PHENOTYPIC VARIATION OF GROWTH TRAJECTORIES IN FINCHES

Evolution cannot proceed without phenotypic variation for selection to act on. This is particularly true of ontogenetic parameters because it is changes in these parameters that give rise to new phenotypes. I analyzed the amount and dimensionality of phenotypic variation on growth trajectories in early ontogeny in three species of finches (Fringillidae) using the recently developed infinite-dimensional model. For two species, eight traits were analyzed, and for a third, six traits. Growth data were analyzed only up to 6 d of age in two species and 8 d of age in the third. The results were very similar for all species and traits. A very large proportion of the phenotypic variation in growth trajectories was confined to a single dimension. This dimension corresponded to a simultaneous increase/decrease at all ages in early ontogeny. The eigenfunctions, each describing a family of similar-shaped growth trajectories, were highly collinear among traits. A high covariance existed among traits at the same and different ages. If some part of the phenotypic variation has an additive genetic basis, then any selection for a change in size at one age in one trait will lead to a response in a size at subsequent ages and in the other traits. This in turn suggests that morphological evolution frequently will move along a multivariate size axis, as has indeed been found in several taxa.     

Extreme land-cover and biodiversity change as an outcome of land abandonment on a Mediterranean island (eastern Adriatic)

Understanding land abandonment and the resulting changes in land cover provides data for suitable reaction to habitat and species losses this process brings. This study aimed to define land-cover types and their biodiversity, record spatio-temporal changes and detect the trajectories and magnitude of these changes. The study was conducted on the island of Molat in the eastern Adriatic Sea. Land cover was defined for different years (1910, 1959, 1986, 2006) using remote sensing and recent vegetation sampling. The obtained land-cover maps were used for spatio-temporal analysis of land-cover change. Open vegetation units of rocky grassland, mesophilous grasslands and farm land dominated in 1910, covering 90% of the island. The observed changes occurred in trajectories through semi-open towards closed vegetation. In 2006, closed vegetation dominated, covering approximately 70% of the island area. The overall land-cover change was extreme, occurring over 90% of the island surface. Biodiversity analysis was related to the present land-cover types and change trajectories, and showed a considerable decline of species richness towards closed vegetation types. All observed changes were correlated to island depopulation and land abandonment. Re-population and encouragement of agro-pastoral activities should reduce habitat and species loss in the process of secondary succession.     

Ontogenetic switches from plant resistance to tolerance: minimizing costs with age?

Changes in herbivory and resource availability during a plant's development should promote ontogenetic shifts in resistance and tolerance, if the costs and benefits of these basic strategies also change as plants develop. We proposed and tested a general model to detect the expression of ontogenetic tradeoffs for these two alternative anti-herbivory strategies in Raphanus sativus . We found that ontogenetic trajectories occur in both resistance and tolerance but in opposite directions. The juvenile stage was more resistant but less tolerant than the reproductive stage. The ontogenetic switch from resistance to tolerance was consistent with the greater vulnerability of young plants to leaf damage and with the costs of resistance and tolerance found at each stage. We posit that the ontogenetic perspective presented here will be helpful in resolving the current debate on the existence and detection of a general resistance–tolerance tradeoff.     

Intra-flock variability in the body reserve dynamics of meat sheep by analyzing BW and body condition score variations over multiple production cycles

Breeding for resilience requires a better understanding of intra-flock variability and the related mechanisms responsible for robustness traits. Among such traits, the animals’ ability to cope with feed fluctuations by mobilizing or restoring body reserves (BR) is a key mechanism in ruminants. The objective of this work was to characterize individual variability in BR dynamics in productive Romane ewes reared in extensive conditions. The BR dynamics profiles were characterized by combining individual longitudinal measurements of BW and body condition scores (BCS) over several production cycles. Historical data, including up to 2628 records per trait distributed in 1146 ewes, underwent cluster analysis. Two to four trajectories were observed for BW depending on the cycle, while three trajectories were found for BCS, whatever the cycle. Most trajectories suggested that BR dynamics were similar but the level of BR may differ between ewes. Nevertheless, some trajectories suggested that both BR dynamics and levels were different for a proportion of ewes. Clustering on BW and BCS profiles adjusted for individual level trends, resulted in differences only in the level of BW or BCS, rather than differences in trajectories. Thus, the overall shape of trajectories was not changed considering or not the individual level trend across cycles. In addition to individual variability, the ewe’s age at first lambing and litter size contributed to the distribution of the ewes between the trajectories. Regarding the entire productive life, three trajectories were observed for BW and BCS changes over three productive cycles. Increase in BW at each cycle suggested that ewes kept growing up until 3 to 4 years old in our conditions. Similar alternation of BCS gains and losses across cycles suggested BR dynamics might be repeatable. Many individual trajectories remained the same throughout a ewe’s life, whatever the age at first lambing, parity or litter size. Our results demonstrate the relevance of using BW and BCS changes for characterizing the diversity of BR mobilization–accretion profiles in sheep in a long timespan perspective.     

Patterns of cranial ontogeny in lacertid lizards: morphological and allometric disparity

We explored the ontogenetic dynamics of the morphological and allometric disparity in the cranium shapes of twelve lacertid lizard species. The analysed species (Darevskia praticola, Dinarolacerta mosorensis, Iberolacerta horvathi, Lacerta agilis, L. trilineata, L. viridis, Podarcis erhardii, P. melisellensis, P. muralis, P. sicula, P. taurica and Zootoca vivipara) can be classified into different ecomorphs: terrestrial lizards that inhabit vegetated habitats (habitats with lush or sparse vegetation), saxicolous and shrub‐climbing lizards. We observed that there was an overall increase in the morphological disparity (MD) during the ontogeny of the lacertid lizards. The ventral cranium, which is involved in the mechanics of jaw movement and feeding, showed higher levels of MD, an ontogenetic shift in the morphospace planes and more variable allometric patterns than more conserved dorsal crania. With respect to ecology, the allometric trajectories of the shrub‐climbing species tended to cluster together, whereas the allometric trajectories of the saxicolous species were highly dispersed. Our results indicate that the ontogenetic patterns of morphological and allometric disparity in the lacertid lizards are modified by ecology and functional constraints and that the identical mechanisms that lead to intraspecific morphological variation also produce morphological divergence at higher taxonomic levels.     

Invasive shrub distribution varies with distance to roads and stand age in eastern deciduous forests in Indiana, USA

We documented the relationship between densities of invasive exotic shrubs, distance to road, and successional age of the forest in 14 forested sites throughout central and southern Indiana. Roadways are increasingly abundant, human-made features that can be conduits for the spread of invasive exotic plants in a number of ecosystems. Little is known, however, about the role of roads in eastern deciduous forest ecosystems where road density is high. Further, it is not known whether the distribution of exotic plants along roads depends on the successional age of the forest. In this study, densities of four of seven exotic shrub species declined with increasing distance to the nearest road across all successional ages. Greater densities of exotic shrubs were found in young and mid-successional forests than mature forests. However, there was no interaction between distance to road and forest age, suggesting that the role of roads in the invasion process does not change across forest successional ages. We outline several potential mechanisms that may drive patterns of shrub distribution along roadside edges as a guide for future research.     

Nutrient concentration-stream discharge relationships during storm events in a first-order stream

The relationship between nutrient element concentration and stream discharge during storm events was studied in a nutrient-rich first order stream. Stream concentrations of NO₃-N, phosphate-P, Ca, and Mg were determined during the course of and following thunderstorms. Nutrient element trajectories were constructed for the elements monitored and some recognizable and reproducible patterns in nutrient concentrations emerged. NO₃-N and phosphate-P generally increased in concentration during the early stages of increasing stream discharge resulting in a general clockwise trajectory. Ca and Mg consistently showed decreases in concentration during rising water, but the pattern of the trajectories was less constant. The patterns seen for NO₃-N and phosphate-P suggest surface run-off as their origin while the patterns for Ca and Mg reflect their primary origin in groundwater. The ability to detect these differences from the analysis of nutrient trajectories suggests the use of this technique for determining the source of other elements in streams.     

Prediction of Antibiotic Resistance Evolution by Growth Measurement of All Proximal Mutants of Beta-Lactamase

The antibiotic resistance crisis continues to threaten human health. Better predictions of the evolution of antibiotic resistance genes could contribute to the design of more sustainable treatment strategies. However, comprehensive prediction of antibiotic resistance gene evolution via laboratory approaches remains challenging. By combining site-specific integration and high-throughput sequencing, we quantified relative growth under the respective selection of cefotaxime or ceftazidime selection in ∼23,000 Escherichia coli MG1655 strains that each carried a unique, single-copy variant of the extended-spectrum β-lactamase gene bla_CTX-M-14 at the chromosomal att HK022 site. Significant synergistic pleiotropy was observed within four subgenic regions, suggesting key regions for the evolution of resistance to both antibiotics. Moreover, we propose PEAR^P and PEAR^R, two deep-learning models with strong clinical correlations, for the prospective and retrospective prediction of bla_CTX-M-14 evolution, respectively. Single to quintuple mutations of bla_CTX-M-14 predicted to confer resistance by PEAR^P were significantly enriched among the clinical isolates harboring bla_CTX-M-14 variants, and the PEAR^R scores matched the minimal inhibitory concentrations obtained for the 31 intermediates in all hypothetical trajectories. Altogether, we conclude that the measurement of local fitness landscape enables prediction of the evolutionary trajectories of antibiotic resistance genes, which could be useful for a broad range of clinical applications, from resistance prediction to designing novel treatment strategies.     

Describing mate preference functions and other function‐valued traits

Mate preferences are important causes of sexual selection. They shape the evolution of sexual ornaments and displays, sometimes maintaining genetic diversity and sometimes promoting speciation. Mate preferences can be challenging to study because they are expressed in animal brains and because they are a function of the features of potential mates that are encountered. Describing them requires taking this into account. We present a method for describing and analysing mate preference functions, and introduce a freely available computer program that implements the method. We give an overview of how the program works, and we discuss how it can be used to visualize and quantitatively analyse preference functions. In addition, we provide an informal review of different methods of testing mate preferences, with recommendations for how best to set up experiments on mate preferences. Although the program was written with mate preferences in mind, it can be used to study any function‐valued trait, and we hope researchers will take advantage of it across a broad range of traits.