Complexity of the Relationship between Environmental Factors, Interspecific Competition, and Intrinsic Traits of the Species in Explaining the Invasive Success of Gobio lozanoi Doadrio & Madeira, 2004

The increase of non-native species in rivers is of great concern. To assess the potential impact of a species it is necessary to consider the ecological state of the receiving ecosystem and the biology of the potentially invasive species. In this work we characterize two populations of Gobio lozanoi Doadrio & Madeira, 2004 (bio-metric and demographic parameter) and the invasibility (as a function of habitat quality, competing species, food supply, etc.) of the two rivers that they inhabit. In addition, biomarkers of energy reserve level are analyzed to investigate their role in the invasiveness of the species. The results show differences in energy reserve levels and invasiveness between the two fish populations, and differences in the potential invasibility of the two tributaries. In the river with lower resistance to invasion, the G. lozanoi population is well-structured, and specimens have higher lipid values. On the contrary, in the river with better ecological status (and therefore greater resistance to invasion) we found lower lipid values, higher protein values and low juvenile survival rate. The lipid level is revealed as a good indicator of invasiveness in populations of alien species, under favorable conditions for invasion.

A co-infection model for HPV and syphilis with optimal control and cost-effectiveness analysis

A co-infection model for human papillomavirus (HPV) and syphilis with cost-effectiveness optimal control analysis is developed and presented. The full co-infection model is shown to undergo the phenomenon of backward bifurcation when a certain condition is satisfied. The global asymptotic stability of the disease-free equilibrium of the full model is shown not to exist when the associated reproduction number is less than unity. The existence of endemic equilibrium of the syphilis-only sub-model is shown to exist and the global asymptotic stability of the disease-free and endemic equilibria of the syphilis-only sub-model was established, for a special case. Sensitivity analysis is also carried out on the parameters of the model. Using the syphilis associated reproduction number, [Formula: see text], as the response function, it is observed that the five-ranked parameters that drive the dynamics of the co-infection model are the demographic parameter [Formula: see text], the effective contact rate for syphilis transmission, [Formula: see text], the progression rate to late stage of syphilis [Formula: see text], and syphilis treatment rates: [Formula: see text] and [Formula: see text] for co-infected individuals in compartments [Formula: see text] and [Formula: see text], respectively. Moreover, when the HPV associated reproduction number, [Formula: see text], is used as the response function, the five most dominant parameters that drive the dynamics of the model are the demographic parameter [Formula: see text], the effective contact rate for HPV transmission, [Formula: see text], the fraction of HPV infected who develop persistent HPV [Formula: see text], the fraction of individuals vaccinated against incident HPV infection [Formula: see text] and the HPV vaccine efficacy [Formula: see text]. Numerical simulations of the optimal control model showed that the optimal control strategy which implements syphilis treatment controls for singly infected individuals is the most cost-effective of all the control strategies in reducing the burden of HPV and syphilis co-infections.

Survival Rates and Capture Heterogeneity of Bottlenose Dolphins (Tursiops truncatus) in the Shannon Estuary, Ireland

Adult survival is arguably the most important demographic parameter for long-lived species as it has a large impact on population growth, and it can be estimated for cetacean populations using natural markings and mark-recapture (MR) modelling. Here we describe a 26-year study of a genetically discrete, resident population of bottlenose dolphins in the Shannon Estuary, Ireland, conducted by an NGO using multiple platforms. We estimated survival rates (SRs) using Cormack-Jolly-Seber models and explored the effects of variable survey effort, multiple researchers, and changes in camera equipment as well as capture heterogeneity induced by changes in marks and site fidelity variation, all common issues affecting longitudinal dolphin studies. The mean adult SR was 0.94 (±0.001 SD) and thus comparable to the estimates reported for other bottlenose dolphin populations. Capture heterogeneity through variation in mark severity was confirmed, with higher capture probabilities for well-marked individuals than for poorly marked individuals and a “transience” effect being detected for less well-marked individuals with 43% only recorded once. Likewise, both SR and capture probabilities were comparatively low for individuals with low site fidelity to the Shannon Estuary, and SR of these individuals additionally decreased even further toward the end of the study, reflecting a terminal bias. This bias was attributed to non-random temporal migration, and, together with high encounter rates in Brandon Bay, supported the hypothesis of range expansion. Our results highlight the importance of consistent and geographically homogenous survey effort and support the differentiation of individuals according to their distinctiveness to avoid biased survival estimates.

Considering Genomic Scans for Selection as Coalescent Model Choice

First inspired by the seminal work of Lewontin and Krakauer (1973. Distribution of gene frequency as a test of the theory of the selective neutrality of polymorphisms. Genetics 74(1):175–195.) and Maynard Smith and Haigh (1974. The hitch-hiking effect of a favourable gene. Genet Res. 23(1):23–35.), genomic scans for positive selection remain a widely utilized tool in modern population genomic analysis. Yet, the relative frequency and genomic impact of selective sweeps have remained a contentious point in the field for decades, largely owing to an inability to accurately identify their presence and quantify their effects—with current methodologies generally being characterized by low true-positive rates and/or high false-positive rates under many realistic demographic models. Most of these approaches are based on Wright–Fisher assumptions and the Kingman coalescent and generally rely on detecting outlier regions which do not conform to these neutral expectations. However, previous theoretical results have demonstrated that selective sweeps are well characterized by an alternative class of model known as the multiple-merger coalescent. Taken together, this suggests the possibility of not simply identifying regions which reject the Kingman, but rather explicitly testing the relative fit of a genomic window to the multiple-merger coalescent. We describe the advantages of such an approach, which owe to the branching structure differentiating selective and neutral models, and demonstrate improved power under certain demographic scenarios relative to a commonly used approach. However, regions of the demographic parameter space continue to exist in which neither this approach nor existing methodologies have sufficient power to detect selective sweeps.

Preferences and demographic parameters of cowpea aphid on advanced lines of semiprostrate cowpea

The objective of this work was to determine the preference and the demographic parameters of cowpea aphid (Aphis craccivora) in advanced lines of semiprostrate cowpea (Vigna unguiculata), and to verify both the existance and type of plant resistance to this insect attack. Aphid preference to 20 cowpea genotypes was tested in a randomized complete block design, with six replicates. Lines showing the highest levels of resistance and susceptibility in the preference tests were selected for use in the demographic parameter tests. Based on aphid birth rate and mortality, fertility life tables were constructed. The MNCO4-792F-123 line was classified as resistant. The lowest values for cowpea aphid intrinsic and finite growth rates were obtained for the MNCO4-792F-123, and the highest ones for MNCO4-782F-108 and 'BRS Novaera' genotypes, whose levels exceeded those of 'Vita 7', the standard genotype for susceptibility. The MNCO4-792F-123 line is the least favorable for the development of cowpea aphid, while MNCO4-782F-108 and 'BRS Novaera' are the most susceptible ones.

Skewed sex ratio in a forest salamander: artefact of the different capture probabilities between sexes or actual ecological trait?

Sex ratio is an essential demographic parameter and distortions from a balanced sex ratio may have contrasting effects on the population dynamics. However, observation of distorted sex ratio using counts or captures may reflect an actual ecological trait of the studied population but may also be an artefact due to different capture probabilities of males and females. We compared results obtained from Counts and Capture-Marking-Recapture (CMR) on both sexes in a population of a forest dwelling salamander,Salamandrina perspicillata, and we investigated if males and females had different capture probabilities. We surveyed available literature to compare information on sex ratio from other populations ofS. perspicillata. The sex ratio from our counts was 0.65 and was significantly male-biased as reported in other studies. The estimated sex ratio from CMR data was 0.57. Although males showed higher recapture rates than females in every capture session, these differences were not statistically significant. Therefore, the skewed sex ratio towards males is not only an artefact due to different capture probabilities between males and females but reflects an actual demographic trait, although the magnitude of the skeweness was overestimated by counts.

Impacts of Recurrent Hitchhiking on Divergence and Demographic Inference in Drosophila

In species with large population sizes such as Drosophila, natural selection may have substantial effects on genetic diversity and divergence. However, the implications of this widespread nonneutrality for standard population genetic assumptions and practices remain poorly resolved. Here, we assess the consequences of recurrent hitchhiking (RHH), in which selective sweeps occur at a given rate randomly across the genome. We use forward simulations to examine two published RHH models for D. melanogaster, reflecting relatively common/weak and rare/strong selection. We find that unlike the rare/strong RHH model, the common/weak model entails a slight degree of Hill-Robertson interference in high recombination regions. We also find that the common/weak RHH model is more consistent with our genome-wide estimate of the proportion of substitutions fixed by natural selection between D. melanogaster and D. simulans (19%). Finally, we examine how these models of RHH might bias demographic inference. We find that these RHH scenarios can bias demographic parameter estimation, but such biases are weaker for parameters relating recently-diverged populations, and for the common/weak RHH model in general. Thus, even for species with important genome-wide impacts of selective sweeps, neutralist demographic inference can have some utility in understanding the histories of recently-diverged populations.

Maximum intrinsic rate of population increase in sharks, rays, and chimaeras: the importance of survival to maturity

The maximum intrinsic rate of population increase (rmax) is a commonly estimated demographic parameter used in assessments of extinction risk. In teleosts, rmax can be calculated using an estimate of spawners per spawner, but for chondrichthyans, most studies have used annual reproductive output (b) instead. This is problematic as it effectively assumes all juveniles survive to maturity. Here, we propose an updated rmax equation that uses a simple mortality estimator that also accounts for survival to maturity: the reciprocal of average life-span. For 94 chondrichthyans, we now estimate that rmax values are on average 10% lower than previously published. Our updated rmax estimates are lower than previously published for species that mature later relative to maximum age and those with high annual fecundity. The most extreme discrepancies in rmax values occur in species with low age at maturity and low annual reproductive output. Our results indicate that chondrichthyans that mature relatively later in life, and to a lesser extent those that are highly fecund, are less resilient to fishing than previously thought.

Maximum intrinsic rate of population increase in sharks, rays, and chimaeras: the importance of survival to maturity

The maximum intrinsic rate of population increase rmax is a commonly estimated demographic parameter used in assessments of extinction risk. In teleosts, rmax can be calculated using an estimate of spawners per spawner, but for chondrichthyans, most studies have used annual reproductive output b instead. This is problematic as it effectively assumes all juveniles survive to maturity. Here, we propose an updated rmax equation that uses a simple mortality estimator which also accounts for survival to maturity: the reciprocal of average lifespan. For 94 chondrichthyans, we now estimate that rmax values are on average 10% lower than previously published. Our updated rmax estimates are lower than previously published for species that mature later relative to maximum age and those with high annual fecundity. The most extreme discrepancies in rmax values occur in species with low age at maturity and low annual reproductive output. Our results indicate that chondrichthyans that mature relatively later in life, and to a lesser extent those that are highly fecund, are less resilient to fishing than previously thought.