Improving inference for nonlinear state-space models of animal population dynamics given biased sequential life stage data.

State-space models (SSMs) are a popular tool for modeling animal abundances. Inference difficulties for simple linear SSMs are well known, particularly in relation to simultaneous estimation of process and observation variances. Several remedies to overcome estimation problems have been studied for relatively simple SSMs, but whether these challenges and proposed remedies apply for nonlinear stage-structured SSMs, an important class of ecological models, is less well understood. Here we identify improvements for inference about nonlinear stage-structured SSMs fit with biased sequential life stage data. Theoretical analyses indicate parameter identifiability requires covariates in the state processes. Simulation studies show that plugging in externally estimated observation variances, as opposed to jointly estimating them with other parameters, reduces bias and standard error of estimates. In contrast to previous results for simple linear SSMs, strong confounding between jointly estimated process and observation variance parameters was not found in the models explored here. However, when observation variance was also estimated in the motivating case study, the resulting process variance estimates were implausibly low (near-zero). As SSMs are used in increasingly complex ways, understanding when inference can be expected to be successful, and what aids it, becomes more important. Our study illustrates (a) the need for relevant process covariates and (b) the benefits of using externally estimated observation variances for inference about nonlinear stage-structured SSMs.

Building matrix population models when individuals are non-identifiable.

Matrix Population Models (MPM) are among the most widely used tools in ecology and evolution. These models consider the life cycle of an individual as composed by states to construct a matrix containing the likelihood of transitions between these states as well as sexual and/or asexual per-capita offspring contributions. When individuals are identifiable one can parametrize an MPM based on survival and fertility data and average development times for every state, but some of this information is absent or incomplete for non-cohort data, or for cohort data when individuals are not identifiable. Here we introduce a simple procedure for the parameterization of an MPM that can be used with cohort data when individuals are non-identifiable; among other aspects our procedure is a novelty in that it does not require information on stage development (or stage residence) times, which current procedures require to be estimated externally, and it is a frequent source of error. We exemplify the procedure with a laboratory cohort dataset from Eratyrus mucronatus (Reduviidae, Triatominae). We also show that even if individuals are identifiable and the duration of each stage is externally estimated with no error, our procedure is simpler to use and yields the same MPM parameter estimates.

Mixing rates in weakly differentiated stocks of greater amberjack (Seriola dumerili) in the Gulf of Mexico.

The greater amberjack (Seriola dumerili) is a commercially and recreationally important marine fish species in the southeastern United States, where it has been historically managed as two non-mixing stocks (Gulf of Mexico and Atlantic). Mark-recapture studies and analysis of mitochondrial DNA have suggested the two stocks are demographically independent; however, little is currently known about when and where spawning occurs in Gulf of Mexico amberjack, and whether stock mixture occurs on breeding grounds. The primary objective of this study was to quantify stock mixture among breeding populations of amberjack collected from the Atlantic and Gulf of Mexico. Genetic data based on 11 loci identified very low, though statistically significant differentiation among Gulf of Mexico samples (GST = 0.007, [Formula: see text] = 0.009; all P = 0.001) and between reproductive adults collected from two spawning areas (GST = 0.007, [Formula: see text] = 0.014; all P = 0.001). Naïve Bayesian mixture analysis supported a single genetic cluster [p(S|data) = 0.734] whereas trained clustering (using Atlantic and Gulf spawning fish) gave the highest support to a two-cluster model (p(S|data) = 1.0). Our results support the argument that the genetic structuring of greater amberjack is more complex than the previously assumed two, non-mixing stock model. Although our data provide evidence of limited population structure, we argue in favour of non-panmixia among reproductive fish collected from the Gulf of Mexico and Florida Keys.

Spatial capture-mark-resight estimation of animal population density.

Sightings of previously marked animals can extend a capture-recapture dataset without the added cost of capturing new animals for marking. Combined marking and resighting methods are therefore an attractive option in animal population studies, and there exist various likelihood-based non-spatial models, and some spatial versions fitted by Markov chain Monte Carlo sampling. As implemented to date, the focus has been on modeling sightings only, which requires that the spatial distribution of pre-marked animals is known. We develop a suite of likelihood-based spatial mark-resight models that either include the marking phase ("capture-mark-resight" models) or require a known distribution of marked animals (narrow-sense "mark-resight"). The new models sacrifice some information in the covariance structure of the counts of unmarked animals; estimation is by maximizing a pseudolikelihood with a simulation-based adjustment for overdispersion in the sightings of unmarked animals. Simulations suggest that the resulting estimates of population density have low bias and adequate confidence interval coverage under typical sampling conditions. Further work is needed to specify the conditions under which ignoring covariance results in unacceptable loss of precision, or to modify the pseudolikelihood to include that information. The methods are applied to a study of ship rats Rattus rattus using live traps and video cameras in a New Zealand forest, and to previously published data.

Fine-Scale Genetic Differentiation in a Salamander Hynobius tokyoensis Living in Fragmented Urban Habitats in and Around Tokyo, Japan.

Salamanders are expected to differentiate genetically among local populations due to their low dispersal ability, and are potentially susceptible to loss of genetic diversity if the population is isolated by habitat fragmentation. The salamander Hynobius tokyoensis is a lowland lentic breeder and endemic to a narrow area of central Japan. In this urban area, H. tokyoensis habitats are extensively fragmented and several populations are threatened with extinction, but information on genetic divergence and loss of genetic diversity is scarce. We performed mitochondrial (cyt b) and microsatellite (five loci) DNA analyses of 815 individuals from 46 populations in 12 regions across their entire distribution range. As a result, populations were clearly separated into northern and southern groups, and genetic differentiation among the 12 regions was also evident. Regional differentiation appears to be affected by a complex geographical history, but the genetic diversity of each population may have also been affected by recent habitat fragmentation. There were positive correlations between the mitochondrial and microsatellite DNA diversities. Some populations have lost genetic diversity in both mitochondrial and microsatellite DNAs; all such populations were at the peripheral edges of the species distribution range. Thus, even in attempts to restore genetic diversity in a small population by the transfer of outside individuals, efforts must be made to avoid genetic pollution.

Stochastic analysis of the extra clustering model for animal grouping.

We consider the extra clustering model which was introduced by Durand et al. (J Theor Biol 249(2):262-270, 2007) in order to describe the grouping of social animals and to test whether genetic relatedness is the main driving force behind the group formation process. Durand and François (J Math Biol 60(3):451-468, 2010) provided a first stochastic analysis of this model by deriving (amongst other things) asymptotic expansions for the mean value of the number of groups. In this paper, we will give a much finer analysis of the number of groups. More precisely, we will derive asymptotic expansions for all higher moments and give a complete characterization of the possible limit laws. In the most interesting case (neutral model), we will prove a central limit theorem with a surprising normalization. In the remaining cases, the limit law will be either a mixture of a discrete and continuous law or a discrete law. Our results show that, except of in degenerate cases, strong concentration around the mean value takes place only for the neutral model, whereas in the remaining cases there is also mass concentration away from the mean.

ProCARs: Progressive Reconstruction of Ancestral Gene Orders.

BACKGROUND: In the context of ancestral gene order reconstruction from extant genomes, there exist two main computational approaches: rearrangement-based, and homology-based methods. The rearrangement-based methods consist in minimizing a total rearrangement distance on the branches of a species tree. The homology-based methods consist in the detection of a set of potential ancestral contiguity features, followed by the assembling of these features into Contiguous Ancestral Regions (CARs). RESULTS: In this paper, we present a new homology-based method that uses a progressive approach for both the detection and the assembling of ancestral contiguity features into CARs. The method is based on detecting a set of potential ancestral adjacencies iteratively using the current set of CARs at each step, and constructing CARs progressively using a 2-phase assembling method. CONCLUSION: We show the usefulness of the method through a reconstruction of the boreoeutherian ancestral gene order, and a comparison with three other homology-based methods: AnGeS, InferCARs and GapAdj. The program, written in Python, and the dataset used in this paper are available at http://bioinfo.lifl.fr/procars/.

Male-biased dispersal causes intersexual differences in the subpopulation structure of the gray-sided vole.

The genetic structure of gray-sided voles was investigated at a spatial scale of 2 km using mtDNA sequences. The control region (674bp) of 162 voles was sequenced and 18 haplotypes were identified. Within 0.5-ha trapping plots (n = 8), the number of haplotypes and gene diversity was significantly greater in males than in females. The fixation index among plots for females (F GP = 0.241) was 3 times as large as that for males (0.075), implying male-biased dispersal. A simulation analysis showed that the observed genetic structure in males could be generated by modifying the observed haplotype distribution of females by adding the effects of local male dispersal. Half of the pairwise F GP (15/28) showed significant differentiation in females, whereas almost none (1/28) were significant in males. Isolation by distance was observed in females, whereas no clear spatial pattern was observed in males. Most pairwise F GP for females were not significant in the short- and intermediate-distance classes (≤1.0 km) as with those for males, whereas all showed significant differentiation in the long-distance class (>1.0 km) for females, but not for males. These findings indicate that the extent of subpopulations within which individuals interact differs between sexes.

Estimation of male gene flow from measures of nuclear and female genetic differentiation.

An approach is provided to estimate male gene flow and the ratio of male to female gene flow, given that there are estimates of diploid, nuclear gene flow and haploid, female gene flow. This approach can be applied to estimates of differentiation (F ST ) from biparentally and maternally inherited markers, assuming the equilibrium island model and equal effective numbers of males and females. Corrections to formulas used previously for California sea lions (González-Suárez M, Flatz R, Aurioles-Gamboa D, Hedrick PW, Gerber LR. 2009. Isolation by distance among California sea lion populations in Mexico: redefining management stocks. Mol Ecol. 18:1088-1099.) and American bison (Halbert ND, Gogan PJP, Hedrick PW, Wahl L, Derr JN. 2012. Genetic population substructure in bison in Yellowstone National Park. J Hered. 103:360-370.) are given and revised values for those species are calculated. The effect of unequal male and female effective population sizes, nonequilibrium conditions, and approximations of differentiation formulas are briefly discussed.

A recent view about encephalomyocarditis virus circulating in compartmentalised animal population in Northern Italy.

Encephalomyocarditis virus (Picornaviridae, Cardiovirus A) is the causative agent of the homonymous disease, which may induce myocarditis, encephalitis and reproductive disorders in various mammals, especially in swine. Despite the disease occurred endemically in pig farms since 1997, the recent increase of death experimented in Northern Italy prompted to furtherly investigate the evolution of the virus and the actual spread of the infection. Italian EMC viruses, collected between 2013 and 2019, showed an overall antigenic stability. The in-house ELISA Monoclonal Antibodies based, able to reveal changes in seven different antigenic sites, showed only sporadic and occasional mutations in considered samples and the subsequent phylogenetic analysis confirmed antigenic panel's remarks. All the isolates could be classified within a unique lineage, which comprise other European strains and confirm that the viruses currently circulating in Italy developed from a unique common ancestor. Despite the demonstrated stability of virus, some putative newly emerged variants were detected through antigenic profile analysis and phylogenesis. Finally, the serosurvey proved that spread of EMCV is greater than the diffusion of fatal infections would suggest, due to subclinical circulation of EMCV. It demonstrated an increase in the proportion of seropositive farms, if compared with previous data with no remarkable differences between farms with and without clinical evidence of disease.

Population genetics of the Washington National Primate Research Center's (WaNPRC) captive pigtailed macaque (Macaca nemestrina) population.

Pigtailed macaques (Macaca nemestrina) provide an important model for biomedical research on human disease and for studying the evolution of primate behavior. The genetic structure of captive populations of pigtailed macaques is not as well described as that of captive rhesus (M. mulatta) or cynomolgus (M. fascicularis) macaques. The Washington National Primate Research Center houses the largest captive colony of pigtailed macaques located in several different housing facilities. Based on genotypes of 18 microsatellite (short tandem repeat [STR]) loci, these pigtailed macaques are more genetically diverse than captive rhesus macaques and exhibit relatively low levels of inbreeding. Colony genetic management facilitates the maintenance of genetic variability without compromising production goals of a breeding facility. The periodic introduction of new founders from specific sources to separate housing facilities at different times influenced the colony's genetic structure over time and space markedly but did not alter its genetic diversity significantly. Changes in genetic structure over time were predominantly due to the inclusion of animals from the Yerkes National Primate Research Center in the original colony and after 2005. Strategies to equalize founder representation in the colony have maximized the representation of the founders' genomes in the extant population. Were exchange of animals among the facilities increased, further differentiation could be avoided. The use of highly differentiated animals may confound interpretations of phenotypic differences due to the inflation of the genetic contribution to phenotypic variance of heritable traits.

The pattern of R2 retrotransposon activity in natural populations of Drosophila simulans reflects the dynamic nature of the rDNA locus.

The pattern and frequency of insertions that enable transposable elements to remain active in a population are poorly understood. The retrotransposable element R2 exclusively inserts into the 28S rRNA genes where it establishes long-term, stable relationships with its animal hosts. Previous studies with laboratory stocks of Drosophila simulans have suggested that control over R2 retrotransposition resides within the rDNA loci. In this report, we sampled 180 rDNA loci of animals collected from two natural populations of D. simulans. The two populations were found to have similar patterns of R2 activity. About half of the rDNA loci supported no or very low levels of R2 transcripts with no evidence of R2 retrotransposition. The remaining half of the rDNA loci had levels of R2 transcripts that varied in a continuous manner over almost a 100-fold range and did support new retrotransposition events. Structural analysis of the rDNA loci in 18 lines that spanned the range of R2 transcript levels in these populations revealed that R2 number and rDNA locus size varied 2-fold; however, R2 activity was not readily correlated with either of these parameters. Instead R2 activity was best correlated with the distribution of elements within the rDNA locus. Loci with no activity had larger contiguous blocks of rDNA units free of R2-insertions. These data suggest a model in which frequent recombination within the rDNA locus continually redistributes R2-inserted units resulting in changing levels of R2 activity within individual loci and persistent R2 activity within the population.

Evaluation of suitable endpoints for assessing the impacts of toxicants at the community level.

Assessment of ecological impacts of toxicants relies currently on extrapolation of effects observed at organismal or population levels. The uncertainty inherent to such extrapolations, together with the impossibility of predicting ecological effects of chemical mixtures, can only be resolved by adopting approaches that consider toxicological endpoints at a community or ecological level. Experimental data from micro- and mesocosms provide estimates of community effect levels, which can then be used to confirm or correct the extrapolations from theoretical methods such as species sensitivity distributions (SSDs) or others. When assessing impacts, the choice of sensitive community endpoints is important. Four community endpoints (species richness, abundance, diversity and similarity indices) were evaluated in their ability to assess impacts of two insecticides, imidacloprid and etofenprox, and their mixture on aquatic and benthic communities from artificial rice paddies. Proportional changes of each community endpoint were expressed by ratios between their values in the treatment and control paddies. Regression lines fitted to the endpoint ratios against the time series of chemical concentrations were used to predict percentile impacts in the communities. The abundance endpoint appears to be the most sensitive indicator of the communities' response, but the Czekanowski similarity index described best the structural changes that occur in all communities. Aquatic arthropods were more sensitive to the mixture of both insecticides than zooplankton and benthic communities. Estimated protective levels for 95% of aquatic species exposed to imidacloprid (<0.01-1.0 µg l(-1)) were slightly lower than predicted by SSD, whereas for etofenprox the protective concentrations in water (<0.01-0.58 µg l(-1)) were an order of magnitude lower than SSD's predictions.

Effect of temperature on behavioural isolation: a study with Drosophila ananassae populations.

Experiments were conducted to study sexual isolation among two natural populations of Drosophila ananassae maintained at 18 degrees C and 24 degrees C for 12 generations in the laboratory to see the effect of this environmental variable on behavioural isolation. Multiple choice technique was used and matings were observed directly in Elens Wattiaux mating chamber. Results showed sexual isolation among strains that were maintained at different temperatures, indicating that temperature may have affected the mating behaviour of the flies which resulted in the induction of ethological isolation among the strains.

Double-observer approach with camera traps can correct imperfect detection and improve the accuracy of density estimation of unmarked animal populations.

Camera traps are a powerful tool for wildlife surveys. However, camera traps may not always detect animals passing in front. This constraint may create a substantial bias in estimating critical parameters such as the density of unmarked populations. We proposed the 'double-observer approach' with camera traps to counter the constraint, which involves setting up a paired camera trap at a station and correcting imperfect detection with a reformulated hierarchical capture-recapture model for stratified populations. We performed simulations to evaluate this approach's reliability and determine how to obtain desirable data for this approach. We then applied it to 12 mammals in Japan and Cameroon. The results showed that the model assuming a beta-binomial distribution as detection processes could correct imperfect detection as long as paired camera traps detect animals nearly independently (Correlation coefficient ≤ 0.2). Camera traps should be installed to monitor a predefined small focal area from different directions to satisfy this requirement. The field surveys showed that camera trap could miss animals by 3-40%, suggesting that current density estimation models relying on perfect detection may underestimate animal density by the same order of magnitude. We hope that our approach will be incorporated into existing density estimation models to improve their accuracy.

A Survey of Chinese Pig Farms and Human Healthcare Isolates Reveals Separate Human and Animal Methicillin-Resistant Staphylococcus aureus Populations.

There has been increasing concern that the overuse of antibiotics in livestock farming is contributing to the burden of antimicrobial resistance in people. Farmed animals in Europe and North America, particularly pigs, provide a reservoir for livestock-associated methicillin-resistant Staphylococcus aureus (LA-MRSA ST398 lineage) found in people. This study is designed to investigate the contribution of MRSA from Chinese pig farms to human infection. A collection of 483 MRSA are isolated from 55 farms and 4 hospitals in central China, a high pig farming density area. CC9 MRSA accounts for 97.2% of all farm isolates, but is not present in hospital isolates. ST398 isolates are found on farms and hospitals, but none of them formed part of the "LA-MRSA ST398 lineage" present in Europe and North America. The hospital ST398 MRSA isolate form a clade that is clearly separate from the farm ST398 isolates. Despite the presence of high levels of MRSA found on Chinese pig farms, the authors find no evidence of them spilling over to the human population. Nevertheless, the ST398 MRSA obtained from hospitals appear to be part of a widely distributed lineage in China. The new animal-adapted ST398 lineage that has emerged in China is of concern.

Evolution in heterogeneous environments: between soft and hard selection.

Since their first formulations about half a century ago, the soft and hard selection models have become classical frameworks to study selection in subdivided populations. These models differ in the timing of density regulation and represent two extreme types of selection: density- and frequency-dependent selection (soft) and density- and frequency-independent selection (hard). Yet only few attempts have been made so far to model intermediate scenarios. Here, we design a model where migration may happen twice during the life cycle: before density regulation with probability d(J) (juvenile migration) and after density regulation with probability d(A) (adult migration). In the first step, we analyze the conditions for the coexistence of two specialists. We find that coexistence is possible under a large range of selection types, even when environmental heterogeneity is low. Then, we investigate the different possible outcomes obtained through gradual evolution. We show that polymorphism is more likely to evolve when the trade-off is weak, environmental heterogeneity is high, migration is low, and in particular when juvenile migration is low relative to adult migration, because the timing of migration affects the magnitude of frequency-dependent selection relative to gene flow. This model may provide a more general theoretical framework to experimentally study evolution in heterogeneous environments.

Genetic analysis of cadherin function in animal morphogenesis.

Cadherins are a superfamily of Ca(2+)-dependent adhesion molecules found in metazoans. Several classes of cadherins have been defined from which two - classic cadherins and Fat-like cadherins - have been studied by genetic approaches. Recent in vivo studies in Caenorhabditis elegans and Drosophila show that cadherins play an active role in a number of distinct morphogenetic processes. Classic cadherins function in epithelial polarization, epithelial sheet or tube fusion, cell migration, cell sorting, and axonal patterning. Fat-like cadherins are required for epithelial morphogenesis, proliferation control, and epithelial planar polarization.

Proton-coupled solute transport in the animal cell plasma membrane.

This review focuses primarily on the progress made in the last couple of years in the understanding of the intestinal peptide transporter, a prototype for H(+)-coupled solute transport systems in the animal cell plasma membrane. The impressive number of transport systems currently known to be energized by the components of the proton-motive force indicates that the role of H+ as the coupling ion for active transport has not been lost during evolution.

Recycling of proteins between the endoplasmic reticulum and Golgi complex.

Several lines of investigation have shown that protein transport from the endoplasmic reticulum to the Golgi is more complex than previously imagined. Dynamic sorting of both membrane and soluble proteins is now believed to occur on the cis side of the Golgi apparatus with some proteins returning to the endoplasmic reticulum while others travel onwards.