Global loss of avian evolutionary uniqueness in urban areas

Urbanization, one of the most important anthropogenic impacts on Earth, is rapidly expanding worldwide. This expansion of urban land‐covered areas is known to significantly reduce different components of biodiversity. However, the global evidence for this effect is mainly focused on a single diversity measure (species richness) with a few local or regional studies also supporting reductions in functional diversity. We have used birds, an important ecological group that has been used as surrogate for other animals, to investigate the hypothesis that urbanization reduces the global taxonomical and/or evolutionary diversity. We have also explored whether there is evidence supporting that urban bird communities are evolutionarily homogenized worldwide in comparison with nonurban ones by means of using evolutionary distinctiveness (how unique are the species) of bird communities. To our knowledge, this is the first attempt to quantify the effect of urbanization in more than one single diversity measure as well as the first time to look for associations between urbanization and phylogenetic diversity at a large spatial scale. Our findings show a strong and globally consistent reduction in taxonomic diversity in urban areas, which is also synchronized with the evolutionary homogenization of urban bird communities. Despite our general patterns, we found some regional differences in the intensity of the effect of cities on bird species richness or evolutionary distinctiveness, suggesting that conservation efforts should be adapted locally. Our findings might be useful for conservationists and policymakers to minimize the impact of urban development on Earth's biodiversity and help design more realistic conservation strategies.     

Pattern and process of biotic homogenization in the New Pangaea

Human activities have reorganized the earth''s biota resulting in spatially disparate locales becoming more or less similar in species composition over time through the processes of biotic homogenization and biotic differentiation, respectively. Despite mounting evidence suggesting that this process may be widespread in both aquatic and terrestrial systems, past studies have predominantly focused on single taxonomic groups at a single spatial scale. Furthermore, change in pairwise similarity is itself dependent on two distinct processes, spatial turnover in species composition and changes in gradients of species richness. Most past research has failed to disentangle the effect of these two mechanisms on homogenization patterns. Here, we use recent statistical advances and collate a global database of homogenization studies (20 studies, 50 datasets) to provide the first global investigation of the homogenization process across major faunal and floral groups and elucidate the relative role of changes in species richness and turnover. We found evidence of homogenization (change in similarity ranging from −0.02 to 0.09) across nearly all taxonomic groups, spatial extent and grain sizes. Partitioning of change in pairwise similarity shows that overall change in community similarity is driven by changes in species richness. Our results show that biotic homogenization is truly a global phenomenon and put into question many of the ecological mechanisms invoked in previous studies to explain patterns of homogenization.     

Morphological evolution: Estimation principles, patterns, and mechanisms

Directions, modes, specializations, and coordination systems of morphofunctional changes are discussed based on modern data. Phylogenetic heterochronies (pedomorphoses and outstripping), which provide the basis for parallel, mosaic, and saltation development and different rates of morphological evolution, are regarded as important events of morphological diversification. The analysis of specificity and relationships of structural levels of organization (including genetic and epigenetic) and the elaboration of evolutionary principles of their dynamic stability are thought to be the most promising fields of modern research.     

Inferring functional linkages between proteins from evolutionary scenarios

Identifying potential protein interactions is of great importance in understanding the topologies of cellular networks, which is much needed and valued in current systematic biological studies. The development of our computational methods to predict protein-protein interactions have been spurred on by the massive sequencing efforts of the genomic revolution. Among these methods is phylogenetic profiling, which assumes that proteins under similar evolutionary pressures with similar phylogenetic profiles might be functionally related. Here, we introduce a method for inferring functional linkages between proteins from their evolutionary scenarios. The term evolutionary scenario refers to a series of events that occurred in speciation over time, which can be reconstructed given a phylogenetic profile and a species tree. Common evolutionary pressures on two proteins can then be inferred by comparing their evolutionary scenarios, which is a direct indication of their functional linkage. This scenario method has proven to have better performance compared with the classical phylogenetic profile method, when applied to the same test set. In addition, predicted results of the two methods are found to be fairly different, suggesting the possibility of merging them in order to achieve a better performance. We analyzed the influence of the topology of the phylogenetic tree on the performance of this method, and found it to be robust to perturbations in the topology of the tree. However, if a completely random tree is incorporated, performance will decline significantly. The evolutionary scenario method was used for inferring functional linkages in 67 species, and 40,006 linkages were predicted. We examine our prediction for budding yeast and find that almost all predicted linkages are supported by further evidence.     

Understanding variation in human fertility: what can we learn from evolutionary demography?

Decades of research on human fertility has presented a clear picture of how fertility varies, including its dramatic decline over the last two centuries in most parts of the world. Why fertility varies, both between and within populations, is not nearly so well understood. Fertility is a complex phenomenon, partly physiologically and partly behaviourally determined, thus an interdisciplinary approach is required to understand it. Evolutionary demographers have focused on human fertility since the 1980s. The first wave of evolutionary demographic research made major theoretical and empirical advances, investigating variation in fertility primarily in terms of fitness maximization. Research focused particularly on variation within high-fertility populations and small-scale subsistence societies and also yielded a number of hypotheses for why fitness maximization seems to break down as fertility declines during the demographic transition. A second wave of evolutionary demography research on fertility is now underway, paying much more attention to the cultural and psychological mechanisms underpinning fertility. It is also engaging with the complex, multi-causal nature of fertility variation, and with understanding fertility in complex modern and transitioning societies. Here, we summarize the history of evolutionary demographic work on human fertility, describe the current state of the field, and suggest future directions.     

The relationship between functional and taxonomic homogenization

Aim Species introductions and extinctions have reorganized the earth's biota, often leaving formerly spatially distinct assemblages more similar in species composition, a process termed biotic homogenization. The study of biotic homogenization has been almost entirely focused on the change in taxonomic similarity between assemblages through time. Here, we provide a trait‐based method for calculating functional similarity through time and compare these trends in functional attributes with those trends generated from a taxonomic perspective. Location Data were produced through computer simulation and gathered from North American Breeding Bird Survey (BBS) data and published accounts of North American birds for 10 locations across the east and west coast of the United States. Methods We simulated change in assemblages with different trait types (binary and continuous), levels of trait overlap, number of traits and species richness to determine the relationship between change in taxonomic similarity (ΔTS) and change in functional similarity (ΔFS). We also assess the relationship between ΔTS and ΔFS for bird assemblages across 10 locales in the USA between 1968 and 2008. We used simple linear regression to determine the slope and correlation between ΔTS and ΔFS and used multiple regression to assess the influence of trait overlap, number of traits, species richness and the ratio of traits to species on the relationship between ΔTS and ΔFS. Results Simulations reveal that trait redundancy governs the relationship between ΔTS and ΔFS. A decrease in trait overlap increases the slope of the regression between ΔTS and ΔFS and an increase in the ratio of traits to species in the regional pool increases the correlation. The relationship between ΔTS and ΔFS for breeding birds is comparable to simulations with low trait redundancy. Main conclusions We show that often losing or gaining species from an assemblage tells us very little about the loss or gain of function, and that this scenario most often occurs when the two assemblages have high trait redundancy. It remains to be seen how prevalent this scenario is within empirical examples; however, the implications for the continued delivery of ecosystem functions in the face of species introductions and extinctions are large.     

Complete gene sequence of spider attachment silk protein (PySp1) reveals novel linker regions and extreme repeat homogenization

Spiders use a myriad of silk types for daily survival, and each silk type has a unique suite of task-specific mechanical properties. Of all spider silk types, pyriform silk is distinct because it is a combination of a dry protein fiber and wet glue. Pyriform silk fibers are coated with wet cement and extruded into “attachment discs” that adhere silks to each other and to substrates. The mechanical properties of spider silk types are linked to the primary and higher-level structures of spider silk proteins (spidroins). Spidroins are often enormous molecules (>250 kDa) and have a lengthy repetitive region that is flanked by relatively short (∼100 amino acids), non-repetitive amino- and carboxyl-terminal regions. The amino acid sequence motifs in the repetitive region vary greatly between spidroin type, while motif length and number underlie the remarkable mechanical properties of spider silk fibers. Existing knowledge of pyriform spidroins is fragmented, making it difficult to define links between the structure and function of pyriform spidroins. Here, we present the full-length sequence of the gene encoding pyriform spidroin 1 (PySp1) from the silver garden spider Argiope argentata. The predicted protein is similar to previously reported PySp1 sequences but the A. argentata PySp1 has a uniquely long and repetitive “linker”, which bridges the amino-terminal and repetitive regions. Predictions of the hydrophobicity and secondary structure of A. argentata PySp1 identify regions important to protein self-assembly. Analysis of the full complement of A. argentata PySp1 repeats reveals extreme intragenic homogenization, and comparison of A. argentata PySp1 repeats with other PySp1 sequences identifies variability in two sub-repetitive expansion regions. Overall, the full-length A. argentata PySp1 sequence provides new evidence for understanding how pyriform spidroins contribute to the properties of pyriform silk fibers.     

MOLECULAR PALAEOBIOLOGY

Abstract:  For more than a generation, molecular biology has been used to approach palaeontological problems, and yet only recently have attempts been made to integrate research utilizing the geological and genomic records in uncovering evolutionary history. We codify this approach as Molecular Palaeobiology for which we provide a synthetic framework for studying the interplay among genotype, phenotype and the environment, within the context of deep time. We provide examples of existing studies where molecular and morphological data have been integrated to provide novel insights within each of these variables, and an account of a case study where each variable has been tackled to understand better a single macroevolutionary event: the diversification of metazoan phyla. We show that the promise of this approach extends well beyond research into the evolutionary history of animals and, in particular, we single out plant evolution as the single greatest opportunity waiting to be exploited by molecular palaeobiology. Although most of our examples consider how novel molecular data and techniques have breathed new life into long-standing palaeontological controversies, we argue that this asymmetry in the balance of molecular and morphological evidence is an artefact of the relative 'newness' of molecular data. In particular, palaeontological data provide unique and crucial roles in unravelling evolutionary history given that extinct taxa reveal patterns of character evolution invisible to molecular biology. Finally, we argue that palaeobiologists, rather than molecular biologists, are best placed to exploit the opportunity afforded by molecular palaeobiology, though this will require incorporating the techniques and approaches of molecular biology into their skill-set.     

Spatial aspects of trait homogenization within the German flora

Aim Biotic homogenization, the replacement of local biota by non‐indigenous and locally expanding species, is among the major effects of species invasions. Almost all studies related to this topic are focused on the species level, on taxonomic homogenization. Homogenization effects on trait diversity (functional homogenization) may be very important for ecosystem functioning, but they are rarely analysed, especially not at different spatial scales within a single study. This paper aims to examine how the presence of alien species (species introduced since 1500 ad ) affects the distribution of ploidy levels in the German flora at different spatial scales. Location Germany. Methods We used a resampling method and the Morisita–Horn dissimilarity index to calculate dissimilarities of ploidy level within and between alien and indigenous plants at three different spatial scales in Germany: (1) the entire country as one location, (2) between grid cells, and (3) within grid cells of a lattice covering Germany. Results We found a significant differentiation effect within grid cells of c. 130 km², with alien plants increasing the variability of ploidy levels. The differentiation effect varies according to the scale used. At the coarsest scale (entire Germany), ploidy levels of alien plants tend to be more homogeneous in composition compared with those of native plants. At the intermediate scale (between grid cells), and even more pronounced at a small scale (within grid cells), ploidy levels are more heterogeneously distributed across Germany than those of native plant species. Main conclusions Homogenization of ploidy levels at a large scale (entire Germany) and differentiation at a small scale (within grid cells) is comparable with the patterns found in taxonomic homogenization analyses. This analysis is a first step towards understanding the impacts of plant invasions on a trait level. Differentiation and homogenization of ploidy levels might mirror the distribution of related ecological traits and therefore might have an impact on ecosystem functioning.     

The effect of low pressure-homogenized lactic cultures on the development of proteolysis in cheese slurry

Summary The aim of this study was to determine the effect of low pressure-homogenization of lactic acid bacteria (LAB) on the development of proteolysis in the slurry medium. For the slurry, the milk was pasteurized at 65 °C for 30 min, cooled to 32 °C and coagulated. The curd obtained was blended; the dry matter was adjusted to 30% by adding distilled water, placed into the flasks and autoclaved. The LAB Lactococcus lactis subsp. lactis, Lactococcus lactis subsp. cremoris, Lactobacillus delbrueckii subsp. bulgaricus, Streptococcus thermophilus, and Lactobacillus helveticus were used in cheese slurry. Homogenization was performed at 30 MPa and 40 °C. The cheese slurries were incubated with and without homogenized cultures at 9 and 30 °C for up to 72 h. During incubation, the changes in trichloroacetic acid-soluble nitrogen (TCA-SN) and phosphotungstic acid-soluble nitrogen (PTA-SN) as well as pH were monitored. The results showed that pH development was slower in the slurries to which homogenized culture was added. Higher TCA-SN and PTA-SN values were obtained from the slurries incubated at 30 °C. Moreover, higher TCA-SN and PTA-SN values were found in the slurries incubated with homogenized mesophilic culture and Lb. helveticus (P<0.05). The results suggested that homogenization of the cultures was a promising method for the acceleration of cheese ripening.     

Postcopulatory sexual selection is associated with accelerated evolution of sperm morphology

Rapid diversification of sexual traits is frequently attributed to sexual selection, though explicit tests of this hypothesis remain limited. Spermatozoa exhibit remarkable variability in size and shape, and studies report a correlation between sperm morphology (sperm length and shape) and sperm competition risk or female reproductive tract morphology. However, whether postcopulatory processes (e.g., sperm competition and cryptic female choice) influence the speed of evolutionary diversification in sperm form is unknown. Using passerine birds, we quantified evolutionary rates of sperm length divergence among lineages (i.e., species pairs) and determined whether these rates varied with the level of sperm competition (estimated as relative testes mass). We found that relative testes mass was significantly and positively associated with more rapid phenotypic divergence in sperm midpiece and flagellum lengths, as well as total sperm length. In contrast, there was no association between relative testes mass and rates of evolutionary divergence in sperm head size, and models suggested that head length is evolutionarily constrained. Our results are the first to show an association between the strength of sperm competition and the speed of sperm evolution, and suggest that postcopulatory sexual selection promotes rapid evolutionary diversification of sperm morphology.     

Revealing hidden evolutionary capacity to cope with global change

The extent to which global change will impact the long‐term persistence of species depends on their evolutionary potential to adapt to future conditions. While the number of studies that estimate the standing levels of adaptive genetic variation in populations under predicted global change scenarios is growing all the time, few studies have considered multiple environments simultaneously and even fewer have considered evolutionary potential in multivariate context. Because conditions will not be constant, adaptation to climate change is fundamentally a multivariate process so viewing genetic variances and covariances over multivariate space will always be more informative than relying on bivariate genetic correlations between traits. A multivariate approach to understanding the evolutionary capacity to cope with global change is necessary to avoid misestimating adaptive genetic variation in the dimensions in which selection will act. We assessed the evolutionary capacity of the larval stage of the marine polychaete Galeolaria caespitosa to adapt to warmer water temperatures. Galeolaria is an important habitat‐forming species in Australia, and its earlier life‐history stages tend to be more susceptible to stress. We used a powerful quantitative genetics design that assessed the impacts of three temperatures on subsequent survival across over 30 000 embryos across 204 unique families. We found adaptive genetic variation in the two cooler temperatures in our study, but none in the warmest temperature. Based on these results, we would have concluded that this species has very little capacity to evolve to the warmest temperature. However, when we explored genetic variation in multivariate space, we found evidence that larval survival has the potential to evolve even in the warmest temperatures via correlated responses to selection across thermal environments. Future studies should take a multivariate approach to estimating evolutionary capacity to cope with global change lest they misestimate a species’ true adaptive potential.     

Eco-evolutionary feedbacks,adaptive dynamics and evolutionary rescue theory

Adaptive dynamics theory has been devised to account for feedbacks between ecological and evolutionary processes. Doing so opens new dimensions to and raises new challenges about evolutionary rescue. Adaptive dynamics theory predicts that successive trait substitutions driven by eco-evolutionary feedbacks can gradually erode population size or growth rate, thus potentially raising the extinction risk. Even a single trait substitution can suffice to degrade population viability drastically at once and cause ‘evolutionary suicide’. In a changing environment, a population may track a viable evolutionary attractor that leads to evolutionary suicide, a phenomenon called ‘evolutionary trapping’. Evolutionary trapping and suicide are commonly observed in adaptive dynamics models in which the smooth variation of traits causes catastrophic changes in ecological state. In the face of trapping and suicide, evolutionary rescue requires that the population overcome evolutionary threats generated by the adaptive process itself. Evolutionary repellors play an important role in determining how variation in environmental conditions correlates with the occurrence of evolutionary trapping and suicide, and what evolutionary pathways rescue may follow. In contrast with standard predictions of evolutionary rescue theory, low genetic variation may attenuate the threat of evolutionary suicide and small population sizes may facilitate escape from evolutionary traps.     

Evolutionarily singular strategies and the adaptive growth and branching of the evolutionary tree

We present a general framework for modelling adaptive trait dynamics in which we integrate various concepts and techniques from modern ESS-theory. The concept of evolutionarily singular strategies is introduced as a generalization of the ESS-concept. We give a full classification of the singular strategies in terms of ESS-stability, convergence stability, the ability of the singular strategy to invade other populations if initially rare itself, and the possibility of protected dimorphisms occurring within the singular strategy's neighbourhood. Of particular interest is a type of singular strategy that is an evolutionary attractor from a great distance, but once in its neighbourhood a population becomes dimorphic and undergoes disruptive selection leading to evolutionary branching. Modelling the adaptive growth and branching of the evolutionary tree can thus be considered as a major application of the framework. A haploid version of Levene's soft selection model is developed as a specific example to demonstrate evolutionary dynamics and branching in monomorphic and polymorphic populations.     

Effects of shrub encroachment on the anuran community in periodically flooded grasslands of the largest Neotropical wetland

In many parts of the world, replacement of natural grasslands by woody plants has resulted in a decrease of pasture areas and in habitat loss for a variety of animal species, including amphibians. Wetlands are especially susceptible to invasive plants, both native and exotic, but the effects of such invasions on animal assemblages remain poorly understood. Here, we present information on the impact of selected environmental variables, especially coverage by the native shrub Combretum laxum Jacq., on the structure of an anuran assemblage in the Pantanal, a huge flood‐pulsed South American wetland. Anurans were surveyed during the rainy season in 17 plots, which differed in extent of C. laxum coverage, leaf litter volume, soil moisture and distance to permanently wet areas. Effects of these environmental variables on the species number, relative abundance and composition of the anuran assemblage were evaluated using multivariate statistical analyses. We captured 1203 anurans, of 21 species from four families. Both the number of species and the relative abundance of anurans were lower in plots with greater C. laxum coverage, which also influenced anuran species composition. Number of species was highest in plots located closest to permanently wet areas, which provide protection from desiccation and other resources during the Pantanal dry season, and so could be considered source areas of anurans. While many anuran species were negatively affected by the homogenization of the landscape caused by shrub encroachment, some seemed to be favoured in such circumstances. For these, dense shrub encroachment into natural grasslands may provide safer migratory routes to permanently wet habitats. Thus, at the mesoscale, a mosaic of areas with different levels of coverage by C. laxum (shrub islands) may aid anuran assemblages in the Pantanal wetlands, facilitating the maintenance of higher beta and gamma diversity.     

An evolutionary space-time model with varying among-site dependencies

It is now widely accepted that sites in a protein do not undergo independent evolutionary processes. The underlying assumption is that proteins are composed of conserved and variable linear domains, and thus rates at neighboring sites are correlated. In this paper, we comprehensively examine the performance of an autocorrelation model of evolutionary rates in protein sequences. We further develop a model in which the level of correlation between rates at adjacent sites is not equal at all sites of the protein. High correlation is expected, for example, in linear functional domains. On the other hand, when we consider nonlinear functional regions (e.g., active sites), low correlation is expected because the interaction between distant sites imposes independence of rates in the linear sequence. Our model is based on a hidden Markov model, which accounts for autocorrelation at certain regions of the protein and rate independence at others. We study the differences between the novel model and models which assume either independence or a fixed level of dependence throughout the protein. Using a diverse set of protein data sets we show that the novel model better fits most data sets. We further analyze the potassium-channel protein family and illustrate the relationship between the dependence of rates at adjacent sites and the tertiary structure of the protein.     

Some Recent Developments in Evolutionary Approaches to the Study of Human Cognition and Behavior

In this paper I review some theoretical exchanges and empiricalresults from recent work on human behavior and cognition in thehope of indicating some productive avenues for critical engagement.I focus particular attention on methodological debates between Evolutionary Psychologists and behavioral ecologists. I argue for a broader and more encompassing approach to the evolutionarily based study of human behavior and cognition than either of these two rivals present.