Miracle-dz/UniFAR-FTUs huggingface dataset:
Validating metabarcoding-based biodiversity assessments with multi-species occupancy models: A case study using coastal marine eDNA

Environmental DNA (eDNA) metabarcoding is an increasingly popular method for rapid biodiversity assessment. As with any ecological survey, false negatives can arise during sampling and, if unaccounted for, lead to biased results and potentially misdiagnosed environmental assessments. We developed a multi-scale, multi-species occupancy model for the analysis of community biodiversity data resulting from eDNA metabarcoding; this model accounts for imperfect detection and additional sources of environmental and experimental variation. We present methods for model assessment and model comparison and demonstrate how these tools improve the inferential power of eDNA metabarcoding data using a case study in a coastal, marine environment. Using occupancy models to account for factors often overlooked in the analysis of eDNA metabarcoding data will dramatically improve ecological inference, sampling design, and methodologies, empowering practitioners with an approach to wield the high-resolution biodiversity data of next-generation sequencing platforms.
Evolution of Microbial Growth Traits Under Serial Dilution

Selection of mutants in a microbial population depends on multiple cellular traits. In serial-dilution evolution experiments, three key traits are the lag time when transitioning from starvation to growth, the exponential growth rate, and the yield (number of cells per unit resource). Here, we investigate how these traits evolve in laboratory evolution experiments using a minimal model of population dynamics, where the only interaction between cells is competition for a single limiting resource. We find that the fixation probability of a beneficial mutation depends on a linear combination of its growth rate and lag time relative to its immediate ancestor, even under clonal interference. The relative selective pressure on growth rate and lag time is set by the dilution factor; a larger dilution factor favors the adaptation of growth rate over the adaptation of lag time. The model shows that yield, however, is under no direct selection. We also show how the adaptation speeds of growth and lag depend on experimental parameters and the underlying supply of mutations. Finally, we investigate the evolution of covariation between these traits across populations, which reveals that the population growth rate and lag time can evolve a nonzero correlation even if mutations have uncorrelated effects on the two traits. Altogether these results provide useful guidance to future experiments on microbial evolution.
A new era in forest restoration monitoring

Monitoring ecological restoration has been historically dependent on traditional inventory methods based on detailed information obtained from field plots. New paradigms are now needed to successfully achieve restoration as a large‐scale, long‐lasting transformative process. Fortunately, advances in technology now allow for unprecedented shifts in the way restoration has been planned, implemented, and monitored. Here, we describe our vision on how the use of new technologies by a new generation of restoration ecologists may revolutionize restoration monitoring in the coming years. The success of the many ambitious restoration programs planned for the coming decade will rely on effective monitoring, which is an essential component of adaptive management and accountability. The development of new remote sensing approaches and their application to a restoration context open new avenues for expanding our capacity to assess restoration performance over unprecedented spatial and temporal scales. A new generation of scientists, which have a background in remote sensing but are getting more and more involved with restoration, will certainly play a key role for making large‐scale restoration monitoring a viable human endeavor in the coming decade—the United Nations' decade on ecosystem restoration.
Temporal changes in abundance–occupancy relationships over 40 years

Abstract Abundance–occupancy (A–O) relationships are widely documented for many organismal groups and regions, and have been used to gain an understanding of regional population and community trends. Monitoring changes in abundance and occupancy over time may be what is required to document changes in conservation status and needs for some species, communities, or areas. We hypothesize that if there is a higher proportion of declining species in one group of species compared with another (e.g., migratory species vs. permanent residents), then a consequence of that difference will be vastly different abundance–occupancy relationships. If this difference persists through time, then the resulting A–O relationships between the groups will continue to diverge. For neotropical migrants, short‐distance migrants, and permanent resident birds of North America, we assess the numbers of declining species over 1969–2009. We further test for differences in the A–O relationship across these three groups, and in rates of change in abundance and occupancy separately. We find significant differences in numbers of declining species across the migratory groups, a significant decline in the A–O relationship for permanent residents, a significant increase for Neotropical migrants, and a nonsignificant decline for short‐distance migrants over the 40 years. Further, abundances are not changing at different rates but occupancies are consistently greater over time for neotropical migrants versus permanent residents, likely driving the changes in A–O relationships observed. In these analyses, we documented changing A–O trends for different groups of species, over a relatively long time period for ecological studies, one of only a few studies to examine A–O relationships over time. Further, we have shown that a temporally unvarying abundance–occupancy relationship is not universal, and we posit that variability in A–O relationships is due to human impacts on habitats, coupled with variation in species' abilities to respond to human impacts.
Sequence and phylogenetic analysis of the mitochondrial genome for red-breasted parakeet Psittacula alexandri (Psittaciformes: Psittacidae)

Abstract In this study, we first sequenced and described the complete mitochondrial genome and phylogeny of Psittacula alexandri. The whole genome of P. alexandri was 16,883 bp in length, and contained 14 protein-coding genes, 22 transfer RNA genes, 2 ribosome RNA genes, and 1 non-coding control regions. The overall base composition of the mitochondrial DNA was 30.87% for A, 22.36% for T, 32.82% for C, and 13.95% for G, with a GC content of 46.77%. A phylogenetic tree strongly supported that P. alexandri closely related with Eclectus roratus by highly probability.
Effects of primary productivity on beta diversity of ecological communities

Abstract Aim Several ecological factors are predicted to affect beta diversity - the dissimilarity of communities among localities or through time. Considering the effect of primary productivity, there is a divergence in the literature concerning if it is positive, negative or hump-shaped. This is relevant considering the discussion on the role of primary productivity on deterministic and stochastic processes shaping ecological communities. The main goal of this study was to review ecological literature to explore causes for variation in the predominant relationship between beta diversity and primary productivity. Methods We have performed a scientometric analysis following the PRISMA statement for systematic reviews and the articles search was made through the ISI Web of Science® database. Results The number of articles approaching the relationship between beta diversity and primary productivity is growing more than expected by the natural growth in published articles. From the 465 articles found, only 38 directly dealt with beta diversity-productivity relationship. From them, we extracted 76 relationships, most of them positive, in almost all factors analyzed. Even so, the proportion of negative studies was higher in aquatic environments. In the Afrotropic region, only negative relationships in terrestrial studies were found. There is a clear inclination towards studies regarding large spatial scales, terrestrial environments, with vertebrates and in the Neartic or Paleartic regions. In aquatic environments there was a clear dominance of studies using small-body organisms, contrasting with terrestrial studies that used more often vertebrates and plants. Conclusions There is an increasing interest in studies concerning this relationship. Positive relations can be explained by several ecological factors, and the more common negative relationships in aquatic environments can be explained by the fact that productivity can cause eutrophication. We also pointed out gaps in the knowledge, especially considering studies in small and medium spatial scales, groups beyond plants and vertebrates in terrestrial environments, and aquatic studies in Afrotropic and Indo – Malaya regions.
Characterization 3333 of tomato (
 Solanum lycopersicum
 ) accessions for resistance to phylotype I and phylotype II strains of the
 Ralstonia solanacearum
 species complex under high temperatures

This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited. © 2019 The Authors. Plant Breeding published by Blackwell Verlag GmbH 1Department of Plant Pathology, University of Florida, Gainesville, FL, USA 2The World Vegetable Center, Shanhua, Taiwan 3Department of Agronomy, National Taiwan University, Taipei, Taiwan 4Gulf Coast Research and Education Center, University of Florida, Wimauma, FL, USA
Comparative evaluation of xylazine, midazolam and xylazine-midazolam combination as preanaesthetics to propofol-halothane anaesthesia in dogs

The study was conducted in 24 selected clinical cases of dogs of either sex and of different breeds, which were divided into three groups viz. A, B and C. All the animals were first administered with atropine sulphate (0.04 mg/kg, i.m.). xylazine (0.5 mg/kg, i.m.) in A group, midazolam (0.5 mg/kg, i.m.) in B group, and xylazine (0.25 mg/kg, i.m.) + midazolam (0.25 mg/kg, i.m.) combination in C group were used as preanaesthetics. Anaesthesia was induced with 1% propofol (i.v., to effect) and maintained with halothane in 100% oxygen in all groups of the animals. Different clinico-physiological, cardiorespiratory and haemodynamic parameters were recorded. On the basis of results, xylazine-midazolam combination was found more suitable preanaesthetic combination than xylazine or midazolam alone for propofol-halothane anaesthesia in dogs.
Role of trait combinations, habitat matrix, and network topology in metapopulation recovery from regional extinction

We studied the role of oceanographic conditions and life history strategies on recovery after extinction in a metapopulation of marine organisms dispersing as pelagic larvae. We combined an age‐structured model with scenarios defined by realistic oceanographic conditions and species distribution along the Irish Sea coast (North Europe). Species life history strategies were modeled combining the dispersal behaviors with two levels of fecundity. Recovery times were quantified after simulating extinction in four regions. Two alternative strategies (high fecundity or larval tidal transport) led to short recovery times, irrespective of the effects of other drivers. Other strategies and low larval survival exacerbated the effects of oceanographic conditions on recovery times: longer times were associated with for example the presence of frontal zones isolating regions of extinction. Recovery times were well explained by the connectivity of each focal population with those located outside the area of extinction (which was higher in the so‐called small world topologies), but not by subsidies (direct connections with populations located nearby). Our work highlights the complexities involved in population recovery: specific trait combinations may blur the effects of the habitat matrix on recovery times; K‐strategists (i.e., with low fecundities) may achieve quick recovery if they possess the appropriate dispersal traits. High larval mortality can exacerbate the effect of oceanographic conditions and lead to heterogeneity in recovery times. Overall, processes driving whole network topologies rather than conditions surrounding local populations are the key to understand patterns of recovery.
The complete chloroplast genome of newly alien medicinal and toxic species, Zaleya pentandra (L.) C.Jeffrey (Aizoaceae), in China

Abstract The first complete chloroplast genome sequences of new intercepted alien weeds in China, pentandra (L.) C. Jeffrey, were reported in this study. The Z. pentandra plastome was 153,239 bp long, with the large single copy (LSC) region of 83,528 bp, the small single copy (SSC) region of 18,081 bp, and two inverted repeat (IR) regions of 25,815 bp. The plastome contained 130 genes, including 85 protein-coding, 8 ribosomal RNA, and 37 transfer RNA genes. The overall GC content was 37.0%. Phylogenetic analysis of 32 representative plastomes within the family Aizoaceae suggests that Zaleya is more closely related to Tetragonia than to Sesuvium which is different previous studies. However, due to the limited chloroplast genome accessions in Aizoaceae at present, the phylogenetic relationship between the subfamilies of the family cannot be further discussed.
Alterations in Human Baroreceptor Reflex Regulation of Blood Pressure Following 15 Days of Simulated Microgravity Exposure

Prolonged exposure to microgravity is known to invoke physiological changes which predispose individuals to orthostatic intolerance upon readaptation to the earth's gravitational field. Attenuated baroreflex responsiveness has been implicated in contributing to this inability to withstand orthostatic stress. To test this hypothesis, eight individuals were exposed to 15 days of simulated microgravity exposure using the 6° head-down bed rest model. Prior to, and after the simulated microgravity exposure, the following were assessed: a) aortic baroreflex function; b) carotid baroreflex function; c) cardiopulmonary baroreflex function; and d) the degree of interaction between the cardiopulmonary and carotid baroreflexes.
Elevational filtering and the evolution of planthoppers (Hemiptera, Fulgoromorpha) in Papua New Guinea

Along elevational gradients, phylogenetic relatedness patterns constitute a considerable source of information and may shed light on ecological processes that structure communities. This study focuses on community phylogenetic structure of planthoppers, specifically the species‐rich and abundant Fulgoromorpha families (Hemiptera, Auchenorrhyncha), Cixiidae and Derbidae + Achilidae, along an elevational gradient on Mount Wilhelm (Papua New Guinea). In order to assess the factors driving planthoppers community composition, we recorded abundance data for planthoppers species at each elevation and we generated a molecular phylogeny of the local species, using Bayesian inference. We analyzed 168 individuals representing 59 local morphospecies. Using a fully resolved and well‐supported phylogeny, we then investigated the phylogenetic structure of the communities by performing a Spatial Analysis of Community Diversity. We show that Cixiidae are phylogenetically clustered along the elevational gradient, whereas Derbidae + Achilidae harbor a random structure, suggesting that local adaptation to elevation shapes community structure of Cixiidae, but not that of Derbidae + Achilidae. Our findings highlight the importance of phylogenies in the study of tropical elevational gradients.
A synthetic approach for assessing the interplay of form and function in the crocodyliform snout

Existing classifications of snout shape within Crocodylia are supported by functional studies, but ecological surveys often reveal a higher than expected diversity of prey items within putatively specialist groups, and research into bite force and predation behaviour does not always reveal significant differences between snout shape groups. The addition of more distantly related crocodyliforms complicates the ecomorphological signal, because these groups often occupy a larger area of morphospace than the crown group alone. Here, we present an expanded classification of snout shapes and diets across Crocodyliformes, bringing together geometric morphometrics, non-hierarchical cluster analyses, phylogenetic analyses, ancestral state reconstructions, ecological surveys of diet, and feeding traces from the fossil record to build and test predictive models for linking snout shape and function across the clade. When applied to living members of the group, these new classifications partition out based on differences in predator body mass and maximal prey size. When applied to fossils, these classifications predict potential prey items and identify possible examples of scavenging. In a phylogenetic context, these ecomorphs reveal differences in dietary strategies and diversity within major crocodyliform clades. Taken together, these patterns suggest that crocodyliform diversity, in terms of both morphology and diet, has been underestimated.
Evidence for widespread selection in shaping the genomic landscape during speciation of Populus

Increasing our understanding of how various evolutionary processes drive the genomic landscape of variation is fundamental to a better understanding of the genomic consequences of speciation. However, the genome-wide patterns of within- and between-species variation have not been fully investigated in most forest tree species despite their global ecological and economic importance. Here, we use whole-genome resequencing data from four Populus species spanning the speciation continuum to reconstruct their demographic histories, investigate patterns of diversity and divergence, infer their genealogical relationships and estimate the extent of ancient introgression across the genome. Our results show substantial variation in these patterns along the genomes although this variation is not randomly distributed but is strongly predicted by the local recombination rates and the density of functional elements. This implies that the interaction between recurrent selection and intrinsic genomic features has dramatically sculpted the genomic landscape over long periods of time. In addition, our findings provide evidence that, apart from background selection, recent positive selection and long-term balancing selection are also crucial components in shaping patterns of genome-wide variation during the speciation process.
What would it take to describe the global diversity of parasites?

How many parasites are there on Earth? Here, we use helminth parasites to highlight how little is known about parasite diversity, and how insufficient our current approach will be to describe the full scope of life on Earth. Using the largest database of host-parasite associations and one of the world’s largest parasite collections, we estimate a global total of roughly 100,000 to 350,000 species of helminth endoparasites of vertebrates, of which 85% to 95% are unknown to science. The parasites of amphibians and reptiles remain the most undescribed, but the majority of missing species are likely parasites of birds and bony fish. Missing species are disproportionately likely to be smaller parasites of smaller hosts in undersampled countries–species that have mostly been understudied over the last century. At current rates, it would take centuries to comprehensively sample, collect, and name vertebrate helminths. While some have suggested that macroecological inference can work around existing data limitations, we argue that patterns described from a small and biased sample of diversity aren’t necessarily reliable, especially as host-parasite networks are increasingly altered by global change. In the spirit of moonshots like the Human Genome Project and the Global Virome Project, we call for a global effort to transform parasitology and describe as much of global parasite diversity as possible. Significance Statement Roughly one in ten parasitic worms has been described by taxonomists, while the majority of species remain unknown to science. Data deficiencies are especially severe for some major groups (reptiles and amphibians) and regions (Africa and Southeast Asia). Decades of work have resulted in much larger, detailed datasets on host-parasite interactions, but their utility is limited by these major data gaps. At current rates, those gaps could take hundreds of years to be filled. We propose that a globally-coordinated project could dramatically speed up this process, playing a critical role in tracking the disease impacts of global change. This work will require new funding streams, and a concerted effort among several research communities.
Seasonal variation in thermal plasticity of an alpine lake Daphnia population

Background: Temperature changes dramatically throughout the growing season in temperate latitudes, and seasonal changes in temperature are especially pronounced in alpine lakes where water stratifies into distinct thermal layers during summer. Hypothesis: Populations are expected to maintain a greater degree of plasticity in more heterogeneous environments, such as when lake stratification occurs. Organism: We studied seasonal variation in plasticity of a population of Daphnia, a key grazer in alpine lakes. Methods: We isolated maternal lines of Daphnia pulicaria from Blue Lake (Sierra Nevada, CA) at four different times throughout the growing season, then measured phenotypic traits and survivorship after individuals were reared at two temperatures (17C and 24C). Results: We found mixed evidence for the role of thermal variation in maintaining plasticity. Thermal plasticity for offspring number and age at maturity varied seasonally; however, inconsistent with our hypothesis, neither response was related to stratification. Similarly, we observed lower plasticity for the clutch interval when the lake experienced peak thermal stratification in mid-summer compared with early-fall conditions. In contrast, plasticity for critical maximum temperature (CT) was highest during peak stratification. As CT is a direct measurement of upper thermal limits, it should be related to maximum temperature experienced in the water column. Thus, this result is consistent with a positive correlation between thermal variation and plasticity. Conclusion: Our results suggest that the degree of plasticity in response to temperature varies throughout the season in relation to thermal stratification, with different life-history traits showing distinct seasonal patterns of plasticity.