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PREMISE OF THE STUDY: We reconstructed aspects of the evolutionary history of Lindleya, a shrubby element in the rose family, as a model for identifying the ancestral area of the biota of the Chihuahuan Desert and for understanding the effect that pre-Pleistocene or Pleistocene climate fluctuations had on the evolution of the plants of this desert. METHODS: We conducted phylogenetic, biogeographic, and phylogeographic analyses based on one nuclear DNA and two plastid markers sequenced for 20 populations comprising 153 accessions and representing the species' entire distribution range. We carried out ecological niche modeling to forecast Lindleya's potential distribution under Current, Last Interglacial, and Last Glacial Maximum conditions. KEY RESULTS: The ancestral area of Lindleya populations was probably in the central and southern parts of the Chihuahuan Desert. Levels of genetic and haplotype variation were the highest in the northernmost and southernmost areas and low levels of genetic variation in the central part. Extended Bayesian skyline plots including all populations identified a slight demographic expansion ~1 Ma. The predicted potential distribution during the Last Glacial Maximum was very restricted. CONCLUSIONS: We suggest that pre-Pleistocene changes had an influence on the divergence of Lindleya populations. We also suggest that the ancestral area for Lindleya was the Chihuahuan Desert and that the uplift of the Trans-Mexican Volcanic Belt isolated the Tehuacán Valley populations. Genetic and demographic analyses as well as and ecological niche modeling indicate that populations of Lindleya experienced genetic bottlenecks and that they have expanded since the Last Glacial Maximum.

Our understanding of the complexity of forces at play in the rise of major angiosperm lineages remains incomplete. The diversity and heterogeneous distribution of most angiosperm lineages is so extraordinary that it confounds our ability to identify simple drivers of diversification. Using machine learning in combination with phylogenetic modelling, we show that five separate abiotic and biotic variables significantly contribute to the diversification of Cactaceae. We reconstruct a comprehensive phylogeny, build a dataset of 39 abiotic and biotic variables, and predict the variables of central importance, while accounting for potential interactions between those variables. We use state-dependent diversification models to confirm that five abiotic and biotic variables shape diversification in the cactus family. Of highest importance are diurnal air temperature range, soil sand content and plant size, with lesser importance identified in isothermality and geographic range size. Interestingly, each of the estimated optimal conditions for abiotic variables were intermediate, indicating that cactus diversification is promoted by moderate, not extreme, climates. Our results reveal the potential primary drivers of cactus diversification, and the need to account for the complexity underlying the evolution of angiosperm lineages. Here, the authors combine machine learning with phylogenetic modeling to assess the impact of 39 abiotic and biotic drivers on Cactaceae evolution. They suggest that cactus diversification was promoted by moderate, rather than extreme climates, as well as soil characteristics and plant size.

Alien species, one of the biggest threats to natural ecosystems worldwide, are of particular concern for oceanic archipelagos such as Galápagos. To enable more effective management of alien species, we reviewed, collated and analysed all available records of alien species for Galápagos. We also assembled a comprehensive dataset on pathways to and among the Galápagos Islands, including tourist and resident numbers, tourist vessels, their itineraries and visitation sites, aircraft capacity and occupancy, air and sea cargo and biosecurity interceptions. So far, 1,579 alien terrestrial and marine species have been introduced to Galápagos by humans. Of these, 1,476 have become established. Almost half of these were intentional introductions, mostly of plants. Most unintentional introductions arrived on plants and plant associated material, followed by transport vehicles, and commodities (in particular fruit and vegetables). The number, frequency and geographic origin of pathways for the arrival and dispersal of alien species to and within Galápagos have increased over time, tracking closely the increase in human population (residents and tourists) on the islands. Intentional introductions of alien species should decline as biosecurity is strengthened but there is a danger that unintentional introductions will increase further as tourism on Galápagos expands. This unique world heritage site will only retain its biodiversity values if the pathways for invasion are managed effectively.

The phenomenal expansion of angiosperms has prompted many investigations into the factors driving their diversification, but there remain significant gaps in our understanding of flowering plant species diversity. Using the crown age of families from five studies, we used a maximum likelihood approach to classify families as having poor, predicted or high species richness (SR) using strict consensus criteria. Using these categories, we looked for associations between family SR and i) the presence of an inferred familial ancestral polyploidization event, ii) 23 life history and floral traits compiled from previously published datasets and papers, and iii) sexual system (dioecy) or genetically determined self-incompatibility (SI) mating system using an updated version of our own database and iv) geographic distribution using a new database describing the global distribution of plant species/families across realms and biomes and inferred range. We find that more than a third of angiosperm families (65%) had predicted SR, a large proportion (30.2%) were species poor, while few (4.8%) had high SR. Families with poor SR were less likely to have undergone an ancestral polyploidization event, exhibited deficits in diverse traits, and were more likely to have unknown breeding systems and to be found in only one or few biomes and realms, especially the Afrotropics or Australasia. On the other hand, families with high SR were more likely to have animal mediated pollination or dispersal, are enriched for epiphytes and taxa with an annual life history, and were more likely to harbour sporophytic SI systems. Mapping the global distribution of georeferenced taxa by their family DR, we find evidence of regions dominated by taxa from lineages with high vs low SR. These results are discussed within the context of the literature describing \"depauperons\" and the factors contributing to low and high biodiversity in angiosperm clades.

Vauquelinia corymbosa (Pyreae, Rosaceae) is a shrubby sclerophyllous species largely restricted to the Chihuahuan Desert, distributed from Texas, Coahuila, and along the Sierra Madre Oriental to Hidalgo. According to a previous taxonomic revision, it comprises six subspecies. Vauquelinia corymbosa has noteworthy morphological variation, mostly in leaf characters, and the majority of its subspecies are restricted to certain areas of the desert. In this study, based on 16 morphometric characters and four anatomical characters collected from 201 specimens of the six subspecies throughout their distribution range,we ran a number of uni-, multivariate, and phylogenetic analyses to determine how many species can be recognized in this species complex. We also analyzed the gaps in morphology across geography to identify whether gaps in morphometric characters are indeed useful to separate species or if they are the result of variation related to geography. The results of the analyses coincided in recognizing that subsp. angustifolia should be considered a separate species and that the remaining subspecies are part of Vauquelinia corymbosa with remarkable morphological variation. Vauquelinia angustifolia has diagnostic characters such as very narrow leaves (0.4–0.6 cm at the middle and 0.2–0.4 cm at the base) and short petioles (1–1.5 cm) and it is restricted to the northeastern region of the Chihuahuan Desert.

Dengue fever is an emerging infectious disease in the Galápagos Islands of Ecuador, with the first cases reported in 2002 and subsequent periodic outbreaks. We report results of a 2014 pilot study conducted in Puerto Ayora (PA) on Santa Cruz Island, and Puerto Baquerizo Moreno (PB) on San Cristobal Island. To assess the socio-ecological risk factors associated with dengue and mosquito vector presence at the household level, we conducted 100 household surveys (50 on each island) in neighborhoods with prior reported dengue cases. Adult mosquitoes were collected inside and outside the home, larval indices were determined through container surveys, and heads of households were interviewed to determine demographics, self-reported prior dengue infections, housing conditions, and knowledge, attitudes, and practices regarding dengue. Multi-model selection methods were used to derive best-fit generalized linear regression models of prior dengue infection, and Aedes aegypti presence. We found that 24% of PB and 14% of PA respondents self-reported a prior dengue infection, and more PB homes than PA homes had Ae. aegypti. The top-ranked model for prior dengue infection included several factors related to human movement, household demographics, access to water quality issues, and dengue awareness. The top-ranked model for Ae. aegypti presence included housing conditions, mosquito control practices, and dengue risk perception. This is the first study of dengue risk and Ae. aegypti presence in the Galápagos Islands.

More than one year since Coronavirus disease 2019 (COVID-19) pandemic outbreak, the gold standard technique for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) detection is still the RT-qPCR. This is a limitation to increase testing capacities, particularly at developing countries, as expensive reagents and equipment are required. We developed a two steps end point RT-PCR reaction with SARS-CoV-2 Nucleocapsid (N) gene and Ribonuclease P (RNase P) specific primers where viral amplicons were verified by agarose gel electrophoresis. We carried out a clinical performance and analytical sensitivity evaluation for this two-steps end point RT-PCR method with 242 nasopharyngeal samples using the CDC RT-qPCR protocol as a gold standard technique. With a specificity of 95.8%, a sensitivity of 95.1%, and a limit of detection of 20 viral RNA copies/uL, this two steps end point RT-PCR assay is an affordable and reliable method for SARS-CoV-2 detection. This protocol would allow to extend COVID-19 diagnosis to basic molecular biology laboratories with a potential positive impact in surveillance programs at developing countries.

Traditional agave spirits such as mezcal or tequila are produced all over Mexico using different species of Agave. Amongst them, A. angustifolia is the most popular given its agricultural extension. A. angustifolia is a wild species extensively distributed from North to Central America, and previous studies show that it is highly related to the tequila agave A. tequilana. In different regions of Mexico, A. angustifolia is cultivated under different types and levels of management, and although traditional producers identify several landraces, for the non-trained eye there are no perceivable differences. After interviews with producers from different localities in Jalisco, Mexico, we sampled A. angustifolia plants classified as different landraces, measured several morphological traits, and characterized their genetic differentiation and diversity at the genome-wide level. We included additional samples identified as A. tequilana and A. rhodacantha to evaluate their relationship with A. angustifolia. In contrast with previous studies, our pool of ca 20K high quality unlinked SNPs provided more information and helped us to distinguish different genetic groups that are congruent with the ethnobotanical landraces. We found no evidence to genetically delimitate A. tequilana, A. rhodacantha and A. angustifolia. Our large genome level dataset allows a better understanding of the genetic identity of important A. angustifolia traditional and autochthonous landraces.

CDC and WHO guidelines for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) diagnosis only recommend synthetic fiber swabs for nasopharyngeal (NP) sampling. We show that cotton-tipped plastic swabs do not inhibit PCR and have equivalent performance to rayon swabs. Cotton-tipped plastic swabs are massively produced worldwide and would prevent swab supply shortages under the current high SARS-CoV-2 testing demands, particularly in developing countries.

BackgroundThe wild ancestors of domesticated rice had red seed, white rice being the result of a mutation in the rice domestication gene Rc. Many pigmented rice landraces are still grown by ethnic communities for their nutritional and cultural value. This study assesses the genetic diversity in a collection of pigmented rice accessions from the Philippines.ResultsWe undertook an analysis of the genetic and colour variation in a collection of 696 pigmented rice accessions held at PhilRice in the Philippines. The collection was reduced to 589 genotypes after removal of accessions with limited passport data or with low SNP marker call rates. Removal of duplicate genotypes resulted in a final, core collection of 307 accessions, representing all administrative districts of the Philippines, and composed predominately of japonica and indica sub-species. No genetic structure was observed in the core collection based on geographic origin. A pairwise comparison of accessions by region indicating that both local and long-distance exchange of rice accessions had occurred. The majority of the genetic variation was within regions (82.38%), rather than between regions (10.23%), with the remaining variation being within rice accession variance (7.39%). The most genetically diverse rice accessions originated from the Cordillera Administrative Region (CAR) in the far north of the Philippines, and in the regions of Davao and Caraga in the southeast. A comparison with pigmented rice accessions from the neighbouring countries Taiwan, Laos, China and India revealed a close relationship between accessions from Taiwan, supporting the hypothesis of southward diffusion of Austronesians from Taiwan to the Philippine. The 14-bp deletion within the gene Rc, known to result in loss of red pigmentation, was found in 30 accessions that still had coloured pericarps. Multi-spectral phenotyping was used to measure seed geometric and colour-appearance traits in 197 accessions from the core collection. The purple and variable purple rice accessions had the lowest values for the seed colour parameters - lightness (L*), intensity, saturation, a* (green – red; redness) and b* (blue – yellow; yellowness).ConclusionThese pigmented rice accessions represent a diverse genetic resource of value for further study and nutritional improvement of commercial rice varieties.