Publications by EEOB faculty August 1 - August 31

September 7, 2016
eeob 2016

Origin of a cryptic lineage in a threatened reptile through isolation and historical hybridization

M G Sovic, A C Fries and H L Gibbs. 2016. Heredity. doi: 10.1038/hdy.2016.56

Abstract

Identifying phylogenetically distinct lineages and understanding the evolutionary processes by which they have arisen are important goals of phylogeography. This information can also help define conservation units in endangered species. Such analyses are being transformed by the availability of genomic-scale data sets and novel analytical approaches for statistically comparing different historical scenarios as causes of phylogeographic patterns. Here, we use genomic-scale restriction-site-associated DNA sequencing (RADseq) data to test for distinct lineages in the endangered Eastern Massasauga Rattlesnake (Sistrurus catenatus). We then use coalescent-based modeling techniques to identify the evolutionary mechanisms responsible for the origin of the lineages in this species. We find equivocal evidence for distinct phylogenetic lineages within S. catenatus east of the Mississippi River, but strong support for a previously unrecognized lineage on the western edge of the range of this snake, represented by populations from Iowa, USA. Snakes from these populations show patterns of genetic admixture with a nearby non-threatened sister species (Sistrurus tergeminus). Tests of historical demographic models support the hypothesis that the genetic distinctiveness of Iowa snakes is due to a combination of isolation and historical introgression between S. catenatus and S. tergeminus. Our work provides an example of how model-based analysis of genomic-scale data can help identify conservation units in rare species.

Multimodal Communication in Wolf Spiders (Lycosidae) An Emerging Model for Study

G.W. Uetz, D.L. Clark, J.A. Roberts. 2016. Advances in the Study of Behavior, 48:117-159. http://dx.doi.org/10.1016/bs.asb.2016.03.003 

Abstract

The subject of communication in spiders is of growing interest to animal behaviorists and evolutionary biologists for many reasons. Com- munication is critical for spiders, as they are predatory and potentially cannibalistic and thus positioned uniquely at the intersection of sexual and natural selection. Spiders have a very different sensory world, or “umwelt” than better-studied taxa (such as vertebrates and insects) and perceive their world through substratum vibration (eg, environmental surfaces or the silk strands of webs), chemotactile or olfactory cues (eg, silk-borne or airborne pheromones), and widely varying visual capabilities (ranging from rudimentary light/dark perception to high-resolution visual acuity). Perhaps as a consequence, spiders exhibit a great diversity of communication behaviors. Spiders also have a relatively simple central nervous system (CNS), yet they can integrate sensory input from multiple sources and systems at the same time. Finally, like many invertebrates, spi- ders are small in size and often easy to work within the laboratory and/or field.

Split scores: a tool to quantify phylogenetic signal in genome-scale data

Elizabeth S. Allman, Laura S. Kubatko, John A. Rhodes. 2016. http://arxiv.org/pdf/1608.00942.pdf

Abstract

Under the general Markov model of sequence evolution on a tree T , each bipartition of the taxa corresponds to a flattening — a rearrangement of the distribution of site pattern frequencies into a matrix. If the bipartition of the taxa is induced by an edge e in the tree T, then this matrix flattening is generically of rank 4. For all other bipartitions of the taxa, the matrix flattening has rank greater than 4. Using this result, we introduce a split score based on the singular value decomposition of a matrix to assess support for splits in sequence data. Using simulation, we explore some of the properties of the split score including its dependence on sequence length, branch length, size of a split and its ability to detect true splits in the underlying tree. Computation of the split score has been implemented in the software package SplitSup. Using a sliding window analysis, split scores are used to detect changes in the evolutionary process in data from primates, mosquitoes, and viruses. [phylogenetic trees, split scores, genome-scale data analysis, general Markov model, matrix flattenings, singular value decomposition].

Population Genetics and Seed Set in Feral, Ornamental Miscanthus sacchariflorus

Evans Mutegi, Allison A. Snow, PhD, Catherine L. Bonin, Emily A. Heaton, Hsiaochi Chang, Carol J. Gernes, Destiny J. Palik, and Maria N. Miriti. 2016. doi = 10.1614/IPSM-D-16-00030.1

Abstract

Ornamental grasses may become invasive weeds depending on their ability to naturalize and out-compete other species. Miscanthus sacchariflorus (Amur silvergrass) is a tall, self-incompatible, non-native grass that has become naturalized in eastern North America, forming monospecific stands and raising concerns about its potential invasiveness. To better understand the extent of clonal and sexual reproduction in feral populations, we examined their population genetic structure, seed production, and ploidy. We surveyed 21 populations in Iowa and Minnesota using eight polymorphic microsatellite markers. Only 34 multilocus genotypes (MLGs) were detected from a total of 390 samples. All of the study populations had more than one MLG, thereby allowing cross-pollination with near neighbors, but most were dominated by one or a few MLGs. Low genetic divergence suggests that all populations may have originated from similar cultivars. Cluster analysis showed that the six populations from Minnesota were extremely similar to each other, while the fifteen populations from Iowa were somewhat more diverse. Seed production was quantified for 20 populations and ploidy for 11 populations. Average seed production was very low (<0.30 seeds per panicle), although most populations did produce seeds. Because the populations were diploid (2x), they also may have the potential to hybridize with ornamental varieties of M. sinensis (Chinese silvergrass), a diploid close relative. Clonal growth, self-incompatibility, and spatial isolation of compatible clones may contribute to pollen-limited seed set in these populations. Low seed set may affect the rate of spread of feral M. sacchariflorus, which appears to disperse vegetatively as well as by seed. Although this species is not widely viewed as invasive, it is worth monitoring as a species that may become more widespread in the future.

Trail-following behavior by males of the wolf spider, Schizocosa ocreata (Hentz)

Ryan D. Bell, J. Andrew Roberts. 2016. J Ethol. doi:10.1007/s10164-016-0486-4

Abstract

Male spiders are able to detect and respond to chemical cues deposited by females in the environment. In many species, detection of these chemicals may be the first indication a male has to the presence of a nearby female. In wolf spiders (Lycosidae), which do not produce webs, females leave a trail of silk and chemical cues as they move through the leaf-litter habitat. Males could increase encounter rates with receptive females if they were able to follow these trails. We used behavioral assays to determine whether male Schizocosa ocreata (Hentz) wolf spiders are able to detect and respond to cues resulting from a single-pass trail by a female, and whether they are able to determine the direction of female travel. Our focal males responded to virgin adult female trails with following behavior, but showed no propensity to follow trails from other conspecifics (subadult females or males). While males were able to follow a female trail, our observations and analysis indicates that they are not able to determine trail directionality.

Events of Increased Biodiversity: Evolutionary Radiations in the Fossil Record. By Pascal Neige.

Hunter, John P. 2016. The Quarterly Review of Biology. doi: 10.1086/688110

Summary

This book is organized into four main chapters. Chapter 1, A Singular Work of Theater, reprises the metaphor of actors on a stage to describe the role of species and environments in the history of life. Neige uses this conceit to introduce Stephen Jay Gould’s concept of contingency in the uniqueness of the actual history of life and the role of chance and random accidents. Chapter 2, The Fossil Record, provides a litany of the major features of the fossil record, both strengths and weaknesses, including Darwin’s reservations. A highlight of this chapter was the discussion of the work of John Phillips who, just one year after the publication Darwin’s On the Origin of Species, produced the first sampling-standardized diversification curve for the history of life (by dividing number of taxa by the thickness of strata). The chapter deals with basics such as the geologic time scale, methods of correcting for sampling biases (emphasis on rarefaction and collectors’ curves), and the recent development of large paleontological databases (big data in deep time). Chapter 3, The Phenomenon of Evolutionary Radiation, deals with the conceptual framework of categorizing and studying radiations. This section is necessary to make sure that readers understand the particular usage of terms in this volume. The subdivision of radiations into adaptive, nonadaptive, and postextinction types seems artificial, however, as the categories grade into one another. Chapter 4, Examples of Evolutionary Radiations, is the core of the book with four carefully chosen case studies: the Cambrian explosion, ammonites, flowering plants, and sea urchins. Unless one has already followed the literature on these groups closely, a reader is sure to learn something new or previously overlooked.

Microbiome Composition and Diversity of the Ice-Dwelling Sea Anemone, Edwardsiella andrillae

Alison E. Murray, Frank R. Rack, Robert Zook, Michael J. M. Williams, Mary L. Higham, Michael Broe, Ronald S. Kaufmann and Marymegan Daly. 2016. Integr. Comp. Biol. doi: 10.1093/icb/icw095

Abstract

Edwardsiella andrillae is a sea anemone (Cnidaria: Anthozoa: Actiniaria) only known to live embedded in the ice at the seawater interface on the underside of the Ross Ice Shelf, Antarctica. Although the anatomy and morphological characteristics of E. andrillae have been described, the adaptations of this species to the under-ice ecosystem have yet to be examined. One feature that may be important to the physiology and ecology of E. andrillae is its microbiome, which may play a role in health and survival, as has been deduced in other metazoans, including anthozoans. Here we describe the microbiome of five specimens of E. andrillae, compare the diversity we recovered to that known for temperate anemones and another Antarctic cnidarian, and consider the phylogenetic and functional implications of microbial diversity for these animals. The E. andrillae microbiome was relatively low in diversity, with seven phyla detected, yet included substantial phylogenetic novelty. Among the five anemones investigated, the distribution of microbial taxa varied; this trait appears to be shared by many anthozoans. Most importantly, specimens either appeared to be dominated by Proteobacteria-affiliated members or by deeply branching Tenericute sequences. There were few closely related sequence types that were common to temperate and Antarctic sea anemone microbiomes, the exception being an Acinetobacter-related representative. Similar observations were made between microbes associated with E. andrillae and an Antarctic soft coral; however, there were several closely-related, low abundance Gammaproteobacteria in both Antarctic microbiomes, particularly from the soft coral, that are also commonly detected in Southern Ocean seawater. Although this preliminary study leaves open many questions concerning microbiome diversity and its role in host ecology, we identify major lineages of microbes (e.g., diverse deep-branching Alphaproteobacteria, Epsilonproteobacteria, and divergent Tenericutes affiliates) that may play critical roles, and we highlight the current understanding and the need for future studies of sea anemone–microbiome relationships.

Entrainment of eclosion and preliminary ontogeny of circadian clock gene expression in the flesh fly, Sarcophaga crassipalpis

Clancy A. Short, , Megan E. Meuti , Qirui Zhang , David L. Denlinger. 2016. http://dx.doi.org/10.1016/j.jinsphys.2016.08.003

Abstract

Timing of circadian activities is controlled by rhythmic expression of clock genes in pacemaker neurons in the insect brain. Circadian behavior and clock gene expression can entrain to both thermoperiod and photoperiod but the availability of such cues, the organization of the brain, and the need for circadian behavior change dramatically during the course of insect metamorphosis. We asked whether photoperiod or thermoperiod entrains the clock during pupal and pharate adult stages by exposing flies to different combinations of thermoperiod and photoperiod and observing the effect on the timing of adult eclosion. This study used qRT-PCR to examine how entrainment and expression of circadian clock genes change during the course of development in the flesh fly, Sarcophaga crassipalpis. Thermoperiod entrains expression of period and controls the timing of adult eclosion, suggesting that the clock gene period may be upstream of the eclosion pathway. Rhythmic clock gene expression is evident in larvae, appears to cease during the early pharate adult stage, and resumes again by the time of adult eclosion. Our results indicate that both patterns of clock gene expression and the cues to which the clock entrains are dynamic and respond to different environmental signals at different developmental stages in S. crassipalpis.

Social-ecological feedbacks lead to unsustainable lock-in in an inland fishery

Sarah Laborde, Alfonso Fernández, Sui Chian Phang, Ian M. Hamilton, Nathaniel Henry, Hahn Chul Jung, Aboukar Mahamat, Mouadjamou Ahmadou, Bruno K. Labara, Saïdou Kari, Michael Durand, Bryan Mark, Paul Scholte, Ningchuan Xiao, Roland Ziebe, Mark Moritz. 2016. http://dx.doi.org/10.1016/j.gloenvcha.2016.08.004

Abstract

This interdisciplinary paper presents an empirical analysis of techno-institutional lock-in in a regional fishery, in the Logone floodplain in the Far North Region of Cameroon. In the Logone floodplain, one fishing technique is spreading exponentially even though it is changing the social, hydrological and ecological dynamics of the system in ways that are largely considered problematic by local communities. We use a complex systems framework to analyze large hydrological and socio-economic datasets. Results show how social-ecological feedbacks foster the spread of the technique and contribute to the process of lock-in. The lock-in leads to a resistance to change despite awareness of the technique’s impact, a situation that may also be described as a social-ecological trap. We identify and explain four kinds of positive feedback loops relating to socio-economic, behavioral, demographic and hydrological processes, respectively. We also identify possible solutions that consider the complexity of the feedback loops across multiple dimensions of the floodplain system.