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Novak, M.

Publications and source records attributed to Novak, M..

35 records · Page 2Linked to original sources

Geometric complexity and the information-theoretic comparison of functional-response models

The assessment of relative model performance using information criteria like AIC and BIC has become routine among functional-response studies, reflecting trends in the broader ecological literature. Such information criteria allow comparison across diverse models because they penalize each models fit by its parametric complexity -- in terms of their number of free parameters -- which allows simpler models to outperform similarly fitting models of higher parametric complexity. However, criteria like AIC and BIC do not consider an additional form of model complexity, referred to as geometric complexity, which relates specifically to the mathematical form of the model. Models of equivalent parametric complexity can differ in their geometric complexity and thereby in their ability to flexibly fit data. Here we use the Fisher Information Approximation to compare, explain, and contextualize how geometric complexity varies across a large compilation of single-prey functional-response models -- including prey-, ratio-, and predator-dependent formulations -- reflecting varying apparent degrees and forms of non-linearity. Because a models geometric complexity varies with the datas underlying experimental design, we also sought to determine which designs are best at leveling the playing field among functional-response models. Our analyses illustrate (1) the large differences in geometric complexity that exist among functional-response models, (2) there is no experimental design that can minimize these differences across all models, and (3) even the qualitative nature by which some models are more or less flexible than others is reversed by changes in experimental design. Failure to appreciate model flexibility in the empirical evaluation of functional-response models may therefore lead to biased inferences for predator-prey ecology, particularly at low experimental sample sizes where its impact is strongest. We conclude by discussing the statistical and epistemological challenges that model flexibility poses for the study of functional responses as it relates to the attainment of biological truth and predictive ability. Contribution to Field StatementThe use of criteria like AIC and BIC for selecting among functional-response models is now standard, well-accepted practice, just as it is in the ecological literature as a whole. The generic desire underlying the use of these criteria is to make the comparison of model performance an unbiased and equitable process by penalizing each models fit to data by its parametric complexity (relating to its number of free parameters). Here we introduce the Fisher Information Approximation to the ecological literature and use it to understand how the geometric complexity of models -- a form of model complexity relating to a models functional flexibility that is not considered by criteria like AIC and BIC -- varies across a large compilation of 40 different single-prey functional-response models. Our results add caution against the simplistic use and interpretation of information-theoretic model comparisons for functional-response experiments, showing just how large an effect that model flexibility can have on inferences of model performance. We therefore use our work to help clarify the challenges that ecologists studying functional responses must face in the attainment of biological truth and predictive ability.

ecology↗

Second Generation Antibodies Neutralize Emerging SARS-CoV-2 Variants of Concern

Recently emerged SARS-CoV-2 variants show resistance to some antibodies that were authorized for emergency use. We employed hybridoma technology combined with authentic virus assays to develop second-generation antibodies, which were specifically selected for their ability to neutralize new variants of SARS-CoV-2. AX290 and AX677, two monoclonal antibodies with non-overlapping epitopes, exhibit subnanomolar or nanomolar affinities to the receptor binding domain of the viral Spike protein carrying amino acid substitutions N501Y, N439K, E484K, K417N, and a combination N501Y/E484K/K417N found in the circulating virus variants. The antibodies showed excellent neutralization of an authentic SARS-CoV-2 virus representing strains circulating in Europe in spring 2020 and also the variants of concern B.1.1.7 and B.1.351. Finally, the combination of the two antibodies prevented the appearance of escape mutations of the authentic SARS-CoV-2 virus. The neutralizing properties were fully reproduced in chimeric mouse-human versions, which may represent a promising tool for COVID-19 therapy.

microbiology↗

An integrative skeletal and paleogenomic analysis of prehistoric stature variation suggests relatively reduced health for early European farmers

Human culture, biology, and health were shaped dramatically by the onset of agriculture ~12,000 years before present (BP). Subsistence shifts from hunting and gathering to agriculture are hypothesized to have resulted in increased individual fitness and population growth as evidenced by archaeological and population genomic data alongside a simultaneous decline in physiological health as inferred from paleopathological analyses and stature reconstructions of skeletal remains. A key component of the health decline inference is that relatively shorter statures observed for early farmers may (at least partly) reflect higher childhood disease burdens and poorer nutrition. However, while such stresses can indeed result in growth stunting, height is also highly heritable, and substantial inter-individual variation in the height genetic component within a population is typical. Moreover, extensive migration and gene flow were characteristics of multiple agricultural transitions worldwide. Here, we consider both osteological and ancient DNA data from the same prehistoric individuals to comprehensively study the trajectory of human stature variation as a proxy for health across a transition to agriculture. Specifically, we compared predicted genetic contributions to height from paleogenomic data and achieved adult osteological height estimated from long bone measurements on a per-individual basis for n=160 ancient Europeans from sites spanning the Upper Paleolithic to the Iron Age (~38,000-2,400 BP). We found that individuals from the Neolithic were shorter than expected (given their individual polygenic height scores) by an average of -4.47 cm relative to individuals from the Upper Paleolithic and Mesolithic (P=0.016). The average osteological vs. expected stature then increased relative to the Neolithic over the Copper (+2.67 cm, P=0.052), Bronze (+3.33 cm, P=0.032), and Iron Ages (+3.95 cm, P=0.094). These results were partly attenuated when we accounted for genome-wide genetic ancestry variation in our sample (which we note is partly duplicative with the individual polygenic score information). For example, in this secondary analysis Neolithic individuals were -3.48 cm shorter than expected on average relative to individuals from the Upper Paleolithic and Mesolithic (P=0.056). We also incorporated observations of paleopathological indicators of non-specific stress that can persist from childhood to adulthood in skeletal remains (linear enamel hypoplasia, cribra orbitalia, and porotic hyperostosis) into our model. Overall, our work highlights the potential of integrating disparate datasets to explore proxies of health in prehistory.

genomics↗

Epilepsy kinase CDKL5 is a DNA damage sensor which controls transcriptional activity at DNA breaks

Mutation of the CDKL5 kinase gene leads to the seizure-prone neurodevelopmental condition CDD (CDKL5 deficiency disorder) and is the most common genetic cause of childhood epilepsy. However, the phospho-targets and roles of CDKL5 are poorly understood, especially in the nucleus. We reveal CDKL5 as a sensor of DNA damage in actively transcribed regions of the nucleus, which phosphorylates transcriptional regulators such as Elongin A (ELOA) on a specific consensus motif. Recruitment of CDKL5 and ELOA to DNA damage sites, and subsequent ELOA phosphorylation, requires both active transcription and synthesis of poly-ADP ribose to which CDKL5 can bind. Critically, CDKL5 is essential for transcriptional control at DNA breaks. Therefore, CDKL5 is a DNA damage-sensing regulator of transcription, with implications for CDKL5-related human diseases. One sentence summaryCDKL5 is a DNA damage-sensing kinase that modulates transcriptional activity near DNA breaks.

cell biology↗

Hidden layers of density dependence in consumer feeding rates

Functional responses relate a consumers feeding rates to variation in its abiotic and biotic environment, providing insight into consumer behavior and fitness, and underpinning population and food-web dynamics. Despite their broad relevance and long-standing history, we show here that the types of density dependence found in classic resource- and consumer-dependent functional-response models equate to strong and often untenable assumptions about the independence of processes underlying feeding rates. We first demonstrate mathematically how to quantify non-independence between feeding and consumer interference and between feeding on multiple resources. We then analyze two large collections of functional-response datasets to show that non-independence is pervasive and borne out in previously-hidden forms of density dependence. Our results provide a new lens through which to view variation in consumer feeding rates and disentangle the biological underpinnings of species interactions in multi-species contexts.

ecology↗

Systematic bias in studies of consumer functional responses

Functional responses are a cornerstone to our understanding of consumer-resource interactions, so how to best describe them using models has been actively debated. Here we focus on the consumer dependence of functional responses to evidence systematic bias in the statistical comparison of functional-response models and the estimation of their parameters. Both forms of bias are universal to nonlinear models (irrespective of consumer dependence) and are rooted in a lack of sufficient replication. Using a large compilation of published datasets, we show that - due to the prevalence of low sample size studies - neither the overall frequency by which alternative models achieve top rank nor the frequency distribution of parameter point estimates should be treated as providing insight into the general form or central tendency of consumer interference. We call for renewed clarity in the varied purposes that motivate the study of functional responses, purposes that can compete with each other in dictating the design, analysis, and interpretation of functional-response experiments.

ecology↗

The Arrival of Steppe and Iranian Related Ancestry in the Islands of the Western Mediterranean

A series of studies have documented how Steppe pastoralist-related ancestry reached central Europe by at least 2500 BCE, while Iranian farmer-related ancestry was present in Aegean Europe by at least 1900 BCE. However, the spread of these ancestries into the western Mediterranean where they have contributed to many populations living today remains poorly understood. We generated genome-wide ancient DNA from the Balearic Islands, Sicily, and Sardinia, increasing the number of individuals with reported data from these islands from 3 to 52. We obtained data from the oldest skeleton excavated from the Balearic islands (dating to [~]2400 BCE), and show that this individual had substantial Steppe pastoralist-derived ancestry; however, later Balearic individuals had less Steppe heritage reflecting geographic heterogeneity or immigration from groups with more European first farmer-related ancestry. In Sicily, Steppe pastoralist ancestry arrived by [~]2200 BCE and likely came at least in part from Spain as it was associated with Iberian-specific Y chromosomes. In Sicily, Iranian-related ancestry also arrived by the Middle Bronze Age, thus revealing that this ancestry type, which was ubiquitous in the Aegean by this time, also spread further west prior to the classical period of Greek expansion. In Sardinia, we find no evidence of either eastern ancestry type in the Nuragic Bronze Age, but show that Iranian-related ancestry arrived by at least [~]300 BCE and Steppe ancestry arrived by [~]300 CE, joined at that time or later by North African ancestry. These results falsify the view that the people of Sardinia are isolated descendants of Europes first farmers. Instead, our results show that the islands admixture history since the Bronze Age is as complex as that in many other parts of Europe.

genomics↗

Temporal shifts in intraspecific and interspecific diet variation: effects of predator body size and identity across seasons in a stream community

Intraspecific variation is increasingly recognized as an important factor in ecological interactions, sometimes exceeding the role of interspecific variation. Few studies, however, have examined how intra-versus interspecific variation affect trophic interactions over time within a seasonally dynamic food web. We collected stomach contents from 2028 reticulate sculpin (Cottus perplexus), 479 cutthroat trout (Oncorhynchus clarkii clarkii), and 107 Pacific giant salamanders (Dicamptodon tenebrosus) in western Oregon streams and compared diets among predator species and size classes over three seasons. Predator body size and species identity both showed strong effects on dietary niche breadth, proportional prey composition, and prey size, with seasonal variation in the relative magnitudes of intraspecific and interspecific diet variation. Size-associated diet variation was high in summer and fall but was heavily outweighed by species-associated diet variation in spring. This pattern was driven primarily by a 50-fold increase in the consumption of terrestrial thrips (Order: Thysanoptera) by cutthroat trout in spring compared to summer and fall. Mean dietary niche breadth generally increased with body size and was roughly half as wide in sculpin as in trout and was intermediate in salamanders. Predator-specific responses to the seasonality of terrestrial prey availability were associated with interspecific differences in foraging mode (e.g., benthic vs drift-feeding) and contributed to temporal variation in the roles of predator size and identity in trophic niche differentiation. Our results thereby demonstrate that intraspecific and interspecific diet variation can exhibit strong seasonality in stream predators, emphasizing the dynamic nature of food webs and the need to incorporate sampling over relevant temporal scales in efforts to understand species interactions.

ecology↗

Food web interaction strength distributions are conserved by greater variation between than within predator-prey pairs

Species interactions in food webs are usually recognized as dynamic, varying across species, space and time due to biotic and abiotic drivers. Yet food webs also show emergent properties that appear consistent, such as a skewed frequency distribution of interaction strengths (many weak, few strong). Reconciling these two properties requires an understanding of the variation in pairwise interaction strengths and its underlying mechanisms. We estimated stream sculpin feeding rates in three seasons at nine sites in Oregon to examine variation in trophic interaction strengths both across and within predator-prey pairs. We considered predator and prey densities, prey body mass, and abiotic factors as putative drivers of within-pair variation over space and time. We hypothesized that consistently skewed interaction strength distributions could result if individual interaction strengths show relatively little variation, or alternatively, if interaction strengths vary but shift in ways that conserve their overall frequency distribution. We show that feeding rate distributions remained consistently and positively skewed across all sites and seasons. The mean coefficient of variation in feeding rates within each of 25 focal species pairs across surveys was less than half the mean coefficient of variation seen across species pairs within a given survey. The rank order of feeding rates also remained relatively conserved across streams, seasons and individual surveys. On average, feeding rates on each prey taxon nonetheless varied by a hundredfold across surveys, with some feeding rates showing more variation in space and others in time. For most species pairs, feeding rates increased with prey density and decreased with high stream flows and low water temperatures. For nearly half of all species pairs, factors other than prey density explained the most variation, indicating that the strength of density dependence in feeding rates can vary greatly among a generalist predators prey species. Our findings show that although individual interaction strengths exhibit considerable variation in space and time, they can nonetheless remain relatively consistent, and thus predictable, compared to the even larger variation that occurs across species pairs. These insights help reconcile how the skewed nature of interaction strength distributions can persist in highly dynamic food webs.

ecology↗

The intrinsic predictability of ecological time series and its potential to guide forecasting

Successfully predicting the future states of systems that are complex, stochastic and potentially chaotic is a major challenge. Model forecasting error (FE) is the usual measure of success; however model predictions provide no insights into the potential for improvement. In short, the realized predictability of a specific model is uninformative about whether the system is inherently predictable or whether the chosen model is a poor match for the system and our observations thereof. Ideally, model proficiency would be judged with respect to the systems intrinsic predictability - the highest achievable predictability given the degree to which system dynamics are the result of deterministic v. stochastic processes. Intrinsic predictability may be quantified with permutation entropy (PE), a model-free, information-theoretic measure of the complexity of a time series. By means of simulations we show that a correlation exists between estimated PE and FE and show how stochasticity, process error, and chaotic dynamics affect the relationship. This relationship is verified for a dataset of 461 empirical ecological time series. We show how deviations from the expected PE-FE relationship are related to covariates of data quality and the nonlinearity of ecological dynamics.\n\nThese results demonstrate a theoretically-grounded basis for a model-free evaluation of a systems intrinsic predictability. Identifying the gap between the intrinsic and realized predictability of time series will enable researchers to understand whether forecasting proficiency is limited by the quality and quantity of their data or the ability of the chosen forecasting model to explain the data. Intrinsic predictability also provides a model-free baseline of forecasting proficiency against which modeling efforts can be evaluated.\n\nGlossaryActive information: The amount of information that is available to forecasting models (redundant information minus lost information; Fig. 1).\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=45 SRC=\"FIGDIR/small/350017_fig1a.gif\" ALT=\"Figure 1A\">\nView larger version (9K):\norg.highwire.dtl.DTLVardef@934d9eorg.highwire.dtl.DTLVardef@ccdc10org.highwire.dtl.DTLVardef@1839ed9org.highwire.dtl.DTLVardef@31bd70_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOFigure 1A.C_FLOATNO The total information content of an observation of a system at a given state in time, St, is depicted by filled circles with past states (St-1 and St-2) represented by shades of grey, i) lack of overlap between past and present states illustrating a case where no information is transmitted from past states (i.e. a purely stochastic system), with low redundancy and high Shannon entropy rate, ii) intermediate overlap indicating a case when some information is transferred from past to present (i.e. a deterministic system strongly driven by stochastic forcing), with intermediate redundancy and Shannon entropy rate, iii) large overlap indicating a case when the current state is mostly determined by the previous state (i.e. a highly deterministic system), with high redundancy and low Shannon entropy rate. Note that both the redundancy and Shannon entropy rate of a system are intrinsic properties of the system and will only change if the system itself changes.\n\nC_FIG Forecasting error (FE): A measure of the discrepancy between a models forecasts and the observed dynamics of a system. Common measures of forecast error are root mean squared error and mean absolute error.\n\nEntropy: Measures the average amount of information in the outcome of a stochastic process.\n\nInformation: Any entity that provides answers and resolves uncertainty about a process. When information is calculated using logarithms to the base two (i.e. information in bits), it is the minimum number of yes/no questions required, on average, to determine the identity of the symbol (Jost 2006). The information in an observation consists of information inherited from the past (redundant information), and of new information.\n\nIntrinsic predictability: the maximum achievable predictability of a system (Beckage et al. 2011).\n\nLost information: The part of the redundant information lost due to measurement or sampling error, or transformations of the data (Fig. 1).\n\nNew information, Shannon entropy rate: The Shannon entropy rate quantifies the average amount of information per observation in a time series that is unrelated to the past, i.e., the new information (Fig. 1).\n\nNonlinearity: When the deterministic processes governing system dynamics depend on the state of the system.\n\nPermutation entropy (PE): permutation entropy is a measure of the complexity of a time series (Bandt & Pompe, 2002) that is negatively correlated with a systems predictability (Garland et al. 2015). Permutation entropy quantifies the combined new and lost information. PE is scaled to range between a minimum of 0 and a maximum of 1.\n\nRealized predictability: the achieved predictability of a system from a given forecasting model.\n\nRedundant information: The information inherited from the past, and thus the maximum amount of information available for use in forecasting (Fig. 1).\n\nSymbols, words, permutations: symbols are simply the smallest unit in a formal language such as the letters in the English alphabet i.e., {\"A\", \"B\",..., \"Z\"}. In information theory the alphabet is more abstract, such as elements in the set {\"up\", \"down\"} or {\"1\", \"2\", \"3\"}. Words, of length m refer to concatenations of the symbols (e.g., up-down-down) in a set. Permutations are the possible orderings of symbols in a set. In this manuscript, the words are the permutations that arise from the numerical ordering of m data points in a time series.\n\nWeighted permutation entropy (WPE): a modification of permutation entropy (Fadlallah et al., 2013) that distinguishes between small-scale, noise-driven variation and large-scale, system-driven variation by considering the magnitudes of changes in addition to the rank-order patterns of PE.

ecology↗

The Genomic Formation of South and Central Asia

The genetic formation of Central and South Asian populations has been unclear because of an absence of ancient DNA. To address this gap, we generated genome-wide data from 362 ancient individuals, including the first from eastern Iran, Turan (Uzbekistan, Turkmenistan, and Tajikistan), Bronze Age Kazakhstan, and South Asia. Our data reveal a complex set of genetic sources that ultimately combined to form the ancestry of South Asians today. We document a southward spread of genetic ancestry from the Eurasian Steppe, correlating with the archaeologically known expansion of pastoralist sites from the Steppe to Turan in the Middle Bronze Age (2300-1500 BCE). These Steppe communities mixed genetically with peoples of the Bactria Margiana Archaeological Complex (BMAC) whom they encountered in Turan (primarily descendants of earlier agriculturalists of Iran), but there is no evidence that the main BMAC population contributed genetically to later South Asians. Instead, Steppe communities integrated farther south throughout the 2nd millennium BCE, and we show that they mixed with a more southern population that we document at multiple sites as outlier individuals exhibiting a distinctive mixture of ancestry related to Iranian agriculturalists and South Asian hunter-gathers. We call this group Indus Periphery because they were found at sites in cultural contact with the Indus Valley Civilization (IVC) and along its northern fringe, and also because they were genetically similar to post-IVC groups in the Swat Valley of Pakistan. By co-analyzing ancient DNA and genomic data from diverse present-day South Asians, we show that Indus Periphery-related people are the single most important source of ancestry in South Asia--consistent with the idea that the Indus Periphery individuals are providing us with the first direct look at the ancestry of peoples of the IVC--and we develop a model for the formation of present-day South Asians in terms of the temporally and geographically proximate sources of Indus Periphery-related, Steppe, and local South Asian hunter-gatherer-related ancestry. Our results show how ancestry from the Steppe genetically linked Europe and South Asia in the Bronze Age, and identifies the populations that almost certainly were responsible for spreading Indo-European languages across much of Eurasia.\n\nOne Sentence SummaryGenome wide ancient DNA from 357 individuals from Central and South Asia sheds new light on the spread of Indo-European languages and parallels between the genetic history of two sub-continents, Europe and South Asia.

genomics↗

Ancient genomes document multiple waves of migration in Southeast Asian prehistory

Southeast Asia is home to rich human genetic and linguistic diversity, but the details of past population movements in the region are not well known. Here, we report genome-wide ancient DNA data from thirteen Southeast Asian individuals spanning from the Neolithic period through the Iron Age (4100-1700 years ago). Early agriculturalists from Man Bac in Vietnam possessed a mixture of East Asian (southern Chinese farmer) and deeply diverged eastern Eurasian (hunter-gatherer) ancestry characteristic of Austroasiatic speakers, with similar ancestry as far south as Indonesia providing evidence for an expansive initial spread of Austroasiatic languages. In a striking parallel with Europe, later sites from across the region show closer connections to present-day majority groups, reflecting a second major influx of migrants by the time of the Bronze Age.

genetics↗

What drives interaction strengths in complex food webs? A test with feeding rates of a generalist stream predator

Describing the mechanisms that drive variation in species interaction strengths is central to understanding, predicting, and managing community dynamics. Multiple factors have been linked to trophic interaction strength variation, including species densities, species traits, and abiotic factors. Yet most empirical tests of the relative roles of multiple mechanisms that drive variation have been limited to simplified experiments that may diverge from the dynamics of natural food webs. Here, we used a field-based observational approach to quantify the roles of prey density, predator density, predator-prey body-mass ratios, prey identity, and abiotic factors in driving variation in feeding rates of reticulate sculpin (Cottus perplexus). We combined data on over 6,000 predator-prey observations with prey identification time functions to estimate 289 prey-specific feeding rates at nine stream sites in Oregon. Feeding rates on 57 prey types showed an approximately log-normal distribution, with few strong and many weak interactions. Model selection indicated that prey density, followed by prey identity, were the two most important predictors of prey-specific sculpin feeding rates. Feeding rates showed a positive, accelerating relationship with prey density that was inconsistent with predator saturation predicted by current functional response models. Feeding rates also exhibited four orders-of-magnitude in variation across prey taxonomic orders, with the lowest feeding rates observed on prey with significant anti-predator defenses. Body-mass ratios were the third most important predictor variable, showing a hump-shaped relationship with the highest feeding rates at intermediate ratios. Sculpin density was negatively correlated with feeding rates, consistent with the presence of intraspecific predator interference. Our results highlight how multiple co-occurring drivers shape trophic interactions in nature and underscore ways in which simplified experiments or reliance on scaling laws alone may lead to biased inferences about the structure and dynamics of species-rich food webs.

ecology↗

The mitotic spindle is chiral due to torques generated by motor proteins

Mitosis relies on forces generated in the spindle, a micro-machine composed of microtubules and associated proteins1,2. Forces are required for the congression of chromosomes to the metaphase plate and separation of chromatids in anaphase3-6. However, torques may also exist in the spindle, yet they have not been investigated. Here we show that the spindle is chiral. Chirality is evident from the finding that microtubule bundles follow a left-handed helical path, which cannot be explained by forces but rather by torques acting in the bundles. STED super-resolution microscopy, as well as confocal microscopy, of human spindles shows that the bundles have complex curved shapes. The average helicity of the bundles with respect to the spindle axis is 1.2{degrees}/m. Inactivation of kinesin-5 (Eg5/Kif11) abolished the chirality of the spindle, suggesting that this motor generates the helical shape of microtubule bundles. To explain the observed shapes, we introduce a theoretical model for the balance of forces and torques acting in the spindle, and show that torque is required to generate the helical shapes. We conclude that torques generated by motor proteins, in addition to forces, exist in the spindle and determine its architecture.

cell biology↗

The Genomic History Of Southeastern Europe

Farming was first introduced to southeastern Europe in the mid-7th millennium BCE - brought by migrants from Anatolia who settled in the region before spreading throughout Europe. To clarify the dynamics of the interaction between the first farmers and indigenous hunter-gatherers where they first met, we analyze genome-wide ancient DNA data from 223 individuals who lived in southeastern Europe and surrounding regions between 12,000 and 500 BCE. We document previously uncharacterized genetic structure, showing a West-East cline of ancestry in hunter-gatherers, and show that some Aegean farmers had ancestry from a different lineage than the northwestern Anatolian lineage that formed the overwhelming ancestry of other European farmers. We show that the first farmers of northern and western Europe passed through southeastern Europe with limited admixture with local hunter-gatherers, but that some groups mixed extensively, with relatively sex-balanced admixture compared to the male-biased hunter-gatherer admixture that prevailed later in the North and West. Southeastern Europe continued to be a nexus between East and West after farming arrived, with intermittent genetic contact from the Steppe up to 2,000 years before the migration that replaced much of northern Europes population.

genetics↗

Exact probabilities for the indeterminacy of complex networks as perceived through press perturbations

We consider the goal of predicting how complex networks respond to chronic (press) perturbations when characterizations of their network topology and interaction strengths are associated with uncertainty. Our primary result is the derivation of exact formulas for the expected number and probability of qualitatively incorrect predictions about a systems responses under uncertainties drawn form arbitrary distributions of error. These formulas obviate the current use of simulations, algorithms, and qualitative modeling techniques. Additional indices provide new tools for identifying which links in a network are most qualitatively and quantitatively sensitive to error, and for determining the volume of errors within which predictions will remain qualitatively determinate (i.e. sign insensitive). Together with recent advances in the empirical characterization of uncertainty in ecological networks, these tools bridge a way towards probabilistic predictions of network dynamics.

ecology↗

Quantifying predator dependence in the functional response of generalist predators.

A longstanding debate concerns whether functional responses are best described by prey-dependent versus ratio-dependent models. Theory suggests that ratio dependence can explain many food web patterns left unexplained by simple prey-dependent models. However, for logistical reasons, ratio dependence and predator dependence more generally have seen infrequent empirical evaluation and then only so in specialist predators, which are rare in nature. Here we develop an approach to simultaneously estimate the prey-specific attack rates and predator-specific interference rates of predators interacting with arbitrary numbers of prey and predator species. We apply the approach to field surveys and two field experiments involving two intertidal whelks and their full suite of potential prey. Our study provides strong evidence for the presence of weak predator dependence that is closer to being prey dependent than ratio dependent over manipulated and natural ranges of species abundances. It also indicates how, for generalist predators, even the qualitative nature of predator dependence can be prey-specific.\n\nAuthor contributionsCW contributed to method development, KC and IS performed the caging experiment, and MN conceived of the study, carried out the fieldwork and analyses, and wrote the manuscript.

ecology↗