Can population genetic structure be predicted from life-history traits?

Population genetic structure is a key parameter in evolutionary biology. Earlier comparative studies have shown that genetic structure depends on species ecological attributes and life-history traits, but species phylogenetic relatedness had not been accounted for. Here we reevaluate the relationships between genetic structure and species traits in seed plants. Each species is characterized by a set of life-history and ecological features as well as by its geographic range size, its heterozygote deficit, and its genetic structure at nuclear and organelle markers to distinguish between pollen- and seed-mediated gene flow. We use both a conventional regression approach and a method that controls for phylogenetic relationships. Once phylogenetic conservatism and covariation among traits are taken into account, genetic structure is shown to be related with only a few synthetic traits, such as mating system for nuclear markers and seed dispersal mode or geographic range size for organelle markers. Along with other studies on invasiveness or rarity, our work illustrates the fact that predicting the fate of species across a broad taxonomic assemblage on the basis of simple traits is rarely possible, a testimony of the highly contingent nature of evolution.     

Are personality differences in a small iteroparous mammal maintained by a life-history trade-off?

Despite increasing interest, animal personality is still a puzzling phenomenon. Several theoretical models have been proposed to explain intraindividual consistency and interindividual variation in behaviour, which have been primarily supported by qualitative data and simulations. Using an empirical approach, I tested predictions of one main life-history hypothesis, which posits that consistent individual differences in behaviour are favoured by a trade-off between current and future reproduction. Data on life-history were collected for individuals of a natural population of grey mouse lemurs (Microcebus murinus). Using open-field and novel-object tests, I quantified variation in activity, exploration and boldness for 117 individuals over 3 years. I found systematic variation in boldness between individuals of different residual reproductive value. Young males with low current but high expected future fitness were less bold than older males with high current fecundity, and males might increase in boldness with age. Females have low variation in assets and in boldness with age. Body condition was not related to boldness and only explained marginal variation in exploration. Overall, these data indicate that a trade-off between current and future reproduction might maintain personality variation in mouse lemurs, and thus provide empirical support of this life-history trade-off hypothesis.     

Can life-history traits predict the response of forb populations to changes in climate variability?

1.  Climate change will cause changes in average temperature and precipitation as well as increased fluctuations around the mean, yet few studies have considered the impacts of altered climate variability on plant populations. We tested whether life-history traits (expected life span, generation time and seed size) can predict plant responses to increased environmental variability across similar plant species sharing the same habitat.
2.  We combined long-term demographic data on 10 prairie forb species with stochastic demography techniques to estimate the effects of potential changes in matrix element means and variances on the long-term stochastic population growth rate.
3.  For all 10 species, recruitment had higher contribution and elasticity values than survival, meaning that climate change is more likely to influence population growth through effects on recruitment than on survival for these relatively short-lived forbs. Species with longer generation times had lower elasticities to increases in matrix element variability.
4.   Synthesis. Our analysis of a unique, long-term data set suggests that longer-lived plant species will be less vulnerable to the effects of future increases in climate variability. While this relationship was previously reported for diverse taxa from many locations, our results show that it also applies within a guild of short-lived species from a single community. The generality of the pattern demonstrates the potential for using life-history traits to make predictions about which species may be the most vulnerable to climate change.     

Does pollution influence small mammal diet in the field? A metabarcoding approach in a generalist consumer

Mammals are mainly exposed to trace metals (TMs) via consuming contaminated food. Several studies have demonstrated relationships between metal concentrations in food and in animal tissues. However, potential effects of TMs on feeding behaviour of wildlife have been poorly documented under field conditions, despite experimental evidence showing that food selection is impacted by resource contamination. Here, we test the hypothesis that the diet of a generalist rodent, the wood mouse (Apodemus sylvaticus), is altered by soil TM contamination in the field. Wood mice were sampled in spring and in autumn along a gradient of soil contamination in the surroundings of a former smelter located in northern France. Available resources in the field were inventoried, and the diet of the animals was analysed using DNA “metabarcoding.” We demonstrated that (a) relationship between the resource richness in the diet and their richness in the field was altered by soil metal contamination. Wood mice specialized their diet along the gradient of soil metal contamination for both plant and invertebrate resources in spring. We also showed that (b) preference for Salicaceae, a plant family accumulating metals, decreased when soil contamination increased. These results suggest that environmental TM pollution could act as a force modulating trophic interactions in terrestrial food webs, thereby affecting wildlife exposure to contaminants by trophic route.     

Starting points for small mammal population recovery after wildfire: recolonisation or residual populations?

Wildfire is a major driver of spatio‐temporal variation in terrestrial ecosystems. Large wildfires are predicted to occur more frequently due to climate change. The mechanisms by which post‐fire recovery proceeds are influenced by the abundance of survivors, and their distribution in relation to habitat variability and refugia. Thus, characterising early post‐fire demographic processes is critical to understanding the demographic and community‐level responses of ecosystems to fire. The Black Saturday fires of February 2009 burnt an area of approximately 3500 km² in Victoria, Australia. We quantified the effects of this high severity forest fire on the habitat, abundance, sex ratio and body mass of two small mammal species, the agile antechinus Antechinus agilis and bush rat Rattus fuscipes. We developed a hypothetical framework to distinguish in situ survival and rapid recolonisation as the processes underlying short‐term post‐fire distributions. These hypotheses were based on expected patterns of abundance over increasing distances from unburnt sources, and the estimated recolonisation capabilities of each species and sex. The agile antechinus and bush rat were present in burnt sites at 30% and 12% of the density observed in unburnt sites. In situ survival, and not recolonisation, was the most plausible explanation for our findings. Abundance and body mass data indicated a greater effect of fire on the bush rat than the agile antechinus. The bush rat showed a shift in topographic association, whereby drainage lines acted as post‐fire refugia. Our findings suggest these species do not depend on recolonisation for recovery, and that the bush rat will follow a nucleated recovery, expanding from topographic refugia. Thus, connectivity‐reducing management activities, such as salvage logging and firebreak and road construction, may not affect the early stages of population recovery in remaining stands of burnt forest. Rather, ongoing recovery is likely to be limited by demographic rates and resource availability.     

How general is cognitive ability in non-human animals? A meta-analytical and multi-level reanalysis approach

General intelligence has been a topic of high interest for over a century. Traditionally, research on general intelligence was based on principal component analyses and other dimensionality reduction approaches. The advent of high-speed computing has provided alternative statistical tools that have been used to test predictions of human general intelligence. In comparison, research on general intelligence in non-human animals is in its infancy and still relies mostly on factor-analytical procedures. Here, we argue that dimensionality reduction, when incorrectly applied, can lead to spurious results and limit our understanding of ecological and evolutionary causes of variation in animal cognition. Using a meta-analytical approach, we show, based on 555 bivariate correlations, that the average correlation among cognitive abilities is low (r = 0.185; 95% CI: 0.087–0.287), suggesting relatively weak support for general intelligence in animals. We then use a case study with relatedness (genetic) data to demonstrate how analysing traits using mixed models, without dimensionality reduction, provides new insights into the structure of phenotypic variance among cognitive traits, and uncovers genetic associations that would be hidden otherwise. We hope this article will stimulate the use of alternative tools in the study of cognition and its evolution in animals.     

Does acoustic environment modify boldness and related life-history traits in field cricket nymphs?

acta ethologica - Between-individual differences in personality and life-history traits can arise from both genetic and environmental factors, with the latter possibly reflecting contrasting...     

Does habitat fragmentation affect temperature-related life-history traits? A laboratory test with a woodland butterfly

Habitat fragmentation may change local climatic conditions leading to altered selection regimes for life-history traits in small ectotherms, including several insects. We investigated temperature-related performance in terms of fitness among populations of the woodland butterfly Pararge aegeria (L.) originating from populations of a closed, continuous woodland landscape versus populations of an open, highly fragmented agricultural landscape in central Belgium. Female fecundity and longevity were evaluated in a temperature-gradient experiment. As predicted, females of woodland landscape origin reached higher maximum daily fecundity and lifetime number of eggs than did agricultural landscape females at low ambient temperatures, but this reversed at high ambient temperature. Egg weight decreased with temperature, and eggs of woodland butterflies were smaller. Contrary to what is generally assumed, remaining thorax mass was a better predictor of lifetime reproductive output than was abdomen mass. Since we used the F2 generation from wild-caught females reared under common garden conditions, the observed effects are likely to rely on intrinsic, heritable variation. Our results suggest that differential selection regimes associated with different landscapes intervene by intraspecific variation in the response of a butterfly to variation in ambient temperature, and may thus be helpful when making predictions of future impacts on how wild populations respond to environmental conditions under a global change scenario, with increasing temperatures and fragmented landscapes.     

Biogeographic and anthropogenic correlates of Aleutian Islands plant diversity: A machine‐learning approach

This is the first comprehensive analysis of vascular plant diversity patterns in the Aleutian Islands to identify and quantify the impact of Aleutian Island distance dispersal barriers, geographical, ecological and anthropogenic factors. Data from public Open Access databases, printed floristic accounts, and from collections made by the primary author were used to develop an Aleutian floristic database. The most common plant distribution pattern was “an eastern origin community”, though it compared similarly to the “Western” and “Widespread” distribution pattern. We established an ecological plant community composition class for each island, based on clustering species assemblage dissimilarity measurements (Jaccard Index), and a measurement of phylogenetic dissimilarity (UniFrac). We modelled these composition classes and species richness values in non‐parametric algorithmic models and concepts (data cloning using machine learning, stochastic boosting‐ TreeNet) based on classic and Aleutians‐specific island biogeography hypotheses. Plant species richness is strongly associated with the equilibrium model variables of area and island isolation, as well as distance to the Alaska Peninsula, and island total stream length. Species composition is strongly associated with the landmass groups during the last glacial maximum, maximum island elevation, island isolation and island area. Phylogenetic composition is associated with island area, distance from the islands to the Chukotka Peninsula, maximum island elevation, island geologic age, and island isolation. This study extends the equilibrium theory of island biogeography by including additional drivers of diversity during the Anthropocene, such as the landmass during the LGM, as well as factors that may be related to anthropogenic extinction rate.     

Is urbanization scrambling the genetic structure of human populations? A case study

Recent population expansion and increased migration linked to urbanization are assumed to be eroding the genetic structure of human populations. We investigated change in population structure over three generations by analysing both demographic and mitochondrial DNA (mtDNA) data from a random sample of 2351 men from 22 Iranian populations. Potential changes in genetic diversity (theta) and genetic distance (F(ST)) over the last three generations were analysed by assigning mtDNA sequences to populations based on the individual's place of birth or that of their mother or grandmother. Despite the fact that several areas included cities of over one million inhabitants, we detected no change in genetic diversity, and only a small decrease in population structure, except in the capital city (Tehran), which was characterized by massive immigration, increased theta and a large decrease in F(ST) over time. Our results suggest that recent erosion of human population structure might not be as important as previously thought, except in some large conurbations, and this clearly has important implications for future sampling strategies.     

Is there a relationship between early genotoxicity and life-history traits in Vicia faba exposed to cadmium-spiked soils?

The Vicia faba-micronucleus test is usually performed to assess the genotoxic potential of pure substances, effluents or water extracts from soil. It is also a relevant, early biological tool to detect mutagenic substances in crude soils. Nevertheless, the physiological meaning of such DNA damage for the plant in the long term remains to be elucidated. To know more about this, two experiments were carried out with the plant model V. faba. In a preliminary short-term experiment, seeds were exposed for five days to a soil spiked with different concentrations of CdCl(2) in order to identify the concentration inducing the highest number of micronuclei without affecting plant growth. Thereafter, a long-term experiment was performed in the soil spiked with such a concentration (i.e. 510μmol CdCl(2) per kg dry soil), in which V. faba seeds were directly sowed and allowed to grow during 151 days. As a result, Cd-spiked soil did not affect seed-emergence time nor the growth-rate of the plants for the first two months. The first signs of toxicity appeared after the 70th day of exposure. Interestingly, exposed plants produced their first flower earlier and had a longer flowering period than did control ones. Nevertheless, total flower production was less abundant in exposed plants than in control plants. Moreover, fruits appeared in control plants whereas no fruit was formed in exposed plants. At last, exposed plants showed a reduced life time. Our results suggest that the micronucleus assay can provide a predictive biomarker of long-term deleterious effects in plants.     

Effects of deforestation on structure and diversity of small mammal communities in the Moravskoslezské Beskydy Mts (Czech Republic)

During 1970s and 1980s, a large area of mountains in the Czech Republic was influenced by long-term industrial air pollution. Among the most degraded areas were the peaks of the Moravskoslezské Beskydy Mts, where vast clearings resulted from emissions and subsequent forest destruction. This study is aimed at determining the degree of deforestation that is necessary to cause changes in structure and species diversity of small mammal communities that were observed previously. Communities of rodents and insectivores were monitored for a minimum of 3 years at two mountain ranges of the Moravskoslezské Beskydy Mts (Czech Republic) by standard mouse snap-traps. The localities (Smrk and Kněhyně) differ by the degree of human disturbance. Clearings on Smrk Mt are very large (> 30 ha) with no remaining original forest growth as a result of intensive air pollution, unlike the same habitat type at Kněhyně Mt, where the clearings are minor (< 3 ha) and contain living solitary trees. Structure and diversity of small mammal communities in clearings were compared with those from original forests and other mountain habitats. Communities of small mammals at clearings in Smrk Mt (with dominatingMicrotus agrestis) are structurally very different from all other habitats, while structure of communities at Kněhyně clearings are very similar to those of original mountain forest (Complete linkage clustering based on Renkonen index). The community of the original mountain spruce forest at Kněhyně had the highest species diversity (according to Shannon-Weaver, Brillouin, and Simpson indices, Shannon evenness, and rarefaction), while species diversity at clearings of Smrk was the lowest. Shannon diversity of community at Kněhyně primeval forest is similar to that of Kněhyně clearings, while at Smrk Mt the forest diversity is higher than that of clearings. The species diversity of mountain forest and clearings at Kněhyně Mt was significantly higher than that in the same habitats at Smrk Mt. Our results obtained in disturbed habitats at Kněhyně and Smrk Mts suggest that the degree of deforestation may influence the presence and/or the degree of community changes. If the forest destruction is relatively small (clearings < 3 ha), the structure and diversity of small mammal communities do not differ from those of original forest.     

Do Australian small mammals respond to native and introduced predator odours?

Abstract Coevolution is thought to have led to many small mammal species avoiding the scent marks of their main mammalian predators, as they provide a reliable cue to predation risk. Most support for this hypothesis comes from northern hemisphere predator/prey systems, however, it is unclear whether this avoidance of predator faecal odour occurs in Australia's mammalian fauna, which has evolved in relative isolation from the rest of the world, and is dominated by marsupials rather than placentals. We tested this theory for an Australian system with marsupial and placental predators and prey, that share a long‐term (>1 million years) or short‐term (<150 years) exposure to each other. The predators were the native marsupial tiger quoll Dasyurus maculatus and the introduced placental red fox Vulpes vulpes. The potential prey were three native rodent species, the bush rat Rattus fuscipes, the swamp rat Rattus lutreolus, the eastern chestnut mouse Pseudomys gracilicaudatus, and the marsupial brown antechinus Antechinus stuartii. Small mammals were captured in Elliott traps with 1/3 of traps treated with fox faeces, 1/3 treated with quoll faeces and the remainder left untreated. The native rodent species all showed avoidance of both tiger quoll and red fox odours whereas the marsupial antechinus showed no responses to either odour. Either predator odour avoidance has not evolved in this marsupial or their reaction to predator odours may be exhibited in ways which are not recognizable through trapping. The avoidance by the rodents of fox odour as well as quoll odour indicates this response may either be due to common components in fox and quoll odour, or it may be a recently evolved response.     

How integrated are behavioral and endocrine stress response traits? A repeated measures approach to testing the stress-coping style model

It is widely expected that physiological and behavioral stress responses will be integrated within divergent stress‐coping styles (SCS) and that these may represent opposite ends of a continuously varying reactive–proactive axis. If such a model is valid, then stress response traits should be repeatable and physiological and behavioral responses should also change in an integrated manner along a major axis of among‐individual variation. While there is some evidence of association between endocrine and behavioral stress response traits, few studies incorporate repeated observations of both. To test this model, we use a multivariate, repeated measures approach in a captive‐bred population of Xiphophorus birchmanni. We quantify among‐individual variation in behavioral stress response to an open field trial (OFT) with simulated predator attack (SPA) and measure waterborne steroid hormone levels (cortisol, 11‐ketotestosterone) before and after exposure. Under the mild stress stimulus (OFT), (multivariate) behavioral variation among individuals was consistent with a strong axis of personality (shy–bold) or coping style (reactive–proactive) variation. However, behavioral responses to a moderate stressor (SPA) were less repeatable, and robust statistical support for repeatable endocrine state over the full sampling period was limited to 11‐ketotestosterone. Although post hoc analysis suggested cortisol expression was repeatable over short time periods, qualitative relationships between behavior and glucocorticoid levels were counter to our a priori expectations. Thus, while our results clearly show among‐individual differences in behavioral and endocrine traits associated with stress response, the correlation structure between these is not consistent with a simple proactive–reactive axis of integrated stress‐coping style. Additionally, the low repeatability of cortisol suggests caution is warranted if single observations (or indeed repeat measures over short sampling periods) of glucocorticoid traits are used in ecological or evolutionary studies focussed at the individual level.     

Is nest‐site availability limiting Lesser Kestrel populations? A multiple scale approach

The Lesser Kestrel, a colonial migratory falcon, is one of the most endangered birds in Europe and, due to a sharp population decline across much of the breeding range, is globally threatened. The reasons for this decline are unclear, but reduced nest-site availability might be a major cause. To test this hypothesis we looked at nest-site availability within Portuguese colonies in rural and urban buildings. Nest holes were larger, longer, higher and older than unoccupied cavities. A typical nest cavity was approximately 29–30 cm long, 300–340 cm high and had an inner chamber 16.5–18 cm wide. Large-scale surveys of existing buildings in Portuguese villages suggested that 85% of sites lacked suitable nest cavities. The model for selection of buildings indicated that Lesser Kestrels prefer buildings with many roof and wall cavities, and that are surrounded by extensive cereal and fallow fields. The villages selected had many old buildings and monuments, were located in areas with few rivers, and a low percentage cover of cereal, olive groves and forest. The conservation implications of these results are discussed.     

Do species populations really start small? New perspectives from the Late Neogene fossil record of African mammals.

This analysis of all known African larger mammals of the past 10 Myr offers new perspectives on the geographical circumstances of speciation. Our central question is: does the fossil evidence support the idea that most new species start as small populations and, if true, how long is the average growth interval until species are established at their mean later size? This simple question is important to unravelling the competing claims of rival models of speciation. We approached it by direct use of fossil data, which, to our knowledge, has not been done previously. We compared the numbers of fossil site records, as a proxy for magnitude of geographical spread, between survivorship intervals across all species. The results show that the average mammal species has indeed started its life in a relatively small population, and thereafter increased rapidly in geographical spread to reach its long-term equilibrium abundance by about 1 million years after origin. Some theoretical implications of these results are discussed.