Quality indexes to assess the reliability of genotypes in studies using noninvasive sampling and multiple‐tube approach

In noninvasive studies, the intersample variance in DNA quality and quantity is large, and produces multilocus genotypes of highly variable quality. Here we propose a standardized method for testing the reliability of the genotyping procedure when using the multiple‐tube approach. The quality indexes generated will allow reliable comparisons among samples, loci, studies, and field and/or laboratory protocols. These indexes represent a powerful tool for the quality management of noninvasive studies.     

Tannic acid-stained microtubules with 12, 13, and 15 protofilaments

Subunit structure in the walls of sectioned microtubules was first noted by Ledbetter and Porter (6), who clearly showed that certain microtubules of plant meristematic cells have 13 wall protofilaments when seen in cross section. Earlier, protofilaments of microtubular elements had been described in negatively stained material, although exact counts of their number were difficult to obtain. In microtubular elements of axonemes, some success has been achieved in visualizing protofilaments in conventionally fixed and sectioned material (8, 10); much less success has been achieved in identifying and counting protofilaments of singlet cytoplasmic microtubules. By using glutaraldehyde-tannic acid fixation, as described by Misuhira and Futaesaku (7), Tilney et al. (12) studied microtubules from a number of sources and found that all have 13 protofilaments comprising their walls. These authors note that "...the number of subunits and their arrangement as protofilaments appear universal...". Preliminary studies of ventral nerve cord of crayfish fixed in glutaraldehyde-tannic acid indicated that axonal microtubules in this material possess only 12 protofilaments (4). On the basis of this observation, tannic acid preparations of several other neuronal and non-neuronal systems were examined. Protofilaments in microtubules from these several cell types are clearly demonstrated, and counts have been made which show that some kinds of microtubules have more or fewer protofilaments than the usual 13 and that at least one kind of microtubule has an even rather than an odd number.     

Successional shifts in tree demographic strategies in wet and dry Neotropical forests

Aim

Tropical forest succession and associated changes in community composition are driven by species demographic rates, but how demographic strategies shift during succession remains unclear. Our goal was to identify generalities in demographic trade-offs and successional shifts in demographic strategies across Neotropical forests that cover a large rainfall gradient and to test whether the current conceptual model of tropical forest succession applies to wet and dry forests.

Location

Mexico and Central America.

Time period

1985–2018.

Major taxa studied

Trees.

Methods

We used repeated forest inventory data from two wet and two dry forests to quantify demographic rates of 781 tree species. For each forest, we explored the main demographic trade-offs and assigned tree species to five demographic groups by performing a weighted principal components analysis to account for differences in sample size. We aggregated the basal area and abundance across demographic groups to identify successional shifts in demographic strategies over the entire successional gradient from very young (<5 years) to old-growth forests.

Results

Across all forests, we found two demographic trade-offs, namely the growth–survival trade-off and the stature–recruitment trade-off, enabling the data-driven assignment of species to five demographic strategies. Fast species dominated early in succession and were then replaced by long-lived pioneers in three forests. Intermediate and slow species increased in basal area over succession in all forests, but, in contrast to the current conceptual model, long-lived pioneers continued to dominate until the old-growth stage in all forests. The basal area of short-lived breeders was low across all successional stages.

Main conclusions

The current conceptual model of Neotropical forest succession should be revised to incorporate the dominance of long-lived pioneers in late-successional and old-growth forests. Moreover, the definition of consistent demographic strategies that show clear dominance shifts across succession substantially improves the mechanistic understanding and predictability of Neotropical forest succession.     

Effect of Periodic Oscillations of Artificial Light Emission on Photosynthetic Activity

The effects of periodic oscillation of artificial light and of the frequency of these oscillations on photosynthetic assimilation has been measured. When the frequency is sufficiently high, the gross CO₂ assimilation in fluctuating light is identical to the assimilation of the leaf under a continuous illumination equal to the efficient intensity of the intermittent light. It is necessary to consider the quality of the sensor used for measuring light intensity, particularly its response velocity.     

Sequence and functional analyses of Haemophilus spp. genomic islands

Background

A major part of horizontal gene transfer that contributes to the diversification and adaptation of bacteria is facilitated by genomic islands. The evolution of these islands is poorly understood. Some progress was made with the identification of a set of phylogenetically related genomic islands among the Proteobacteria, recognized from the investigation of the evolutionary origins of a Haemophilus influenzae antibiotic resistance island, namely ICEHin1056. More clarity comes from this comparative analysis of seven complete sequences of the ICEHin1056 genomic island subfamily.

Results

These genomic islands have core and accessory genes in approximately equal proportion, with none demonstrating recent acquisition from other islands. The number of variable sites within core genes is similar to that found in the host bacteria. Furthermore, the GC content of the core genes is similar to that of the host bacteria (38% to 40%). Most of the core gene content is formed by the syntenic type IV secretion system dependent conjugative module and replicative module. GC content and lack of variable sites indicate that the antibiotic resistance genes were acquired relatively recently. An analysis of conjugation efficiency and antibiotic susceptibility demonstrates that phenotypic expression of genomic island-borne genes differs between different hosts.

Conclusion

Genomic islands of the ICEHin1056 subfamily have a longstanding relationship with H. influenzae and H. parainfluenzae and are co-evolving as semi-autonomous genomes within the 'supragenomes' of their host species. They have promoted bacterial diversity and adaptation through becoming efficient vectors of antibiotic resistance by the recent acquisition of antibiotic resistance transposons.