreased with increasing fish age, probably as an effect of sexual maturation of older fish, and differential allocation of protein and lipid among different size-groups of brown trout. After adjusting for variation in temperature, season, and fish mass, there was still significant among-site variation in growth rate. A significant part of this variation was due to variation in brown trout density and the presence or absence of Alpine bullhead Cottus poecilopus . Growth rate decreased with increasing brown trout density, and was lower in the presence than in the absence of Alpine bullhead after correcting for variation in brown trout density. This last result may indicate the presence of interspecific competition.     

When peers are not peers and don't know it: The Dunning‐Kruger effect and self‐fulfilling prophecy in peer‐review

The fateful combination of (i) the Dunning‐Kruger effect (ignorance of one's own ignorance) with (ii) the nonlinear dynamics of the echo‐chamber between reviewers and editors fuels a self‐reinforcing collective delusion system that sometimes spirals uncontrollably away from objectivity and truth. Escape from this subconscious meta‐ignorance is a formidable challenge but if achieved will help correct a central deficit of the peer‐review process that stifles innovation and paradigm shifts.     

Interspecific hybridization causes long‐term phylogenetic discordance between nuclear and mitochondrial genomes in freshwater fishes

Classification, phylogeography and the testing of evolutionary hypotheses rely on correct estimation of species phylogeny. Early molecular phylogenies often relied on mtDNA alone, which acts as a single linkage group with one history. Over the last decade, the use of multiple nuclear sequences has often revealed conflict among gene trees. This observation can be attributed to hybridization, lineage sorting, paralogy or selection. Here, we use 54 groups of fishes from 48 studies to estimate the degree of concordance between mitochondrial and nuclear gene trees in two ecological grades of fishes: marine and freshwater. We test the hypothesis that freshwater fish phylogenies should, on average, show more discordance because of their higher propensity for hybridization in the past. In keeping with this idea, concordance between mitochondrial and nuclear gene trees (as measured by proportion of components shared) is on average 50% higher in marine fishes. We discuss why this difference almost certainly results from introgression caused by greater historical hybridization among lineages in freshwater groups, and further emphasize the need to use multiple nuclear genes, and identify conflict among them, in estimation of species phylogeny.     

Nuclear and mitochondrial phylogenetic analysis of big‐scale sand smelt Atherina boyeri complex in Greece

Genetic differentiation and phylogenetic relationships of big‐scale sand smelt Atherina boyeri specimens from 23 sampling sites in Greece and one from a lake in Turkey were investigated. A total of 2180 base pairs (bp) corresponding to the partial sequence of the mitochondrial gene cytochrome oxidase I (coI), cytochrome b (cytb) and control region, as well as of the nuclear protein‐coding gene rhodopsin (rh), were determined for the 143 specimens studied. Phylogenetic analysis of each gene segment separately and of the combined dataset revealed the existence of three different and well divergent lineages in Greece. The first corresponds to the lagoon form, in which a clear distinction between the Aegean and Ionian Sea was observed. The other two correspond to the punctuated and non‐punctuated marine forms that have been previously reported. The fact that in the present study a population without black spots on the flanks is clustered with the punctuated form and vice versa, however, suggests that differences in colour pattern do not seem to be a sufficient marker to discriminate the two marine forms. In contrast, the presence of a different length insertion between transfer RNA (tRNA) glutamic acid (tRNA^glu) and cytb genes in the lagoon and in one of the two forms of marine populations, and its absence from the rest marine‐form specimens confirms that this character is conserved and capable to be used for distinguishing the different forms. Even though the divergence values among the different forms were high, their phylogenetic relationships were not able to be resolved.     

Complete mitochondrial genomes from four subspecies of common chaffinch (Fringilla coelebs): New inferences about mitochondrial rate heterogeneity,neutral theory,and phylogenetic relationships within the order Passeriformes

We describe whole mitochondrial genome sequences from four subspecies of the common chaffinch (Fringilla coelebs), and compare them to 31 publicly available mitochondrial genome sequences from other Passeriformes. Rates and patterns of mitochondrial gene evolution are analyzed at different taxonomic levels within this avian order, and evidence is adduced for and against the nearly neutral theory of molecular evolution and the role of positive selection in shaping genetic variation of this small but critical genome. We find evidence of mitochondrial rate heterogeneity in birds as in other vertebrates, likely due to differences in mutational pressure across the genome. Unlike in gadine fish and some of the human mitochondrial work we do not observe strong support for the nearly neutral theory of molecular evolution; instead evidence from molecular clocks, distribution of dN/dS ratios at different levels of the taxonomic hierarchy and in different lineages, McDonald–Kreitman tests within Fringillidae, and site-specific tests of selection within Passeriformes, all point to a role for positive selection, especially for the complex I NADH dehydrogenase genes. The protein-coding mitogenome phylogeny of the order Passeriformes is broadly consistent with previously-reported molecular findings, but provides support for a sister relationship between the superfamilies Muscicapoidea and Passeroidea on a short basal internode of the Passerida where relationships have been difficult to resolve. An unexpected placement of the Paridae (represented by Hume's groundpecker) within the Muscicapoidea was observed. Consistent with other molecular studies the mtDNA phylogeny reveals paraphyly within the Muscicapoidea and a sister relationship of Fringilla with Carduelis rather than Emberiza.     

Landscape heterogeneity drives intra‐population niche variation and reproduction in an arctic top predator

While intra‐population variability in resource use is ubiquitous, little is known of how this measure of niche diversity varies in space and its role in population dynamics. Here we examined how heterogeneous breeding environments can structure intra‐population niche variation in both resource use and reproductive output. We investigated intra‐population niche variation in the Arctic tundra ecosystem, studying peregrine falcon (Falco peregrinus tundrius, White) breeding within a terrestrial‐marine gradient near Rankin Inlet, Nunavut, Canada. Using stable isotope analysis, we found that intra‐population niches varied at the individual level; we examined within‐nest and among‐nest variation, though only the latter varied along the terrestrial‐marine gradient (i.e., increased among‐nest variability among birds nesting within the marine environment, indicating higher degree of specialization). Terrestrial prey species (small herbivores and insectivores) were consumed by virtually all falcons. Falcons nesting within the marine environment made use of marine prey (sea birds), but depended heavily on terrestrial prey (up to 90% of the diet). Using 28‐years of peregrine falcon nesting data, we found a positive relationship between the proportion of terrestrial habitat surrounding nest sites and annual nestling production, but no relationship with the likelihood of successfully rearing at least one nestling reaching 25 days old. Annually, successful inland breeders raised 0.47 more young on average compared to offshore breeders, which yields potential fitness consequences for this long‐living species. The analyses of niche and reproductive success suggest a potential breeding cost for accessing distant terrestrial prey, perhaps due to additional traveling costs, for those individuals with marine nest site locations. Our study indicates how landscape heterogeneity can generate proximate (niche variation) and ultimate (reproduction) consequences on a population of generalist predator. We also show that within‐individual and among‐individual variation are not mutually exclusive, but can simultaneously arise and structure intra‐population niche variation.     

Small‐ and large‐scale heterogeneity in genetic variation across the collard flycatcher genome: implications for estimating genetic diversity in nonmodel organisms

Population genetic studies in nonmodel organisms are often hampered by a lack of reference genomes that are essential for whole‐genome resequencing. In the light of this, genotyping methods have been developed to effectively eliminate the need for a reference genome, such as genotyping by sequencing or restriction site‐associated DNA sequencing (RAD‐seq). However, what remains relatively poorly studied is how accurately these methods capture both average and variation in genetic diversity across an organism's genome. In this issue of Molecular Ecology Resources, Dutoit et al. (2016) use whole‐genome resequencing data from the collard flycatcher to assess what factors drive heterogeneity in nucleotide diversity across the genome. Using these data, they then simulate how well different sequencing designs, including RAD sequencing, could capture most of the variation in genetic diversity. They conclude that for evolutionary and conservation‐related studies focused on the estimating genomic diversity, researchers should emphasize the number of loci analysed over the number of individuals sequenced.     

Estimating dispersal distributions at multiple scales: within‐colony and among‐colony dispersal rates,distances and directions in European Shags Phalacrocorax aristotelis

Knowledge of the rate, distance and direction of dispersal within and among breeding areas is required to understand and predict demographic and genetic connectivity and resulting population and evolutionary dynamics. However dispersal rates, and the full distributions of dispersal distances and directions, are rarely comprehensively estimated across all spatial scales relevant to wild populations. We used re‐sightings of European Shags Phalacrocorax aristotelis colour‐ringed as chicks on the Isle of May (IoM), UK, to quantify rates, distances and directions of dispersal from natal to subsequent breeding sites both within IoM (within‐colony dispersal) and across 27 other breeding colonies covering 1045 km of coastline (among‐colony dispersal). Additionally, we used non‐breeding season surveys covering 895 km of coastline to estimate breeding season detection probability and hence potential bias in estimated dispersal parameters. Within IoM, 99.6% of individuals dispersed between their natal and observed breeding nest‐site. The distribution of within‐colony dispersal distances was right‐skewed; mean distance was shorter than expected given random settlement within IoM, yet some individuals dispersed long distances within the colony. The distribution of within‐colony dispersal directions was non‐uniform but did not differ from expectation given the spatial arrangement of nest‐sites. However, 10% of all 460 colour‐ringed adults that were located breeding had dispersed to a different colony. The maximum observed dispersal distance (170 km) was much smaller than the maximum distance surveyed (690 km). The distribution of among‐colony dispersal distances was again right‐skewed. Among‐colony dispersal was directional, and differed from random expectation and from the distribution of within‐colony dispersal directions. Non‐breeding season surveys suggested that the probability of detecting a colour‐ringed adult at its breeding location was high in the northeastern UK (98%). Estimated dispersal rates and distributions were therefore robust to incomplete detection. Overall, these data demonstrate skewed and directionally divergent dispersal distributions across small (within‐colony) and large (among‐colony) scales, indicating that dispersal could create genetic and demographic connectivity within the study area.