Systematic identification of gene families for use as markers for phylogenetic and phylogeny- driven ecological studies of bacteria and archaea and their major subgroups

Systematic identification of gene families for use as markers for phylogenetic and phylogeny- driven ecological studies of bacteria and archaea and their major subgroups
Dongying Wu, Guillaume Jospin, Jonathan A. Eisen
(Submitted on 2 Jul 2013)

With the astonishing rate that the genomic and metagenomic sequence data sets are accumulating, there are many reasons to constrain the data analyses. One approach to such constrained analyses is to focus on select subsets of gene families that are particularly well suited for the tasks at hand. Such gene families have generally been referred to as marker genes. We are particularly interested in identifying and using such marker genes for phylogenetic and phylogeny-driven ecological studies of microbes and their communities. We therefore refer to these as PhyEco (for phylogenetic and phylogenetic ecology) markers. The dual use of these PhyEco markers means that we needed to develop and apply a set of somewhat novel criteria for identification of the best candidates for such markers. The criteria we focused on included universality across the taxa of interest, ability to be used to produce robust phylogenetic trees that reflect as much as possible the evolution of the species from which the genes come, and low variation in copy number across taxa. We describe here an automated protocol for identifying potential PhyEco markers from a set of complete genome sequences. The protocol combines rapid searching, clustering and phylogenetic tree building algorithms to generate protein families that meet the criteria listed above. We report here the identification of PhyEco markers for different taxonomic levels including 40 for all bacteria and archaea, 114 for all bacteria, and much more for some of the individual phyla of bacteria. This new list of PhyEco markers should allow much more detailed automated phylogenetic and phylogenetic ecology analyses of these groups than possible previously.

Native climate uniformly influences temperature-dependent growth rate in Drosophila embryos

Native climate uniformly influences temperature-dependent growth rate in Drosophila embryos
Steven G. Kuntz, Michael B. Eisen
(Submitted on 22 Jun 2013)

It is well known that temperature affects both the timing and outcome of animal development, and there is considerable evidence that species have adapted so that their embryos develop appropriately in the climates in which they live. There have, however, been relatively few studies comparing development in related species with different optimal developmental temperatures. To determine the species-specific impact of temperature on the rate, order, and proportionality of major stages of embryonic development, we used time-lapse imaging to track the developmental progress of embryos in 11 Drosophila species at seven precisely maintained temperatures between 17.5C and 32.5C, and used a combination of automated and manual annotation to determine the timing of 34 milestones during embryogenesis. Developmental timing is highly temperature-dependent in all species. Tropical species, including cosmopolitan species of tropical origin like D. melanogaster, accelerate development with increasing temperature up to 27.5C, above which growth slowing from heat-stress becomes increasingly significant. D. mojavensis, a sub-tropical fly, exhibits an amplified slow-down with lower temperatures, while D. virilis, a temperate fly, exhibits slower growth than tropical species at all temperatures. The alpine species D. persimilis and D. pseudoobscura grow as rapidly as tropical flies at cooler temperatures, but exhibit diminished acceleration above 22.5C and have drastically slowed development by 30C. Though the fractional developmental time of major events is affected by heat-shock, developmental stages are otherwise uniformly affected by temperature, independent of species. Our results suggest that climate has a major effect on developmental timing and comparisons should be performed based on developmental stage rather than time.

Simpsonian ‘Evolution by Jumps’ in an Adaptive Radiation of Anolis Lizards

Simpsonian ‘Evolution by Jumps’ in an Adaptive Radiation of Anolis Lizards
Jonathan M. Eastman, Daniel Wegmann, Christoph Leuenberger, Luke J. Harmon
(Submitted on 18 May 2013)

In his highly influential view of evolution, G. G. Simpson hypothesized that clades of species evolve in adaptive zones, defined as collections of niches occupied by species with similar traits and patterns of habitat use. Simpson hypothesized that species enter new adaptive zones in one of three ways: extinction of competitor species, dispersal to a new geographic region, or the evolution of a key trait that allows species to exploit resources in a new way. However, direct tests of Simpson’s hypotheses for the entry into new adaptive zones remain elusive. Here we evaluate the fit of a Simpsonian model of jumps between adaptive zones to phylogenetic comparative data. We use a novel statistical approach to show that anoles, a well-studied adaptive radiation of Caribbean lizards, have evolved by a series of evolutionary jumps in trait evolution. Furthermore, as Simpson predicted, trait axes strongly tied to habitat specialization show jumps that correspond with the evolution of key traits and/or dispersal between islands in the Greater Antilles. We conclude that jumps are commonly associated with major adaptive shifts in the evolutionary radiation of anoles.

Genomic evidence of rapid and stable adaptive oscillations over seasonal time scales in Drosophila

Genomic evidence of rapid and stable adaptive oscillations over seasonal time scales in Drosophila
Alan O. Bergland, Emily L. Behrman, Katherine R. O’Brien, Paul S. Schmidt, Dmitri A. Petrov
(Submitted on 20 Mar 2013)

In many species, genomic data have revealed pervasive adaptive evolution indicated by the near fixation of beneficial alleles. However, when selection pressures are highly variable along a species range or through time adaptive alleles may persist at intermediate frequencies for long periods. So called balanced polymorphisms have long been understood to be an important component of standing genetic variation yet direct evidence of the ubiquity of balancing selection has remained elusive. We hypothesized that environmental fluctuations between seasons in a North American orchard would impose temporally variable selection on Drosophila melanogaster and consequently maintain allelic variation at polymorphisms adaptively evolving in response climatic variation. We identified hundreds of polymorphisms whose frequency oscillates among seasons and argue that these loci are subject to strong, temporally variable selection. We show that adaptively oscillating polymorphisms are often millions of years old, predating the divergence between D. melanogaster and D. simulans and that a subset of these polymorphisms respond predictably to an acute frost event. Taken together, our results demonstrate that rapid temporal fluctuations in climate over generational scales is a predominant force that maintains adaptive alleles and promotes genetic diversity.

Our paper: Oh sister, where art thou? Indirect fitness benefit could maintain a host defense trait

This guest post is by Pleuni Pennings on the paper “Oh sister, where art thou? Indirect fitness benefit could maintain a host defense trait”, available from the arXiv here. This is cross-posted from her website here

Tobias Pamminger, Susanne Foitzik, Dirk Metzler and I analyzed the small scale spatial structure of ants of the species Temnothorax longispinosus. These ants are the host of a slavemaking ant. The slavemakers go on raids, and steal young from the host species to work as slaves in their nests. We wanted to know whether the slaves still have relatives in the nearby nests. If they do, then their behavior – which influences the slavemakers – could have an effect on their relatives and therefore on their indirect fitness.

To find out if slaves are related to their neighbours, we collected lots of ant nests (they nest in acorns), both in New York and in West Virginia, marked exactly where we found them and genotyped them at six microsatellites.

Ants in acorn

Photograph by Andreas Gros
Temnothorax longispinosus in acorn

US2009 132

We put little flags at the exact location of an ant nest to measure the distances between the nests.

Microsat Data

This is one of the figures from the manuscript. Plot R (from West Virginia) is is shown to demonstrate the distribution of colonies within a plot and to show the distribution of alleles of one of the six microsatellite loci (GT1) among colonies. Each colony is represented by a pie-diagram with the frequencies of different GT1 alleles amongst the genotyped individuals of the colony. R3 is a slavemaker nest (we genotyped the slaves, not the slavemakers) and shares most of its alleles with the free nest R7. R13 and R15 are free living host colonies in close proximity and appear to be related.

Our main conclusion is that the enslaved ants are indeed related to their neighbors. The manuscript can be found on the arXiv here:

The manuscript was peer-reviewed at Peerage of Science, a new and very useful community of scientists who agree to review each others papers fairly. See

The manuscript is part of Tobias Pamminger’s PhD thesis. Tobias defends his thesis this week in Mainz!! Congrats Tobias!

Tobias came up with the awesome title for the paper “Oh sister, where art thou? Indirect fitness benefit could maintain a host defense trait.”

Plump Cutthroat Trout and Thin Rainbow Trout in a Lentic Ecosystem

Plump Cutthroat Trout and Thin Rainbow Trout in a Lentic Ecosystem

Joshua Courtney, Jessica Abbott, Kerri Schmidt, Michael Courtney
(Submitted on 17 Oct 2012)

Background: Much has been written about introduced rainbow trout (Oncorhynchus mykiss) interbreeding and outcompeting cutthroat trout (Oncorhynchus clarkii). However, the specific mechanisms by which rainbow trout and their hybrids outcompete cutthroat trout have not been thoroughly explored, and the published data is limited to lotic ecosystems. Materials and Methods: Samples of rainbow trout and cutthroat trout were obtained from a lentic ecosystem by angling. The total length and weight of each fish was measured and the relative weight of each fish was computed (Anderson R.O., Neumann R.M. 1996. Length, Weight, and Associated Structural Indices, Pp. 447-481. In: Murphy B.E. and Willis D.W. (eds.) Fisheries Techniques, second edition. American Fisheries Society.), along with the mean and uncertainty in the mean for each species. Data from an independent source (K.D. Carlander, 1969. Handbook of Freshwater Fishery Biology, Volume One, Iowa University Press, Ames.) was also used to generate mean weight-length curves, as well as 25th and 75th percentile curves for each species to allow further comparison. Results: The mean relative weight of the rainbow trout was 72.5 (+/- 2.1); whereas, the mean relative weight of the cutthroat trout was 101.0 (+/- 4.9). The rainbow trout were thin; 80% weighed below the 25th percentile. The cutthroat trout were plump; 86% weighed above the 75th percentile, and 29% were above the heaviest recorded specimens at a given length in the Carlander (1969) data set. Conclusion: This data casts doubt on the hypothesis that rainbow trout are strong food competitors with cutthroat trout in lentic ecosystems. On the contrary, in the lake under study, the cutthroat trout seem to be outcompeting rainbow trout for the available food.