Foraging Decisions in Risk-Uniform Landscapes

Behaviour is shaped by evolution as to maximise fitness by balancing gains and risks. Models on decision making in biology, psychology or economy have investigated choices among options which differ in gain and/or risk. Meanwhile, there are decision contexts with uniform risk distributions where options are not differing in risk while the overall risk level may be high. Adequate predictions for the emerging investment patterns in risk uniformity are missing. Here we use foraging behaviour as a model for decision making. While foraging, animals often titrate food and safety from predation and prefer safer foraging options over riskier ones. Risk uniformity can occur when habitat structures are uniform, when predators are omnipresent or when predators are ideal-free distributed in relation to prey availability. However, models and empirical investigations on optimal foraging have mainly investigated choices among options with different predation risks. Based on the existing models on local decision making in risk-heterogeneity we test predictions extrapolated to a landscape level with uniform risk distribution. We compare among landscapes with different risk levels. If the uniform risk is low, local decisions on the marginal value of an option should lead to an equal distribution of foraging effort. If the uniform risk is high, foraging should be concentrated on few options, due to a landscape-wide reduction of the value of missed opportunity costs of activities other than foraging. We provide experimental support for these predictions using foraging small mammals in artificial, risk uniform landscapes. In high risk uniform landscapes animals invested their foraging time in fewer options and accepted lower total returns, compared to their behaviour in low risk-uniform landscapes. The observed trade off between gain and risk, demonstrated here for food reduction and safety increase, may possibly apply also to other contexts of economic decision making

Ecological Determinants of Avian Productivity and Aviation Risk in Semi-natural Grasslands

Growing concerns about climate change, foreign oil dependency, and environmental quality have fostered interest in perennial native grasses (e.g. switchgrass [Panicum virgatum]) for bioenergy production while also maintaining biodiversity and ecosystem function. However, biofuel cultivation in marginal landscapes such as airport grasslands may have detrimental effects on aviation safety as well as demography and conservation efforts for grassland birds including Dickcissels (Spiza americana). In 2011–2013 I studied the response of avian populations to vegetation composition and harvest frequency of switchgrass monocultures and native warm-season grass (NWSG) mixtures at B. Bryan farms in Clay Co. MS, USA. Four treatments incorporating switchgrass and NWSG with single and multiple annual harvesting were established on 16 experimental plots. I examined the relative abundance, aviation risk, and conservation value of birds associated with these treatments, evaluated contributions of habitat attributes and individual male quality towards territory productivity and determined effects of harvest regimens on nest success, nest density, and productivity for Dickcissels. Avian relative abundance was greater in switchgrass plots during winter months, whereas NWSG was favored by species during the breeding season. Conversely, treatment differences in aviation risk and conservation value were not biologically significant. Only 2.6% of observations included avian species of high risk to aircraft, suggesting that it may be feasible to use semi-natural grasslands at airports to provide grassland bird habitat while concurrently minimizing aviation risk. Regarding individual and habitat quality effects on nest survival and productivity, male song rate was not an effective surrogate for individual quality in demographic models. However, nest survival declined with increasing territory size and territories established earlier in the season had greater territory productivity relative to later arriving males, providing evidence that some metric of individual quality is important for grassland bird reproduction. Additionally, vegetation composition and harvest frequencies influenced nest density and productivity, but not nest survival. Native warm season grasses contained 54–64 times more nests relative to switchgrass treatments, and nest density was 10% greater in single harvest plots. My results suggest semi-natural grasslands can support grassland bird conservation while allowing for biofuel production and aviation risk management in airport landscapes

Genetics of Local Adaptation in theThree-spined Stickleback

Spatial differentiation in phenotypic traits is commonly observed in the wild, but both the proximate (cf. environmental vs. genetic) and ultimate (cf. adaptive vs. stochastic) causes underlying this differentiation often remain obscure. Studies focussed on the genetic basis of this differentiation can inform us about these issues, especially if the genetic variants under investigation can be linked with information about their functional role(s) and/or gauged against expectations derived from evolutionary null models. However, due to the difficulties in deciphering and studying the genetic basis of phenotypic variability and differentiation in quantitative traits especially in marine vertebrates the occurrence and scale of local adaptation in them is still poorly understood. Yet, identifying patterns of adaptive divergence and the ecological factors that have contributed to them is essential for understanding how natural selection can maintain local adaptation in the face of gene flow. In this thesis I used a genome-wide set of candidate gene-based microsatellite markers, in combination with quantitative genetic approaches, to explore the patterns of adaptive diversity and divergence among stickleback populations from a variety of habitats ranging from global to local geographic scales. Through comparisons of several independent, isolated pairs of marine and freshwater populations, I found that selection is acting on many genomic regions harbouring genes whose putative functions are related to a wide variety of physiological processes. I also found indications that adaptation to freshwater environments may have been achieved through different genetic pathways in different populations. Importantly, the design of my study was such that alternative demographic explanations for observed patterns could be excluded. Focussing on populations within the physically continuous, yet environmentally heterogeneous marine habitat, I further investigated whether selection is acting strongly enough to promote adaptive population structuring despite high gene flow. Signatures of selection were detected in several candidate genes, along with clear evidence for adaptive differentiation in a phenotypic trait (lateral plate number). Analysis of population structure with only these outlier loci uncovered a higher degree of differentiation than was evident in neutral loci, and in some cases, patterns of adaptive differentiation were correlated with environmental variables likely to act as selective agents in the marine environment (viz. salinity and temperature). Evidence for local adaptation among Baltic Sea sticklebacks was confirmed in a common garden experiment, which demonstrated a loss of fitness in populations native to low salinity regions when exposed to high salinity treatments. Overall, the results from this thesis point to the conclusion that adaptive genetic and phenotypic differentiation is common, even in continuous marine habitats lacking obvious physical barriers to dispersal and gene flow. These results are particularly noteworthy, firstly from the perspective that earlier studies conducted using neutral marker genes have largely overlooked the patterns and magnitude of divergence, and secondly due to the comprehensive geographic coverage of the investigations.Maantieteellinen muuntelu eliöiden ilmiasullisissa ominaisuuksissa on tavallista. Ymmärryksemme tämän muuntelun proksimaattisista ja ultimaattista syistä on kuitenkin vajavaista: useinkaan ei ole selvää missä määrin ilmiasulliset erot johtuvat geneettisistä erilaistumisesta ja missä määrin ilmiasullisesta plastisuudesta. Myös luonnonvalinnan ja geneettisen satunnaisajautumisen suhteellinen merkitys geneettisten erojen selittäjänä on yleensä tuntematon, samoin kuin se, jos ja kuinka luonnonvalinta kykenee ylläpitämään paikallisia sopeumia geenivirrasta huolimatta. Tutkimukset populaatioiden välisen ilmiasullisen erilaistumisen perinnöllisestä taustasta yhdessä merkkigeenitutkimusten kanssa tarjoavatkin mahdollisuuksia lisätä ymmärrystämme näistä seikoista. Tarve tämän ymmärryksen kartoittamiselle korostuu erityisesti merikalojen kohdalla, joiden biologiset ominaisuudet ovat rajoittaneet niiden perinnöllisyyden ja paikallisten sopeumien tutkimusta. Käytin tässä väitöskirjatyössä suurta määrää kandidaattigeeneihin ankkuroituja mikrosatelliitti ja SNP merkkigeenejä yhdessä kvantitatiivisen genetiikan menetelmien kanssa selvittääkseni kolmipiikin (Gasterosteus aculeatus) geneettistä erilaistumista ja sen evoluutiivisiä syitä. Tutkimusten maantieteellinen mittakaava vaihteli Itämeren piirin kattavista tutkimuksista maailmanlaajuiseen tarkasteluun sekä meri- että makean veden populaatioissa. Parittaisten meri- ja makean veden populaatioiden vertailu maailmanlaajuisessa mittakaavassa paljasti ison joukon luonnonvalinnan alla olleita fysiologisesti merkittäviä geenejä, jotka ovat todennäköisesti mahdollistaneet kolmipiikkien sopeutumisen makeaan veteen. Valinnan alla olleet geenit eivät olleet aina samoja populaatioparista toiseen, mikä on tulkittavissa osoitukseksi siitä, että sopeutuminen makeaan veteen on voinut tapahtua eri populaatioissa vaihtoehtoisten geneettisten mekanismien avulla. Tutkimukset meripopulaatioiden geneettisestä erilaistumisesta paljastivat, että voimakkaasta geenivirrasta huolimatta, myös meripopulaatiot olivat voimakkaasti toisistaan erilaistuneita. Erilaistuminen ilmeni sekä kandidaattigeeneihin sitoutuneissa merkkigeeneissä, että myös ilmiasullisessa ominaisuudessa (kylkikilpien määrä), jonka ilmenemistä säätelevä geeni on tunnettu. Nämä tulokset tukevat tulkintaa, jonka mukaan kolmipiikin meripopulaatiot ovat paikallisesti sopeutuneita. Tätä tulkintaa tukivat myös valinnan alla olleiden lokusten alleelifrekvenssien korrelaatiot ympäristön suolapitoisuuden kanssa, sekä myös laboratoriossa tehdyt kasvatuskokeet, joissa eri alkuperää olevien kolmipiikkien kelpoisuutta testattiin eri suolapitoisuuksissa mittavien faktorikokeiden avulla. Yleisesti ottaen voidaan sanoa että tähän väitöskirjaan sisältyvien tutkimusten tulokset tukevat näkemystä, jonka mukaan kolmipiikkipopulaatiot niin meressä kuin makeissakin vesissä ovat sekä ilmiasullisesti että perinnöllisesti sopeutuneet paikallisiin olosuhteisiin. Sopeutumista on tapahtunut myös valtamerissä, joista geenivirtaa rajoittavat esteet puuttuvat. Nämä havainnot ovat merkille pantavia siinä perspektiivissä, että aiemmat neutraaleja merkkigeenejä hyödyntäneet tutkimukset eivät ole tätä erilaistumista kyenneet todentamaan. Lisäarvoa havainnoille antavat käytettyjen aineistojen laajuus ja maantieteellinen kattavuus

Direct and indirect effects of environmental drivers on reindeer reproduction

The impact of climate change on the dynamics of populations has been well documented and is widespread. However, weather variability influences populations both directly and indirectly, and is mediated by species interactions. This complexity may impede proper climate impact assessments. Hence, predicting the consequences of climate change may require including processes that occur both with time lags and across trophic levels. Based on our current understanding of the mechanisms linking local climate and trophic interactions in tundra ecosystems, we used a state-space formulation of a mediation model that allowed for assessing the relative contribution of direct and indirect environmental (weather and trophic) effects on reindeer Rangifer tarandus reproductive success. Our study showed that the mediator effect of body condition caused delayed but predictable effects of weather, plant productivity, and reindeer densities on reproductive success. Furthermore, these predictors also affected reproductive success directly and with the same sign, suggesting that direct and indirect effects pulled in the same direction with respect to their combined total effect on reproductive success. Hence, poor weather conditions not only affect calf production negatively the same year, but also increase the likelihood of poor reproductive success the subsequent year. The results support the expectation that calf slaughter mass (as a proxy for herd body condition) is an important indicator of the state of reindeer herds with respect to their production potential and resilience to weather events and climate change. Finally, the model framework employed in the present study can be further developed as a potential vehicle for near-term forecasting, and thereby constitutes a useful tool for adaptive management

The genomic impact of deleterious mutations in isolation with migration models

Tese de mestrado, Biologia Evolutiva e do Desenvolvimento, Universidade de Lisboa, Faculdade de Ciências, 2019The effects of background selection (BGS), i.e. the effect that purifying selection due to removal of deleterious mutations at given site has on linked neutral sites, is well understood in single population models. For recessive deleterious mutations, heterozygotes can have a higher fitness leading to associative overdominance (AOD). Previous studies suggest that BGS may increase genomic differentiation, misleading genomic scans that rely on high differentiation regions to detect genes involved in local adaptation. However, little is known about the interaction of BGS and AOD with gene flow. To characterize the genomic impact of BGS, AOD and migration we used a forward-in-time simulator implemented in the program SLiM 3.2. We considered an isolation with migration model with two populations of constant size. To understand the relative impact of each parameter we used various combinations of migration rates, recombination rates, selective coefficients and dominance coefficients. We find that, in relation to neutral expectations, co-dominant deleterious mutations decrease within population diversity and increase genetic differentiation (FST) between populations, although with high migration (2Nem>10) FST does not deviate from neutral expectation. Consistent with the effect of AOD, for recessive deleterious mutations we found an increase of neutral diversity for selective coefficients s between 0.0001 and 0.1, when recombination rate is lower than the mutation rate. AOD also leads to a decrease in population differentiation (FST), with higher migration rates decreasing the magnitude of this effect. Thus, BGS and AOD can lead to heterogeneous genomic patterns and bias the detection of divergent selection

Challenges for the estimation of uncertainty of measurements made in situ

In situ measurements are made without the removal of a physical sample and have many advantages over traditional ex situ measurements, made on a removed sample usually in a remote laboratory. The quality of ex situ measurements is usually expressed primarily in terms of their measurement uncertainty, including that arising during the sampling process. However, estimates of uncertainty for in situ measurement values have not usually included this uncertainty from sampling (UfS). It is argued that the making of an in situ measurement inevitably includes the taking of an ‘undisturbed sample’ that generates UfS, which should be included in the estimate of measurement uncertainty. Because undisturbed samples are not prepared or mixed, as is usual for removed samples, the heterogeneity of the analyte concentration in the sampling target is the primary source of UfS. Existing methods for estimating UfS for ex situ measurements can broadly be applied to in situ measurements. However, four extra challenges that limit the design and uptake of uncertainty estimation for in situ methods are identified, and possible solutions and actions required are discussed. Examples of in situ measurements considered include Pb in top soil by hand-held PXRF, 137Cs at a nuclear site by portable gamma-ray spectrometry, and bilirubin in new-born infants by hand-held reflectance photometry

Three-Dimensional Bedrock Channel Evolution with Smoothed Particle Hydrodynamics

Bedrock channels are responsible for balancing and communicating tectonic and climatic signals across landscapes, but it is difficult and dangerous to observe and measure the flows responsible for removing weakly-attached blocks of bedrock from the channel boundary. Consequently, quantitative descriptions of the dynamics of bedrock removal are scarce. Detailed numerical simulation of violent flows in three dimensions has been historically challenging due to technological limitations, but advances in computational fluid dynamics aided by high-performance computing have made it practical to generate approximate solutions to the governing equations of fluid dynamics. From these numerical solutions we gain detailed knowledge of the motions and forces of flowing water, which deepens our understanding of earth processes responsible for shaping landscapes. By simulating hydraulic forces generated by flowing water in bedrock channels with interconnected zones of weakness, I explore the implications of fluvial stresses, boulder impact, and rock fabric heterogeneity on landscape form. I use a Smoothed Particle Hydrodynamics (SPH) solver to simulate flow over landscapes and I use stress-strength analysis to calculate earth fabric failure using the Failure Earth Response Model (FERM). SPH modeling is used to simulate the hydraulic mobilization of a boulder in a bedrock channel and to quantify the forces associated with its subsequent rolling, sliding, and impact two-meter freefall. FERM model results reveal that strength gradients in fractured bedrock topographies exert more control on volume of eroded material and channel form than the overall strength of the surrounding bedrock. Finally, SPH model results are calibrated with three-dimensional water velocity measurements collected by an acoustic doppler current profiler in the Penobscot River. SPH modeling is used to explore the influence of in-stream logging structures on channel velocity, which has implications for the habitat of federally-protected diadromous fish species in the Penobscot River. Model results show that even at low discharges, the presence of in-stream structures changes the velocity structure at ~102 m length scales

Modeling infectious disease dynamics in the complex landscape of global health.

Despite some notable successes in the control of infectious diseases, transmissible pathogens still pose an enormous threat to human and animal health. The ecological and evolutionary dynamics of infections play out on a wide range of interconnected temporal, organizational, and spatial scales, which span hours to months, cells to ecosystems, and local to global spread. Moreover, some pathogens are directly transmitted between individuals of a single species, whereas others circulate among multiple hosts, need arthropod vectors, or can survive in environmental reservoirs. Many factors, including increasing antimicrobial resistance, increased human connectivity and changeable human behavior, elevate prevention and control from matters of national policy to international challenge. In the face of this complexity, mathematical models offer valuable tools for synthesizing information to understand epidemiological patterns, and for developing quantitative evidence for decision-making in global health