Publications by EEOB faculty February 1 - February 28

March 23, 2015

An updated classification of Orchidaceae

Mark W. Chase, Kenneth M. Cameron, John V. Freudenstein, Alec M. Pridgeon, Gerardo Salazar, Cássio van den Berg, and André Schuiteman. 2015. Botanical Journal of the Linnean Society. 177(2):151–174. DOI: 10.1111/boj.12234


Since the last classification of Orchidaceae in 2003, there has been major progress in the determination of relationships, and we present here a revised classification including a list of all 736 currently recognized genera. A number of generic changes have occurred in Orchideae (Orchidoideae), but the majority of changes have occurred in Epidendroideae. In the latter, almost all of the problematic placements recognized in the previous classification 11 years ago have now been resolved. In Epidendroideae, we have recognized three new tribes (relative to the last classification): Thaieae (monogeneric) for Thaia, which was previously considered to be the only taxon incertae sedis; Xerorchideae (monogeneric) for Xerorchis; and Wullschlaegelieae for achlorophyllous Wullschlaegelia, which had tentatively been placed in Calypsoeae. Another genus, Devogelia, takes the place of Thaia as incertae sedis in Epidendroideae. Gastrodieae are clearly placed among the tribes in the neottioid grade, with Neottieae sister to the remainder of Epidendroideae. Arethuseae are sister to the rest of the higher Epidendroideae, which is unsurprising given their mostly soft pollinia. Tribal relationships within Epidendroideae have been much clarified by analyses of multiple plastid DNA regions and the low-copy nuclear gene Xdh. Four major clades within the remainder of Epidendroideae are recognized: Vandeae/Podochileae/Collabieae, Cymbidieae, Malaxideae and Epidendreae, the last now including Calypsoinae (previously recognized as a tribe on its own) and Agrostophyllinae s.s. Agrostophyllinae and Collabiinae were unplaced subtribes in the 2003 classification. The former are now split between two subtribes, Agrostophyllinae s.s. and Adrorhizinae, the first now included in Epidendreae and the second in Vandeae. Collabiinae, also probably related to Vandeae, are now elevated to a tribe along with Podochileae. Malaxis and relatives are placed in Malaxidinae and included with Dendrobiinae in Malaxideae. The increased resolution and content of larger clades, recognized here as tribes, do not support the ‘phylads’ in Epidendroideae proposed 22 years ago by Dressler.

Freudenstein Lab

AftrRAD: a pipeline for accurate and efficient de novo assembly of RADseq data

Michael G. Sovic, Anthony C. Fries and H. Lisle Gibbs. 2015. Molecular Ecology Resources. DOI: 10.1111/1755-0998.12378


An increase in studies using restriction site-associated DNA sequencing (RADseq) methods has led to a need for both the development and assessment of novel bioinformatic tools that aid in the generation and analysis of these data. Here, we report the availability of AftrRAD, a bioinformatic pipeline that efficiently assembles and genotypes RADseq data, and outputs these data in various formats for downstream analyses. We use simulated and experimental data sets to evaluate AftrRAD's ability to perform accurate de novo assembly of loci, and we compare its performance with two other commonly used programs, stacks and pyrad. We demonstrate that AftrRAD is able to accurately assemble loci, while accounting for indel variation among alleles, in a more computationally efficient manner than currently available programs. AftrRAD run times are not strongly affected by the number of samples in the data set, making this program a useful tool when multicore systems are not available for parallel processing, or when data sets include large numbers of samples.

Gibbs Lab

Long-term plant responses to climate are moderated by biophysical attributes in a North American desert

Seth M. Munson, Robert H. Webb, David C. Housman, Kari E. Veblen, Kenneth E. Nussear, Erik A. Beever, Kristine B. Hartney, Maria N. Miriti, Susan L. Phillips, Robert E. Fulton and Nita G. Tallent. 2015. DOI: 10.1111/1365-2745.12381


Recent elevated temperatures and prolonged droughts in many already water-limited regions throughout the world, including the southwestern United States, are likely to intensify according to future climate-model projections. This warming and drying can negatively affect perennial vegetation and lead to the degradation of ecosystem properties.To better understand these detrimental effects, we formulate a conceptual model of dryland ecosystem vulnerability to climate change that integrates hypotheses on how plant species will respond to increases in temperature and drought, including how plant responses to climate are modified by landscape, soil and plant attributes that are integral to water availability and use. We test the model through a synthesis of fifty years of repeat measurements of perennial plant species cover in large permanent plots across the Mojave Desert, one of the most water-limited ecosystems in North America.Plant species ranged in their sensitivity to precipitation in different seasons, capacity to increase in cover with high precipitation and resistance to decrease in cover with low precipitation. Our model successfully explains how plant responses to climate are modified by biophysical attributes in the Mojave Desert. For example, deep-rooted plants were not as vulnerable to drought on soils that allowed for deep-water percolation, whereas shallow-rooted plants were better buffered from drought on soils that promoted water retention near the surface. Our results emphasize the importance of understanding climate–vegetation relationships in the context of biophysical attributes that influence water availability and provide an important forecast of climate-change effects, including plant mortality and land degradation in dryland regions throughout the world.

Functional circadian clock genes are essential for the overwintering diapause of the Northern house mosquito, Culex pipiens

Megan E. Meuti, Mary Stone, Tomoko Ikeno, and David L. Denlinger. 2015. J Exp Biol 218:412-422. doi: 10.1242/​jeb.113233


The short day lengths of late summer are used to program the overwintering adult diapause (dormancy) of the Northern house mosquito, Culex pipiens. Here, we investigated the role of clock genes in initiating this diapause and asked whether the circadian cycling of clock gene expression persists during diapause. We provide evidence that the major circadian clock genes continue to cycle throughout diapause and after diapause has been terminated. RNA interference (RNAi) was used to knock down the core circadian clock genes and to then assess the impact of the various clock genes on the ability of females to enter diapause. RNAi directed against negative circadian regulators (period, timeless and cryptochrome2) caused females that were reared under diapause-inducing, short day conditions to avert diapause. In contrast, knocking down the circadian-associated gene pigment dispersing factor caused females that were reared under diapause-averting, long day conditions to enter a diapause-like state. Our results implicate the circadian clock in the initiation of diapause in C. pipiens.

Evidence for alternative male morphs in a Tanganyikan cichlid fish

J. K. Hellmann, C. M. O'Connor, I. Y. Ligocki, T. M. Farmer, T. J. Arnold, A. R. Reddon, K. A. Garvy, S. E. Marsh-Rollo, S. Balshine and I. M. Hamilton. 2015. Journal of Zoology. DOI: 10.1111/jzo.12222


Teleost fish show tremendous variation in breeding systems. In particular, indeterminate growth and external fertilization create great disparities in reproductive success among males, which drive the evolution of male reproductive polymorphisms. Here, we present evidence for alternative male reproductive tactics in Neolamprologus modestus, a substrate-spawning African cichlid fish. We observed two types of males in our study site: (1) males that guarded large territories comprised of smaller subterritories of several females and (2) males that did not hold territories and were vigorously attacked by the guarding males upon intrusion into the guarding male's territory. We hypothesized that these intruder males constitute an alternative male phenotype. To test this hypothesis, we collected both territorial males and these intruder males to determine if there were differences in overall body size, gonad size, age or hormone profiles between the two male phenotypes that would be consistent with alternative reproductive tactics in this species. We also collected guarded offspring from territorial male and female pairs to determine if there was any extra-pair paternity in N. modestus that could indicate the possibility of alternative reproductive tactics. We found that intruder males were significantly smaller in body size and had significantly larger testes in absolute and relative mass compared with territorial paired males. While we assigned no paternity to any collected intruder males, we found that extra-pair paternity occurred in eight of the 12 collected broods and accounted for c. 27% of all offspring across all broods. Finally, the two sets of males did not differ significantly in age or in circulating androgen levels, suggesting that individuals may not change morphs within their lifetime, but instead may adopt distinct life history strategies. Collectively, we provide strong evidence that intruder N. modestus males represent an alternative small-bodied male morph that may practice alternative reproductive tactics.

Hamilton Lab

The evolution of phylogeographic data sets

Ryan C. Garrick, Isabel A. S. Bonatelli, Chaz Hyseni, Ariadna Morales, Tara A. Pelletier, Manolo F. Perez, Edwin Rice, Jordan D. Satler, Rebecca E. Symula, Maria Tereza C. Thomé and Bryan C. Carstens. 2015. Molecular Ecology 24 (6):1164–1171. DOI: 10.1111/mec.13108


Empirical phylogeographic studies have progressively sampled greater numbers of loci over time, in part motivated by theoretical papers showing that estimates of key demographic parameters improve as the number of loci increases. Recently, next-generation sequencing has been applied to questions about organismal history, with the promise of revolutionizing the field. However, no systematic assessment of how phylogeographic data sets have changed over time with respect to overall size and information content has been performed. Here, we quantify the changing nature of these genetic data sets over the past 20 years, focusing on papers published in Molecular Ecology. We found that the number of independent loci, the total number of alleles sampled and the total number of single nucleotide polymorphisms (SNPs) per data set has improved over time, with particularly dramatic increases within the past 5 years. Interestingly, uniparentally inherited organellar markers (e.g. animal mitochondrial and plant chloroplast DNA) continue to represent an important component of phylogeographic data. Single-species studies (cf. comparative studies) that focus on vertebrates (particularly fish and to some extent, birds) represent the gold standard of phylogeographic data collection. Based on the current trajectory seen in our survey data, forecast modelling indicates that the median number of SNPs per data set for studies published by the end of the year 2016 may approach ~20 000. This survey provides baseline information for understanding the evolution of phylogeographic data sets and underscores the fact that development of analytical methods for handling very large genetic data sets will be critical for facilitating growth of the field.


Carstens Lab

Joint control of terrestrial gross primary productivity by plant phenology and physiology

Jianyang Xia, Shuli Niu, Philippe Ciais, Ivan A. Janssens, Jiquan Chen, Christof Ammann, Altaf Arain, Peter D. Blanken, Alessandro Cescatti, Damien Bonal, Nina Buchmann, Peter S. Curtis, Shiping Chen, Jinwei Dong, Lawrence B. Flanagan, Christian Frankenberg, Teodoro Georgiadis, Christopher M. Gough, Dafeng Hui, Gerard Kiely, Jianwei Li, Magnus Lund, Vincenzo Magliulo, Barbara Marcolla, Lutz Merbold, Leonardo Montagnani, Eddy J. Moors, Jørgen E. Olesen, Shilong Piao, Antonio Raschi, Olivier Roupsard, Andrew E. Suyker, Marek Urbaniak, Francesco P. Vaccari, Andrej Varlagin, Timo Vesala, Matthew Wilkinson, Ensheng Weng, Georg Wohlfahrt, Liming Yan, and Yiqi Luo. 2015. PNAS 12(9): 2788–2793. doi: 10.1073/pnas.1413090112


Terrestrial gross primary productivity (GPP) varies greatly over time and space. A better understanding of this variability is necessary for more accurate predictions of the future climate–carbon cycle feedback. Recent studies have suggested that variability in GPP is driven by a broad range of biotic and abiotic factors operating mainly through changes in vegetation phenology and physiological processes. However, it is still unclear how plant phenology and physiology can be integrated to explain the spatiotemporal variability of terrestrial GPP. Based on analyses of eddy–covariance and satellite-derived data, we decomposed annual terrestrial GPP into the length of the CO2 uptake period (CUP) and the seasonal maximal capacity of CO2 uptake (GPPmax). The product of CUP and GPPmax explained >90% of the temporal GPP variability in most areas of North America during 2000–2010 and the spatial GPP variation among globally distributed eddy flux tower sites. It also explained GPP response to the European heatwave in 2003 (r2 = 0.90) and GPP recovery after a fire disturbance in South Dakota (r2 = 0.88). Additional analysis of the eddy–covariance flux data shows that the interbiome variation in annual GPP is better explained by that in GPPmax than CUP. These findings indicate that terrestrial GPP is jointly controlled by ecosystem-level plant phenology and photosynthetic capacity, and greater understanding of GPPmax and CUP responses to environmental and biological variations will, thus, improve predictions of GPP over time and space.

Curtis Lab

Imidazole derivative KK-42 boosts pupal diapause incidence and delays diapause termination in several insect species

Yanqun Liu, Qirui Zhang, David L. Denlinger. 2015. Journal of Insect Physiology 74:38–44. doi:10.1016/j.jinsphys.2015.02.003


The imidazole derivative KK-42 is a synthetic insect growth regulator known previously to be capable of averting embryonic diapause in several Lepidoptera, but whether it also affects diapauses occurring in other developmental stages remains unknown. In the present study, we examined the effect of KK-42 on pupal diapause in two species of Lepidoptera, the Chinese oak silkworm Antheraea pernyi and the corn earworm Helicoverpa zea, and in one species of Diptera, the flesh fly Sarcophaga crassipalpis. In A. pernyi, KK-42 delayed pupal diapause termination under the long day conditions that normally break diapause in this species. Likewise, in H. zea, KK-42 delayed termination of pupal diapause, a diapause that, in this species, is normally broken by high temperature. KK-42-treated pupae of these two species eventually terminated diapause and successfully emerged as adults, but the timing of diapause termination was significantly delayed. KK-42 also significantly increased the incidence of pupal diapause in H. zea and S. crassipalpis when administered to larvae that were environmentally programmed for diapause, but it was not capable of inducing pupal diapause in H. zea if larvae were reared under environmental conditions that do not normally evoke the diapause response. Experiments with H. zea showed that the effect of KK-42 on pupal diapause was dose- and stage-dependent, but not temperature-dependent. Results presented here are consistent with a link between KK-42 and the ecdysteroid signaling pathway that regulates pupal diapause.

Insect capa neuropeptides impact desiccation and cold tolerance

Selim Terhzaz, Nicholas M. Teets, Pablo Cabrero, Louise Henderson, Michael G. Ritchie, Ronald J. Nachman, Julian A. T. Dow, David L. Denlinger, and Shireen-A. Davies. 2015. PNAS 12(9): 2882–2887. doi: 10.1073/pnas.1501518112


The success of insects is linked to their impressive tolerance to environmental stress, but little is known about how such responses are mediated by the neuroendocrine system. Here we show that the capability (capa) neuropeptide gene is a desiccation- and cold stress-responsive gene in diverse dipteran species. Using targeted in vivo gene silencing, physiological manipulations, stress-tolerance assays, and rationally designed neuropeptide analogs, we demonstrate that the Drosophila melanogaster capa neuropeptide gene and its encoded peptides alter desiccation and cold tolerance. Knockdown of the capa gene increases desiccation tolerance but lengthens chill coma recovery time, and injection of capa peptide analogs can reverse both phenotypes. Immunohistochemical staining suggests that capa accumulates in the capa-expressing Va neurons during desiccation and nonlethal cold stress but is not released until recovery from each stress. Our results also suggest that regulation of cellular ion and water homeostasis mediated by capa peptide signaling in the insect Malpighian (renal) tubules is a key physiological mechanism during recovery from desiccation and cold stress. This work augments our understanding of how stress tolerance is mediated by neuroendocrine signaling and illustrates the use of rationally designed peptide analogs as agents for disrupting protective stress tolerance.