Information dropout patterns in restriction site associated DNA phylogenomics and a comparison with multilocus Sanger data in a species-rich moth genus

A rapid shift from traditional Sanger sequencing-based molecular methods to the phylogenomic approach with large numbers of loci is underway. Among phylogenomic methods, restriction site associated DNA (RAD) sequencing approaches have gained much attention as they enable rapid generation of up to thousands of loci randomly scattered across the genome and are suitable for nonmodel species. RAD data sets however suffer from large amounts of missing data and rapid locus dropout along with decreasing relatedness among taxa. The relationship between locus dropout and the amount of phylogenetic information retained in the data has remained largely uninvestigated. Similarly, phylogenetic hypotheses based on RAD have rarely been compared with phylogenetic hypotheses based on multilocus Sanger sequencing, even less so using exactly the same species and specimens. We compared the Sanger-based phylogenetic hypothesis (8 loci; 6172 bp) of 32 species of the diverse moth genus Eupithecia (Lepidoptera, Geometridae) to that based on double-digest RAD sequencing (3256 loci; 726,658 bp). We observed that topologies were largely congruent, with some notable exceptions that we discuss. The locus dropout effect was strong. We demonstrate that number of loci is not a precise measure of phylogenetic information since the number of single-nucleotide polymorphisms (SNPs) may remain low at very shallow phylogenetic levels despite large numbers of loci. As we hypothesize, the number of SNPs and parsimony informative SNPs (PIS) is low at shallow phylogenetic levels, peaks at intermediate levels and, thereafter, declines again at the deepest levels as a result of decay of available loci. Similarly, we demonstrate with empirical data that the locus dropout affects the type of loci retained, the loci found in many species tending to show lower interspecific distances than those shared among fewer species. We also examine the effects of the numbers of loci, SNPs, and PIS on nodal bootstrap support, but could not demonstrate with our data our expectation of a positive correlation between them. We conclude that RAD methods provide a powerful tool for phylogenomics at an intermediate phylogenetic level as indicated by its broad congruence with an eight-gene Sanger data set in a genus of moths. When assessing the quality of the data for phylogenetic inference, the focus should be on the distribution and number of SNPs and PIS rather than on loci.Peer reviewe

Avoiding perceived past resource use of potential competitors affects niche dynamics in a bird community

Social information use is usually considered to lead to ecological convergence among involved con- or heterospecific individuals. However, recent results demonstrate that observers can also actively avoid behaving as those individuals being observed, leading to ecological divergence. This phenomenon has been little explored so far, yet it can have significant impact on resource use, realized niches and species co-existence. In particular, the time-scale and the ecological context over which such shifts can occur are unknown. We examined with a long-term (four years) field experiment whether experimentally manipulated, species-specific, nest-site feature preferences (symbols on nest boxes) are transmitted across breeding seasons and affect future nest-site preferences in a guild of three cavity-nesting birds.</p

The past and the present in decision-making: the use of conspecific and heterospecific cues in nest site selection

Nest-site selection significantly affects fitness, so adaptations for assessment of the qualities of available sites are expected. The assessment may be based on personal or social information, social information referring to the observed location and performance of both con- and heterospecific individuals. Contrary to large-scale breeding habitat selection, small-scale nest-site selection within habitat patches is insufficiently understood. We analyzed nest-site selection in the migratory collared flycatcher Ficedula albicollis in relation to present and past cues provided by conspecifics and by resident tits within habitat patches by using long-term data. Collared flycatchers preferred nest boxes that were occupied by conspecifics in the previous year. This preference was strongest in breeding pairs where both individuals bred in the same forest patch in the previous year. The results also suggest preference for nest boxes close to boxes where conspecifics had a high breeding success in the previous year, and for nest boxes which are presently surrounded by a high number of breeding great tits Parus major. The results indicate social information use in nest-site selection at a small spatial scale, where collared flycatchers use conspecific cues with a time lag of one year and heterospecific cues instantly.</p

Titmice are a better indicator of bird density in Northern European than in Western European forests

Publisher Copyright: © 2022 The Authors. Ecology and Evolution published by John Wiley & Sons Ltd.Population sizes of many birds are declining alarmingly and methods for estimating fluctuations in species’ abundances at a large spatial scale are needed. The possibility to derive indicators from the tendency of specific species to co-occur with others has been overlooked. Here, we tested whether the abundance of resident titmice can act as a general ecological indicator of forest bird density in European forests. Titmice species are easily identifiable and have a wide distribution, which makes them potentially useful ecological indicators. Migratory birds often use information on the density of resident birds, such as titmice, as a cue for habitat selection. Thus, the density of residents may potentially affect community dynamics. We examined spatio-temporal variation in titmouse abundance and total bird abundance, each measured as biomass, by using long-term citizen science data on breeding forest birds in Finland and France. We analyzed the variation in observed forest bird density (excluding titmice) in relation to titmouse abundance. In Finland, forest bird density linearly increased with titmouse abundance. In France, forest bird density nonlinearly increased with titmouse abundance, the association weakening toward high titmouse abundance. We then analyzed whether the abundance (measured as biomass) of random species sets could predict forest bird density better than titmouse abundance. Random species sets outperformed titmice as an indicator of forest bird density only in 4.4% and 24.2% of the random draws, in Finland and France, respectively. Overall, the results suggest that titmice could act as an indicator of bird density in Northern European forest bird communities, encouraging the use of titmice observations by even less-experienced observers in citizen science monitoring of general forest bird density.Peer reviewe

Do large-scale associations in birds imply biotic interactions or environmental filtering?

Aim There has been a wide interest in the effect of biotic interactions on species' occurrences and abundances at large spatial scales, coupled with a vast development of the statistical methods to study them. Still, evidence for whether the effects of within-trophic-level biotic interactions (e.g. competition and heterospecific attraction) are discernible beyond local scales remains inconsistent. Here, we present a novel hypothesis-testing framework based on joint dynamic species distribution models and functional trait similarity to dissect between environmental filtering and biotic interactions. Location France and Finland. Taxon Birds. Methods We estimated species-to-species associations within a trophic level, independent of the main environmental variables (mean temperature and total precipitation) for common species at large spatial scale with joint dynamic species distribution (a multivariate spatiotemporal delta model) models. We created hypotheses based on species' functionality (morphological and/or diet dissimilarity) and habitat preferences about the sign and strength of the pairwise spatiotemporal associations to estimate the extent to which they result from biotic interactions (competition, heterospecific attraction) and/or environmental filtering. Results Spatiotemporal associations were mostly positive (80%), followed by random (15%), and only 5% were negative. Where detected, negative spatiotemporal associations in different communities were due to a few species. The relationship between spatiotemporal association and functional dissimilarity among species was negative, which fulfils the predictions of both environmental filtering and heterospecific attraction. Main conclusions We showed that processes leading to species aggregation (mixture between environmental filtering and heterospecific attraction) seem to dominate assembly rules, and we did not find evidence for competition. Altogether, our hypothesis-testing framework based on joint dynamic species distribution models and functional trait similarity is beneficial in ecological interpretation of species-to-species associations from data covering several decades and biogeographical regions.Peer reviewe

Ecological and evolutionary consequences of selective interspecific information use

Recent work has shown that animals frequently use social information from individuals of their own species as well as from other species; however, the ecological and evolutionary consequences of this social information use remain poorly understood. Additionally, information users may be selective in their social information use, deciding from whom and how to use information, but this has been overlooked in an interspecific context. In particular, the intentional decision to reject a behaviour observed via social information has received less attention, although recent work has indicated its presence in various taxa. Based on existing literature, we explore in which circumstances selective interspecific information use may lead to different ecological and coevolutionary outcomes between two species, such as explaining observed co-occurrences of putative competitors. The initial ecological differences and the balance between the costs of competition and the benefits of social information use potentially determine whether selection may lead to trait divergence, convergence or coevolutionary arms race between two species. We propose that selective social information use, including adoption and rejection of behaviours, may have far-reaching fitness consequences, potentially leading to community-level eco-evolutionary outcomes. We argue that these consequences of selective interspecific information use may be much more widespread than has thus far been considered

Apolipoprotein A-I mimetic peptide 4F blocks sphingomyelinase-induced LDL aggregation

Lipolytic modification of LDL particles by SMase generates LDL aggregates with a strong affinity for human arterial proteoglycans and may so enhance LDL retention in the arterial wall. Here, we evaluated the effects of apoA-I mimetic peptide 4F on structural and functional properties of the SMase-modified LDL particles. LDL particles with and without 4F were incubated with SMase, after which their aggregation, structure, and proteoglycan binding were analyzed. At a molar ratio of L-4F to apoB-100 of 2.5 to 20: 1, 4F dose-dependently inhibited SMase-induced LDL aggregation. At a molar ratio of 20: 1, SMase-induced aggregation was fully blocked. Binding of 4F to LDL particles inhibited SMase-induced hydrolysis of LDL by 10% and prevented SMase-induced LDL aggregation. In addition, the binding of the SMase-modifi ed LDL particles to human aortic proteoglycans was dose-dependently inhibited by pretreating LDL with 4F. The 4F stabilized apoB-100 conformation and inhibited SMase-induced conformational changes of apoB-100. Molecular dynamic simulations showed that upon binding to protein-free LDL surface, 4F locally alters membrane order and fluidity and induces structural changes to the lipid layer. Collectively, 4F stabilizes LDL particles by preventing the SMase-induced conformational changes in apoB-100 and so blocks SMase-induced LDL aggregation and the resulting increase in LDL retention.Peer reviewe

The roles of temperature, nest predators and information parasites for geographical variation in egg covering behaviour of tits (Paridae)

Aim Nest building is widespread among animals. Nests may provide receptacles for eggs, developing offspring and the parents, and protect them from adverse environmental conditions. Nests may also indicate the quality of the territory and its owner and can be considered as an extended phenotype of its builder(s). Nests may, thus, function as a sexual and social signal. Here, we examined ecological and abiotic factors-temperature, nest predation and interspecific information utilization-shaping geographical variation in a specific nest structure-hair and feather cover of eggs-and its function as an extended phenotype before incubation in great (Parus major) and blue tits (Cyanistes caeruleus) across Europe. We also tested whether egg covering is associated with reproductive success of great tits. Location Fourteen different study sites and 28 populations across Europe. Taxon Parus major, Cyanistes caeruleus. Methods We recorded clutch coverage estimates and collected egg covering nest material from the tit nests. We also measured nest specific breeding parameters and phenotypic measurements on adults. We tested whether mean spring temperatures, nest predation rates and flycatcher (Ficedulaspp) densities in the study areas explain the large-scale geographical variation of clutch coverage and reproductive success of tits. Results The degree of egg coverage of great tits increased with lower mean spring temperature, higher nest predation rate and higher flycatcher density. We did not find egg covering of blue tits to be associated with any of the ecological or abiotic factors. Moreover, egg covering of great tits was not associated with reproductive success in our cross-sectional data, yet a rigorous assessment of fitness effects would require long-term data. Main conclusions Our findings suggest that, in great tits, egg covering may simultaneously provide thermal insulation against cold temperatures during egg-laying in spring and also represent a counter-adaptation to reduce information parasitism by flycatchers and nest predation. Hence, geographical variation in interspecific interactions, and consequently in co-evolutionary processes, may affect the evolution of nest characteristics besides environmental conditions

Evolution of insect life histories in relation to time constraints in seasonal environments:polymorphism and clinal variation

Abstract Both the length of the season that is favourable for insect growth and reproduction and the number of generations emerging per season (voltinism) increase with decreasing latitude. Thus, time constraints on reproduction and juvenile development decrease with decreasing latitude, except where voltinism changes and time constraints suddenly increase as the season must be shared with one more generation. I studied the evolution of insect life histories in relation to time constraints from two perspectives: polymorphism and clinal variation. Life history polymorphism in seasonal environments was studied with the butterfly Pieris napi that has discrete life history strategies, and polymorphic natural populations. Experimental studies showed that asymmetric intraspecific larval competition and divergent timing of reproduction between the strategies may promote the maintenance of polymorphism. A simulation model showed that the divergent timing of reproduction between the strategies is sufficient to maintain polymorphism even in the absence of intraspecific competition. Clinal variation was studied empirically with four geometrid moths (Cabera exanthemata, Cabera pusaria, Chiasmia clathrata and Lomaspilis marginata) and generally in theory. Due to latitudinal saw-tooth variation in time constraints, traditional theory predicts a saw-tooth cline in body size and development time. A common garden experiment with the four geometrid moths did not support the traditional theory even when a saw-tooth cline in body size was found, suggesting that the theory is based on unrealistic assumptions. A theoretical analysis showed that reproductive effort should be high in populations under intense time constraints and low in populations experiencing no time constraints, resulting in a saw-tooth cline. In the four geometrid moths, support for these predictions was found, although the observed clinal variation deviated from the predicted pattern. The results imply that clinal variation is expected in almost any continuous life history trait, whereas polymorphism of different strategies may emerge when life histories fall into discrete categories. When inferring the evolution of a single trait, complex interdependencies among several traits should be considered, as well as the possibility that the time constraints are not similar for each generation in multivoltine populations.Tiivistelmä Hyönteisten kasvu ja kehitys ovat pääsääntöisesti mahdollisia vain kesän aikana. Etelään päin mentäessä kesä pitenee, ja saman kesän aikana kehittyvien hyönteissukupolvien määrä kasvaa. Kesän pituus aiheuttaa lisääntymiseen ja toukkien kasvuun kohdistuvan aikarajoitteen, joka heikkenee etelään päin siirryttäessä. Aikarajoite kuitenkin tiukkenee siellä, missä yksi uusi sukupolvi ehtii juuri kehittymään saman kesän aikana, sillä kesä on nyt jaettava useamman sukupolven kesken. Väitöstyössä tarkastelin hyönteisten elinkierto-ominaisuuksien evoluutiota suhteessa aikarajoitteisiin sekä diskreetin että jatkuvan muuntelun näkökulmista. Diskreettiä muuntelua tutkin lanttuperhosella (Pieris napi), jolla esiintyy diskreettejä elinkiertostrategioita. Kokeellisesti osoitin, että toukkien välinen kilpailu on epäsymmetristä, mikä yhdessä eri elinkiertostrategioiden erilaisen lisääntymisen ajoittumisen kanssa voi ylläpitää diskreettiä muuntelua. Simulaatiomalli osoitti, että erilaiset elinkiertostrategiat voivat säilyä populaatiossa pelkästään niiden erilaisen lisääntymisen ajoittumisen ansiosta. Elinkierto-ominaisuuksien jatkuvaa muuntelua tutkin neljän mittariperhosen (Cabera exanthemata, Cabera pusaria, Chiasmia clathrata ja Lomaspilis marginata) avulla ja teoreettisesti yleisellä tasolla. Aikaisempi teoria ennustaa ruumiinkoon ja kehitysajan muuntelevan sahalaitakuvion mukaisesti siirryttäessä pohjoisesta etelään, koska aikarajoitteet muuntelevat samalla tavalla. Tämä teoria perustunee epärealistisiin oletuksiin, koska kokeelliset tulokset eivät tukeneet teoriaa silloinkaan, kun mittariperhosten ruumiinkoko muunteli ennustetulla tavalla. Teoreettinen tutkimus osoitti, että myös lisääntymispanostuksen tulisi muunnella sahalaitakuvion mukaisesti suhteessa kesän pituuteen siten, että se on korkeimmillaan siellä, missä aikarajoitteet ovat tiukat. Mittariperhosten tutkiminen antoi jossain määrin tukea tälle ennusteelle. Tulosten perusteella jatkuvaa maantieteellistä muuntelua ennustetaan elinkierto-ominaisuuksille, jotka muuntelevat jatkuvalla asteikolla. Erilaiset elinkiertostrategiat voivat sen sijaan säilyä populaatiossa, jos elinkierto-ominaisuuksien muuntelu on diskreettiä. Eri ominaisuuksien monimutkaiset vuorovaikutukset sekä eri sukupolvien mahdollisesti kokemat erilaiset aikarajoitteet olisi syytä tuntea, kun tarkastelun kohteena on yksittäisen ominaisuuden evoluutio

Evolution of searching effort for resources: a missing piece of the puzzle in the ideal free distribution paradigm

Animals commonly search for information about available resources to select a breeding or foraging site or a mate. Searching can be costly, which is why even random selection of resources may pay off. However, the evolution of searching effort in relation to key ecological factors and its ecological consequences remain insufficiently understood. We build a model to analyze the evolution of searching effort for resources in relation to key ecological factors; the cost of information acquisition, the cost of competition and the distribution of resource qualities. Evolutionarily stable searching effort decreased with increasing cost of information acquisition, eventually resulting in a random choice of resources. With a very low cost of information acquisition, evolutionarily stable searching effort increased with increasing proportion of low-quality resources in the available resource distribution, while the opposite was predicted with a higher cost of information acquisition. Cost of competition had only a negligible effect on the evolution of searching effort, except that increasing cost of competition increased investment in information acquisition when a resource distribution was biased towards high-quality resources. Informed resource selection (above-zero investment in information acquisition) resulted in skewed distribution of individuals across resources. Consequently, expected fitness became more similar across resources with decreasing cost of information acquisition and associated increase in searching effort, thus approaching the prediction of the classical ideal free distribution (IFD) model stating that individuals distribute themselves so that fitness is invariant across resources. However, we predict a positive correlation between fitness and resource quality with biologically more realistic parameter values, contradicting the IFD model. Costly information acquisition may, thus, explain why IFD is not always found in empirical studies. Generally, our results imply that avoidance of poor choices is more important for the evolution of information acquisition strategies than making the very best choices.202