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IMEG SEMINARS
Spring 2008
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| Previous IMEG
Seminars and Abstracts: |
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Date |
Speaker |
| 01/16/08 |
Speaker:
Dr. Ilana Baums -
Department of Biology
Title:
Comparative genomics in
non-model organisms: the role of dispersal in the ecology and
evolution of reef corals
Abstract: Our
view of the role of dispersal in the ecology and evolution of reef
corals has changed dramatically over the last decade due in part to
advances in molecular genetics. It was previously thought that
dispersal of floating propagules (larvae) via ocean currents would
routinely connect even distant populations (1000s of km). New
molecular markers contradict this notion: most ecologically relevant
dispersal occurs over shorter distances. In the Caribbean,
bio-physical models emphasize the importance of the timing of larval
release with respect to the occurrence of transient oceanographic
features in determining scales of larval dispersal. We identified one
such oceanographic feature, an eddy that develops over the summer
months in the Mona Passage as a potential barrier to larval dispersal.
Though narrow (113 km wide), the Mona Passage divides Caribbean coral
populations into an eastern and western province (Baums et al.2005).
Within each province, patterns of fragmentation (a form of asexual
reproduction) indicate that certain genets may outcompete others
locally (<< 1km) and led us to hypothesize that fine-scale
site-adaptation exists in these corals (Baums et al. 2006). The
biology of the animal precludes the use of traditional transplantation
experiments and quantitative genetic methods to further test this
hypothesis. Instead, we are taking a comparative transcriptome
approach (Toth et al. 2007). Challenges include frequent
hybridization among coral species and a dearth of genomic data for
related organisms (but see Putnam et al. 2007). The finding of
site-adaptation in corals with planktonic larvae would have important
consequences for the restoration of coral reefs, indicating that
careful matching of propagules to transplantation sites is necessary.
References:Baums
IB, Miller MW, Hellberg ME (2005) Regionally isolated populations of
an imperiled Caribbean coral, Acropora palmata. Molecular Ecology 14,
1377-1390.
Baums IB, Miller MW, Hellberg ME (2006) Geographic variation in clonal
structure in a reef building Caribbean coral, Acropora palmata.
Ecological Monographs 76, 503-519.
Putnam NH, Srivastava M, Hellsten U, et al. (2007) Sea anemone genome
reveals ancestral eumetazoan gene repertoire and genomic organization.
Science 317, 86-94.
Toth AL, Varala K, Newman TC, et al. (2007) Wasp Gene Expression
Supports an
Evolutionary Link Between Maternal Behavior and Eusociality. Science,
1146647. |
| 01/23/08 |
Speaker:
Xiaofan Zhou - Department
of Biology
Title:
Phylogenetic Analyses of Two
Histone Demethylase Gene Families
Abstract: Histone
methylation has been recognized as an important way to regulate
chromatin structure and gene expression in eukaryotes for a long time.
However, not until the identification of two families of histone
demethylase, the KDM1 (previously known as LSD1) and JmjC-domain
containing proteins in recent years, this modification was found to be
reversible. These two families of proteins have different functional
domains and different substrate specificities. Whereas increasing
number of new members are proved to have histone demethylase activity,
only limited is known about the origin and evolution history of these
two families. In this study, we collected KDM1-like and JmjC-domain
containing proteins in both eukaryotes and prokaryotes, and performed
systematic phylogenetic analyses. Our results indicate two distinct
patterns of evolution; the KDM1-like histone demethylase originated
through acquiring a SWIRM domain in the common ancestor of eukaryotes,
and then experienced limited expansion in plants while maintained two
copies in most animals except for insects which lost one. The JmjC-domain
containing proteins can be divided into more than ten subfamilies, and
each has different domain architecture and substrate specificity. At
least seven subfamilies have already existed before the divergence of
eukaryotes, and then most subfamilies were expanded through gene
duplication. Our work also provides reference for the further
functional studies on histone demethylase.
References:
Shi Y, Whetstine JR. (2007).
“Dynamic regulation of histone lysine methylation by demethylases.”
Mol Cell. 25(1):1-14.
Klose RJ, Kallin EM, Zhang Y (2006). “JmjC-domain-containing proteins
and histone demethylation.” Nat Rev Genet. 7(9):715-27. |
| 01/30/08 |
Speaker:
Dr. Hiroki Goto,
Lei Peng, and Kateryna D. Makova - Department of Biology and
Center for Comparative Genomics and Bioinformatics
Title:
Evolution of X-degenerate Y
chromosome genes in greater apes: Conservation of gene content in
human and gorilla, but not chimpanzee
Abstract: Compared
with the X chromosome, the human Y chromosome is considerably
diminished in size and has lost most of its functional genes, leading
to predictions that it might become extinct within only a few million
years. Although several population genetic models explaining Y
chromosome degeneration have been proposed, their relative importance
for the evolution of this chromosome in apes remains puzzling.
Interestingly, for the X-degenerate region on the Y chromosome, human
retained all 16 genes, while chimpanzee lost 4 of the 16 genes since
the divergence of the two species. To uncover the evolutionary forces
governing ape Y chromosome degeneration, we determined the complete
sequences of the coding exons and their splice sites for 16 gorilla Y
chromosome genes located in the X-degenerate region. We discovered
that all studied reading frames and splice sites were intact and thus,
this genomic region experienced no gene loss in the gorilla lineage
after its divergence from the human-chimpanzee-gorilla common
ancestor. Higher nucleotide divergence was observed in the chimpanzee
than human lineage and this difference was more pronounced for the
genes with disruptive mutations, suggesting a lack of functional
constraints for these genes in chimpanzee. Surprisingly, our results
indicate that the human and gorilla orthologs of the genes disrupted
in chimpanzee evolve under relaxed functional constraints and might
not be essential for all apes. Taking mating patterns and effective
population sizes of human, chimpanzee, and gorilla into account, we
concluded that genetic hitchhiking associated with positive selection
due to sperm competition might explain a rapid decline in the Y
chromosome gene number in chimpanzee. Since we found no evidence of
positive selection acting on the X-degenerate genes, such selection
likely targets other genes on the chimpanzee Y chromosome.
References: Hughes JF et al. (2005)
Conservation of Y-linked genes during human evolution revealed by
comparative sequencing in chimpanzee. Nature 437:100-103.
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| 02/06/08 |
Speaker:
Jill Duarte - Department of
Biology
Title:
Phylogenetic Utility of
Conserved Single Copy Nuclear Genes in Flowering Plants
Abstract:
Given the prevalence of gene
duplication in flowering plants, the presence of approximately 600
widely conserved single copy genes in flowering plants is a surprising
observation. In this talk, I will focus on one aspect of our current
research on these fascinating components of the plant genome, namely,
their potential utility as protein-coding nuclear genes that can be
used as novel phylogenetic markers. Using the PlantTribes database (http://fgpdev.huck.psu.edu/tribe.pl),
we have identified proteins that are single copy in two or more
genomes. To investigate the phylogenetic utility of these genes, we
have selected approximately twenty genes that have good representation
in EST databases. To study how they perform as phylogenetic markers,
we have used them in a series of phylogenetic analyses at various
taxanomic levels: Brassicaceae, basal angiosperms, and seed plants.
The results from these studies indicates that although duplications of
these genes can persist in some lineages, a single expressed copy is
typical and these genes contain a sufficient amount of phylogenetic
signal, in spite of typically short coding sequences.
References:
Sang, T. 2002. Utility of
low-copy nuclear gene sequences in plant phylogenetics. Critical
Reviews in Biochemistry and Molecular Biology 37:121-147.
Small, R. L., R. C. Cronn,
and J. F. Wendel. 2004. Use of nuclear genes for phylogeny
reconstruction in plants. Australian Systematic Botany 17:145-170.
Soltis, D. E., and P. S.
Soltis. 1998. Choosing an approach and an appropriate gene for
phylogenetic analysis. Pp. 1-42 in D. E. Soltis, P. S. Soltis,
and J. J. Doyle, eds. Molecular systematics of
Plants II. DNA Sequencing. Kluwer Academic
Publishers, Boston.
Strand, A. E., J. Leebens-Mack,
and B. G. Milligan. 1997. Nuclear DNA-based markers for plant
evolutionary biology. Molecular Ecology 6:113-118.
Wall, P. K., Leebens-Mack,
J., Muller, K. F., Field, D., Altman, N. S., and dePamphilis, C. W.
2008. PlantTribes: a gene and gene family resource for comparative
genomics in plants. Nucleic Acids
Research, 36: D970-6.
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02/13/08 |
Speaker:
Dr. Beth
Shapiro - Department of Biology
Title:
Investigating extinction
using ancient DNA
Abstract:
The recent advent of ancient
DNA (aDNA) techniques makes it possible to directly observe
evolutionary and population genetic changes in species and communities
through time. DNA extracted from hair, teeth and bones of animal
remains, as well as directly from soil cores, can be used to
reconstruct changes in population size and structure potentially as
far back as the most recent common ancestor of the sampled sequences.
While significant limitations to the technique remain, for example the
potential for DNA damage and modern contamination to interfere with
experiments and confound phylogenetic analysis, and the almost
complete reliance on mitochondrial DNA markers due to the low-copy
number of nuclear DNA, aDNA has shown significant promise as a method
for examining molecular evolutionary processes in populations. I will
discuss the application of aDNA techniques to investigating the cause
of the megafaunal mass extinction that occurred at the Pleistocene/
Holocene boundary (ca 10 thousand years ago; ka BP). I will describe
the use of maximum likelihood and Bayesian techniques for
reconstructing population history for five large mammals that were
once abundant in the Siberian and North American arctic: bison (Bison
priscus), horses (Equus caballus), cave lions (Panthera
spelea), brown bears (Ursus arctos) and mammoths (Mammuthus
primigenius). Our results indicate that climate change, rather
than over-hunting by humans, was the driving force behind the
extinction events, with significant losses of genetic diversity in all
of these species beginning just prior to the onset of glacial
conditions, ca. 25-30 ka BP. We also demonstrate multiple, distinct
periods of population turnover over the most recent 60 ka BP,
suggesting repeated periods of local extinctions and replacements,
large-scale migration between regions and transient barriers to gene
flow. These results demonstrate the power of serially sampled data
from measurably evolving populations to uncover significantly
different demographic scenarios than it is possible to observe with
modern data alone.
References:
Barnes I, Shapiro B,
Kuznetsova T, Sher A, Guthrie D, Lister A, Thomas MG. Genetic
structure and extinction of the woolly mammoth Mammuthus primigenius
(Blum.). Current Biology 17: 1072-1075 (2007).
Drummond AJ, Pybus OG, Shapiro B, Rambaut A. Bayesian coalescent
inference of past population dynamics from molecular sequences.
Molecular Biology and Evolution 22: 1185-1192 (2005).
Shapiro B, Drummond AJ, Rambaut A, Wilson MC, Matheus P, Sher AV,
Pybus OG, Gilbert MTP, Barnes I, Binladen J, Willerslev E, Hansen A,
Baryshnikov GF, Burns JA, Davydov S, Driver JC, Froese D, Harington
CR, Keddie G, Kosintsev P, Kunz ML, Martin LD, Stephenson RO, Storer
J, Tedford R, Zimov S, Cooper A. Rise and fall of the Beringian steppe
bison. Science 306: 1561-1565 (2004).
Hofreiter M, Serre D, Poinar HN, Kuch M, Paabo S. Ancient DNA. Nature
Reviews Genetics 2: 353-359. |
| 02/20/08 |
Speaker:
Dr. Steve
Schaeffer - Department of Biology
Title: Chromosomal
Rearrangements inferred from the 12 Drosophila Genomes Project
Abstract: Comparative genomics offers an
unprecedented opportunity to examine how gene order evolves on
chromosomes and its significance. The recent completion of 12
Drosophila genomes has been used to develop computational methods
for assembling eukaryotic genomes and to test these scaffold
assemblies using the polytene chromosomal maps. I will discuss how
the assembly scaffolds from the 11 non-D. melanogaster
genomes were anchored to the polytene maps with computational and
physical mapping approaches. These maps were a critical first step in
the examination of gene order evolution.
Gene order data among the divergent Drosophila
species was analyzed with a variety of graphical and statistical
approaches. Comparison of syntenic blocks across this large genomic
dataset confirms that genetic elements are largely (95%) localized to
the same Muller element across genus Drosophila species and
paracentric inversions serve as the dominant mechanism for shuffling
the order of genes along a chromosome. Gene order scrambling between
species is in accordance with the estimated evolutionary distances
between them and we find it to approximate an exponential process over
time (linear with alternate divergence rates). Our results provide
estimated chromosomal evolution rates across this set of species based
on whole-genome synteny analysis, which are found to be higher than
those previously reported. Analysis of conserved syntenic blocks
across these genomes suggests clustering based on various criteria,
including function and various patterns of embryonic expression
correlation in D. melanogaster. On the other hand, an analysis
of the disruption of syntenic blocks between species allowed the
identification of fixed inversion breakpoints and estimates of
breakpoint re-usage.
References:
Drosophila 12 Genomes Consortium.
2007. Evolution of genes and genomes on the Drosophila
phylogeny. Nature 450:203-218. |
| 02/27/08 |
Speaker:
Dr. George
Zhang - Department of Ecology and Evolutionary Biology, University of
Michigan
Title: Metabolic
network analysis for understanding
evolution
Abstract: "I
plan to present the results from two studies that both utilize the
flux balance analysis (FBA) of metabolic networks. The first is about
functional redundancy of metabolic reactions and its evolutionary
maintenance. The second is about the biological basis of epistasis.
The two studies have not been published, but below are brief
summaries. "
On metabolic redundancy
Cellular life is a highly redundant complex
system, yet the evolutionary maintenance of the redundancy remains
unexplained. We infer that 37-47% of metabolic reactions in E. coli
and yeast can be individually removed without blocking the production
of any biomass component under any nutritional condition. However,
the majority of these redundant reactions are preserved, because they
have differential maximal efficiencies at different conditions or
their loss causes a fitness reduction that can only be recovered via
evolution. The remaining redundancies are attributable to pleiotropic
effects or recent horizontal gene transfers. Thus, redundant
reactions need not be kept as backups and the genetic robustness of
metabolic networks is likely an evolutionary byproduct.
On epistasis
Epistasis, a term coined by Bateson nearly 100
years ago, refers to the phenomenon that the effect of a gene on a
trait is masked or enhanced by one or more other genes. Fisher soon
extended the concept to mean non-independent or non-multiplicative
effects of genes. The direction, magnitude, and prevalence of
epistasis is important for understanding gene function and
interaction, speciation, evolution of sex and recombination, evolution
of ploidy, mutation load, genetic buffering, human disease, and
drug-drug interaction. Although high-throughput epistasis data from
model organisms are being generated and used to construct genetic
networks, to what extent epistasis reflects functional intimacy of
involved genes is unclear. We here address this question in the
Escherichia coli metabolic network, where both epistasis and
functional relationships of biochemical reactions can be evaluated
through systemic analysis. We found that negative or synergistic
epistasis in fitness occurs mainly between nonessential reactions with
overlapping functions, whereas positive or antagonistic epistasis
usually involves essential reactions, is highly abundant, and
surprisingly, often occurs between reactions without overlapping
functions. These observations, together with theoretical
considerations of their causes, require the distinction of the concept
of genetic interaction from non-multiplicative gene effects and
necessitate reconsideration of evolutionary theories that depend on
prevalent negative epistasis."
References:
Price ND,
Reed JL,
Palsson BŘ. Nat Rev Microbiol.
2004 Nov; 2(11):886-97. Genome-scale models of microbial cells:
evaluating the consequences of constraints. |
|
03/05/08
|
Speaker:
Solny
Adalsteinsson - Department of Biology
Title: Molecular
Phylogenetics and Biogeography of the Snake Family Leptotyphlopidae
Abstract:
The threadsnakes (Leptotyphlopidae)
comprise one of the last major groups of terrestrial vertebrates for
which essentially nothing is known of its evolutionary history, from
molecules or morphology. They include the world’s smallest snakes
and occur mainly in South America, Africa, and southwest Asia. The
family consists of two genera and 104 species. These are burrowing
snakes that have no fossil record and greatly reduced scale features,
making even morphological analysis difficult. Most are about the
diameter and shape of a spaghetti noodle and many of the species are
known from only one or a few specimens. We were fortunate to assemble
a relatively large collection of tissue samples for molecular analysis
(mitochondrial and nuclear gene sequences), and the results will be
presented. They reveal some unexpected geographic patterns and a
surprisingly large number of cryptic species.
Reference:
Vidal, N., A. Azvolinsky, C.
Cruaud, and S. B. Hedges. 2008. Origin of tropical American burrowing
reptiles by transatlantic rafting. Biology Letters
4:115-118.
|
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03/12/08
|
SPRING BREAK NO IMEG SEMINAR
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| 03/19/08 |
Speaker:
Melissa Wilson
- Department of Biology
Title: Evolution
and Survival on Eutherian Sex Chromosomes
Abstract: Since
the two eutherian sex chromosomes diverged from an ancestral
autosomal pair, the X has remained relatively gene-rich, while the Y
lost most of its genes through the accumulation of deleterious
mutations in nonrecombining regions. Presently, it is unclear when
the sex chromosomes acquired their unique evolutionary rates, what
is distinctive about the genes remaining on the Y chromosome, and
whether X-Y gene divergence paralleled that of paralogs located on
autosomes. To tackle these questions, here we juxtaposed the
evolution of nine X and Y homologous genes (gametologs) in human and
mouse with their autosomal orthologs in opossum and platypus. We
discovered that genes on the X and Y acquired distinct evolutionary
rates immediately following the suppression of recombination between
the two sex chromosomes. The Y-linked genes evolved at higher rates,
while the X-linked genes maintained the lower evolutionary rates of
the ancestral autosomal genes. We further established that,
surprisingly, the surviving gametologs had less radical and fewer
overall amino acid changes than did autosomal paralogs. Curiously,
in contrast to expectations, most Y gametologs evolved under
stronger purifying selection than the quickly evolving copies of
autosomal duplicate pairs. Finally, after evaluating expression and
functional laboratory experiments, we concluded that, to be retained
on both the X and the Y, gametologs evolved unique mRNA and protein
expression patterns as well as separate functions.
Reference:
Wyckoff, G. J., Li, J.,
and C. Wu. 2002. Molecular evolution of functional genes on the
mammalian Y chromosome. Mol. Biol. Evol. 19(9)1633-1636.
|
| 03/26/08 |
Speaker:
Yan Zhang -
Department of Biology
Title:
Striking
convergence of plastid genome in independent nonphotosynthetic
lineages
Abstract:
Parasitic plants are
valuable models for studying genes and genome evolution. Under relaxed
functional constraint, the plastid genomes of some parasitic plants
have undergone great reduction in gene content and exhibited
accelerated rates of evolution for the remaining genes. For example,
the fully sequenced plastid genome of the nonphotosynthetic plant
Epifagus virginiana (Orobanchaceae) displays extreme genome
reduction; it lacks functional copies of all photosynthetic and ndh
genes, all four RNA polymerase genes, nearly half of the tRNA genes,
and one third of the ribosomal protein genes. Accelerated evolution is
observed in Epifagus. Recent complete sequences of the plastid
genome of Cuscuta, an independent lineage of parasitic plant,
reveal plastid genomes distinctly different from Epifagus, but
species of this group retain a minimal photosynthetic ability. To
understand whether genome evolution is similar in other independent
lineages of nonphotosynthetic plants, the plastid genome of
Pholisma arenarium (Lennoaceae/Boraginaceae) has been fully
sequenced.. The plastid genomes of Ehretia acuminata (Boraginaceae),
a photosynthetic relative of Pholisma, and Mimulus guttatus
(Phrymaceae), a photosynthetic relative of Epifagus, were
also sequenced. The plastid genome of Pholisma shows a
pattern of gene loss that is strikingly similar to that observed in
Epifagus. All of the photosynthetic genes (with the notable
exception of rbcL and psaI) and ndh genes are
lost, as are the RNA polymerase genes and some components of the
translation apparatus. The gene losses in Pholisma are a
perfect subset of those observed in Epifagus, and the remaining
genes are also evolving at accelerated rates, but not as accelerated
as Epifagus. The results indicate parallel evolution of the two
independent lineages of nonphotosynthetic plants and also suggest that
photosynthesis has been lost more recently in the lineage including
Pholisma.
References:
Barkman, T.J., J.R. McNeal,
S.H. Lim, G. Coat, H.B. Croom, N. Young, and C.W. dePamphilis. 2007.
Mitochondrial DNA suggests 11 origins of parasitism in angiosperms and
reveals genomic chimerism in parasitic plants. BMC Evolutionary
Biology, 7:248.
McNeal, J.R., J.V. Kuehl, J.L. Boore and C.W. dePamphilis. 2007.
Complete plastid genome sequences suggest strong selection for
retention of photosynthetic genes in the parasitic plant genus
Cuscuta. BMC Plant Biology, 7:57.
McNeal, J.R., K. Arumugunathan, J.V. Kuehl, J.L. Boore and C.W.
dePamphilis. 2007. Systematics and plastid genome evolution of the
cryptically photosynthetic parasitic plant genus Cuscuta (Convolvulaceae).
BMC Biology, 5:55.
Young, N.D. and C.W. dePamphilis. 2005. Rate variation in parasitic
plants: correlated and uncorrelated patterns among plastid genes of
different function. BMC Evolutionary Biology, 5:16. |
|
04/02/08 |
Speaker:
Dr. Hiroshi Akashi
- Department
of Biology
Title:
Biosynthetic constraints and
molecular evolution: Lineage-specific codon usage and protein
evolution in the Drosophila melanogaster subgroup
Abstract:
Selection pressures related
to biosynthetic, as opposed to functional, constraints may act
globally in protein as well as “silent” DNA evolution. In yeast and
Drosophila, both amino acid usage and rates of protein evolution show
striking associations with gene expression levels. Genome-scale
analyses of four closely related Drosophila lineages show that
mutation patterns and selection intensity for codon bias vary
frequently on the time-scale of molecular evolution. Strong
departures from steady-state amino acid composition in lineages
showing changes in synonymous codon usage suggest that similar forces
(such as selection for translational accuracy and efficiency) may act
on codon usage and protein evolution.
References:
Akashi, H., 2001
Gene expression and molecular evolution. Current Opinions in Genetics
and Development 11: 660-666.
Akashi, H., W.Y. Ko,
S. Piao, A. John, P. Goel, C. F. Lin, and A. Vitins, 2006 Molecular
evolution in the Drosophila melanogaster species subgroup: Frequent
parameter fluctuations on the time-scale of molecular divergence.
Genetics 172: 1711-1726. |
| 04/09/08 |
Speaker:
Dr. Masafumi
Nozawa - Department of Biology
Title: Copy
number changes of histone genes during the evolution of humans and
chimpanzees
Abstract: Recent
studies have shown that genomic drift (i.e., random changes of gene
copy number) is an important mechanism in the evolution of sensory
receptor gene families. However, the importance of genomic drift
remains unclear for other multigene families. In this study, we have
therefore examined the magnitude of genomic drift in histone gene
family, which is thought to be one of the most conserved gene
families, using human and chimpanzee data. The results showed that
both humans and chimpanzees showed ~100 functional histone genes in
their genomes. Interestingly, we also found a considerable number of
histone pseudogenes (~100) in both genomes. Although the extent of
copy number variation among human individuals in histone genes was
much smaller than that in sensory receptor genes, ~20% of histone
genes were still polymorphic with respect to copy number among 270
individuals. In addition, there was no significant difference in the
proportion of copy number polymorphic genes between functional and
nonfunctional histone genes. When the evolutionary changes of the
number of histone genes were estimated after the divergence of humans
and chimpanzees, we found many gains and losses of histone genes,
although the total numbers of histone genes have been stable during
the evolution of humans and chimpanzees. From these results, we
conclude that a part of copy number changes have randomly occurred
even in the highly constrained histone gene family.
References:
Redon R, et al. (2006) Global variation in copy number
in the human genome. Nature 444: 444-454.
Nei M. (2007) The new mutation theory of phenotypic
evolution. Proc Natl Acad Sci USA 104: 12235-12242.
Niimura Y and Nei M. (2007). Extensive gains and losses
of olfactory receptor genes in mammalian evolution. PLoS ONE 2: e708.
Nozawa M, Kawahara Y, and Nei M. (2007) Genomic drift
and copy number variation of sensory receptor genes in humans. Proc
Natl Acad Sci USA 104: 20421-20426. |
| 04/16/08 |
Speaker:
Dr. Webb
Miller -
CANCELLED
Title:
Abstract:
References:
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|
04/23/08 |
Speaker:
Dr. Webb
Miller - Department of Biology and Yu Zhang - Department of BMB
Title:
Primate Gene Clusters
Abstract:
We will discuss a
collaborative project to sequence and analyze 14 tandem gene clusters
in up to 7 primates. The data will be added to that from human,
chimpanzee, gorilla (if it is ready), orangutan, rhesus and marmoset.
Computational methods to reconstruct the evolutionary history of these
clusters will be described, including methods to identify
gene-conversion events.
References:
No references to post
|
| 04/30/08 |
Speaker:
Dr. Benjamin
Dickins
Title:
Evolved and evolving
overlapping reading frames in viruses
Abstract:
Viral genomes often encode
multiple proteins in overlapping reading frames. Since regions
containing overlaps can encode more protein functions and can share
regulatory features, overlaps may have evolved in response to
selection for genomic and/or regulatory compression (though more
frequent emergence in compact, gene-dense genomes cannot be excluded).
With a rapid life-cycle and fecund reproductive strategy, viruses
offer an excellent system within which to study the biology of
overlaps and the dynamics of selection more generally. For example,
one study used variation in codon bias between overlapping and
non-overlapping gene segments in the Microviridae to evaluate the
evolutionary order of overlap emergence [1].
To explore the effects of selection more directly,
I will describe planned experiments, on the Microvirid PhiX174, in
which selection is relieved on one member of an overlapping gene pair
and the impact of this on substitutions occurring during continuous
selection on naive bacterial hosts explored. To evaluate compression
hypotheses for the emergence of overlaps, I will also present a
preliminary analysis of the properties of overlaps in this and other
virus families.
References:
[1] Pavesi, A. (2006) Origin
and evolution of overlapping genes in the family Microviridae. Journal
of General Virology. 87: 1013. |
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