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. Subsequent experiments focused on A. vaga because the complete genome of this species has been sequenced. These experiments showed similarly rapid declines in fitness; however, we cannot rule out the possibility that reisolation lines die because of fitness variation unrelated to the number of detrimental mutations. To test this, we will dehydrate and rehydrate animals and compare their survival to that of controls in daily reisolation lines. This dehydration-rehydration cycle is known to cause chromosomes to fragment and then re-join, possibly with attendant repair or replacement of detrimental alleles. Work in Claudia Ricci's lab (Universithy of Milan) previously showed that long-term culture of bdelloids in populations of small (unspecified, but > 1) population size caused decline in fitness that could be reversed by a dehydration-rehydration cycle.
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 in bdelloid rotifers, 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). Next I used the K/q ratio to delimit species in an assortment of sexually-reproducing eukaryotes (Birky 2013). Currently I am extending this to bacteria. Note that this project is basically DNA barcoding, but the rationale and methodology are based on well-established population genetic theory and are thus completely different from that employed by the Barcode of Life project.
The 2005 paper also describes evidence that some species are adapted to different ecological niches, which was extended to a larger sample of bdelloids with a different method in papers from Tim's lab. Also in my 2005 paper, 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.
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, analyzed by EEB graduate student Erica Sommers, 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. It is possible that oceans represent significant barriers to the dispersal of bdelloids.
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