The influence of fluctuating population densities on evolutionary dynamics

Intraspecies dynamics underlie the apparent stability of two important skin microbiome species

Adult human facial skin microbiomes are remarkably similar at the species level, dominated by Cutibacterium acnes and Staphylococcus epidermidis, yet each person harbors a unique community of strains. Understanding how person-specific communities assemble is critical for designing microbiome-based therapies. Here, using 4,055 isolate genomes and 356 metagenomes, we reconstruct on-person evolutionary history to reveal on- and between-person strain dynamics. We find that multiple cells are typically involved in transmission, indicating ample opportunity for migration. Despite this accessibility, family members share only some of their strains. S. epidermidis communities are dynamic, with each strain persisting for an average of only 2 years. C. acnes strains are more stable and have a higher colonization rate during the transition to an adult facial skin microbiome, suggesting this window could facilitate engraftment of therapeutic strains. These previously undetectable dynamics may influence the design of microbiome therapeutics and motivate the study of their effects on hosts.

Population Dynamics of the Exotic Flatworm Obama nungara in an Invaded Garden

Population dynamics and the way abundance fluctuates over time may be key determinants of the invasion success of an introduced species. Fine-scale temporal monitoring of invasive species is rarely carried out due to the difficulties in collecting data regularly and over a long period. Thanks to the collaboration of an amateur naturalist, a unique dataset on the abundance of the invasive land flatworm Obama nungara was obtained during a 4-year survey of a French private garden, where up to 1585 O. nungara were recorded in 1 month. Daily monitoring data revealed high population size fluctuations that may be explained by meteorological factors as well as intra- and inter-specific interactions. Bayesian modeling confirmed that O. nungara's abundance fluctuates depending on temperature, humidity, and precipitation. Population growth seems to be favored by mild winters and precipitation while it is disadvantaged by drought. These exogenous factors affect both directly this species, which is sensitive to desiccation, and indirectly since they are known to affect the populations of its prey (earthworms and terrestrial gastropods). We also suggested the important resilience of O. nungara population in this site, which was able to recover from a drastic demographic bottleneck due to a severe drought, as well to systematic removal by the owner of the site. These findings highlight the potentially high invasiveness of O. nungara and raise concerns about the major threat these invasive flatworms pose to the populations of their prey.

Unstable environment of coastal lagoons drives genetic variation in the amphipod Quadrivisio lutzi

The freshwater/brackish amphipod Quadrivisio lutzi inhabits coastal lagoons, highly unstable environments subject to sudden inflow of marine water. Our aim was to evaluate how the genetic composition varies in these populations. Brazilian populations were compared by 16S rRNA and COI gene sequences. The genetic structure of four Rio de Janeiro amphipod populations was evaluated during the period of 2011-2019 by COI. Rio de Janeiro population was compared with Alagoas and São Paulo populations, which was genetically distinct, at species level (16S, d > 7%; COI, d >14%). The genetic structure in Rio de Janeiro showed the Imboassica subpopulation as the most divergent (Imboassica & Carapebus, F ST = 0.238), followed by Lagamar population (Lagamar & Carapebus, F ST = 0.049). The geographic distance and urbanization around these lagoons explain the degree of genetic isolation of these amphipod subpopulations. Paulista and Carapebus populations were not structured. Temporal variation in haplotype number and frequency were evident in both populations that were evaluated (Carapebus and Imboassica). Changes in salinity and water volume variation at these lagoons may be responsible for the observed changes in genetic composition, which may be the results of genetic drift effects over temporally fluctuating size subpopulations, without loss of genetic diversity.

The costs and benefits of dispersal in small populations

Dispersal has three major effects on adaptation. First, gene flow mixes alleles adapted to different environments, potentially hindering (swamping) adaptation. Second, it brings in other variants and inflates genetic variance: this aids adaptation to spatially (and temporally) varying environments but if selection is hard, it lowers the mean fitness of the population. Third, neighbourhood size, which determines how weak genetic drift is, increases with dispersal-when genetic drift is strong, increase of the neighbourhood size with dispersal aids adaptation. In this note, I focus on the role of dispersal in environments that change gradually across space, and when local populations are quite small such that genetic drift has a significant effect. Using individual-based simulations, I show that in small populations, even leptokurtic dispersal benefits adaptation by reducing the power of genetic drift. This has implications for management of fragmented or marginal populations: the beneficial effect of increased dispersal into small populations is stronger than swamping of adaption under a broad range of conditions, including a mixture of local and long-distance dispersal. However, when environmental gradient is steep, heavily fat-tailed dispersal will swamp continuous adaptation so that only patches of locally adapted subpopulations remain. This article is part of the theme issue 'Species' ranges in the face of changing environments (Part II)'.