How to Quantify Urbanization When Testing for Urban Evolution?

Author(s):  
Marta Szulkin ◽  
Colin J. Garroway ◽  
Michela Corsini ◽  
Andrzej Z. Kotarba ◽  
Davide Dominoni

Research in urban evolution requires that the features of cities are accurately captured for input into evolutionary models. Until recently, the evolutionary effects of cities have often been addressed using single sites, dichotomous urban–rural contrasts or, to a lesser extent, using urban gradients. However, urbanization does not produce a homogenous spatial continuum: cities are highly heterogeneous environments, with sharp and often non-linear environmental changes related to the amount of impervious surface, green vegetation, air pollution, light, noise, or contrasted temperature profiles. The comprehensive quantification of urban heterogeneity in space and time is essential for exploring the origins of organismal variation and adaptation in cities, and to best identify the strength and directionality of selective pressures and neutral processes occurring in populations of urban organisms. This chapter reviews frameworks that can be used to describe and quantify urbanization—these include classical ecological frameworks, the understudied temporal dimension of urban evolutionary biology, and the concept of replicated insight into urban-driven evolutionary processes. The chapter further discusses how axes of variation capturing the urban environment can be quantified with univariate and multivariate approaches, and presents quantitative results on how urbanization is captured in published studies of urban evolution. Finally, it discusses study design and statistical approaches of interest when testing for urban evolution: these include the question of model selection and variable fitting, spatial autocorrelation, and appropriate scale use in studies of urban evolution.

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Handuo Shi ◽  
Yan Hu ◽  
Pascal D. Odermatt ◽  
Carlos G. Gonzalez ◽  
Lichao Zhang ◽  
...  

AbstractThe steady-state size of bacterial cells correlates with nutrient-determined growth rate. Here, we explore how rod-shaped bacterial cells regulate their morphology during rapid environmental changes. We quantify cellular dimensions throughout passage cycles of stationary-phase cells diluted into fresh medium and grown back to saturation. We find that cells exhibit characteristic dynamics in surface area to volume ratio (SA/V), which are conserved across genetic and chemical perturbations as well as across species and growth temperatures. A mathematical model with a single fitting parameter (the time delay between surface and volume synthesis) is quantitatively consistent with our SA/V experimental observations. The model supports that this time delay is due to differential expression of volume and surface-related genes, and that the first division after dilution occurs at a tightly controlled SA/V. Our minimal model thus provides insight into the connections between bacterial growth rate and cell shape in dynamic environments.


2013 ◽  
Vol 10 (87) ◽  
pp. 20130559 ◽  
Author(s):  
Adam Lampert ◽  
Alan Hastings

Critical population phase transitions, in which a persistent population becomes extinction-prone owing to environmental changes, are fundamentally important in ecology, and their determination is a key factor in successful ecosystem management. To persist, a species requires a suitable environment in a sufficiently large spatial region. However, even if this condition is met, the species does not necessarily persist, owing to stochastic fluctuations. Here, we develop a model that allows simultaneous investigation of extinction due to either stochastic or deterministic reasons. We find that even classic birth–death processes in spatially extended ecosystems exhibit phase transitions between extinction-prone and persistent populations. Sometimes these are first-order transitions, which means that environmental changes may result in irreversible population collapse. Moreover, we find that higher migration rates not only lead to higher robustness to stochastic fluctuations, but also result in lower sustainability in heterogeneous environments by preventing efficient selection for suitable habitats. This demonstrates that intermediate migration rates are optimal for survival. At low migration rates, the dynamics are reduced to metapopulation dynamics, whereas at high migration rates, the dynamics are reduced to a multi-type branching process. We focus on species persistence, but our results suggest a unique method for finding phase transitions in spatially extended stochastic systems in general.


2000 ◽  
Vol 12 (3) ◽  
pp. 257-257 ◽  
Author(s):  
Andrew Clarke

Theodosius Dobzhansky once remarked that nothing in biology makes sense other than in the light of evolution, thereby emphasising the central role of evolutionary studies in providing the theoretical context for all of biology. It is perhaps surprising then that evolutionary biology has played such a small role to date in Antarctic science. This is particularly so when it is recognised that the polar regions provide us with an unrivalled laboratory within which to undertake evolutionary studies. The Antarctic exhibits one of the classic examples of a resistance adaptation (antifreeze peptides and glycopeptides, first described from Antarctic fish), and provides textbook examples of adaptive radiations (for example amphipod crustaceans and notothenioid fish). The land is still largely in the grip of major glaciation, and the once rich terrestrial floras and faunas of Cenozoic Gondwana are now highly depauperate and confined to relatively small patches of habitat, often extremely isolated from other such patches. Unlike the Arctic, where organisms are returning to newly deglaciated land from refugia on the continental landmasses to the south, recolonization of Antarctica has had to take place by the dispersal of propagules over vast distances. Antarctica thus offers an insight into the evolutionary responses of terrestrial floras and faunas to extreme climatic change unrivalled in the world. The sea forms a strong contrast to the land in that here the impact of climate appears to have been less severe, at least in as much as few elements of the fauna show convincing signs of having been completely eradicated.


2018 ◽  
Vol 48 (3) ◽  
pp. 43-64
Author(s):  
Amy Rose Green ◽  
Adriana Tulissi ◽  
Seth Erais ◽  
Sharon Lynn Cairns ◽  
Debbie Bruckner

Post-secondary institutions are increasingly recognizing the need to foster intercultural competence (ICC) in students; however, the ways in which these institutions can do so has not been fully explored. The purpose of the current mixed methods study was to investigate changes in post-secondary students’ ICC (N = 35) following participation in an interreligious and intercultural diversity program, based upon changes in students’ scores on the Intercultural Development Inventory (IDI). A thematic analysis of post-program questionnaires was used to triangulate the data and provide more insight into changes experienced by participants. Quantitative results revealed significant increases in students’ overall ICC, and significant decreases in the discrepancy between students’ perceived ICC and their actual ICC. Qualitative results revealed five overall themes: (1) shifting perspectives, (2) enhancing intercultural engagement skills, (3) connecting, (4) inspiring action, and (5) personal growth. Implications for research and practice are discussed.


2021 ◽  
Vol 14 ◽  
Author(s):  
Umer Saleem Bhat ◽  
Navneet Shahi ◽  
Siju Surendran ◽  
Kavita Babu

One of the reasons that most multicellular animals survive and thrive is because of the adaptable and plastic nature of their nervous systems. For an organism to survive, it is essential for the animal to respond and adapt to environmental changes. This is achieved by sensing external cues and translating them into behaviors through changes in synaptic activity. The nervous system plays a crucial role in constantly evaluating environmental cues and allowing for behavioral plasticity in the organism. Multiple neurotransmitters and neuropeptides have been implicated as key players for integrating sensory information to produce the desired output. Because of its simple nervous system and well-established neuronal connectome, C. elegans acts as an excellent model to understand the mechanisms underlying behavioral plasticity. Here, we critically review how neuropeptides modulate a wide range of behaviors by allowing for changes in neuronal and synaptic signaling. This review will have a specific focus on feeding, mating, sleep, addiction, learning and locomotory behaviors in C. elegans. With a view to understand evolutionary relationships, we explore the functions and associated pathophysiology of C. elegans neuropeptides that are conserved across different phyla. Further, we discuss the mechanisms of neuropeptidergic signaling and how these signals are regulated in different behaviors. Finally, we attempt to provide insight into developing potential therapeutics for neuropeptide-related disorders.


2021 ◽  
Author(s):  
Anna E. Weinmann ◽  
Susan T. Goldstein ◽  
Maria V. Triantaphyllou ◽  
Martin R. Langer

<p>Benthic foraminifera are important indicators for ecological studies. The assemblage composition of local communities can be used to analyze influences of environmental variables such as temperature, salinity, pH, and others. In recent years, the experimental propagule method has emerged as an effective tool to evaluate the influence of these variables on assemblage dynamics of benthic foraminifera. Propagules (tiny juveniles) of benthic foraminifera are widespread and can survive outside of a species’ natural distribution range. Their ability to become dormant and be re-activated once local conditions become suitable, is an important driver behind the capacity of foraminiferal assemblages to react quickly to environmental changes. In the laboratory, the propagules are first separated from the coarser fractions by sieving and then cultured under different conditions.</p><p>In the present study, we analyzed the effect of ocean pH on the composition of shallow-water assemblages from Corfu Island (Greece). Like other calcifying organisms, assemblages of foraminifera are susceptible to pH variations and have revealed compositional shifts along natural or experimental pH gradients. Our experimental set-up included four pH treatments between 6.5 and 8.5 at constant temperature and salinity (22°C and 38 ppt) for 5 weeks.</p><p>At the conclusion of the cultivation experiment, we found high numbers of grown specimens (825–1564 per replicate) and a high survivability rate throughout all treatments (78–87%). Higher pH (7.8 and 8.5) resulted in assemblages that were dominated by monothalamous and porcelaneous species, whereas lower pH (6.5 and 7.2) lead to a reduction in porcelaneous and an increase in agglutinated species. Several taxa showed significant positive or negative correlations with decreasing pH values.</p><p>Our results are congruent with previous findings that reported compositional shifts from calcareous to agglutinated taxa with decreasing pH (both from culture and field observations). Our study also indicates that the activation of propagules is an important mechanism behind assemblage dynamics in shallow-water foraminifera. As such, it offers an improved insight into potential resilience and recovery mechanisms of foraminiferal assemblages with regard to local or seasonal pH variations as well as ongoing ocean acidification.</p>


Author(s):  
Chesla Ann Lenkaitis ◽  
Shannon M. Hilliker

Situated cognition is a theory where engagement in a social activity is essential to learning. Applied to teacher education, this theory is important as teacher candidates need clinical experiences throughout their curriculum. This chapter uses games as a context for teacher candidates to develop a vocabulary curriculum to support native and foreign language learning. Twenty-nine teacher candidates participated in the study. Pre- and post-surveys with both Likert-scale and open-ended questions comprise the data set for the study. Results show that groups created vocabulary lists with different amounts of words for games played during each session. Quantitative results reveal how helpful teacher candidates rated the game for language teaching while from qualitative data, three themes emerged: 1) vocabulary needed, 2) communicative aspect of the game, and 3) unsure of helpfulness. This study provides insight into the ways games can provide teacher candidates a way to explore ideas about using them for vocabulary in language teaching.


Animals ◽  
2020 ◽  
Vol 10 (8) ◽  
pp. 1309
Author(s):  
Veronika Kharzinova ◽  
Arsen Dotsev ◽  
Anastasiya Solovieva ◽  
Olga Sergeeva ◽  
Georgiy Bryzgalov ◽  
...  

To examine the genetic diversity and population structure of domestic reindeer, using the BovineHD BeadChip, we genotyped reindeer individuals belonging to the Nenets breed of the five main breeding regions, the Even breed of the Republic of Sakha, the Evenk breed of the Krasnoyarsk and Yakutia regions, and the Chukotka breed of the Chukotka region and its within-breed ecotype, namely, the Chukotka–Khargin, which is bred in Yakutia. The Chukotka reindeer was shown to have the lowest genetic diversity in terms of the allelic richness and heterozygosity indicators. The principal component analysis (PCA) results are consistent with the neighbor-net tree topology, dividing the reindeer into groups according to their habitat location and origin of the breed. Admixture analysis indicated a genetic structuring of two groups of Chukotka origin, the Even breed and most of the geographical groups of the Nenets breed, with the exception of the Murmansk reindeer, the gene pool of which was comprised of the Nenets and apparently the native Sami reindeer. The presence of a genetic component of the Nenets breed in some reindeer inhabiting the Krasnoyarsk region was detected. Our results provide a deeper insight into the current intra-breeding reindeer genetic diversity, which is an important requirement for future reindeer herding strategies and for animal adaptation to environmental changes.


mSystems ◽  
2020 ◽  
Vol 5 (3) ◽  
Author(s):  
Vaughn S. Cooper ◽  
Erin Honsa ◽  
Hannah Rowe ◽  
Christopher Deitrick ◽  
Amy R. Iverson ◽  
...  

ABSTRACT Experimental evolution is a powerful technique to understand how populations evolve from selective pressures imparted by the surrounding environment. With the advancement of whole-population genomic sequencing, it is possible to identify and track multiple contending genotypes associated with adaptations to specific selective pressures. This approach has been used repeatedly with model species in vitro, but only rarely in vivo. Herein we report results of replicate experimentally evolved populations of Streptococcus pneumoniae propagated by repeated murine nasal colonization with the aim of identifying gene products under strong selection as well as the population genetic dynamics of infection cycles. Frameshift mutations in one gene, dltB, responsible for incorporation of d-alanine into teichoic acids on the bacterial surface, evolved repeatedly and swept to high frequency. Targeted deletions of dltB produced a fitness advantage during initial nasal colonization coupled with a corresponding fitness disadvantage in the lungs during pulmonary infection. The underlying mechanism behind the fitness trade-off between these two niches was found to be enhanced adherence to respiratory cells balanced by increased sensitivity to host-derived antimicrobial peptides, a finding recapitulated in the murine model. Additional mutations that are predicted to affect trace metal transport, central metabolism, and regulation of biofilm production and competence were also selected. These data indicate that experimental evolution can be applied to murine models of pathogenesis to gain insight into organism-specific tissue tropisms. IMPORTANCE Evolution is a powerful force that can be experimentally harnessed to gain insight into how populations evolve in response to selective pressures. Herein we tested the applicability of experimental evolutionary approaches to gain insight into how the major human pathogen Streptococcus pneumoniae responds to repeated colonization events using a murine model. These studies revealed the population dynamics of repeated colonization events and demonstrated that in vivo experimental evolution resulted in highly reproducible trajectories that reflect the environmental niche encountered during nasal colonization. Mutations impacting the surface charge of the bacteria were repeatedly selected during colonization and provided a fitness benefit in this niche that was counterbalanced by a corresponding fitness defect during lung infection. These data indicate that experimental evolution can be applied to models of pathogenesis to gain insight into organism-specific tissue tropisms.


2004 ◽  
Vol 70 (12) ◽  
pp. 7260-7268 ◽  
Author(s):  
Anika Marceau ◽  
Monique Zagorec ◽  
Stéphane Chaillou ◽  
Thérèse Méra ◽  
Marie-Christine Champomier-Vergès

ABSTRACT Lactobacillus sakei is a lactic acid bacterium widely represented in the natural flora of fresh meat. The aim of this study was to analyze the differences in protein expression during environmental changes encountered during technological processes in which L. sakei is involved in order to gain insight into the ability of this species to grow and survive in such environments. Using two-dimensional electrophoresis, we observed significant variation of a set of 21 proteins in cells grown at 4°C or in the presence of 4% NaCl. Six proteins could be identified by determination of their N-terminal sequences, and the corresponding gene clusters were studied. Two proteins belong to carbon metabolic pathways, and four can be clustered as general stress proteins. A phenotype was observed at low temperature for five of the six mutants constructed for these genes. The survival of four mutants during stationary phase at 4°C was affected, and surprisingly, one mutant showed enhanced survival during stationary phase at low temperatures.


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