The origin and speciation of orchids.

Orchids constitute one of the most spectacular radiations of flowering plants. However, their origin, spread across the globe, and hotspots of speciation remain uncertain due to the lack of an up-to-date phylogeographic analysis. We present a new Orchidaceae phylogeny based on combined high-throughput and Sanger sequencing data, covering all five subfamilies, 17/22 tribes, 40/49 subtribes, 285/736 genera, and c. 7% (1921) of the 29 524 accepted species, and use it to infer geographic range evolution, diversity, and speciation patterns by adding curated geographical distributions from the World Checklist of Vascular Plants. The orchids' most recent common ancestor is inferred to have lived in Late Cretaceous Laurasia. The modern range of Apostasioideae, which comprises two genera with 16 species from India to northern Australia, is interpreted as relictual, similar to that of numerous other groups that went extinct at higher latitudes following the global climate cooling during the Oligocene. Despite their ancient origin, modern orchid species diversity mainly originated over the last 5 Ma, with the highest speciation rates in Panama and Costa Rica. These results alter our understanding of the geographic origin of orchids, previously proposed as Australian, and pinpoint Central America as a region of recent, explosive speciation.

From Undergraduate Research to Graduation: Measuring the Robustness of the Pathway at a Hispanic-Serving Institution.

Based on several regression specifications that control for a host of covariates, this article demonstrates that the quantity of undergraduate research experience was by far the most important determinant for increased graduation rates at a 100% Hispanic-serving institution. Our finding also shows a causal relationship confirmed by propensity score matching analyses. Results underscore the high impact but sometimes underestimated contribution of undergraduate research to academic success, even for teaching-oriented colleges.

Utilizando varias regresiones que controlan por un grupo de variables controles, este artículo sugiere que la cantidad de experiencia en investigación durante los estudios sub-graduados es el determinante más significativo para el aumento en la tasa de graduación en una institución donde todos sus estudiantes son hispanos. Nuestros hallazgos también indican una relación causal confirmada por el modelo Propensity Score Matching. Los resultados subrayan el alto, pero algunas veces subestimado, impacto de la investigacion de sub-graduada en el éxito académico estudiantil, aún en universidades orientadas a la enseñanza.

Post-Hurricane Distress Scale (PHDS): Determination of General and Disorder-Specific Cutoff Scores.

The Post-Hurricane Distress Scale (PHDS) was developed to assess mental health risk in the aftermath of hurricanes. We derive both disorder-specific cutoff values and a single nonspecific cutoff for the PHDS for field use by disaster relief and mental health workers. Data from 672 adult residents of Puerto Rico, sampled 3 to 12 months after Hurricane Maria, were collected. Participants completed a five-tool questionnaire packet: PHDS, Kessler K6, Patient Health Questionnaire 9, Generalized Anxiety Disorder 7, and Post-Traumatic Stress Disorder Checklist for DSM V (PCL-5). ROC curves, AUC values, sensitivities, specificities, Youden's index, and LR+ ratios are reported. The recommended single cutoff value for the PHDS is 41, whereby a respondent with a PHDS score of 41 or above is deemed high-risk for a mental health disorder. The single field use PHDS cutoff demonstrated high specificity (0.80), an LR + ratio (2.84), and a sensitivity of 0.56. The mean ROC values of PHDS for Kessler K6, Patient Health Questionnaire 9, Generalized Anxiety Disorder 7, and PCL-5 were all above 0.74. The derived cutoff for the PHDS allows efficient assessment of respondents' and/or a community's risk status for mental health disorders in the aftermath of hurricanes and natural disasters.

Incidence, prevalence, and economic burden of sarcoidosis in Puerto Rico: Estimates from a government health insurance claims database.

OBJECTIVES: To estimate the epidemiology of sarcoidosis in Puerto Rico. METHODS: Patients with a diagnosis of sarcoidosis between January 2015 and December 2018 were selected from the Puerto Rico Health Insurance Administration Administración de Seguros de Salud de Puerto Rico claims database. The International Classification of Diseases-Tenth Revision coding for sarcoidosis was used for case detection and utilization of health care services. Cases by sex and age were evaluated. RESULTS: A total of 488 individuals with sarcoidosis were identified over the 4-year study. The median age at diagnosis was 59 years old. The average annual incidence rate was 9.9/100,000. The baseline prevalence was 14.9 per 100,000. Females represented 68.4% of the cases. Patients with lung and unspecified sarcoidosis predominate with 45.6% and 28.2% of cases, respectively. Overall, the yearly cost of health care utilization and medications per patient was $234 and $13,638, respectively. CONCLUSIONS: Annual incidence rate and the median age of sarcoidosis in Puerto Ricans are among the highest and oldest reported globally. The demographic profile of sarcoidosis in Puerto Rico presents a patient in the mid-to advanced age, mostly female. While costs for medications were relatively high for a patient with sarcoidosis, the economic burden of the disease to the national health care system is not substantial.

Microbiota dispersion in the Uyuni salt flat (Bolivia) as determined by community structure analyses

Soil microbial communities are an important component of biological diversity and terrestrial ecosystems which is responsible for processes such as decomposition, mineralization of nutrients, and accumulation of organic matter. One of the factors that provide information on the mechanisms regulating biodiversity is spatial scaling. We characterized the microbial communities using 16S rRNA gene sequences from DNA isolated from halite at various locations and correlated these to geographic distance in the Uyuni salt flat (Bolivia). Sequences from each site were analyzed to determine any spatial patterns of diversity, as well as to describe the microbial communities. Results suggest that different taxa are able to disperse over Uyuni's surface crust regardless of distance. As expected, ubiquitous taxa included members of Halobacteriaceae such as Haloarcula, Halorubrum, Halorhabdus, Halolamina, and halophilic bacteria Salinibacter, Halorhodospira, and unclassified members of the Gammaproteobacteria. Archaeal communities were homogeneous across the salt flat. In contrast, bacterial communities present strong local variations which could be attributed to external factors. Likely sources for these variations are the Rio Grande river influent in the south shore and the Tunupa volcano influencing the northern area

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Microbiota dispersion in the Uyuni salt flat (Bolivia) as determined by community structure analyses.

Soil microbial communities are an important component of biological diversity and terrestrial ecosystems which is responsible for processes such as decomposition, mineralization of nutrients, and accumulation of organic matter. One of the factors that provide information on the mechanisms regulating biodiversity is spatial scaling. We characterized the microbial communities using 16S rRNA gene sequences from DNA isolated from halite at various locations and correlated these to geographic distance in the Uyuni salt flat (Bolivia). Sequences from each site were analyzed to determine any spatial patterns of diversity, as well as to describe the microbial communities. Results suggest that different taxa are able to disperse over Uyuni's surface crust regardless of distance. As expected, ubiquitous taxa included members of Halobacteriaceae such as Haloarcula, Halorubrum, Halorhabdus, Halolamina, and halophilic bacteria Salinibacter, Halorhodospira, and unclassified members of the Gammaproteobacteria. Archaeal communities were homogeneous across the salt flat. In contrast, bacterial communities present strong local variations which could be attributed to external factors. Likely sources for these variations are the Rio Grande river influent in the south shore and the Tunupa volcano influencing the northern area.

From the cage to the wild: introductions of Psittaciformes to Puerto Rico.

Introduced psittacine birds can become highly invasive. In this study, we assessed invasions of Psittaciformes in Puerto Rico. We reviewed the literature, public databases, citizen science records, and performed in situ population surveys across the island to determine the historical and current status and distribution of psittacine species. We used count data from Ebird to determine population trends. For species whose populations were increasing, we modelled their potential distribution using niche modeling techniques. We found 46 Psittaciformes in Puerto Rico, of which 26% are only present as pets, at least 29 species have been reported in the wild, and of those, there is evidence that at least 12 species are breeding. Our results indicate that most introduced species which have been detected as established still persist, although mostly in localized areas and small populations. Clear evidence of invasiveness was found for Brotogeris versicolurus and Myiopsitta monachus, which have greatly expanded their range in recent years. Psittacara erythrogenys and Eupsittacula canicularis also showed population increases, although to a lesser degree. The niche models predicted suitable areas for the four species, and also indicate the potential for range expansion. We discuss the factors leading to invasion success, assess the potential impacts, and we discuss possible management strategies and research prospects.

Invasive plant species in the West Indies: geographical, ecological, and floristic insights.

The level of invasion (number or proportion of invasive species) in a given area depends on features of the invaded community, propagule pressure, and climate. In this study, we assess the invasive flora of nine islands in the West Indies to identify invasion patterns and evaluate whether invasive species diversity is related to geographical, ecological, and socioeconomic factors. We compiled a database of invasive plant species including information on their taxonomy, origin, pathways of introduction, habitats, and life history. This database was used to evaluate the similarity of invasive floras between islands and to identify invasion patterns at regional (West Indies) and local (island) scales. We found a total of 516 alien plant species that are invasive on at least one of the nine islands studied, with between 24 to 306 invasive species per island. The invasive flora on these islands includes a wide range of taxonomic groups, life forms, and habitats. We detected low similarity in invasive species diversity between islands, with most invasive species (>60%) occurring on a single island and 6% occurring on at least five islands. To assess the importance of different models in predicting patterns of invasive species diversity among islands, we used generalized linear models. Our analyses revealed that invasive species diversity was well predicted by a combination of island area and economic development (gross domestic product per capita and kilometers of paved roadways). Our results provide strong evidence for the roles of geographical, ecological, and socioeconomic factors in determining the distribution and spread of invasive species on these islands. Anthropogenic disturbance and economic development seem to be the major drivers facilitating the spread and predominance of invasive species over native species.

Spatial asymmetries in connectivity influence colonization-extinction dynamics.

Movement has broad implications for many areas of biology, including evolution, community and population ecology. Movement is crucial in metapopulation ecology because it facilitates colonization and reduces the likelihood of local extinction via rescue effects. Most metapopulation modeling approaches describe connectivity using pair-wise Euclidean distances resulting in the simplifying assumption of a symmetric connectivity pattern. Yet, assuming symmetric connectivity when populations show net asymmetric movement patterns may result in biased estimates of colonization and extinction, and may alter interpretations of the dynamics and conclusions regarding the viability of metapopulations. Here, we use a 10-year time series on a wind-dispersed orchid Lepanthes rupestris that anchors its roots in patches of moss growing on trees or boulders along streams, to test for the role of connectivity asymmetries in explaining the colonization-extinction dynamics of this orchid in a network of 975 patches. We expected that wind direction could highly alter dispersal direction in this orchid. To account for this potential asymmetry, we modified the connectivity measure traditionally used in metapopulation models to allow for asymmetric effective distances between patches and subsequently estimated colonization and extinction probabilities using a dynamic occupancy modeling approach. Asymmetric movement was prevalent in the L. rupestris metapopulation and incorporating potential dispersal asymmetries resulted in higher colonization estimates in larger patches and more accurate models. Accounting for dispersal asymmetries may reveal connectivity effects where they were previously assumed to be negligible and may provide more reliable conclusions regarding the role of connectivity in patch dynamics.

Immunomodulator-based enhancement of anti smallpox immune responses.

BACKGROUND: The current live vaccinia virus vaccine used in the prevention of smallpox is contraindicated for millions of immune-compromised individuals. Although vaccination with the current smallpox vaccine produces protective immunity, it might result in mild to serious health complications for some vaccinees. Thus, there is a critical need for the production of a safe virus-free vaccine against smallpox that is available to everyone. For that reason, we investigated the impact of imiquimod and resiquimod (Toll-like receptors agonists), and the codon-usage optimization of the vaccinia virus A27L gene in the enhancement of the immune response, with intent of producing a safe, virus-free DNA vaccine coding for the A27 vaccinia virus protein. METHODS: We analyzed the cellular-immune response by measuring the IFN-γ production of splenocytes by ELISPOT, the humoral-immune responses measuring total IgG and IgG2a/IgG1 ratios by ELISA, and the TH1 and TH2 cytokine profiles by ELISA, in mice immunized with our vaccine formulation. RESULTS: The proposed vaccine formulation enhanced the A27L vaccine-mediated production of IFN-γ on mouse spleens, and increased the humoral immunity with a TH1-biased response. Also, our vaccine induced a TH1 cytokine milieu, which is important against viral infections. CONCLUSION: These results support the efforts to find a new mechanism to enhance an immune response against smallpox, through the implementation of a safe, virus-free DNA vaccination platform.

When stable-stage equilibrium is unlikely: integrating transient population dynamics improves asymptotic methods.

BACKGROUND AND AIMS: Evaluation of population projection matrices (PPMs) that are focused on asymptotically based properties of populations is a commonly used approach to evaluate projected dynamics of managed populations. Recently, a set of tools for evaluating the properties of transient dynamics has been expanded to evaluate PPMs and to consider the dynamics of populations prior to attaining the stable-stage distribution, a state that may never be achieved in disturbed or otherwise ephemeral habitats or persistently small populations. This study re-evaluates data for a tropical orchid and examines the value of including such analyses in an integrative approach. METHODS: Six small populations of Lepanthes rubripetala were used as a model system and the R software package popdemo was used to produce estimates of the indices for the asymptotic growth rate (lambda), sensitivities, reactivity, first-time step attenuation, maximum amplification, maximum attenuation, maximal inertia and maximal attenuation. The response in lambda to perturbations of demographic parameters using transfer functions and multiple perturbations on growth, stasis and fecundity were also determined. The results were compared with previously published asymptotic indices. KEY RESULTS: It was found that combining asymptotic and transient dynamics expands the understanding of possible population changes. Comparison of the predicted density from reactivity and first-time step attenuation with the observed change in population size in two orchid populations showed that the observed density was within the predicted range. However, transfer function analysis suggests that the traditional approach of measuring perturbation of growth rates and persistence (inertia) may be misleading and is likely to result in erroneous management decisions. CONCLUSIONS: Based on the results, an integrative approach is recommended using traditional PPMs (asymptotic processes) with an evaluation of the diversity of dynamics that may arise when populations are not at a stable-stage distribution (transient processes). This method is preferable for designing rapid and efficient interventions after disturbances, and for developing strategies to establish new populations.

Bayesian estimates of transition probabilities in seven small lithophytic orchid populations: maximizing data availability from many small samples.

Predicting population dynamics for rare species is of paramount importance in order to evaluate the likelihood of extinction and planning conservation strategies. However, evaluating and predicting population viability can be hindered from a lack of data. Rare species frequently have small populations, so estimates of vital rates are often very uncertain due to lack of data. We evaluated the vital rates of seven small populations from two watersheds with varying light environment of a common epiphytic orchid using Bayesian methods of parameter estimation. From the Lefkovitch matrices we predicted the deterministic population growth rates, elasticities, stable stage distributions and the credible intervals of the statistics. Populations were surveyed on a monthly basis between 18-34 months. In some of the populations few or no transitions in some of the vital rates were observed throughout the sampling period, however, we were able to predict the most likely vital rates using a Bayesian model that incorporated the transitions rates from the other populations. Asymptotic population growth rate varied among the seven orchid populations. There was little difference in population growth rate among watersheds even though it was expected because of physical differences as a result of differing canopy cover and watershed width. Elasticity analyses of Lepanthes rupestris suggest that growth rate is more sensitive to survival followed by growth, shrinking and the reproductive rates. The Bayesian approach helped to estimate transition probabilities that were uncommon or variable in some populations. Moreover, it increased the precision of the parameter estimates as compared to traditional approaches.

Microbial quality of tropical inland waters and effects of rainfall events.

Novel markers of fecal pollution in tropical waters are needed since conventional methods recommended for other geographical regions may not apply. To address this, the prevalence of thermotolerant coliforms, enterococci, coliphages, and enterophages was determined by culture methods across a watershed. Additionally, human-, chicken-, and cattle-specific PCR assays were used to identify potential fecal pollution sources in this watershed. An enterococcus quantitative PCR (qPCR) assay was tested and correlated with culture methods at three sites since water quality guidelines could incorporate this technique as a rapid detection method. Various rainfall events reported before sample collection at three sites were considered in the data analyses. Thermotolerant coliforms, enterococci, coliphages, and enterophages were detected across the watershed. Human-specific Bacteroides bacteria, unlike the cattle- and chicken-specific bacteria, were detected mostly at sites with the corresponding fecal impact. Enterococci were detected by qPCR as well, but positive correlations with the culture method were noted at two sites, suggesting that either technique could be used. However, no positive correlations were noted for an inland lake tested, suggesting that qPCR may not be suitable for all water bodies. Concentrations of thermotolerant coliforms and bacteriophages were consistently lower after rainfall events, pointing to a possible dilution effect. Rainfall positively correlated with enterococci detected by culturing and qPCR, but this was not the case for the inland lake. The toolbox of methods and correlations presented here could be potentially applied to assess the microbial quality of various water types.

Riding across the selection landscape: fitness consequences of annual variation in reproductive characteristics.

Evolutionary models estimating phenotypic selection in character size usually assume that the character is invariant across reproductive bouts. We show that variation in the size of reproductive traits may be large over multiple events and can influence fitness in organisms where these traits are produced anew each season. With data from populations of two orchid species, Caladenia valida and Tolumnia variegata, we used Bayesian statistics to investigate the effect on the distribution in fitness of individuals when the fitness landscape is not flat and when characters vary across reproductive bouts. Inconsistency in character size across reproductive periods within an individual increases the uncertainty of mean fitness and, consequently, the uncertainty in individual fitness. The trajectory of selection is likely to be muddled as a consequence of variation in morphology of individuals across reproductive bouts. The frequency and amplitude of such changes will certainly affect the dynamics between selection and genetic drift.

Variation in endophytic fungi from roots and leaves of Lepanthes (Orchidaceae).

Little is known about non-mycorrhizal endophytic fungi in tropical orchids; still less is known about how endophytes vary within and between individual orchid plants. Fungal endophytes were isolated from roots and leaves of epiphytic and lithophytic orchids in the genus Lepanthes; seven species, from rainforests in Puerto Rico, were sampled. The endophytes observed most frequently were Xylaria species and Rhizoctonia-like fungi, found in 29% of roots and 19% of leaves, and 45 % of roots and 31 % of leaves, respectively. Five deuteromycete genera were also isolated, occurring in 19 % of roots and 43 % of leaves (combined). At least nine species of Xylaria were found, with several species sometimes occurring in a single plant. Differences between roots and leaves in frequency of Xylaria and Rhizoctonia isolates were not significant, although differences among orchid species in number and types of endophytes were. Heterogeneity of endophytes in single plants and plant organs was greater than differences between species. Many Lepanthes species are very restricted in distribution, and knowledge of their interactions with endophytes might be useful in species management.