The relative strength of selection on modifiers of genetic architecture under migration load

Gene flow between populations adapting to differing local environmental conditions creates a "migration load" because individuals might disperse to habitats where their survival is low or because they might reproduce with locally maladapted individuals. The amount by which the mean relative population fitness is kept below one creates an opportunity for modifiers of the genetic architecture to spread due to selection. Prior work that separately considered modifiers changing dispersal or recombination rates, or altering dominance or epistasis, has typically focused on the direction of selection rather than its absolute magnitude. We here develop methods to determine the strength of selection on modifiers of the genetic architecture, including modifiers of the dispersal rate, after populations evolved local adaptation. We consider scenarios with up to five loci contributing to local adaptation and derive a matrix model for the deterministic spread of modifiers. We find that selection for modifiers of epistasis and dominance is stronger than selection for decreased recombination, and that selection for partial reductions in recombination are extremely weak, regardless of the number of loci contributing to local adaptation. The spread of modifiers for a reduction in dispersal depends on the number of loci, pre-existing epistasis and extent of migration load. We identify a novel effect, that modifiers of dominance are more strongly selected when they are unlinked to the locus that they modify. Overall, these results help explain population differentiation and reproductive isolation and provide a benchmark to compare selection on genetic architecture modifiers in finite population sizes and under demographic stochasticity.

Error Distribution Model to Standardize LPUE, CPUE and Survey-Derived Catch Rates of Target and Non-Target Species

Indices of abundance are usually a key input parameter used for fitting a stock assessment model, as they provide abundance estimates representative of the fraction of the stock that is vulnerable to fishing. These indices can be estimated from catches derived from fishery-dependent sources, such as catch per unit effort (CPUE) and landings per unit effort (LPUE), or from scientific survey data (e.g., relative population number—RPN). However, fluctuations in many factors (e.g., vessel size, period, area, gear) may affect the catch rates, bringing the need to evaluate the appropriateness of the statistical models for the standardization process. In this research, we analyzed different generalized linear models to select the best technique to standardize catch rates of target and non-target species from fishery dependent (CPUE and LPUE) and independent (RPN) data. The examined error distribution models were gamma, lognormal, tweedie, and hurdle models. For hurdle, positive observations were analyzed assuming a lognormal (hurdle–lognormal) or gamma (hurdle–gamma) error distribution. Based on deviance table analyses and diagnostic checks, the hurdle–lognormal was the statistical model that best satisfied the underlying characteristics of the different data sets. Finally, catch rates (CPUE, LPUE and RPN) of the thornback ray Raja clavata, blackbelly rosefish Helicolenus dactylopterus, and common mora Mora moro from the NE Atlantic (Azores region) were standardized. The analyses confirmed the spatial and temporal nature of their distribution.

Water vole (Arvicola amphibious) as an object of long-term biomonitoring in a floodplain area (Western Siberia, Russia)

The paper is devoted to the dynamics of the water vole population in the conditions of total deforestation of valley forests and their subsequent restoration. We analyzed the relative population of small mammals in the typical biotopes in the Tom River basin (Western Siberia) on the border of the forest-steppe and taiga zones. From 1978 to 2019, 1,139 water voles Arvicola amphibius (Linnaeus, 1758) (synonym of A. terrestris) were caught with 50-meter trapping grooves; for 788 individuals we assessed the condition of non-metric features (phenes) of the skull. It was found that changes in the population level are non-cyclical, while against the background of a generally low occurrence of the species in the region, the population level increased tenfold in some years. It was shown that such episodic population surges can significantly impact the structure of the community of small mammals. In the valley of the Tom River, the water vole prefers inhabit wet meadows and ecotone areas between the meadow and the dark coniferous taiga forest. During the years of population surges, the water vole intensely occupies new nesting sites due to the dispersal activity of young animals but at the same time retains the original biotopic preferences. Dispersal of the species takes place in waterlogged wetlands. Most of the animals caught during the peak of their numbers were young animals of late broods born from overwintered individuals. The conducted phenetic analysis revealed the heterogeneity of young animals during the population surge, which allowed us to assume the participation of several populations in the formation of the peak. In the final surge year, the surge was characterized by an extremely low percentage of participation in the breeding of young females and the appearance of a large number of weakened animals, which led to crisis in the species population and the disappearance of the water vole from the captures. The research shows that one cannot predict the success of this process at the current stage; therefore, after flooding, it is necessary to continue monitoring.

Molecular interaction and partitioning in α-keratin using 1 H NMR spin-lattice ( T 1 ) relaxation times

The interactions between small molecules and keratins are poorly understood. In this paper, a nuclear magnetic resonance method is presented to measure changes in the 1 H T 1 relaxation times of small molecules in human hair keratin to quantify their interaction with the fibre. Two populations of small-molecule compounds were identified with distinct relaxation times, demonstrating the partitioning of the compounds into different keratin environments. The changes in relaxation time for solvent in hair compared with bulk solvent were shown to be related to the molecular weight (MW) and the partition coefficient, LogP, of the solvent investigated. Compounds with low MWs and high hydrophilicities had greater reductions in their T 1 relaxation times and therefore experienced increased interactions with the hair fibre. The relative population sizes were also calculated. This is a significant step towards modelling the behaviour of small molecules in keratinous materials and other large insoluble fibrous proteins.

Reactive/Less-cooperative individuals advance population’s synchronization: Modeling of Dictyostelium discoideum concerted signaling during aggregation phase

Orchestrated chemical signaling of single cells sounds to be a linchpin of emerging organization and multicellular life form. The social amoeba Dictyostelium discoideum is a well-studied model organism to explore overall pictures of grouped behavior in developmental biology. The chemical waves secreted by aggregating Dictyostelium is a superb example of pattern formation. The waves are either circular or spiral in shape, according to the incremental population density of a self-aggregating community of individuals. Here, we revisit the spatiotemporal patterns that appear in an excitable medium due to synchronization of randomly firing individuals, but with a more parsimonious attitude. According to our model, a fraction of these individuals are less involved in amplifying external stimulants. Our simulations indicate that the cells enhance the system’s asymmetry and as a result, nucleate early sustainable spiral territory zones, provided that their relative population does not exceed a tolerable threshold.

rGAI: An R package for fitting the generalised abundance index to seasonal count data

1. The Generalised Abundance Index (GAI) provides a useful tool for estimating relative population sizes and trends of seasonal invertebrates from species’ count data, and offers potential for inferring which external factors may influence phenology and demography through parametric descriptions of seasonal variation. 2. We provide an R package that extends previous software with the ability to include covariates when fitting parametric GAI models, where seasonal variation is described by either a mixture of Normal distributions or a stopover model which provides estimates of lifespan. The package also generalises the model to allow any number of broods/generations in the target population within a defined season. The option to perform bootstrapping, either parametrically or non-parametrically, is also provided. 3. The new package allows models to be far more flexible when describing seasonal variation, which may be dependent on site-specific environmental factors or consist of many broods/generations which may overlap, as demonstrated by two case studies. 4. Our open-source software, available at \href{https://github.com/calliste-fagard-jenkin/GAI}{https://github.com/calliste-fagard-jenkin/rGAI}, makes this extension widely and freely available, allowing the complexity of GAI models used by ecologists and applied statisticians to increase accordingly.

Relative species abundance and population densities of the past; developing multi-species occupancy models for fossil data

The number of individuals of species within communities varies, but estimating abundance, given incomplete and biased sampling, is challenging. Here, we describe a new occupancy model in a hierarchical Bayesian framework with random effects, where multi-species occupancy and detection are modeled as a means to estimate relative species abundance and relative population densities. The modelling framework is suited for occupancy data for temporal samples of fossil communities with repeated sampling including multiple species with similar preservation potential. We demonstrate our modelling framework using a fossil community of benthic organisms to estimate changing relative species abundance dynamics and relative population densities of focal species in 9 (geological) time-intervals over 2.3 million years. We also explored potential explanatory factors (paleoenvironmental proxies) and temporal autocorrelation that could provide extra information on unsampled time-intervals. The modelling framework is applicable across a wide range of questions on species-level dynamics in (palaeo)ecological community settings.

Assessing (a)symmetry in multilingualism: The case of Mano and Kpelle in Guinea

Aims and objectives: The paper studies Kpelle–Mano bilingualism in the broader context of local multilingual repertoires and assesses symmetry in the patterns of language use. Methodology: We combine natural speech sampling with ethnographic observations, interviews, sociolinguistic surveys and elicitation tasks. Data and analysis: The data analyzed includes 88 questionnaire responses, targeted elicitation with 21 individuals, as well as corpus collection and ethnographic observations over the course of fieldwork from 2008 onwards. Findings: Neither Mano nor Kpelle has an overt prestige value. Marriage patterns and economic activity are symmetrical, and both languages can be in certain cases chosen as a means of interethnic communication. However, bilingualism is typically unreciprocated, and the Mano speak Kpelle more often than the other way round. Contact-induced change is almost exclusively unidirectional, with Kpelle influencing Mano. We suggest relative population size as the main explanatory factor. In contrast, both Mano and Kpelle are in an asymmetric relationship with Maninka, which is frequently used by urban Mano and Kpelle speakers. Even if some Maninka claim to speak Kpelle to a certain extent, they rarely use it in real life. Originality: This paper is a report on a previously unstudied multilingual setting. We stress the theoretical and the empirical importance of the patrilect. In addition to its being the defining identity feature, the patrilect is also the main predictor defining the language choice in communication and the volume of the repertoire. Significance: We applied long-term participant observation in various social settings to obtain a fine-grained account of the rules governing language choice, which a typical background questionnaire would overlook. We also sampled natural and elicited speech of L1 and L2 speakers of Mano and Kpelle, a method that yields better results than proficiency tests because it captures interference in grammar, which has far-reaching consequences for contacting languages.

Infective prey leads to a partial role reversal in a predator-prey interaction

An infective prey has the potential to infect, kill and consume its predator. Such a prey-predator relationship fundamentally differs from the predator-prey interaction because the prey can directly profit from the predator as a growth resource. Here we present a population dynamics model of partial role reversal in the predator-prey interaction of two species, the bottom dwelling marine deposit feeder sea cucumber Apostichopus japonicus and an important food source for the sea cucumber but potentially infective bacterium Vibrio splendidus. We analyse the effects of different parameters, e.g. infectivity and grazing rate, on the population sizes. We show that relative population sizes of the sea cucumber and V. Splendidus may switch with increasing infectivity. We also show that in the partial role reversal interaction the infective prey may benefit from the presence of the predator such that the population size may exceed the value of the carrying capacity of the prey in the absence of the predator. We also analysed the conditions for species extinction. The extinction of the prey, V. splendidus, may occur when its growth rate is low, or in the absence of infectivity. The extinction of the predator, A. japonicus, may follow if either the infectivity of the prey is high or a moderately infective prey is abundant. We conclude that partial role reversal is an undervalued subject in predator-prey studies.