BIOE 402. Medical Technology Assessment. 2 or 3 hours. Bioentrepreneur course. Assessment of medical technology in the context of commercialization. Objectives, competition, market share, funding, pricing, manufacturing, growth, and intellectual property; many issues unique to biomedical products. Course Information: 2 undergraduate hours. 3 graduate hours. Prerequisite(s): Junior standing or above and consent of the instructor.

“Bioinformatics” 특집을 내면서

Current global patterns of biodiversity result from processes that operate over both space and time and thus require an integrated macroecological and macroevolutionary perspective. Molecular time trees have advanced our understanding of the tempo and mode of diversification and have identified remarkable adaptive radiations across the tree of life. However, incomplete joint phylogenetic and geographic sampling has limited broad-scale inference. Thus, the relative prevalence of rapid radiations and the importance of their geographic settings in shaping global biodiversity patterns remain unclear. Here we present, analyse and map the first complete dated phylogeny of all 9,993 extant species of birds, a widely studied group showing many unique adaptations. We find that birds have undergone a strong increase in diversification rate from about 50 million years ago to the near present. This acceleration is due to a number of significant rate increases, both within songbirds and within other young and mostly temperate radiations including the waterfowl, gulls and woodpeckers. Importantly, species characterized with very high past diversification rates are interspersed throughout the avian tree and across geographic space. Geographically, the major differences in diversification rates are hemispheric rather than latitudinal, with bird assemblages in Asia, North America and southern South America containing a disproportionate number of species from recent rapid radiations. The contribution of rapidly radiating lineages to both temporal diversification dynamics and spatial distributions of species diversity illustrates the benefits of an inclusive geographical and taxonomical perspective. Overall, whereas constituent clades may exhibit slowdowns, the adaptive zone into which modern birds have diversified since the Cretaceous may still offer opportunities for diversification.

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The global diversity of birds in space and time

To better determine the history of modern birds, we performed a genome-scale phylogenetic analysis of 48 species representing all orders of Neoaves using phylogenomic methods created to handle genome-scale data. We recovered a highly resolved tree that confirms previously controversial sister or close relationships. We identified the first divergence in Neoaves, two groups we named Passerea and Columbea, representing independent lineages of diverse and convergently evolved land and water bird species. Among Passerea, we infer the common ancestor of core landbirds to have been an apex predator and confirm independent gains of vocal learning. Among Columbea, we identify pigeons and flamingoes as belonging to sister clades. Even with whole genomes, some of the earliest branches in Neoaves proved challenging to resolve, which was best explained by massive protein-coding sequence convergence and high levels of incomplete lineage sorting that occurred during a rapid radiation after the Cretaceous-Paleogene mass extinction event about 66 million years ago.

/pdf/whole-genome-analyses-resolve-early-branches-in-the-tree-of-2wufsv5juy.pdf

Whole-genome analyses resolve early branches in the tree of life of modern birds

Although reconstruction of the phylogeny of living birds has progressed tremendously in the last decade, the evolutionary history of Neoaves--a clade that encompasses nearly all living bird species--remains the greatest unresolved challenge in dinosaur systematics. Here we investigate avian phylogeny with an unprecedented scale of data: >390,000 bases of genomic sequence data from each of 198 species of living birds, representing all major avian lineages, and two crocodilian outgroups. Sequence data were collected using anchored hybrid enrichment, yielding 259 nuclear loci with an average length of 1,523 bases for a total data set of over 7.8 × 10(7) bases. Bayesian and maximum likelihood analyses yielded highly supported and nearly identical phylogenetic trees for all major avian lineages. Five major clades form successive sister groups to the rest of Neoaves: (1) a clade including nightjars, other caprimulgiforms, swifts, and hummingbirds; (2) a clade uniting cuckoos, bustards, and turacos with pigeons, mesites, and sandgrouse; (3) cranes and their relatives; (4) a comprehensive waterbird clade, including all diving, wading, and shorebirds; and (5) a comprehensive landbird clade with the enigmatic hoatzin (Opisthocomus hoazin) as the sister group to the rest. Neither of the two main, recently proposed Neoavian clades--Columbea and Passerea--were supported as monophyletic. The results of our divergence time analyses are congruent with the palaeontological record, supporting a major radiation of crown birds in the wake of the Cretaceous-Palaeogene (K-Pg) mass extinction.

A comprehensive phylogeny of birds (Aves) using targeted next-generation DNA sequencing

Modern attempts to produce biogeographic maps focus on the distribution of species, and the maps are typically drawn without phylogenetic considerations. Here, we generate a global map of zoogeographic regions by combining data on the distributions and phylogenetic relationships of 21,037 species of amphibians, birds, and mammals. We identify 20 distinct zoogeographic regions, which are grouped into 11 larger realms. We document the lack of support for several regions previously defined based on distributional data and show that spatial turnover in the phylogenetic composition of vertebrate assemblages is higher in the Southern than in the Northern Hemisphere. We further show that the integration of phylogenetic information provides valuable insight on historical relationships among regions, permitting the identification of evolutionarily unique regions of the world.

https://science.sciencemag.org/content/sci/339/6115/74.full.pdf

An Update of Wallace’s Zoogeographic Regions of the World

Deep avian evolutionary relationships have been difficult to resolve as a result of a putative explosive radiation. Our study examined ∼32 kilobases of aligned nuclear DNA sequences from 19 independent loci for 169 species, representing all major extant groups, and recovered a robust phylogeny from a genome-wide signal supported by multiple analytical methods. We documented well-supported, previously unrecognized interordinal relationships (such as a sister relationship between passerines and parrots) and corroborated previously contentious groupings (such as flamingos and grebes). Our conclusions challenge current classifications and alter our understanding of trait evolution; for example, some diurnal birds evolved from nocturnal ancestors. Our results provide a valuable resource for phylogenetic and comparative studies in birds.

/pdf/a-phylogenomic-study-of-birds-reveals-their-evolutionary-313fuwnxzf.pdf

A Phylogenomic Study of Birds Reveals Their Evolutionary History

Conservation efforts are most effective when we have complete demographic information for a species of concern. Nevertheless, fundamental gaps in our knowledge of demography still exist for many taxa. For passerine birds, the period of time directly after young birds leave the nest and before they disperse and/or migrate (i.e., the post-fledging period) remains an understudied life stage. We reviewed the literature on survival of passerine birds during the post-fledging period to synthesize current knowledge on survival rates and the factors affecting these rates, and conducted a sensitivity analysis to explore the relationship between population growth and post-fledging survival across the range of rates reported in the literature. Fledgling age was a strong predictor of survival, with the highest mortality occurring during the first 3 weeks after birds fledged. Among species, survival ranged from 0.23 to 0.87 during the first 3 weeks post-fledging and increased with adult body mass and nestling period duration. The relatively high proportion (12 of 19; 63%) of studies that detected at least 1 habitat effect on survival indicates that management focused on post-fledging habitat can improve survival. Sensitivity analyses indicated that post-fledging survival rates less than approximately 0.4 require unrealistic overwinter survival rates of juveniles to prevent population decline, unless adult survival rates and seasonal fecundity are high. Post-fledging survival is a useful metric for monitoring passerine populations because it sets the ceiling on first-year survival, responds to habitat management, and leads to more comprehensive demographic models for songbirds. Published 2014. This article is a U.S. Government work and is in the public domain in the USA.

https://www.fs.fed.us/nrs/pubs/jrnl/2014/nrs_2014_cox_001.pdf

Post-fledging survival in passerine birds and the value of post-fledging studies to conservation

Rates of nest predation for birds vary between and within species across multiple spatial scales, but we have a poor understanding of which predators drive such patterns. We video-monitored nests and identified predators at 120 nests of the Acadian Flycatcher (Empidonax virescens) and the Indigo Bunting (Passerina cyanea) at eight study sites in Missouri and Illinois, USA, during 2007–2010. We used an information-theoretic approach to evaluate hypotheses concerning factors affecting predator-specific and overall rates of predation at landscape, edge, and nest-site scales. We found support for effects of landscape forest cover and distance to habitat edge. Predation by Brown-headed Cowbirds (Molothrus ater) increased, and predation by rodents decreased as landscape forest cover decreased. Predation by raptors, rodents, and snakes increased as the distance to forest edges decreased, but the effect was modest and conditional upon the top-ranked model. Despite the predator-specific patterns we detected, there was no support for these effects on overall rates of predation. The interactions between breeding birds, nest predators, and the landscapes in which they reside are scale-dependent and context-specific, and may be resistant to broad conceptual management recommendations.

https://www.nrs.fs.fed.us/pubs/jrnl/2012/nrs_2012_cox_002.pdf

Landscape forest cover and edge effects on songbird nest predation vary by nest predator

Photo and video technology has become increasingly useful in the study of avian nesting ecology. However, researchers interested in using camera systems are often faced with insufficient information on the types and relative advantages of available technologies. We reviewed the literature for studies of nests that used cameras and summarized them based on study objective and the type of technology used. We also designed and tested two video systems that we used for three nest predator and behavioral studies. We found 327 studies that recorded 255 bird species spanning 19 orders. Cameras were most commonly used to study nest predators (n 114), feeding ecology (n 103), and adult behavior (n 81). Most systems (69%) were partially or completely user-built. Systems that recorded in real time ( 25 frames per second), time-lapse ( 25 fps), and still images were all common, though their use tended to vary by study objective. Using the time-lapse digital video recording systems we designed, we monitored 184 nests of 15 different species. We generally found these low-cost systems (US$350–725 per unit) to be reliable. Sources of data loss were variable by study but included digital recorder malfunction, power failure, and video cable damage due to rodents. Our review of the literature and our own experiences suggest that researchers carefully consider their objectives and study systems when choosing camera technology. To facilitate selection of the appropriate system, we describe general video system design and offer recommendations for researchers based on commercially available system components.

/pdf/development-of-camera-technology-for-monitoring-nests-50p551eby1.pdf

Development of camera technology for monitoring nests

. Understanding how weather influences survival and reproduction is an important component of forecasting how climate change will influence wildlife population viability. Nest predation is the primary source of reproductive failure for passerine birds and can change in response to temperature. However, it is unclear which predator species are responsible for such patterns because predation events are rarely observed. We investigated whether temperature influenced predator-specific rates of nest predation by analyzing data from six prior studies conducted between 1997 and 2010 in Texas, Illinois, and Missouri that used constant-surveillance video systems to identify predators at the nests of Golden-cheeked Warblers (Setophaga chrysoparia), Blackcapped Vireos (Vireo atricapilla), Indigo Buntings (Passerina cyanea), and Acadian Flycatchers (Empidonax virescens). Rates of nest predation by snakes and birds increased as daily maximum temperatures increased, whereas predation by mammals was essentially ...

https://www.fs.fed.us/nrs/pubs/jrnl/2013/nrs_2013_cox_002.pdf

W. Andrew Cox

Papers

A Phylogenomic Study of Birds Reveals Their Evolutionary History

Post-fledging survival in passerine birds and the value of post-fledging studies to conservation

Landscape forest cover and edge effects on songbird nest predation vary by nest predator

Development of camera technology for monitoring nests

The Effects of Temperature on Nest Predation by Mammals, Birds, and Snakes