Previous IMEG Seminars and Abstracts:
Speaker: Dr. Ilana
Baums - Department of Biology
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
Evolutionary Link Between Maternal Behavior and Eusociality. Science,
Zhou - Department of Biology
Title: Phylogenetic Analyses of Two
Histone Demethylase Gene Families
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.
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.
Hiroki Goto, Lei Peng, and Kateryna D. Makova -
Department of Biology and Center for Comparative Genomics and
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.
JF et al. (2005) Conservation of Y-linked genes during human evolution revealed
by comparative sequencing in chimpanzee. Nature 437:100-103.
Duarte - Department of Biology
Title: Phylogenetic Utility of Conserved
Single Copy Nuclear Genes in Flowering Plants
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
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.
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:
Beth Shapiro - Department of Biology
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
Hofreiter M, Serre D, Poinar HN, Kuch M, Paabo S. Ancient DNA. Nature
Reviews Genetics 2: 353-359.
Steve Schaeffer - Department of Biology
Rearrangements inferred from the 12 Drosophila Genomes Project
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.
Speaker: Dr. George
Zhang - Department of Ecology and Evolutionary Biology, University of
Title: Metabolic network
analysis for understanding evolution
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.
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
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.
Adalsteinsson - Department of Biology
Phylogenetics and Biogeography of the Snake Family Leptotyphlopidae
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
worldâ€™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
BREAK NO IMEG SEMINAR
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.
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.
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
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
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
Masafumi Nozawa - Department of Biology
Title: Copy number
changes of histone genes during the evolution of humans and chimpanzees
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.
R, et al. (2006) Global variation in copy number in the human genome. Nature
M. (2007) The new mutation theory of phenotypic evolution. Proc Natl Acad
Sci USA 104: 12235-12242.
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.
Webb Miller - CANCELLED
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
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 .
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
Pavesi, A. (2006) Origin and evolution of overlapping genes in the family
Microviridae. Journal of General Virology. 87: 1013.