485 research outputs found
A phylogeny of birds based on over 1,500 loci collected by target enrichment and high-throughput sequencing
Evolutionary relationships among birds in Neoaves, the clade comprising the
vast majority of avian diversity, have vexed systematists due to the ancient,
rapid radiation of numerous lineages. We applied a new phylogenomic approach to
resolve relationships in Neoaves using target enrichment (sequence capture) and
high-throughput sequencing of ultraconserved elements (UCEs) in avian genomes.
We collected sequence data from UCE loci for 32 members of Neoaves and one
outgroup (chicken) and analyzed data sets that differed in their amount of
missing data. An alignment of 1,541 loci that allowed missing data was 87%
complete and resulted in a highly resolved phylogeny with broad agreement
between the Bayesian and maximum-likelihood (ML) trees. Although results from
the 100% complete matrix of 416 UCE loci were similar, the Bayesian and ML
trees differed to a greater extent in this analysis, suggesting that increasing
from 416 to 1,541 loci led to increased stability and resolution of the tree.
Novel results of our study include surprisingly close relationships between
phenotypically divergent bird families, such as tropicbirds (Phaethontidae) and
the sunbittern (Eurypygidae) as well as between bustards (Otididae) and turacos
(Musophagidae). This phylogeny bolsters support for monophyletic waterbird and
landbird clades and also strongly supports controversial results from previous
studies, including the sister relationship between passerines and parrots and
the non-monophyly of raptorial birds in the hawk and falcon families. Although
significant challenges remain to fully resolving some of the deep relationships
in Neoaves, especially among lineages outside the waterbirds and landbirds,
this study suggests that increased data will yield an increasingly resolved
avian phylogeny.Comment: 30 pages, 1 table, 4 figures, 1 supplementary table, 3 supplementary
figure
Inferring Species Trees Directly from Biallelic Genetic Markers: Bypassing Gene Trees in a Full Coalescent Analysis
The multi-species coalescent provides an elegant theoretical framework for
estimating species trees and species demographics from genetic markers.
Practical applications of the multi-species coalescent model are, however,
limited by the need to integrate or sample over all gene trees possible for
each genetic marker. Here we describe a polynomial-time algorithm that computes
the likelihood of a species tree directly from the markers under a finite-sites
model of mutation, effectively integrating over all possible gene trees. The
method applies to independent (unlinked) biallelic markers such as well-spaced
single nucleotide polymorphisms (SNPs), and we have implemented it in SNAPP, a
Markov chain Monte-Carlo sampler for inferring species trees, divergence dates,
and population sizes. We report results from simulation experiments and from an
analysis of 1997 amplified fragment length polymorphism (AFLP) loci in 69
individuals sampled from six species of {\em Ourisia} (New Zealand native
foxglove)
Racial and Socioeconomic Disparities in Melanoma Incidence Rates in Georgia: 2000-2011
Background: The objective of this research was to investigate melanoma incidence rates and health outcomes in Georgia over time and by race, socio-economic status (SES), and gender.
Methods: Age-adjusted melanoma incidence rates were obtained from the Georgia Comprehensive Cancer Registry SEER*Stat Database (2000-2011). To compare incidence rates across counties, and public health districts and by race, SES and gender, maps were generated using Geographic Information Systems (GIS). A cluster analysis was performed by use of SaTScan, and maps were created to visualize clusters of melanoma cases.
Results: In Georgia, from 2000-2011, age-adjusted incidence rates for melanoma were higher among Whites than Blacks (28.0 vs. 1.1 per 100,000 population). For both races, high rates were found to be associated with high SES. For Whites, high rates were concentrated in urban areas relative to Blacks in rural areas. Clusters of melanoma incident cases were found mainly in the north central region of Georgia.
Conclusions: For Georgia, results for map comparisons are consistent with previous research findings that higher melanoma incidence rates are associated with high SES for Whites and, to a lesser extent, for Blacks. Melanoma interventions in Georgia should focus on urban White and rural Black at-risk populations, especially those with high SES
Tuberculosis before and after the Black Death (1346 – 1353 CE) in the Hospital of St John the Evangelist in Cambridge, England
This article was published with Open Access under the Elsevier/Jisc Open Access agreement The authors would like to thank all of the members of the ‘After the Plague’ project, and the Cambridge Archaeological Unit for their help and support. We would also like to thank György Pálfi for organising the ICEPT-3 conference, at which the initial findings of this research were presented and for inviting us to contribute to this special issue. This research was funded by the Wellcome Trust (Award no 2000368/Z/15/Z) and St John's College, Cambridge.Peer reviewedPublisher PD
Ultraconserved elements are novel phylogenomic markers that resolve placental mammal phylogeny when combined with species-tree analysis
Phylogenomics offers the potential to fully resolve the Tree of Life, but increasing genomic coverage also reveals conflicting evolutionary histories among genes, demanding new analytical strategies for elucidating a single history of life. Here, we outline a phylogenomic approach using a novel class of phylogenetic markers derived from ultraconserved elements and flanking DNA. Using species-tree analysis that accounts for discord among hundreds of independent loci, we show that this class of marker is useful for recovering deep-level phylogeny in placental mammals. In broad outline, our phylogeny agrees with recent phylogenomic studies of mammals, including several formerly controversial relationships. Our results also inform two outstanding questions in placental mammal phylogeny involving rapid speciation, where species-tree methods are particularly needed. Contrary to most phylogenomic studies, our study supports a first-diverging placental mammal lineage that includes elephants and tenrecs (Afrotheria). The level of conflict among gene histories is consistent with this basal divergence occurring in or near a phylogenetic \u27\u27anomaly zone\u27\u27 where a failure to account for coalescent stochasticity will mislead phylogenetic inference. Addressing a long-standing phylogenetic mystery, we find some support from a high genomic coverage data set for a traditional placement of bats (Chiroptera) sister to a clade containing Perissodactyla, Cetartiodactyla, and Carnivora, and not nested within the latter clade, as has been suggested recently, although other results were conflicting. One of the most remarkable findings of our study is that ultraconserved elements and their flanking DNA are a rich source of phylogenetic information with strong potential for application across Amniotes. © 2012 by Cold Spring Harbor Laboratory Press
Ultraconserved elements anchor thousands of genetic markers spanning multiple evolutionary timescales
Although massively parallel sequencing has facilitated large-scale DNA sequencing, comparisons among distantly related species rely upon small portions of the genome that are easily aligned. Methods are needed to efficiently obtain comparable DNA fragments prior to massively parallel sequencing, particularly for biologists working with non-model organisms. We introduce a new class of molecular marker, anchored by ultraconserved genomic elements (UCEs), that universally enable target enrichment and sequencing of thousands of orthologous loci across species separated by hundreds of millions of years of evolution. Our analyses here focus on use of UCE markers in Amniota because UCEs and phylogenetic relationships are well-known in some amniotes. We perform an in silico experiment to demonstrate that sequence flanking 2030 UCEs contains information sufficient to enable unambiguous recovery of the established primate phylogeny. We extend this experiment by performing an in vitro enrichment of 2386 UCE-anchored loci from nine, non-model avian species. We then use alignments of 854 of these loci to unambiguously recover the established evolutionary relationships within and among three ancient bird lineages. Because many organismal lineages have UCEs, this type of genetic marker and the analytical framework we outline can be applied across the tree of life, potentially reshaping our understanding of phylogeny at many taxonomic levels. © The Author(s) 2012. Published by Oxford University Press, on behalf of the Society of Systematic Biologists. All rights reserved
- …