Jesualdo A. Fuentes-González’s research while affiliated with Florida International University and other places

The evolution of modern humans is as fascinating as it is complicated. Various environmental and socio-political factors have played a significant role in shaping different migratory paths and lifestyles in ancient times and the establishment of current sub-populations around the globe. These factors have impacted the molecular evolution of mitochondrial DNA (mtDNA). To account for the role of genetic background and variable sites in shaping the migratory and evolutionary paths, we analyzed the ancient mtDNA as spatiotemporal co-mutation networks. Haplogroup-based analysis of the variable sites suggests a transition from hunter-gatherer to agrarian lifestyle during the Copper-Bronze transition period. Furthermore, the genetic interaction networks showed that COX and CYB genes behaved diversely with time and that there is an interplay of the genetic interactions with NADH Dehydrogenase genes specific to each age. We performed a phylogeny (tree) based gene network analysis and examined polymorphism to divergence ratios to complement the co-mutation networks. The tree-based gene networks exhibit similar topology with reduced co-mutation among the genes. The more traditional polymorphism/divergence analysis indicated that the CYB gene has been under long-term purifying selection. In contrast, other genes (ATP6, COX, NADH hydrogenases) have undergone episodes of purifying selection corresponding to different ages. We believe this network-based exploratory study provides insights into early lifestyle transitions and haplogroup establishment of the current human population.

The PCMBase R package is a powerful computational tool that enables efficient calculations of likelihoods for a wide range of phylogenetic Gaussian models. Taking advantage of it, we redesigned the R package mvSLOUCH. Here, we demonstrate how the new version of the package can be used to thoroughly examine the evolution and adaptation of traits in a large dataset of 1252 vascular plants through the use of multivariate Ornstein–Uhlenbeck processes. The results of our analysis demonstrate the ability of the modelling framework to distinguish between various alternative hypotheses regarding the evolution of functional traits in angiosperms.

The mechanisms of the induction of extremotolerant states, a.k.a. cryptobiosis, in tardigrades are beginning to be explored. Armored tardigrades (Class: Heterotardigrada) living in limnoterrestrial environments are highly associated with desiccation-tolerant moss or lichen substrates that themselves produce numerous specialized metabolites during desiccation. Here we show that some of these metabolites can induce reversible cryptobiosis in their coexisting heterotardigrades in a dose-dependent manner. Coexisting eutardigrades, nematodes and rotifers however, show no such response to these molecules. The response-inducing metabolites belong to a class of soft-electrophilic flavonoid compounds, suggesting that they possibly interact with electrophile-responsive heterotardigrade proteomes related to their specific cryptobiotic traits. The ability to control when biological material enters a protective state increases the scope of bioengineering avenues to mitigate increasing environmental unpredictability on Earth and to inform near-future space-travel endeavors.

Adams and Collyer (2018) argue that contemporary multivariate (Gaussian) phylogenetic comparative methods are prone to favouring more complex models of evolution and sometimes rotation invariance can be an issue. Here we dissect the concept of rotation invariance and point out that, depending on the understanding, this can be an issue with any method that relies on numerical instead of analytical estimation approaches. We relate this to the ongoing discussion concerning phylogenetic principal components analysis. Contrary to what Adams and Collyer (2018) found, we do not observe a bias against the simpler Brownian motion process in simulations when we use the new, improved, likelihood evaluation algorithm employed by mvSLOUCH, which allows for studying much larger phylogenies and more complex model setups.

Models based on the Ornstein-Uhlenbeck process have become standard for the comparative study of adaptation. Cooper et al. (2016) have cast doubt on this practice by claiming statistical problems with fitting Ornstein-Uhlenbeck models to comparative data. Specifically, they claim that statistical tests of Brownian motion may have too high Type I error rates and that such error rates are exacerbated by measurement error. In this note, we argue that these results have little relevance to the estimation of adaptation with Ornstein-Uhlenbeck models for three reasons. First, we point out that Cooper et al. (2016) did not consider the detection of distinct optima (e.g. for different environments), and therefore did not evaluate the standard test for adaptation. Second, we show that consideration of parameter estimates, and not just statistical significance, will usually lead to correct inferences about evolutionary dynamics. Third, we show that bias due to measurement error can be corrected for by standard methods. We conclude that Cooper et al. (2016) have not identified any statistical problems specific to Ornstein-Uhlenbeck models, and that their cautions against their use in comparative analyses are unfounded and misleading. [adaptation, Ornstein-Uhlenbeck model, phylogenetic comparative method.].

Microbial diversity positively influences community resilience of the host microbiome. However, extinction risk factors such as habitat specialization, narrow environmental tolerances, and exposure to anthropogenic disturbance may homogenize host-associated microbial communities critical for stress responses including disease defense. In a dataset containing 43 threatened and 90 non-threatened amphibian species across two biodiversity hotspots (Brazil’s Atlantic Forest and Madagascar), we found that threatened host species carried lower skin bacterial diversity, after accounting for key environmental and host factors. The consistency of our findings across continents suggests the broad scale at which low bacteriome diversity may compromise pathogen defenses in species already burdened with the threat of extinction.

The causes and consequences of the evolution of placentotrophy (post-fertilization nutrition of developing embryos of viviparous organisms by means of a maternal placenta) in non-mammalian vertebrates are still not fully understood. In particular, in the fish family Poeciliidae there is an evolutionary link between placentotrophy and superfetation (ability of females to simultaneously bear embryos at distinct developmental stages), with no conclusive evidence for which of these two traits facilitates the evolution of more advanced degrees of the other. Using a robust phylogenetic comparative method based on Ornstein–Uhlenbeck models of adaptive evolution and data from 36 poeciliid species, we detected a clear causality pattern. The evolution of extensive placentotrophy has been facilitated by the preceding evolution of more simultaneous broods. Therefore, placentas became increasingly complex as an adaptive response to evolutionary increases in the degree of superfetation. This finding represents a substantial contribution to our knowledge of the factors that have shaped placental evolution in poeciliid fishes.

Zoologists have long tried to culture the limnoterrestrial heterotardigrades associated with bryophytes and lichens without success. By carefully observing heterotardigrades in the genera Echiniscus, Pseudechiniscus, and Viridiscus over many months, we determined that these organisms feed on chloroplasts and cytoplasm from the cells of moss (typically moss protonema), and on the single‐celled green algae associated with the moss (typically Chlorella vulgaris). We also determined that the cryptogams they associate with, and hence the heterotardigrades themselves, spend more time in a dried state than do most eutardigrades, which are more easily cultured. Taking these observations into account, we varied food, water, and desiccation cycle conditions with the aim of developing a viable culturing protocol for heterotardigrades. We used this experimentally derived protocol to maintain laboratory cultures of the tardigrades Echiniscus sp., Pseudechiniscus aff. P. ramazzotti and Viridiscus viridianus, which regularly produced new eggs and hatchlings. Both moss and algae from their natural habitats were used as food sources, and a small layer of rain or spring water was added every morning and allowed to partially evaporate overnight. Furthermore, the organisms were more likely to lay eggs on a dense mat of moss protonema, grown by inserting tips of moss branches into a solidified KCM–agar medium. The medium also provided a walking substrate for the tardigrades, and possibly a source of cations. Crucially, the cultures were allowed to dry out completely every 10 days for a period of at least 3 days. Moss in the culture dish significantly improved the chances of the tardigrades coming out of their desiccation‐resistant states successfully. The ability to culture heterotardigrades makes these organisms available for modern genomics and other studies with implications for understanding desiccation resistance mechanisms beyond those studied in a few model eutardigrade species.

Background and aims – Tracheophyte leaf morphology is well studied but it is unclear if the findings generalize to poikilohydric plants. We tested combinations of hypotheses to determine if microhabitat characteristics, including light exposure, moisture availability, and substrate slope, controlled for morphological differences between upright and prostrate growth forms, affect phyllid surface area and costa length of mosses.Material and methods – We quantified mean phyllid surface-area and costa lengths for four replicates of 38 moss species from Alabama. Phylogenetic comparative methods that model adaptation were used to evaluate the relative evidence for each hypothesis using information criteria. To further explore mechanistic explanations involving substrate slope, we tested whether mosses on vertical substrates differed from those on horizontal substrates in the average amount of water-retaining, nutrient-rich litter they accumulated.Key results – Substrate slope and growth form combined were the best predictors of phyllid surface area. Mosses growing on vertical substrates exhibited smaller phyllid surface area for both growth forms. Although growth form and phyllid length best explained costa length variation, a more complex model including substrate slope performed nearly as well. Within the prostrate growth forms, species growing on vertical substrates exhibit longer relative costa than those on horizontal substrates. We also estimated rapid rates of adaptation for both traits.Conclusion – The smaller phyllid surface area of both upright and prostrate growth forms is possibly an adaptive response to reduced habitat moisture-retention or nutrient quality that vertical substrates offer. The longer costa lengths of prostrate mosses growing on vertical surfaces relative to prostrate mosses on horizontal surfaces, possibly make up for the decreased ability of smaller phyllids to rapidly reabsorb water when it is available. Further work is required to determine if it is truly substrate slope itself that matters or other variables associated with the differences in slope, and to determine how general this phenomenon is.

Background: Tardigradologists have long tried to culture limnoterrestrial heterotardigrades without success. This is likely because they depend on specific conditions in their microhabitats. Most limnoterrestrial heterotardigrades are found associated with bryophytes and lichens (collectively cryptogams). In contrast to eutardigrades, many of which are easily cultured, heterotardigrades are found in cryptogams that prefer drier and sunnier habitats and that tend to grow on the vertical surfaces of boulders, cliffs, or tree trunks. By carefully observing heterotardigrades in the Echniscus and Viridiscus genera over many months, we determined that these organisms feed on chloroplasts and cytoplasm of both moss cells (typically moss protonema) and single-celled green algae associated with the moss (typically Chlorella vulgaris). We also determined that the cryptogams they associate with, and hence the heterotardigrades themselves, spend more time in a dried state than most eutardigrade species. Taking these observations into account we varied food, water, and desiccation cycle conditions with the aim of developing a culturing protocol for heterotardigrades. Results: We have maintained laboratory cultures of several generations and counting of Echiniscus, Pseudechniscus and Viridiscus genera tardigrades using the following experimentally derived protocol: Both moss and algae from their natural habitats are required as food sources and a small layer of rain or spring water is added every morning and allowed to evaporate some overnight. Furthermore, the organisms are more likely to lay eggs on a dense mat of moss protonema, grown by inserting tips of moss branches into a solidified KCM / agar medium. The medium also provides a walking substrate for the tardigrades, and possibly a source of cations. Crucially, the cultures must be allowed to dry out completely every ten days for a period of at least three days. Moss in the culture dish significantly improves the chances of the tardigrades coming out of their desiccation-resistant states successfully. Conclusions: We conclude that periodic drying out, moss and algae are all required to successfully culture heterotardigrades. Furthermore, drying must occur slowly, and the moss protonema enables this by retaining moisture thereby slowing evaporation. We suspect our protocol will work for most limnoterrestrial heterotardigrades with minor tweaking of culturing conditions.