Genetic variation in an ephemeral mudflat species: The role of the soil seed bank and dispersal in river and secondary anthropogenic habitats

Many ephemeral mudflat species, which rely on a soil seed bank to build up the next generation, are endangered in their natural habitat due to the widespread regulation of rivers. The aim of the present study was to elucidate the role of the soil seed bank and dispersal for the maintenance of genetic diversity in populations of near‐natural river habitats and anthropogenic habitats created by traditional fish farming practices using Cyperus fuscus as a model. Using microsatellite markers, we found no difference in genetic diversity levels between soil seed bank and above‐ground population and only moderate differentiation between the two fractions. One possible interpretation is the difference in short‐term selection during germination under specific conditions (glasshouse versus field) resulting in an ecological filtering of genotypes out of the reservoir in the soil. River populations harbored significantly more genetic diversity than populations from the anthropogenic pond types. We suggest that altered levels and patterns of dispersal together with stronger selection pressures and historical bottlenecks in anthropogenic habitats are responsible for the observed reduction in genetic diversity. Dispersal is also supposed to largely prohibit genetic structure across Europe, although there is a gradient in private allelic richness from southern Europe (high values) to northern, especially north‐western, Europe (low values), which probably relates to postglacial expansion out of southern and/or eastern refugia.     

Whole‐genome resequencing reveals the pleistocene temporal dynamics of Branchiostoma belcheri and Branchiostoma floridae populations

Global climatic fluctuations governed the ancestral demographic histories of species and contributed to place the current population status into a more extensive ecological and evolutionary context. Genetic variations will leave unambiguous signatures in the patterns of intraspecific genetic variation in extant species since the genome of each individual is an imperfect mosaic of the ancestral genomes. Here, we report the genome sequences of 20 Branchiostoma individuals by whole‐genome resequencing strategy. We detected over 140 million genomic variations for each Branchiostoma individual. In particular, we applied the pairwise sequentially Markovian coalescent (PSMC) method to estimate the trajectories of changes in the effective population size (N_e) of Branchiostoma population during the Pleistocene. We evaluated the threshold of sequencing depth for proper inference of demographic histories using PSMC was ≥25×. The PSMC results highlight the role of historical global climatic fluctuations in the long‐term population dynamics of Branchiostoma. The inferred ancestral N_e of the Branchiostoma belcheri populations from Zhanjiang and Xiamen (China) seawaters was different in amplitude before the first (mutation rate = 3 × 10^?9) or third glaciation (mutation rate = 9 × 10^?9) of the Pleistocene, indicating that the two populations most probably started to evolve in isolation in their respective seas after the first or third glaciation of the Pleistocene. A pronounced population bottleneck coinciding with the last glacial maximum was observed in all Branchiostoma individuals, followed by a population expansion occurred during the late Pleistocene. Species that have experienced long‐term declines may be especially vulnerable to recent anthropogenic activities. Recently, the industrial pollution and the exploitation of sea sand have destroyed the harmonious living environment of amphioxus species. In the future, we need to protect the habitat of Branchiostoma and make full use of these detected genetic variations to facilitate the functional study of Branchiostoma for adaptation to local environments.     

Effects of thermal and oxygen conditions during development on cell size in the common rough woodlice Porcellio scaber

During development, cells may adjust their size to balance between the tissue metabolic demand and the oxygen and resource supply: Small cells may effectively absorb oxygen and nutrients, but the relatively large area of the plasma membrane requires costly maintenance. Consequently, warm and hypoxic environments should favor ectotherms with small cells to meet increased metabolic demand by oxygen supply. To test these predictions, we compared cell size (hindgut epithelium, hepatopancreas B cells, ommatidia) in common rough woodlice (Porcellio scaber) that were developed under four developmental conditions designated by two temperatures (15 or 22°C) and two air O₂ concentrations (10% or 22%). To test whether small‐cell woodlice cope better under increased metabolic demand, the CO₂ production of each woodlouse was measured under cold, normoxic conditions and under warm, hypoxic conditions, and the magnitude of metabolic increase (MMI) was calculated. Cell sizes were highly intercorrelated, indicative of organism‐wide mechanisms of cell cycle control. Cell size differences among woodlice were largely linked with body size changes (larger cells in larger woodlice) and to a lesser degree with oxygen conditions (development of smaller cells under hypoxia), but not with temperature. Developmental conditions did not affect MMI, and contrary to predictions, large woodlice with large cells showed higher MMI than small woodlice with small cells. We also observed complex patterns of sexual difference in the size of hepatopancreatic cells and the size and number of ommatidia, which are indicative of sex differences in reproductive biology. We conclude that existing theories about the adaptiveness of cell size do not satisfactorily explain the patterns in cell size and metabolic performance observed here in P. scaber. Thus, future studies addressing physiological effects of cell size variance should simultaneously consider different organismal elements that can be involved in sustaining the metabolic demands of tissue, such as the characteristics of gas‐exchange organs and O₂‐binding proteins.     

Interspecific variation and elevated CO2 influence the relationship between plant chemical resistance and regrowth tolerance

To understand how comprehensive plant defense phenotypes will respond to global change, we investigated the legacy effects of elevated CO₂ on the relationships between chemical resistance (constitutive and induced via mechanical damage) and regrowth tolerance in four milkweed species (Asclepias). We quantified potential resistance and tolerance trade‐offs at the physiological level following simulated mowing, which are relevant to milkweed ecology and conservation. We examined the legacy effects of elevated CO₂ on four hypothesized trade‐offs between the following: (a) plant growth rate and constitutive chemical resistance (foliar cardenolide concentrations), (b) plant growth rate and mechanically induced chemical resistance, (c) constitutive resistance and regrowth tolerance, and (d) regrowth tolerance and mechanically induced resistance. We observed support for one trade‐off between plant regrowth tolerance and mechanically induced resistance traits that was, surprisingly, independent of CO₂ exposure. Across milkweed species, mechanically induced resistance increased by 28% in those plants previously exposed to elevated CO_2. In contrast, constitutive resistance and the diversity of mechanically induced chemical resistance traits declined in response to elevated CO₂ in two out of four milkweed species. Finally, previous exposure to elevated CO₂ uncoupled the positive relationship between plant growth rate and regrowth tolerance following damage. Our data highlight the complex and dynamic nature of plant defense phenotypes under environmental change and question the generality of physiologically based defense trade‐offs.     

Application of leaf size and leafing intensity scaling across subtropical trees

Understanding the scaling between leaf size and leafing intensity (leaf number per stem size) is crucial for comprehending theories about the leaf costs and benefits in the leaf size–twig size spectrum. However, the scaling scope of leaf size versus leafing intensity changes along the twig leaf size variation in different leaf habit species remains elusive. Here, we hypothesize that the numerical value of scaling exponent for leaf mass versus leafing intensity in twig is governed by the minimum leaf mass versus maximum leaf mass (M _min versus M _max) and constrained to be ≤−1.0. We tested this hypothesis by analyzing the twigs of 123 species datasets compiled in the subtropical mountain forest. The standardized major axis regression (SMA) analyses showed the M _min scaled as the 1.19 power of M _max and the ‐α (−1.19) were not statistically different from the exponents of M _min versus leafing intensity in whole data. Across leaf habit groups, the M _max scaled negatively and isometrically with respect to leafing intensity. The pooled data''s scaling exponents ranged from −1.14 to −0.96 for M _min and M _max versus the leafing intensity based on stem volume (LIV). In the case of M _min and M _max versus the leafing intensity based on stem mass (LIM), the scaling exponents ranged from −1.24 to −1.04. Our hypothesis successfully predicts that the scaling relationship between leaf mass and leafing intensity is constrained to be ≤−1.0. More importantly, the lower limit to scaling of leaf mass and leafing intensity may be closely correlated with M _min versus M _max. Besides, constrained by the maximum leaf mass expansion, the broad scope range between leaf size and number may be insensitive to leaf habit groups in subtropical mountain forest.     

Comparison of size-structured and species-level trophic networks reveals antagonistic effects of temperature on vertical trophic diversity at the population and species level

It is predicted that warmer conditions should lead to a loss of trophic levels, as larger bodied consumers, which occupy higher trophic levels, experience higher metabolic costs at high temperature. Yet, it is unclear whether this prediction is consistent with the effect of warming on the trophic structure of natural systems. Furthermore, effects of temperature at the species level, which arise through a change in species composition, may differ from those at the population level, which arise through a change in population structure. We investigate this by building species-level trophic networks, and size-structured trophic networks, as a proxy for population structure, for 18 648 stream fish communities, from 4 145 234 individual fish samples, across 7024 stream locations in France from 1980 to 2008. We estimated effects of temperature on total trophic diversity (total number of nodes), vertical trophic diversity (mean and maximum trophic level) and distribution of biomass across trophic level (correlation between trophic level and biomass) in these networks. We found a positive effect of temperature on total trophic diversity in both species- and size-structured trophic networks. We found that maximum trophic level and biomass distribution decreased in species-level and size-structured trophic networks, but the mean trophic level decreased only in size-structured trophic networks. These results show that warmer temperatures associate with a lower vertical trophic diversity in size-structured networks, and a higher one in species-level networks. This suggests that vertical trophic diversity is shaped by antagonistic effects of temperature on population structure and on species composition. Our results hence demonstrate that effects of temperature do not only differ across trophic levels, but also across levels of biological organisation, from population to species level, implying complex changes in network structure and functioning with warming.     

Reproductive biology of the white marlin (Kajikia albida) in the southwestern and equatorial Atlantic Ocean

The present work describes the reproductive biology of the white marlin (Kajikia albida) caught in the southwestern and equatorial Atlantic Ocean. The gonads of 924 fish were collected by observers on board Brazilian tuna longliners, between November 2004 and December 2006. The spawning season was assessed by the monthly frequency distribution of distinct stages of maturity and monthly mean female gonadosomatic index GSI. Sixty-one percent (n = 656) of the fish examined were female, with a Lower Jaw Fork Length (LJFL) between 83 and 236 cm (mean = 155.5 ± 16.63). The 268 males had a LJFL between 90 and 220 cm (mean = 152.3 ± 34.62). Although the northeastern region of Brazil does not appear to be a significant spawning area for the species, the results suggest a higher reproductive activity in the third quarter of the year. Using a Bayesian logistic model approach, length at 50% maturity was estimated at 145.04 cm (credibility interval of 95%, 143.94–146.09 cm), for females, and at 140.03 cm (credibility interval of 95%, 137.28–142.52 cm), for males.     

Identifying Primate ACE2 Variants That Confer Resistance to SARS-CoV-2

SARS-CoV-2 infects humans through the binding of viral S-protein (spike protein) to human angiotensin I converting enzyme 2 (ACE2). The structure of the ACE2-S-protein complex has been deciphered and we focused on the 27 ACE2 residues that bind to S-protein. From human sequence databases, we identified nine ACE2 variants at ACE2–S-protein binding sites. We used both experimental assays and protein structure analysis to evaluate the effect of each variant on the binding affinity of ACE2 to S-protein. We found one variant causing complete binding disruption, two and three variants, respectively, strongly and mildly reducing the binding affinity, and two variants strongly enhancing the binding affinity. We then collected the ACE2 gene sequences from 57 nonhuman primates. Among the 6 apes and 20 Old World monkeys (OWMs) studied, we found no new variants. In contrast, all 11 New World monkeys (NWMs) studied share four variants each causing a strong reduction in binding affinity, the Philippine tarsier also possesses three such variants, and 18 of the 19 prosimian species studied share one variant causing a strong reduction in binding affinity. Moreover, one OWM and three prosimian variants increased binding affinity by >50%. Based on these findings, we proposed that the common ancestor of primates was strongly resistant to and that of NWMs was completely resistant to SARS-CoV-2 and so is the Philippine tarsier, whereas apes and OWMs, like most humans, are susceptible. This study increases our understanding of the differences in susceptibility to SARS-CoV-2 infection among primates.