437 research outputs found
A phylogenomic perspective on the radiation of ray-finned fishes based upon targeted sequencing of ultraconserved elements
Ray-finned fishes constitute the dominant radiation of vertebrates with over
30,000 species. Although molecular phylogenetics has begun to disentangle major
evolutionary relationships within this vast section of the Tree of Life, there
is no widely available approach for efficiently collecting phylogenomic data
within fishes, leaving much of the enormous potential of massively parallel
sequencing technologies for resolving major radiations in ray-finned fishes
unrealized. Here, we provide a genomic perspective on longstanding questions
regarding the diversification of major groups of ray-finned fishes through
targeted enrichment of ultraconserved nuclear DNA elements (UCEs) and their
flanking sequence. Our workflow efficiently and economically generates data
sets that are orders of magnitude larger than those produced by traditional
approaches and is well-suited to working with museum specimens. Analysis of the
UCE data set recovers a well-supported phylogeny at both shallow and deep
time-scales that supports a monophyletic relationship between Amia and
Lepisosteus (Holostei) and reveals elopomorphs and then osteoglossomorphs to be
the earliest diverging teleost lineages. Divergence time estimation based upon
14 fossil calibrations reveals that crown teleosts appeared ~270 Ma at the end
of the Permian and that elopomorphs, osteoglossomorphs, ostarioclupeomorphs,
and euteleosts diverged from one another by 205 Ma during the Triassic. Our
approach additionally reveals that sequence capture of UCE regions and their
flanking sequence offers enormous potential for resolving phylogenetic
relationships within ray-finned fishes
Target enrichment of ultraconserved elements from arthropods provides a genomic perspective on relationships among Hymenoptera
Gaining a genomic perspective on phylogeny requires the collection of data
from many putatively independent loci collected across the genome. Among
insects, an increasingly common approach to collecting this class of data
involves transcriptome sequencing, because few insects have high-quality genome
sequences available; assembling new genomes remains a limiting factor; the
transcribed portion of the genome is a reasonable, reduced subset of the genome
to target; and the data collected from transcribed portions of the genome are
similar in composition to the types of data with which biologists have
traditionally worked (e.g., exons). However, molecular techniques requiring RNA
as a template are limited to using very high quality source materials, which
are often unavailable from a large proportion of biologically important insect
samples. Recent research suggests that DNA-based target enrichment of conserved
genomic elements offers another path to collecting phylogenomic data across
insect taxa, provided that conserved elements are present in and can be
collected from insect genomes. Here, we identify a large set (n1510) of
ultraconserved elements (UCE) shared among the insect order Hymenoptera. We use
in silico analyses to show that these loci accurately reconstruct relationships
among genome-enabled Hymenoptera, and we design a set of baits for enriching
these loci that researchers can use with DNA templates extracted from a variety
of sources. We use our UCE bait set to enrich an average of 721 UCE loci from
30 hymenopteran taxa, and we use these UCE loci to reconstruct phylogenetic
relationships spanning very old (220 MYA) to very young (1 MYA)
divergences among hymenopteran lineages. In contrast to a recent study
addressing hymenopteran phylogeny using transcriptome data, we found ants to be
sister to all remaining aculeate lineages with complete support
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
Ultraconserved elements (UCEs) illuminate the population genomics of a recent, high-latitude avian speciation event
Using a large, consistent set of loci shared by descent (orthologous) to study relationships among taxa would revolutionize among-lineage comparisons of divergence and speciation processes. Ultraconserved elements (UCEs), highly conserved regions of the genome, offer such genomic markers. The utility of UCEs for deep phylogenetics is clearly established and there are mature analytical frameworks available, but fewer studies apply UCEs to recent evolutionary events, creating a need for additional example datasets and analytical approaches. We used UCEs to study population genomics in snow and McKayβs buntings (Plectrophenax nivalis and P. hyperboreus). Prior work suggested divergence of these sister species during the last glacial maximum (βΌ18β74 Kya). With a sequencing depth of βΌ30Γ from four individuals of each species, we used a series of analysis tools to genotype both alleles, obtaining a complete dataset of 2,635 variable loci (βΌ3.6 single nucleotide polymorphisms/locus) and 796 invariable loci. We found no fixed allelic differences between the lineages, and few loci had large allele frequency differences. Nevertheless, individuals were 100% diagnosable to species, and the two taxa were different genetically (FST = 0.034; P = 0.03). The demographic model best fitting the data was one of divergence with gene flow. Estimates of demographic parameters differed from published mtDNA research, with UCE data suggesting lower effective population sizes (βΌ92,500β240,500 individuals), a deeper divergence time (βΌ241,000 years), and lower gene flow (2.8β5.2 individuals per generation). Our methods provide a framework for future population studies using UCEs, and our results provide additional evidence that UCEs are useful for answering questions at shallow evolutionary depths
Using Microsatellite DNA to Understand Bobwhite Behavior and Population Structure (Post Abstract)
Northern bobwhite (Colinus virginianus) have a flexible mating system with varying degrees of parental investment in offspring. Questions of relatedness of mates and the dynamics of covey membership have not been answered. It is not known how different patterns of mating systems impact productivity of bobwhite populations. In addition to behaviors, the genetic structure of bobwhite populations likely varies across landscapes, and may depend on the distribution and abundance of habitat types. These issues have critical conservation and management implications, such as the impact of habitat fragmentation on gene flow. Recent advances in molecular techniques provide an opportunity to investigate these questions through examination of small, repetitive, highly variable regions of DNA known as microsatellites. Microsatellites provide the fine-scale resolution needed to objectively understand certain population structures and reproductive strategies. Microsatellite analysis techniques have been used successfully to research relatedness and extra-pair paternity of a number of species. Therefore, we have begun to investigate the genetic basis for many northern bobwhite behaviors related to reproduction. Our primary objectives are to determine: (1) relatedness of individuals within coveys and groups over time, (2) relatedness between reproductive pairs relative to random pairings, (3) relatedness of chicks in broods, (4) rates of extrapair fertilization, (5) rates of intra-specific nest parasitism, and (6) the relatedness of incubating birds to their eggs. To do so, we have developed a series of microsatellite markers for northern bobwhites. We radiomarked approximately 75% of bobwhites on our study area at Tall Timbers Research Station. We collected body feathers from adults and 1.5 mm patagial micro-biopsies from each chick (4 days old) found brooding with radiomarked adults for microsatellite analysis. We are determining relatedness and parentage, based on these microsatellite data, using programs RELATEDNESS and CERVUS. Additionally, we are testing our tissue collection techniques on a pen-reared population of bobwhites to determine the efficiency of DNA amplification via the polymerase chain reaction for 4 tissue collection techniques: patagial micro-biopsy, down and feather shaft, egg tooth, and egg membrane. Additionally, we are pairing pen-reared adult hens and males for different periods of time to determine the presence of sperm storage and test for evidence of sperm competition. Further, we are crossing individuals of known relatedness over several generations to test the accuracy of paternity inferences calculated by CERVUS with respect to bobwhite microsatellite data. Finally, by collecting feathers from hunterkilled bobwhites throughout the Red Hills and the southeast, we will compare the genetic structure of the bobwhite population(s) of the Red Hills, likely the last panmictic population in the southeast, to more isolated, declining populations. In our poster we present a detailed description of this research along with first year results
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