Comparison of Methods for Species-Tree Inference in the Sawfly Genus Neodiprion (Hymenoptera: Diprionidae)

Conifer-feeding sawflies in the genus Neodiprion provide an excellent opportunity to investigate the origin and maintenance of barriers to reproduction, but obtaining a phylogenetic estimate for comparative studies of Neodiprion speciation has proved difficult. Specifically, nonmonophyly within and discordance between individual gene trees, both of which are common in groups that diverged recently and/or rapidly, make it impossible to infer a species tree using methods that are designed to estimate gene trees. Therefore, in this study, we estimate relationships between members of the lecontei species group using four approaches that are intended to estimate species, not gene, trees: (1) minimize deep coalescences (MDC), (2) shallowest divergences (SD), (3) Bayesian estimation of species trees (BEST), and (4) a novel approach that combines concatenation with monophyly constraints (CMC). Multiple populations are sampled for most species and all four methods incorporate this intraspecific variation into estimates of interspecific relationships. We investigate the sensitivity of each method to taxonomic sampling, and, for the BEST method, we assess the impact of prior choice on species-tree inference. We also compare species-tree estimates to one another and to a morphologically based hypothesis to identify clades that are supported by multiple analyses and lines of evidence. We find that both taxonomic sampling and method choice impact species-tree estimates and that, for these data, the BEST method is strongly influenced by and branch-length priors. We also find that the CMC method is the least sensitive to taxonomic sampling. Finally, although interspecific genetic variation is low due to the recent divergence of the lecontei group, our results to date suggest that incomplete lineage sorting and interspecific gene flow are the main factors complicating species-tree inference in Neodiprion. Based on these analyses, we propose a phylogenetic hypothesis for the lecontei group. Finally, our results suggest that, even for very challenging groups like Neodiprion, an underlying species-tree signal can be extracted from multi-locus data as long as intraspecific variation is adequately sampled and methods that focus on the estimation of species trees are used. [Bayesian estimation of species trees (BEST); concatenation with monophyly constraints (CMC); gene-tree discordance; hybridization; introgression; lineage sorting; minimize deep coalescences (MDC); shallowest divergences (SD).]Organismic and Evolutionary Biolog

Phenology of Antler Casting and Occurrence of Late-Breeding in Nebraska White-Tailed Deer

White-tailed deer (Odocoileus virginianus) in Nebraska primarily breed in November (stimulated by photoperiod), but this season extends into December and January for unfertilized females and healthy fawns reaching the appropriate breeding weight by winter. Variation in the typical mating period can be attributed to geographic region, skewed sex ratios, and fawns reaching sexual maturity during their first year of birth. During April of 2019, we observed late season breeding by a male white-tailed deer in the central Platte River valley and documented late antler casting for this same late-copulating male. An additional male was observed in April of 2020 still retaining antlers within the region. To understand the irregularity of these observations relative to the central Platte River valley, we documented observations of early and late antler casting utilizing long-term cast antler collection and camera trap data. We were able to establish a baseline for antler casting phenology within this region to denote a shift in average casting timeframe (more than one month later than previously recorded in this region) and document early and the latest known antler casting within the literature. Herein, we detail the variation in antler casting phenology for white-tailed deer in this region, and the latest known occurrence of natural breeding in the state. Our findings help us better understand the life history of the Nebraska white-tailed deer population and can assist state wildlife biologists and property managers as they assess seasonal harvest regulations and adaptively manage the changing resource

Are flightless Galapaganus weevils older than the Galapagos islands they inhabit?

The 15 species in the weevil genus Galapaganus Lanteri 1992 (Entiminae: Curculionidae: Coleoptera) are distributed on coastal Peril and Ecuador and include 10 flightless species endemic to the Galapagos islands. These beetles thus provide a promising system through which to investigate the patterns and processes of evolution on Darwin's archipelago. Sequences of the mtDNA locus encoding cytochrome oxidase subunit I (COI) were obtained from samples of seven species occurring in different ecological zones of the oldest south-eastern islands: San Cristobal, Espanola and Floreana, and the central island Santa Cruz. The single most parsimonious tree obtained shows two well-supported clades that correspond to the species groups previously defined by morphological characters. Based on a mtDNA clock calibrated for arthropods, the initial speciation separating the oldest species, G. galapagoensis (Linell) on the oldest island, San Cristobal, from the remaining species in the Galapagos occurred about 7.2 Ma. This estimate exceeds geological ages of the extant emerged islands, although it agrees well with molecular dating of endemic Galapagos iguanas, geckos and lizards. An apparent explanation for the disagreement between geological and molecular time-frames is that about 7 Ma there were emerged islands which subsequently disappeared under ocean waters. This hypothesis has gained support from the recent findings of 11 -Myr-old submarine seamounts (sunken islands), south-east of the present location of the archipelago. Some species within the darwini group may have differentiated on the extant islands, 1-5 Ma.Facultad de Ciencias Naturales y Muse

Are flightless Galapaganus weevils older than the Galapagos islands they inhabit?

The 15 species in the weevil genus Galapaganus Lanteri 1992 (Entiminae: Curculionidae: Coleoptera) are distributed on coastal Peril and Ecuador and include 10 flightless species endemic to the Galapagos islands. These beetles thus provide a promising system through which to investigate the patterns and processes of evolution on Darwin's archipelago. Sequences of the mtDNA locus encoding cytochrome oxidase subunit I (COI) were obtained from samples of seven species occurring in different ecological zones of the oldest south-eastern islands: San Cristobal, Espanola and Floreana, and the central island Santa Cruz. The single most parsimonious tree obtained shows two well-supported clades that correspond to the species groups previously defined by morphological characters. Based on a mtDNA clock calibrated for arthropods, the initial speciation separating the oldest species, G. galapagoensis (Linell) on the oldest island, San Cristobal, from the remaining species in the Galapagos occurred about 7.2 Ma. This estimate exceeds geological ages of the extant emerged islands, although it agrees well with molecular dating of endemic Galapagos iguanas, geckos and lizards. An apparent explanation for the disagreement between geological and molecular time-frames is that about 7 Ma there were emerged islands which subsequently disappeared under ocean waters. This hypothesis has gained support from the recent findings of 11 -Myr-old submarine seamounts (sunken islands), south-east of the present location of the archipelago. Some species within the darwini group may have differentiated on the extant islands, 1-5 Ma.Facultad de Ciencias Naturales y Muse

Whole-genome amplification in double-digest RADseq results in adequate libraries but fewer sequenced loci

Whole-genome amplification by multiple displacement amplification (MDA) is a promising technique to enable the use of samples with only limited amount of DNA for the construction of RAD-seq libraries. Previous work has shown that, when the amount of DNA used in the MDA reaction is large, double-digest RAD-seq (ddRAD) libraries prepared with amplified genomic DNA result in data that are indistinguishable from libraries prepared directly from genomic DNA. Based on this observation, here we evaluate the quality of ddRAD libraries prepared from MDA-amplified genomic DNA when the amount of input genomic DNA and the coverage obtained for samples is variable. By simultaneously preparing libraries for five species of weevils (Coleoptera, Curculionidae), we also evaluate the likelihood that potential contaminants will be encountered in the assembled dataset. Overall, our results indicate that MDA may not be able to rescue all samples with small amounts of DNA, but it does produce ddRAD libraries adequate for studies of phylogeography and population genetics even when conditions are not optimal. We find that MDA makes it harder to predict the number of loci that will be obtained for a given sequencing effort, with some samples behaving like traditional libraries and others yielding fewer loci than expected. This seems to be caused both by stochastic and deterministic effects during amplification. Further, the reduction in loci is stronger in libraries with lower amounts of template DNA for the MDA reaction. Even though a few samples exhibit substantial levels of contamination in raw reads, the effect is very small in the final dataset, suggesting that filters imposed during dataset assembly are important in removing contamination. Importantly, samples with strong signs of contamination and biases in heterozygosity were also those with fewer loci shared in the final dataset, suggesting that stringent filtering of samples with significant amounts of missing data is important when assembling data derived from MDA-amplified genomic DNA. Overall, we find that the combination of MDA and ddRAD results in high-quality datasets for population genetics as long as the sequence data is properly filtered during assembly.Organismic and Evolutionary Biolog

Chiral carbene–borane adducts: precursors for borenium catalysts for asymmetric FLP hydrogenations

The carbene derived from (1R,3S)-camphoric acid was used to prepare the borane adduct with Piers’ borane 7. Subsequent hydride abstraction gave the borenium cation 8. Adducts with 9-BBN and the corresponding (1R,3S)-camphoric acid-derived carbene bearing increasingly sterically demanding N-substituents (R = Me 9, Et 10, i-Pr 11) and the corresponding borenium cations 12–14 were also prepared. These cations were not active as catalysts in hydrogenation, although 9–11 were shown to undergo carbene ring expansion reactions at 50 °C to give species 15–17. The IBOX-carbene precursors 18 and 19 derived from amino alcohols (S)-valinol and (S)-tert-leucinol (R = i-Pr, t-Bu) were used to prepare borane adducts 20–23. Reaction of the carbenes 1,3-dimethylimidazol-2-ylidene (IMe), 1,3-di-iso-propylimidazol-2-ylidene (IPr) 1-benzyl-3-methylimidazol-2-ylidene (IBnMe), 1-methyl-3-phenylimidazol-2-ylidene (IPhMe) and 1-tert-butyl-3-methylimidazol-2-ylidene (ItBuMe) with diisopinocampheylborane (Ipc2BH) gave chiral adducts: (IMe)(Ipc2BH) 24, (IPr)(Ipc2BH) 25, (IBnMe)(Ipc2BH) 26, (IPhMe)(Ipc2BH) 27, and (ItBuMe)(Ipc2BH) 28. Triazolylidene-type adducts including the (10)-phenyl-9-borabicyclo [3.3.2]decane adduct of 1,3,4-triphenyl-1H-1,2,3-triazolium, rac-29 and the 9-BBN derivative of (S)-2-amino-2′-methoxy-1,1′-binaphthalene-1,2,3-triazolium 34a/b were also prepared. In catalytic studies of these systems, while several species were competent catalysts for imine reduction, in general, low enantioselectivities, ranging from 1–20% ee, were obtained. The implications for chiral borenium cation catalyst design are considered

Are flightless Galapaganus weevils older than the Galapagos islands they inhabit?

The 15 species in the weevil genus Galapaganus Lanteri 1992 (Entiminae: Curculionidae: Coleoptera) are distributed on coastal Peril and Ecuador and include 10 flightless species endemic to the Galapagos islands. These beetles thus provide a promising system through which to investigate the patterns and processes of evolution on Darwin's archipelago. Sequences of the mtDNA locus encoding cytochrome oxidase subunit I (COI) were obtained from samples of seven species occurring in different ecological zones of the oldest south-eastern islands: San Cristobal, Espanola and Floreana, and the central island Santa Cruz. The single most parsimonious tree obtained shows two well-supported clades that correspond to the species groups previously defined by morphological characters. Based on a mtDNA clock calibrated for arthropods, the initial speciation separating the oldest species, G. galapagoensis (Linell) on the oldest island, San Cristobal, from the remaining species in the Galapagos occurred about 7.2 Ma. This estimate exceeds geological ages of the extant emerged islands, although it agrees well with molecular dating of endemic Galapagos iguanas, geckos and lizards. An apparent explanation for the disagreement between geological and molecular time-frames is that about 7 Ma there were emerged islands which subsequently disappeared under ocean waters. This hypothesis has gained support from the recent findings of 11 -Myr-old submarine seamounts (sunken islands), south-east of the present location of the archipelago. Some species within the darwini group may have differentiated on the extant islands, 1-5 Ma.Facultad de Ciencias Naturales y Muse

Using iron oxide nanoparticles to diagnose CNS inflammatory diseases and PCNSL

Abstract OBJECTIVE: The study goal was to assess the benefits and potential limitations in the use of ultrasmall superparamagnetic iron oxide (USPIO) nanoparticles in the MRI diagnosis of CNS inflammatory diseases and primary CNS lymphoma. METHODS: Twenty patients with presumptive or known CNS lesions underwent MRI study. Eighteen patients received both gadolinium-based contrast agents (GBCAs) and 1 of 2 USPIO contrast agents (ferumoxytol and ferumoxtran-10) 24 hours apart, which allowed direct comparative analysis. The remaining 2 patients had only USPIO-enhanced MRI because of a renal contraindication to GBCA. Conventional T1- and T2-weighted MRI were acquired before and after contrast administration in all patients, and perfusion MRI for relative cerebral blood volume (rCBV) assessment was obtained in all 9 patients receiving ferumoxytol. RESULTS: USPIO-enhanced MRI showed an equal number of enhancing brain lesions in 9 of 18 patients (50%), more enhancing lesions in 2 of 18 patients (11%), and fewer enhancing lesions in 3 of 18 patients (17%) compared with GBCA-enhanced MRI. Four of 18 patients (22%) showed no MRI enhancement. Dynamic susceptibility-weighted contrast-enhanced perfusion MRI using ferumoxytol showed low rCBV (ratio <1.0) in 3 cases of demyelination or inflammation, modestly elevated rCBV in 5 cases of CNS lymphoma or lymphoproliferative disorder (range: 1.3-4.1), and no measurable disease in one case. CONCLUSIONS: This study showed that USPIO-enhanced brain MRI can be useful in the diagnosis of CNS inflammatory disorders and lymphoma, and is also useful for patients with renal compromise at risk of nephrogenic systemic fibrosis who are unable to receive GBCA

Investigating the Information Systems Heterarchy

This article assesses how one IS organization is changing in response to the increased globalization of software development and posits the emergence of a new form of multi-national enterprise (MNE)—the heterarchy. Data from two projects create new insights into the structures and behaviors of ISMNEs as they adapt to global systems development. The article identifies four primary dimensions of impact—cultural, economic, operational, and organizational—and suggests how such organizations are evolvin

Ethanol Distribution, Dispensing, and Use: Analysis of a Portion of the Biomass-to-Biofuels Supply Chain Using System Dynamics

The Energy Independence and Security Act of 2007 targets use of 36 billion gallons of biofuels per year by 2022. Achieving this may require substantial changes to current transportation fuel systems for distribution, dispensing, and use in vehicles. The U.S. Department of Energy and the National Renewable Energy Laboratory designed a system dynamics approach to help focus government action by determining what supply chain changes would have the greatest potential to accelerate biofuels deployment. The National Renewable Energy Laboratory developed the Biomass Scenario Model, a system dynamics model which represents the primary system effects and dependencies in the biomass-to-biofuels supply chain. The model provides a framework for developing scenarios and conducting biofuels policy analysis. This paper focuses on the downstream portion of the supply chain–represented in the distribution logistics, dispensing station, and fuel utilization, and vehicle modules of the Biomass Scenario Model. This model initially focused on ethanol, but has since been expanded to include other biofuels. Some portions of this system are represented dynamically with major interactions and feedbacks, especially those related to a dispensing station owner’s decision whether to offer ethanol fuel and a consumer’s choice whether to purchase that fuel. Other portions of the system are modeled with little or no dynamics; the vehicle choices of consumers are represented as discrete scenarios. This paper explores conditions needed to sustain an ethanol fuel market and identifies implications of these findings for program and policy goals. A large, economically sustainable ethanol fuel market (or other biofuel market) requires low end-user fuel price relative to gasoline and sufficient producer payment, which are difficult to achieve simultaneously. Other requirements (different for ethanol vs. other biofuel markets) include the need for infrastructure for distribution and dispensing and widespread use of high ethanol blends in flexible-fuel vehicles