THE BIRKY LAB

Department of Ecology and Evolutionary Biology

The University of Arizona

Dedicated to the study of molecular evolution and genetics.

 

Links

Bill Birky's Home Page  

 Department of Ecology and Evolutionary Biology

University of Arizona


Publications 

Required Reading for Lab People

BdelloidMovieShort.mov
EEB Seminar
Seminar given to EBio department at the University of Colorado  10-21-2011

 Lab People

 

Bill Birky
Professsor Emeritus, Dept. of Ecology and Evolutionary Biology



Jose Lujano
Undergraduate, Dept. of Ecology and Evolutionary Biology



Former lab people at UA

Images

   

Fluorescence microscopy image of live female Philodina roseola stained with DAPI, which binds specifically to DNA to reveal nuclei.

   

Macrotrachela sonorensis rediscovered! I found this unusual animal in a sample of microbiotic soil from the desert near my house. It has an unusual head which swells and contracts when the animal is feeding on detritus, like a rubber bulb exerting suction. This species has been reported only once before, from Sonora, Mexico, by Aydin Orstan (1995 Southwestern Naturalist 40:255).


     

Rotaria species (left and center); Philodina species (right)

Philodina spp. from Scotia Marsh, Arizona

Current Research Projects

Mutation Accumulation in an Ancient Asexual Organism

In a mutation accumulation (MA) experiment, a number of single asexual animals are isolated and examined daily. When an animal reproduces, a single offspring is kept and the parent is discarded. This is repeated for many generations. In each line, the effective population size is 1. New mutations occur in each generation and accumulate because there is no natural selection or random genetic drift to eliminate them. Deleterious mutations greatly outnumber advantageous mutations, and as they accmulate in each line the fitness of the animals in that line decreases. One by one, they cease to reproduce. These experiments have been applied to protists such as Paramecium aurelia and multicellular organisms such as the nematode Caenorhabditis elegans. In our first experiment with the strictly asexual bdelloid rotifer Adineta vaga, the lines survived only 12 generations on average, and a maximum of 22 generations. In a prallel experiment Philodina roseola lines became extinct even faster. A second experiment with Adineta vaga is underway and is showing nearly as rapid a decline in fitness. We will do controls to rule out the (unlikely) possibility that the animals' environment is deteriorating, look for increased fitness in mass cultures due to compensating or advantageous mutations, and test whether dessication and rehydration or freezing at -80C and thawing can "rejuvenate" lines. Our lab cultures of P. roseola and A. vaga have been reared in laboratories for many years and may have already accumulated a substantial load of detrimental mutations. Therefore we will also isolate dessicated animals of several species from nature, rehydrate them in the lab, and see if they have they survive longer in MA experiments.

Speciation in an Ancient Asexual Organism

One of the major problems of biology is why most organisms reproduce sexually at least part of the time. Theory and some experimental evidence suggests that the loss of sexual reproduction should reduce the effectiveness natural selection. Asexual lineages should accumulate detrimental mutations, leading to extinction. They should also have difficulty retaining and fixing advantageous mutations, which would make it difficult to adapt to new environments and speciate. In fact the definition of species in asexual organisms is controversial, since the "biological" species definition cannot be applied. We are studying the long-term consequences of the loss of asexual reproduction, and the preliminary results are exciting! The bdelloid rotifers are a widespread group of freshwater invertebrates which have been reproducing asexually for at least 40 million years and undergone substantial differentiation into species differing in morphology, habitat, and behavior. (See the movie at BdelloidMovieShort.mov.)

We are collecting bdelloid rotifers and amplifying and sequencing a fragment of the mitochondrial coxI gene from each isolate. Together with Tim Barraclough and Austin Burt (Barraclough, Birky, and Burt 2003), we used basic population genetic theory to show that asexual organisms, like sexual organisms, should fall into clusters representing independently evolving lineages. We devised a new species concept, the Evolutionary Genetic Species Concept, for asexuals which describes clusters that are comparable to biological species in sexual organisms. We also devised a species criterion that uses the ratio of the sequence difference between two clades to the mean sequence difference between sequences within one clade. This K/q ratio, together with the number of specimens in each clade, can be used to detemine the probability that the specimens came from two different species. This work was described in a preliminary paper (Birky et al. 05) and a more complete paper (Birky et al. 2010) where it is applied not only to bdelloid rotifers but also to several other groups of asexual animals and protists. With Tim Barraclough (Silwood Park), I applied the K/q ratio and Tim's GMYC method to bdelloid rotifers and oribatid mites, finding that the two methods agree in identifying the majority of species from cox1 sequences (Birky and Barraclough 2009).

The paper also describes evidence that some species are adapted to different ecological niches. Analyses of the same DNA sequences used for phylogenetic analysis found that anciently asexual bdelloid rotifer lineage showed about the same intensity of selection (measured by Ka/Ks) as their sexual sister group, the monogonont rotifers.

Our Evolutionary Genetic Species Concept and criterion appear to be applicable to other asexual organisms, including the eukaryotic protist Giardia and at least some bacterial species.

Natural Selection and Sex

Now that we can identify species in bdelloid rotifers, we can compare them with their sexual relatives, the monogonont rotifers, to study the volutionary advantage of sex. The great geneticist H. J. Muller showed that asexual organisms should accumulate detrimental mutations due to random drift, more so than their sexual relatives. We can test this using the cox1 gene sequences that we use for phylogenetic analysis. If the asexual bdelloids accumulate more detrimental mutations than the sexual monogononts, this should be reflected in a higher ratio of nonsynonymous to synonymous substitutions (Ka/Ks) along the long evolutionary branches connecting species to their ancestors. Matt Meselson's lab showed that this effect was not seen in nuclear genes, and our preliminary work verified this with the cox1 gene in a large sample of bdelloids. With collaborator (and former graduate student) Heather Maughan, we are extending this analysis to a largr sample of bdelloids and monogononts. The results to date verify that Ka/Ks is similar in the asexual and sexual groups. Now the big puzzle is how bdelloids have managed to escape the ratchet.

Genetic Diversity and Sex

We have also found that the nucleotide diversity of the cox1 gene in bdelloids is similar to that of other invertebrates, both macroscopic and microscopic. This suggests that the effective population size is modest, even though the census population size is immense. Evidently bdelloids have not escaped Muller's ratchet by having extremely large effective population sizes.

Frozen Rotifers

Bdelloid rotifers are remarkably tough. Among other things, they withstand dessication and disperse by blowing around in the wind when dessicated. Moreover, they have been found in temporary waters in Antarctica and on the top of 12,000-foot mountains in the U.S. Former undergrad student Julia Perry found that bdelloids also survive freezing at -80C, in culture medium without cryoprotectants or any other special treatment. We have found good survival and reproduction after freezing for more than 2.5 years. Undergrad Alex Podolsky has investigated some of the factors that do, or do not, affect survival after frezing at -80C. Remarkably, they do not survive freezing at -20C, perhaps because it is too slow and ice crystals form.

Testing the "Everything is Everywhere" Hypothesis

We are now able to test an important hypothesis in biogeography, the Everything is Everywhere hypothesis. This hypothesis says that microscopic organisms have such large population sizes that every species can be found everywhere, although the local environment determines whether a species thrives at a particular location. Some of the data favoring this hypothesis are based on species identified by morphology, which is often a misleading criterion, especially for microscopic organisms. Our preliminary data suggest that although many or most bdelloid rotifer species disperse broadly and rapidly, not all do so and most of the species we find in the U.S. are not found in collections from Europe, Africa, and elsewhere.

Rotifer Systematics

Our collection includes a number of new species. We have four species of Abrochtha, of which at least three are new; we collaborated with Claudia Ricci, Giulio Melone, and Diego Fontaneto of the University of Milan to describe the new species (Birky et al. 2011). Two of them are cryptic species, distinguishable by genotype but not be phenotype.

Link to the labs of collaborator Claudia Ricci's web site at the University of Milan: http://users.unimi.it/ricci/rotifer.htm

DNA Barcoding

DNA barcoding is the use of DNA sequences to identify specimens to species, and to discover new species. It has previously been applied only to sexual organisms and primarily uses the mitochondrial cox1gene. These efforts are controversial because mitochondral gene phylogenies do not necessarily agree with nuclear gene phylogenies. However, this objection does not apply to asexual organisms in which all genes are completely linked and mitochondrial genes necessarily have the same phylogenetic history as nuclear genes and individuals. Our theoretical model of speciation suggested a new method of delimiting evolutionary species, using the ratio of sequence differences between clades to the mean sequence difference within clades (the K/theta ratio). application to bdelloid rotifers and to a number of other asexual organisms shows that barcoding works well with asexual and clonal organisms, which includes many parasites and microorganisms of medical and agricultural importance. In preparation is a paper applying the K/theta ratio to delimit species in sexual organisms. In these organisms, sequences of mitochondrial or chloroplast genes detect earlier stages of speciation than do most nuclear genes.

DNA barcode of Philodina roseola; each color represents a different base in the cox1 sequence.

 

Link to the Barcode Blog: http://phe.rockefeller.edu/barcode/blog/

 

A Curious Incident

A recent paper did computer simulations which the authors interpreted as showing that aquatic organisms smaller than 1 mm cannot form species (Rossberg et al. 2013 Proc. Roy. Soc. B 280,20131248). The authors also re-plotted data from several experimental papers which they said supported their conclusion. Given that many papers that have demonstrated the existence of species in microscopic eukaryotes, including my own, and even given formal names to some of these species, this came as a surprise! It reminded me of the (possibly apocryphal) story of the engineer who showed mathematically that bumblebees can't fly. A critique which describes methodological errors in Rossberg et al. has been accepted by the Proceedings (Morgan, Bass, Bik, Birky, et al. 2014 A critique of Rossberg et al.: noise obscures the genetic signal of meiobiotal ecospecies in ecogenomic datasets.). In addition to those errors, I also believe that they have confused the large census population sizes of microscopic organisms with the much smaller effective population sizes.

 Rotifer Links:

WheelBase, a web site for rotifer studies

 

Some Representative Publications

Most of the links for downloading pdf files are broken; I'll repair them as soon as possible.

Birky, C. William, Jr., and John J. Gilbert, 1971 Parthenogenesis in rotifers: the control of sexual and asexual reproduction. Am. Zoologist 11:245-266.

Birky, C. William, Jr.,1973 On the origin of mitochondrial mutants: Evidence for intracellular selection of mitochondria in the origin of antibiotic-resistant cells in yeast. Genetics 74:421-432. Birky73IntracellSelectMito.pdf

Thrailkill, Kathryn M., C. William Birky, Jr., Gudrun Lückemann, and Klaus Wolf, 1980 Intracellular population genetics: Evidence for random drift of mitochondrial allele frequencies in Saccharomyces cerevisiae and Schizosaccharomyces pombe. Genetics 96:237-262. Thrailkill80MitoDrift.pdf

Birky, C. William, Jr., Karen P. VanWinkle-Swift, Barbara B. Sears, John E. Boynton, and Nicholas W. Gillham, 1981 Frequency distributions for chloroplast genes in Chlamydomonas zygote clones: Evidence for random drift. Plasmid 6:173-192. Birky81ChlamyCpRandomDrift.pdf

Birky, C. William, Jr., Takeo Maruyama, and Paul Fuerst, 1983 An approach to population and evolutionary genetic theory for genes in mitochondria and chloroplasts, and some results. Genetics 103:513-527. Birky83OrgPopGenTheory1.pdf

Banks, Jo Ann, and C. William Birky, Jr., 1985 Chloroplast DNA diversity is low in a wild plant, Lupinus texensis. Proc. Nat. Acad. Sci. USA 82:6950-6954. Banks85LupineCpDiversity.pdf

Birky, C. William, Jr., and J. Bruce Walsh, 1988 Effects of linkage on rates of molecular evolution. Proc. Nat. Acad. Sci. USA 85:6414-6418. Birky88Linkage&EvolRates.pdf

Birky, C. William, Jr., Paul Fuerst, and Takeo Maruyama, 1989 Organelle gene diversity under migration, mutation, and drift: Equilibrium expectations, approach to equilibrium, effects of heteroplasmic cells, and comparison to nuclear genes. Genetics 121:613-627. Birky89OrgPopGenTheory2.pdf

Birky, C. William, Jr., 1995 Uniparental inheritance of mitochondria and chloroplast genes: mechanisms and evolution. Proc. Nat. Acad. Sci. USA 92:11331-11338. Birky95UPI.pdf

Rumpf, Robert, Dawne Vernon, David Schreiber, and C. William Birky, Jr., 1996 Evolutionary consequences of the loss of photosynthesis in Chlamydomonadaceae: Phylogenetic analysis of Rrn18 (18S rDNA) in 13 Polytoma strains (Chlorophyta). J. Phycol. 32:119-126. Rumpf96PolytomaPhylogeny.pdf

Birky, C. William, Jr., 1996 Heterozygosity, heteromorphy, and phylogenetic trees in asexual eukaryotes. Genetics 144:427-437. Birky96Heterozygosity.pdf

Birky, C. William, Jr., 1999 An even broader perspective on the evolution of sex. J. Evol. Biol. 12:1013-1016. Birky99BroaderPerspective.pdf

Birky, C. William, Jr., 2001 The inheritance of genes in mitochondria and chloroplasts: Laws, mechanisms, and models. Annu. Rev. Genet. 35:125-148. Birky01AnnRevGenet.pdf

Vernon, Dawne, Robin Gutell, Jaime Cannone, Robert Rumpf, and C. William Birky, Jr., 2001. Accelerated evolution of functional plastid rRNA and elongation factor genes due to reduced protein synthetic load after the loss of photosynthesis in the chlorophyte alga Polytoma.. Mol. Biol. Evol. 18:1810-1822. Vernon01PolyRates.pdf

Lizhi Yu, C.. William Birky, Jr., and Rodney D. Adam, 2002. The two nuclei of Giardia each have complete copies of the genome as demonstrated by fluorescence in situ hybridization. Eukaryotic Cell 1:191-199. Yu02Giardia.pdf

Maughan, H., C. W. Birky,Jr, W. L. Nicholson, W. D. Rosenzweig, and R. H. Vreeland, 2002.The paradox of the "ancient' bacterium which contains "modern" protein-coding genes. Molecular Biology and Evolution 19:1637-1639. Maughan02BacillusPermians.pdf

Barraclough, Timothy G., C. William Birky, Jr., and Austin Burt, 2003 Diversification in sexual and asexual organisms. Evolution 57:2166-2172. BarraBirkyBurt2003.pdf

Birky, C. William, Jr. (2004) Bdelloid rotifers revisited. Proceedings of the National Academy of Sciences USA 101:2651-2652. Birky04BdelloidsRevisited.pdf

Birky, C. William, Jr. (2005) Sex: Is Giardia doing it in the dark?. Current Biology 15:R56-R56. Birky05SexInGiardia?.pdf

Maughan , Heather (2004) Stochastic processes influence stationary-phase decisions in Bacillus subtilis. Journal of Bacteriology 186:2212-2214. Maughan04StchstcVariatn&Sel.pdf

Birky, C. William, Jr., Cynthia Wolf, Heather Maughan, Linnea Herbertson, Elena Henry (2005) Speciation and selection without sex. Hydrobiologia 546:29-45. Birky05RotiferaX.pdf

Birky, C. William, Jr. (2008) Uniparental inheritance of organelle genes. Curr. Biol. 18:R692-R695. 

Birky, C. William, Jr., Timothy G. Barraclough (2009) Asexual Speciation. In Lost Sex. The Evolutionary Biology of Parthenogenesis. Peter Van Dijk, Koen Martens, Isa Schön (eds.) Springer. pp. 201-216.

Birky, C. William, Jr. (2009). Sex and evolution in eukaryotes. in Reproduction and Developmental Biology, edited by Andre Pires da Silva, in Encyclopedia of Life Support Systems (EOLSS), Developed under the auspices of the UNESCO, Eolss Publishers, Oxford, UK, [http://www.eolss.net]

Birky, C. William, Jr. (2010) Giardia sex? Yes, but how and how much? Trends Parasitol. 26:70-74.

Birky, C. William, Jr. (2010) Positively negative evidence for asexuality. J. Hered. 101(Supplement 1): 542-545.

Birky, C. William, Jr., Joshua Adams, Marlea Gemmel, Julia Perry (2010) Using population genetic theory and DNA sequences for species detection and identification in asexual organisms. PLoS One. 5:e10609.

Birky, C. William, Jr., Claudia Ricci, Giulio Melone, Diego Fontaneto (2011) Integrating DNA and traditional taxonomy to describe diversity in poorly studied microscopic animals: new species of the genus Abrochtha Bryce, 1910 (Rotifera: Bdelloidea: Philodinavidae). Zool. J. Linnean  Soc. 161:723-734.

Birky, C. William, Jr. (2013) Species detection and identification in sexual organisms using population genetic theory and DNA sequences. PLoS One 8(1):e52544.

Morgan, M.J., Bass, D., Bik, H., Birky, C.W., Blaxter, M., Crisp, M.D., Derycke, S., Fitch, D., Fontaneto, D., Hardy, C.M., King, A.J., Kiontke, K.C., Moens, T., Pawlowski, J.W., Porazinska, D., Tang, C.Q., Thomas, W.K., Yeates, D.K., Creer, S. 2014 A critique of Rossberg et al.: noise obscures the genetic signal of meiobiotal ecospecies in ecogenomic datasets. Proc. Roy. Soc. B (accepted).

Go to Research History for a summary of Bill's previous research (this will be updated soon). Go to Publications for a complete list of Bill's papers.

Some files are in pdf format. You can view them with the Acrobat Reader software, available free at http://www.adobe.com.