Center for the Study of Evolution in Action

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Sullivan J.,University of Idaho | Sullivan J.,Center for the Study of Evolution in Action | Demboski J.R.,Denver Museum of Nature and Science | Bell K.C.,University of New Mexico | And 5 more authors.
Heredity | Year: 2014

Increasing data have supported the importance of divergence with gene flow (DGF) in the generation of biological diversity. In such cases, lineage divergence occurs on a shorter timescale than does the completion of reproductive isolation. Although it is critical to explore the mechanisms driving divergence and preventing homogenization by hybridization, it is equally important to document cases of DGF in nature. Here we synthesize data that have accumulated over the last dozen or so years on DGF in the chipmunk (Tamias) radiation with new data that quantify very high rates of mitochondrial DNA (mtDNA) introgression among para-and sympatric species in the T. quadrivittatus group in the central and southern Rocky Mountains. These new data (188 cytochrome b sequences) bring the total number of sequences up to 1871; roughly 16% (298) of the chipmunks we have sequenced exhibit introgressed mtDNA. This includes ongoing introgression between subspecies and between both closely related and distantly related taxa. In addition, we have identified several taxa that are apparently fixed for ancient introgressions and in which there is no evidence of ongoing introgression. A recurrent observation is that these introgressions occur between ecologically and morphologically diverged, sometimes non-sister taxa that engage in well-documented niche partitioning. Thus, the chipmunk radiation in western North America represents an excellent mammalian example of speciation in the face of recurrent gene flow among lineages and where biogeography, habitat differentiation and mating systems suggest important roles for both ecological and sexual selection. © 2014 Macmillan Publishers Limited All rights reserved.


PubMed | University of Wisconsin - Madison, Dana-Farber Cancer Institute, Rice University, Michigan State University and 6 more.
Type: | Journal: BMC genomics | Year: 2015

With its unique ability to produce high-voltage electric discharges in excess of 600 volts, the South American strong voltage electric eel (Electrophorus electricus) has played an important role in the history of science. Remarkably little is understood about the molecular nature of its electric organs.We present an in-depth analysis of the genome of E. electricus, including the transcriptomes of eight mature tissues: brain, spinal cord, kidney, heart, skeletal muscle, Sachs electric organ, main electric organ, and Hunters electric organ. A gene set enrichment analysis based on gene ontology reveals enriched functions in all three electric organs related to transmembrane transport, androgen binding, and signaling. This study also represents the first analysis of miRNA in electric fish. It identified a number of miRNAs displaying electric organ-specific expression patterns, including one novel miRNA highly over-expressed in all three electric organs of E. electricus. All three electric organ tissues also express three conserved miRNAs that have been reported to inhibit muscle development in mammals, suggesting that miRNA-dependent regulation of gene expression might play an important role in specifying an electric organ identity from its muscle precursor. These miRNA data were supported using another complete miRNA profile from muscle and electric organ tissues of a second gymnotiform species.Our work on the E. electricus genome and eight tissue-specific gene expression profiles will greatly facilitate future research on determining the coding and regulatory sequences that specify the function, development, and evolution of electric organs. Moreover, these data and future studies will be informed by the first comprehensive analysis of miRNA expression in an electric fish presented here.


News Article | November 29, 2016
Site: www.chromatographytechniques.com

Biologists have discovered that the evolution of a new species can occur rapidly enough for them to observe the process in a simple laboratory flask. In a month-long experiment using a virus harmless to humans, biologists working at the University of California San Diego and at Michigan State University documented the evolution of a virus into two incipient species—a process known as speciation that Charles Darwin proposed to explain the branching in the tree of life, where one species splits into two distinct species during evolution. “Many theories have been proposed to explain speciation, and they have been tested through analyzing the characteristics of fossils, genomes, and natural populations of plants and animals,” said Justin Meyer, an assistant professor of biology at UC San Diego and the first author of a study that will be published in the December 9 issue of Science.“However, speciation has been notoriously difficult to thoroughly investigate because it happens too slowly to directly observe. Without direct evidence for speciation, some people have doubted the importance of evolution and Darwin’s theory of natural selection.” Meyer’s study, which also appeared last week in an early online edition of Science, began while he was a doctoral student at Michigan State University, working in the laboratory of Richard Lenski, a professor of microbial ecology there who pioneered the use of microorganisms to study the dynamics of long-term evolution. “Even though we set out to study speciation in the lab, I was surprised it happened so fast,” said Lenski, a co-author of the study. “Yet the deeper Justin dug into things—from how the viruses infected different hosts to their DNA sequences—the stronger the evidence became that we really were seeing the early stages of speciation.” “With these experiments, no one can doubt whether speciation occurs,” Meyer added. “More importantly, we now have an experimental system to test many previously untestable ideas about the process.” To conduct their experiment, Meyer, Lenski and their colleagues cultured a virus—known as “bacteriophage lambda”—capable of infecting E. coli bacteria using two receptors, molecules on the outside of the cell wall that viruses use to attach themselves and then infect cells. When the biologists supplied the virus with two types of cells that varied in their receptors, the virus evolved into two new species, one specialized on each receptor type. “The virus we started the experiment with, the one with the nondiscriminatory appetite, went extinct. During the process of speciation, it was replaced by its more evolved descendants with a more refined palette,” explained Meyer. Why did the new viruses take over? “The answer is as simple as the old expression, ‘a jack of all trades is a master of none’,” explained Meyer. “The specialized viruses were much better at infecting through their preferred receptor and blocked their ‘jack of all trades’ ancestor from infecting cells and reproducing. The survival of the fittest led to the emergence of two new specialized viruses.” Meyer’s study was conducted over six years in two separate labs. The first experiments were performed at Michigan State, supported in part by BEACON, the National Science Foundation’s Center for the Study of Evolution in Action, and the analyses were completed at UC San Diego. Other co-authors of the study included MSU’s Devin Dobias, now a graduate student at Washington University; Sarah Medina, an undergraduate at UC San Diego, and Animesh Gupta and Lisa Servilio, UC San Diego graduate students working in Meyer’s laboratory.


News Article | November 29, 2016
Site: www.eurekalert.org

Biologists have discovered that the evolution of a new species can occur rapidly enough for them to observe the process in a simple laboratory flask. In a month-long experiment using a virus harmless to humans, biologists working at the University of California San Diego and at Michigan State University documented the evolution of a virus into two incipient species--a process known as speciation that Charles Darwin proposed to explain the branching in the tree of life, where one species splits into two distinct species during evolution. "Many theories have been proposed to explain speciation, and they have been tested through analyzing the characteristics of fossils, genomes, and natural populations of plants and animals," said Justin Meyer, an assistant professor of biology at UC San Diego and the first author of a study that will be published in the December 9 issue of Science. "However, speciation has been notoriously difficult to thoroughly investigate because it happens too slowly to directly observe. Without direct evidence for speciation, some people have doubted the importance of evolution and Darwin's theory of natural selection." Meyer's study, which also appeared last week in an early online edition of Science, began while he was a doctoral student at Michigan State University, working in the laboratory of Richard Lenski, a professor of microbial ecology there who pioneered the use of microorganisms to study the dynamics of long-term evolution. "Even though we set out to study speciation in the lab, I was surprised it happened so fast," said Lenski, a co-author of the study. "Yet the deeper Justin dug into things--from how the viruses infected different hosts to their DNA sequences--the stronger the evidence became that we really were seeing the early stages of speciation." "With these experiments, no one can doubt whether speciation occurs," Meyer added. "More importantly, we now have an experimental system to test many previously untestable ideas about the process." To conduct their experiment, Meyer, Lenski and their colleagues cultured a virus--known as "bacteriophage lambda"--capable of infecting E. coli bacteria using two receptors, molecules on the outside of the cell wall that viruses use to attach themselves and then infect cells. When the biologists supplied the virus with two types of cells that varied in their receptors, the virus evolved into two new species, one specialized on each receptor type. "The virus we started the experiment with, the one with the nondiscriminatory appetite, went extinct. During the process of speciation, it was replaced by its more evolved descendants with a more refined palette," explained Meyer. Why did the new viruses take over? "The answer is as simple as the old expression, 'a jack of all trades is a master of none'," explained Meyer. "The specialized viruses were much better at infecting through their preferred receptor and blocked their 'jack of all trades' ancestor from infecting cells and reproducing. The survival of the fittest led to the emergence of two new specialized viruses." Meyers's study was conducted over six years in two separate labs. The first experiments were performed at Michigan State, supported in part by BEACON, the National Science Foundation's Center for the Study of Evolution in Action, and the analyses were completed at UC San Diego. Other co-authors of the study included MSU's Devin Dobias, now a graduate student at Washington University; Sarah Medina, an undergraduate at UC San Diego, and Animesh Gupta and Lisa Servilio, UC San Diego graduate students working in Meyer's laboratory.


Eisthen H.L.,Michigan State University | Eisthen H.L.,Center for the Study of Evolution in Action | Theis K.R.,Center for the Study of Evolution in Action | Theis K.R.,University of Michigan | Theis K.R.,Wayne State University
Philosophical Transactions of the Royal Society B: Biological Sciences | Year: 2016

Animals ubiquitously interact with environmental and symbiotic microbes, and the effects of these interactions on animal physiology are currently the subject of intense interest. Nevertheless, the influence of microbes on nervous system evolution has been largely ignored. We illustrate here how taking microbes into account might enrich our ideas about the evolution of nervous systems. For example, microbes are involved in animals’ communicative, defensive, predatory and dispersal behaviours, and have likely influenced the evolution of chemoand photosensory systems. In addition, we speculate that the need to regulate interactions with microbes at the epithelial surface may have contributed to the evolutionary internalization of the nervous system. © 2015 The Author(s) Published by the Royal Society. All rights reserved.


News Article | November 29, 2016
Site: phys.org

In a month-long experiment using a virus harmless to humans, biologists working at the University of California San Diego and at Michigan State University documented the evolution of a virus into two incipient species—a process known as speciation that Charles Darwin proposed to explain the branching in the tree of life, where one species splits into two distinct species during evolution. "Many theories have been proposed to explain speciation, and they have been tested through analyzing the characteristics of fossils, genomes, and natural populations of plants and animals," said Justin Meyer, an assistant professor of biology at UC San Diego and the first author of a study that will be published in the December 9 issue of Science. "However, speciation has been notoriously difficult to thoroughly investigate because it happens too slowly to directly observe. Without direct evidence for speciation, some people have doubted the importance of evolution and Darwin's theory of natural selection." Meyer's study, which also appeared last week in an early online edition of Science, began while he was a doctoral student at Michigan State University, working in the laboratory of Richard Lenski, a professor of microbial ecology there who pioneered the use of microorganisms to study the dynamics of long-term evolution. "Even though we set out to study speciation in the lab, I was surprised it happened so fast," said Lenski, a co-author of the study. "Yet the deeper Justin dug into things—from how the viruses infected different hosts to their DNA sequences—the stronger the evidence became that we really were seeing the early stages of speciation." "With these experiments, no one can doubt whether speciation occurs," Meyer added. "More importantly, we now have an experimental system to test many previously untestable ideas about the process." To conduct their experiment, Meyer, Lenski and their colleagues cultured a virus—known as "bacteriophage lambda"—capable of infecting E. coli bacteria using two receptors, molecules on the outside of the cell wall that viruses use to attach themselves and then infect cells. When the biologists supplied the virus with two types of cells that varied in their receptors, the virus evolved into two new species, one specialized on each receptor type. "The virus we started the experiment with, the one with the nondiscriminatory appetite, went extinct. During the process of speciation, it was replaced by its more evolved descendants with a more refined palette," explained Meyer. Why did the new viruses take over? "The answer is as simple as the old expression, 'a jack of all trades is a master of none'," explained Meyer. "The specialized viruses were much better at infecting through their preferred receptor and blocked their 'jack of all trades' ancestor from infecting cells and reproducing. The survival of the fittest led to the emergence of two new specialized viruses." Meyers's study was conducted over six years in two separate labs. The first experiments were performed at Michigan State, supported in part by BEACON, the National Science Foundation's Center for the Study of Evolution in Action, and the analyses were completed at UC San Diego. Explore further: Researchers show how new viruses evolve, and in some cases, become deadly More information: J. R. Meyer et al, Ecological speciation of bacteriophage lambda in allopatry and sympatry, Science (2016). DOI: 10.1126/science.aai8446


Rosenblum E.B.,University of Idaho | Rosenblum E.B.,University of California at Berkeley | Rosenblum E.B.,Center for the Study of Evolution in Action | Sarver B.A.J.,University of Idaho | And 8 more authors.
Evolutionary Biology | Year: 2012

Understanding the rate at which new species form is a key question in studying the evolution of life on earth. Here we review our current understanding of speciation rates, focusing on studies based on the fossil record, phylogenies, and mathematical models. We find that speciation rates estimated from these different studies can be dramatically different: some studies find that new species form quickly and often, while others find that new species form much less frequently. We suggest that instead of being contradictory, differences in speciation rates across different scales can be reconciled by a common model. Under the "ephemeral speciation model", speciation is very common and very rapid but the new species produced almost never persist. Evolutionary studies should therefore focus on not only the formation but also the persistence of new species. © 2012 The Author(s).


Pennell M.W.,University of Idaho | Pennell M.W.,Center for the Study of Evolution in Action | Sarver B.A.J.,University of Idaho | Sarver B.A.J.,Center for the Study of Evolution in Action | And 2 more authors.
PLoS ONE | Year: 2012

An early burst of speciation followed by a subsequent slowdown in the rate of diversification is commonly inferred from molecular phylogenies. This pattern is consistent with some verbal theory of ecological opportunity and adaptive radiations. One often-overlooked source of bias in these studies is that of sampling at the level of whole clades, as researchers tend to choose large, speciose clades to study. In this paper, we investigate the performance of common methods across the distribution of clade sizes that can be generated by a constant-rate birth-death process. Clades which are larger than expected for a given constant-rate branching process tend to show a pattern of an early burst even when both speciation and extinction rates are constant through time. All methods evaluated were susceptible to detecting this false signature when extinction was low. Under moderate extinction, both the γ-statistic and diversity-dependent models did not detect such a slowdown but only because the signature of a slowdown was masked by subsequent extinction. Some models which estimate time-varying speciation rates are able to detect early bursts under higher extinction rates, but are extremely prone to sampling bias. We suggest that examining clades in isolation may result in spurious inferences that rates of diversification have changed through time. © 2012 Pennell et al.


PubMed | Center for the Study of Evolution in Action and Max Planck Institute for Human Development
Type: | Journal: Scientific reports | Year: 2016

When humans fail to make optimal decisions in strategic games and economic gambles, researchers typically try to explain why that behaviour is biased. To this end, they search for mechanisms that cause human behaviour to deviate from what seems to be the rational optimum. But perhaps human behaviour is not biased; perhaps research assumptions about the optimality of strategies are incomplete. In the one-shot anonymous symmetric ultimatum game (UG), humans fail to play optimally as defined by the Nash equilibrium. However, the distinction between kin and non-kin-with kin detection being a key evolutionary adaption-is often neglected when deriving the optimal strategy. We computationally evolved strategies in the UG that were equipped with an evolvable probability to discern kin from non-kin. When an opponent was not kin, agents evolved strategies that were similar to those used by humans. We therefore conclude that the strategy humans play is not irrational. The deviation between behaviour and the Nash equilibrium may rather be attributable to key evolutionary adaptations, such as kin detection. Our findings further suggest that social preference models are likely to capture mechanisms that permit people to play optimally in an evolutionary context. Once this context is taken into account, human behaviour no longer appears irrational.


Swanson E.M.,Michigan State University | Dworkin I.,Michigan State University | Dworkin I.,Center for the Study of Evolution in Action | Holekamp K.E.,Michigan State University | Holekamp K.E.,Center for the Study of Evolution in Action
Proceedings of the Royal Society B: Biological Sciences | Year: 2011

Size-related traits are common targets of natural selection, yet there is a relative paucity of data on selection among mammals, particularly from studies measuring lifetime reproductive success (LRS). We present the first phenotypic selection analysis using LRS on size-related traits in a large terrestrial carnivore, the spotted hyena, which displays a rare pattern of female-biased sexual size dimorphism (SSD). Using path analysis, we investigate the operation of selection to address hypotheses proposed to explain SSD in spotted hyenas. Ideal size measures are elusive, and allometric variation often obfuscates interpretation of size proxies. We adopt a novel approach integrating two common methods of assessing size, and demonstrate lifetime selection on sizerelated traits that scale hypoallometrically with overall body size. Our data support selection on hypoallometric traits in hyenas, but not on traits exhibiting isometric or hyperallometric scaling relationships, or on commonly used measures of overall body size. Our results represent the first estimate of lifetime selection on a large carnivore, and suggest a possible route for maintenance of female-biased SSD in spotted hyenas. Finally, our results highlight the importance of choosing appropriate measures when estimating animal body size, and suggest caution in interpreting selection on size-related traits as selection on size itself. © 2011 The Royal Society.

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