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► Genetic and geospatial data complement one another in phylogeography. ► Practical examples to illustrate how these data can be integrated. ► Variety of tools and approaches can be ...applied to many biological systems.
The field of phylogeography continues to grow in terms of power and accessibility. Initially uniting population genetics and phylogenetics, it now spans disciplines as diverse as geology, statistics, climatology, ecology, physiology, and bioinformatics to name a few. One major and recent integration driving the field forward is between “statistical phylogeography” and Geographic Information Systems (GIS) (
Knowles, 2009). Merging genetic and geospatial data, and their associated methodological toolkits, is helping to bring explicit hypothesis testing to the field of phylogeography. Hypotheses derived from one approach can be reciprocally tested with data derived from the other field and the synthesis of these data can help place demographic events in an historical and spatial context, guide genetic sampling, and point to areas for further investigation. Here, we present three practical examples of empirical analysis that integrate statistical genetic and GIS tools to construct and test phylogeographic hypotheses. Insights into the evolutionary mechanisms underlying recent divergences can benefit from simultaneously considering diverse types of information to iteratively test and reformulate hypotheses. Our goal is to provide the reader with an introduction to the variety of available tools and their potential application to typical questions in phylogeography with the hope that integrative methods will be more broadly and commonly applied to other biological systems and data sets.
ABSTRACT
We investigate changes in the quality and cost of audit services surrounding PCAOB Rule 3211, which requires disclosure of audit partner names in Form AP. To isolate changes due to Rule 3211 ...from other confounding factors, we use difference-in-differences analyses with separate control groups, including a group of companies that disclosed partner identities prior to Rule 3211. Our study also incorporates several measures from prior literature to proxy for various dimensions of audit quality. Evidence from the difference-in-differences analyses reveals that any immediate impact of Rule 3211 on audit quality or fees is limited to specific dimensions of audit quality, specific control groups, and/or specific company characteristics. We reach this conclusion after considering alternative research designs and evaluating confidence intervals for statistically insignificant coefficients. We caution that our findings only provide initial evidence and further research is necessary to evaluate other potential impacts of Rule 3211.
Bacteria within the genus
can be abundant in showerheads, and the inhalation of aerosolized mycobacteria while showering has been implicated as a mode of transmission in nontuberculous mycobacterial ...(NTM) lung infections. Despite their importance, the diversity, distributions, and environmental predictors of showerhead-associated mycobacteria remain largely unresolved. To address these knowledge gaps, we worked with citizen scientists to collect showerhead biofilm samples and associated water chemistry data from 656 households located across the United States and Europe. Our cultivation-independent analyses revealed that the genus
was consistently the most abundant genus of bacteria detected in residential showerheads, and yet mycobacterial diversity and abundances were highly variable. Mycobacteria were far more abundant, on average, in showerheads receiving municipal water than in those receiving well water and in U.S. households than in European households, patterns that are likely driven by differences in the use of chlorine disinfectants. Moreover, we found that water source, water chemistry, and household location also influenced the prevalence of specific mycobacterial lineages detected in showerheads. We identified geographic regions within the United States where showerheads have particularly high abundances of potentially pathogenic lineages of mycobacteria, and these "hot spots" generally overlapped those regions where NTM lung disease is most prevalent. Together, these results emphasize the public health relevance of mycobacteria in showerhead biofilms. They further demonstrate that mycobacterial distributions in showerhead biofilms are often predictable from household location and water chemistry, knowledge that advances our understanding of NTM transmission dynamics and the development of strategies to reduce exposures to these emerging pathogens.
Bacteria thrive in showerheads and throughout household water distribution systems. While most of these bacteria are innocuous, some are potential pathogens, including members of the genus
that can cause nontuberculous mycobacterial (NTM) lung infection, an increasing threat to public health. We found that showerheads in households across the United States and Europe often harbor abundant mycobacterial communities that vary in composition depending on geographic location, water chemistry, and water source, with households receiving water treated with chlorine disinfectants having particularly high abundances of certain mycobacteria. The regions in the United States where NTM lung infections are most common were the same regions where pathogenic mycobacteria were most prevalent in showerheads, highlighting the important role of showerheads in the transmission of NTM infections.
Abstract Background Systemic capillary leak syndrome is a highly rare disorder of unknown cause. The disease is characterized by episodes of transient vascular collapse, which leads to hypotensive ...shock and anasarca. Previous treatment of this potentially devastating condition has been largely ineffective. We evaluated intravenous immunoglobulin prophylactic therapy in a cohort of 29 patients with systemic capillary leak syndrome in a longitudinal follow-up study. Methods All patients received treatments at the discretion of their primary providers and retrospectively via questionnaire-recorded symptoms beginning with their first documented episode of systemic capillary leak syndrome to May 31, 2014. Results A total of 22 of 29 patients responded to the questionnaire, and 18 of the 22 respondents received monthly prophylaxis with intravenous immunoglobulin during the study period for a median interval of 32 months. The median annual attack frequency was 2.6 per patient before intravenous immunoglobulin therapy and 0 per patient after initiation of intravenous immunoglobulin prophylaxis ( P = .0001). A total of 15 of 18 subjects with a history of 1 or more acute systemic capillary leak syndrome episodes experienced no further symptoms while taking intravenous immunoglobulin therapy. Conclusions Intravenous immunoglobulin prophylaxis is associated with a dramatic reduction in the occurrence of systemic capillary leak syndrome attacks in most patients, with minimal side effects. A prospective, randomized trial may be necessary to fully assess the benefits of intravenous immunoglobulin for systemic capillary leak syndrome and to determine the optimal dosage and duration of therapy.
Multidrug resistance–associated proteins (Mrps) are adenosine triphosphate–dependent transporters that efflux chemicals out of cells. In the liver, Mrp2 transports bilirubin‐glucuronide, glutathione ...(GSH), and drug conjugates into bile, whereas Mrp3 and Mrp4 efflux these entities into blood. The purpose of this study was to determine whether oxidative conditions (that is, the disruption of hepatic GSH synthesis) or the administration of nuclear factor‐E2–related factor‐2 (Nrf2) activators (oltipraz and butylated hydroxyanisole) can induce hepatic Mrp transporters and whether that induction is through the Nrf2 transcriptional pathway. Livers from hepatocyte‐specific glutamate‐cysteine ligase catalytic subunit–null mice had increased nuclear Nrf2 levels, marked gene and protein induction of the Nrf2 target gene NAD(P)H:quinone oxidoreductase 1, as well as Mrp2, Mrp3, and Mrp4 expression. The treatment of wild‐type and Nrf2‐null mice with oltipraz and butylated hydroxyanisole demonstrated that the induction of Mrp2, Mrp3, and Mrp4 is Nrf2‐dependent. In Hepa1c1c7 cells treated with the Nrf2 activator tert‐butyl hydroquinone, chromatin immunoprecipitation with Nrf2 antibodies revealed the binding of Nrf2 to antioxidant response elements in the promoter regions of mouse Mrp2 −185 base pairs (bp), Mrp3 (−9919 bp), and Mrp4 (−3767 bp). Conclusion: The activation of the Nrf2 regulatory pathway stimulates the coordinated induction of hepatic Mrps. (HEPATOLOGY 2007.)
Phylogeographic divergence and population genetic diversity within species reflect the impacts of habitat connectivity, demographics, and landscape level processes in both the recent and distant ...past. Characterizing patterns of differentiation across the geographic range of a species provides insight on the roles of organismal and environmental traits in evolutionary divergence and future population persistence. This is particularly true of habitat specialists where habitat availability and resource dependence may result in pronounced genetic structure as well as increased population vulnerability. We use DNA sequence data as well as microsatellite genotypes to estimate range-wide phylogeographic divergence, historical population connectivity, and historical demographics in an endemic habitat specialist, the dunes sagebrush lizard (Sceloporus arenicolus). This species is found exclusively in dune blowouts and patches of open sand within the shinnery oak-sand dune ecosystem of southeastern New Mexico and adjacent Texas. We find evidence of phylogeographic structure consistent with breaks and constrictions in suitable habitat at the range-wide scale. In addition, we find support for a dynamic and variable evolutionary history across the range of S. arenicolus. Populations in the Monahans Sandhills have deeply divergent lineages consistent with long-term demographic stability. In contrast, populations in the Mescalero Sands are not highly differentiated, though we do find evidence of demographic expansion in some regions and relative demographic stability in others. Phylogeographic history and population genetic differentiation in this species has been shaped by the configuration of habitat patches within a geologically complex and historically dynamic landscape. Our findings identify regions as genetically distinctive conservation units as well as underscore the genetic and demographic history of different lineages of S. arenicolus.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
PURPOSEIntra-articular distal radius fractures are common and can be associated with carpal instability. Failure to address articular fragments linked to maintaining carpal stability can lead to ...radiocarpal subluxation or dislocation. The purpose of this study was to evaluate the size of a dorsal osteotomy in the dorsal/volar plane of the lunate facet that leads to dorsal carpal subluxation. METHODSDorsal lunate facet fractures were simulated twice in each of nine fresh-frozen cadavers. After completing a partial dorsal osteotomy in the radial/ulnar plane between the scaphoid and lunate facets, an osteotomy in the dorsal/volar plane was completed. Using a cutting jig, first an estimated 5-mm osteotomy, and then a 10-mm osteotomy (from the dorsal rim of the distal radius) were completed. The wrist was mounted in a custom jig and loaded with 100 N. Displacement of the lunate in the dorsal/volar plane compared with displacement in an intact specimen was evaluated and used to assess carpal subluxation. RESULTSLunate translation was 0 mm ± 0 mm in the intact state. The 5-mm osteotomy averaged 29% of the distal radius dorsal lunate facet in the dorsal/volar plane, and lunate translation was 0.7 mm ± 1.7 mm. The 10-mm osteotomy averaged 54% of the dorsal lunate facet in the dorsal/volar plane, and lunate translation was 2.8 mm ± 2.6 mm. Assuming a linear relationship from the osteotomies created, an osteotomy of an estimated ≥40% of the distal radius in the dorsal to volar plane resulted in substantial dorsal subluxation, although this specific osteotomy was not assessed in our study. CONCLUSIONSSequentially increased dorsal osteotomies of the dorsal lunate facet result in increased dorsal carpal subluxation. CLINICAL RELEVANCEDistal radius fractures that include >40% of the "dorsal critical corner" are at risk for dorsal carpal subluxation and may require supplementary fixation.
Frequent aspirin use has been associated with reduced ovarian cancer risk, but no study has comprehensively assessed for effect modification. We leveraged harmonized, individual-level data from 17 ...studies to examine the association between frequent aspirin use and ovarian cancer risk, overall and across subgroups of women with other ovarian cancer risk factors.
Nine cohort studies from the Ovarian Cancer Cohort Consortium (n = 2,600 cases) and eight case-control studies from the Ovarian Cancer Association Consortium (n = 5,726 cases) were included. We used Cox regression and logistic regression to assess study-specific associations between frequent aspirin use (≥ 6 days/week) and ovarian cancer risk and combined study-specific estimates using random-effects meta-analysis. We conducted analyses within subgroups defined by individual ovarian cancer risk factors (endometriosis, obesity, family history of breast/ovarian cancer, nulliparity, oral contraceptive use, and tubal ligation) and by number of risk factors (0, 1, and ≥ 2).
Overall, frequent aspirin use was associated with a 13% reduction in ovarian cancer risk (95% CI, 6 to 20), with no significant heterogeneity by study design (
= .48) or histotype (
= .60). Although no association was observed among women with endometriosis, consistent risk reductions were observed among all other subgroups defined by ovarian cancer risk factors (relative risks ranging from 0.79 to 0.93, all
-heterogeneity > .05), including women with ≥ 2 risk factors (relative risk, 0.81; 95% CI, 0.73 to 0.90).
This study, the largest to-date on aspirin use and ovarian cancer, provides evidence that frequent aspirin use is associated with lower ovarian cancer risk regardless of the presence of most other ovarian cancer risk factors. Risk reductions were also observed among women with multiple risk factors, providing proof of principle that chemoprevention programs with frequent aspirin use could target higher-risk subgroups.
Aim
Island biotas provide opportunities to study colonization and adaptation to novel environments. Islands, especially near‐shore islands, may have a long record of human habitation such that some ...lineages result from human‐assisted introductions. Here, we combine phylogenetic analyses with fossil data and historical specimen records to reconstruct colonization histories, characterize among‐island divergence and assess the role of humans in shaping the evolutionary history of lizards inhabiting a near‐shore island archipelago.
Location
Channel Islands and adjacent mainland of California, United States.
Taxa
Western fence lizard (Sceloporus occidentalis), southern alligator lizard (Elgaria multicarinata), common side‐blotched lizard (Uta stansburiana).
Methods
We sequenced mitochondrial DNA (ND1, cyt‐b) from each of three lizard species, covering their entire island distributions plus the adjacent mainland. For each, we estimated diversity within and among each island, obtained maximum likelihood bootstrapped phylogenies, constructed haplotype networks and tested for population expansion. We used museum specimen records and microfossil evidence to infer colonization scenarios.
Results
Sceloporus occidentalis is characterized by a single island‐colonization event, and exhibits the deepest divergences from mainland relatives and the highest among‐island divergence. Elgaria multicarinata and Uta stansburiana each have at least three distinct colonization events, with fossil and historical data indicating that some of these occurred after humans arrived to the islands.
Main Conclusions
The evolution of Channel Island lineages for two lizard taxa has been mediated by ancient and contemporary anthropogenic activity, while the evolution of the third is shaped by natural dispersal and vicariance caused by sea‐level rise. Genetic divergence corroborates the treatment of S. occidentalis as an endemic island species, Sceloporus becki. The unique histories of these three taxa are synthesized with other Channel Island lineages highlighting that taxa inhabiting islands with long histories of human activity should be carefully studied to assess the role of people in facilitating colonization and subsequent gene flow.
Objetivo
Las biotas de islas proveen oportunidades para estudiar la colonización y la adaptación a ambientes novedosos. Las islas, en especial aquellas cerca de la costa, pueden tener un largo historial de actividad humana, de tal modo que muchos linajes pueden ser resultado de introducciones asistidas por humanos. En este estudio combinamos análisis filogenéticos con registros fósiles y registros históricos de especímenes en las islas para reconstruir la historia de colonizaciones, caracterizar la divergencia entre las islas, y evaluar el rol de los humanos en amoldar la historia evolutiva de lagartijas que habitan este archipielago.
Localidad
Las Islas Channel, adyacentes a California continental, EEUU.
Taxa
Sceloporus occidentalis, Elgaria multicarinata, y Uta stansburiana.
Métodos
Secuenciamos ADN mitocondrial (ND1 y cyt‐b) de múltiples especímenes de tres especies de lagartijas, y abarcando la totalidad de su distribución en las islas y parte del continente aledaño. Para cada especie, estimamos la diversidad dentro y entre islas, obtuvimos filogenias de máxima verosimilitud, contruimos redes de haplotipos e hicimos pruebas de expansión poblacional. Usamos registros fósiles y registros de museos para inferir distintos escenarios de colonización.
Resultados
Sceloporus occidentalis se caracteriza por tener un solo evento de colonización, y exhibe la mayor divergencia con respecto al continente y también entre las islas. Elgaria multicarinata y Uta stansburiana tienen al menos tres eventos de colonización, y los registros fósiles y de especímenes sugieren que algunos de estos eventos ocurrieron luego de que los humanos llegaran a las islas.
Conclusiones
La evolución de los linajes de las islas Channel para dos de las especies de lagartijas ha sido mediado por actividad antropogénica tanto reciente como antigua, mientras que la evolución de la tercera especie parece ser mediada por eventos naturales y por vicarianza debido a la subida del nivel del mar. La divergencia genética corrobora el tratamiento de S. occidentalis como una especie endémica de las islas Channel, S. becki. Las historias únicas de estas tres especies son contextualizadas con otros linajes de las islas Channel, resaltando que las especies que habitan islas con larga historia de actividad antropogénica deben ser estudiadas minuciosamente para poder evaluar el rol de los humanos en facilitar tanto colonizaciones como flujo génico posterior.
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