EEOB Publications July 1- July 31

August 4, 2020

EEOB Publications July 1- July 31

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Otolith microchemistry shows natal philopatry of walleye in western Lake Erie

Kuan-YuChen, Stuart A. Ludsin, Benjamin J. Marcek, John W. Olesik, Elizabeth A. Marschall. 2020. Journal of Great Lakes Research. https://doi.org/10.1016/j.jglr.2020.06.006

Abstract

Natal philopatry is important to the structure of fish populations because it can lead to local adaptations among component stocks of a mixed population, reducing the risk of recruitment failure. By contrast, straying between component stocks may bolster declining populations or allow for colonization of new habitat. To examine rates of natal philopatry and straying among western Lake Erie walleye (Sander vitreus) stocks, we used the concentration of strontium [Sr] in otolith cores to determine the natal origin of adults captured at three major spawning sites: the Sandusky (n = 62) and Maumee (n = 55) rivers and the Ohio reef complex (n = 50) during the 2012–2013 spawning seasons. Mean otolith core [Sr] was consistently and significantly higher for individuals captured in the Sandusky River than for those captured in the Maumee River or Ohio reef complex. Although logistic regression indicates that no individuals with a Maumee River or Ohio reef complex origin were captured in the Sandusky River, quadratic discriminant analysis suggests low rates of straying of fish between the Maumee and Sandusky rivers. Our results suggest little straying and high rates of natal philopatry in the Sandusky River walleye stock. Similar rates of natal philopatry may also exist across western Lake Erie walleye stocks, demonstrating a need for stock-specific management.


The Influence of Arbuscular Mycorrhizal Fungi on Plant Reproduction

Alison E. Bennett & Heiler C. Meek. 2020. Journal of Chemical Ecology. https://doi.org/10.1007/s10886-020-01192-4

Abstract

Arbuscular mycorrhizal (AM) fungi can influence all components of plant reproduction including pollen delivery, pollen germination, pollen tube growth, fertilization, and seed germination. AM fungi associate with plant roots, uptake nutrients, and prime plants for faster defense responses. Our literature review first identified four testable hypotheses describing how AM fungi could alter pollen delivery: (1) We hypothesize AM fungi promote floral display size. The influence of AM fungi on flower size and number is supported by literature, however there are no studies on floral color. (2) We hypothesize AM fungi promote pollen and nectar quality and quantity, and, as reported before, AM fungi promote male fitness over female fitness. (3) We hypothesize AM fungi promote both earlier and longer flowering times, but we found no consistent trend in the data for earlier or later or longer flowering times. (4) We hypothesize AM fungi alter floral secondary chemistry and VOCs, and find there is clear evidence for the alteration of floral chemistry but little data on VOCs. Second, we focus on how AM fungi could alter pollen germination, pollen tube growth, and fertilization, and present three testable hypotheses. We found evidence that AM fungi influence pollen germination and pollen tube growth, production of seeds, and seed germination. However, while most of these influences are positive they are not conclusive, because studies have been conducted in small numbers of systems and groups. Therefore, we conclude that the majority of research to date may not be measuring the influence of AM fungi on the most important components of plant reproduction: pollen germination, pollen tube growth, fertilization, and seed germination.


The molecular basis of venom resistance in a rattlesnake‐squirrel predator‐prey system

H. Lisle Gibbs, Libia Sanz, Alicia Pérez, Alexander Ochoa, Alyssa T.B. Hassinger, Matthew L. Holding, Juan J. Calvete. 2020. Molecular Ecology. https://doi.org/10.1111/mec.15529

Abstract

Understanding how interspecific interactions mould the molecular basis of adaptations in coevolving species is a long‐sought goal of evolutionary biology. Venom in predators and venom resistance proteins in prey are coevolving molecular phenotypes, and while venoms are highly complex mixtures it is unclear if prey respond with equally complex resistance traits. Here, we use a novel molecular methodology based on protein affinity columns to capture and identify candidate blood serum resistance proteins (“venom interactive proteins” [VIPs]) in California Ground Squirrels (Otospermophilus beecheyi ) that interact with venom proteins from their main predator, Northern Pacific Rattlesnakes (Crotalus o. oreganus ). This assay showed that serum‐based resistance is both population‐ and species‐specific, with serum proteins from ground squirrels showing higher binding affinities for venom proteins of local snakes compared to allopatric individuals. Venom protein specificity assays identified numerous and diverse candidate prey resistance VIPs but also potential targets of venom in prey tissues. Many specific VIPs bind to multiple snake venom proteins and, conversely, single venom proteins bind multiple VIPs, demonstrating that a portion of the squirrel blood serum “resistome” involves broad‐based inhibition of nonself proteins and suggests that resistance involves a toxin scavenging mechanism. Analyses of rates of evolution of VIP protein homologues in related mammals show that most of these proteins evolve under purifying selection possibly due to molecular constraints that limit the evolutionary responses of prey to rapidly evolving snake venom proteins. Our method represents a general approach to identify specific proteins involved in co‐evolutionary interactions between species at the molecular level.


Climate change influences mycorrhizal fungal–plant interactions, but conclusions are limited by geographical study bias

Alison E. Bennett  Aimée T. Classen. 2020. Ecology. https://doi.org/10.1002/ecy.2978

Abstract

Climate change is altering the interactions among plants and soil organisms in ways that will alter the structure and function of ecosystems. We reviewed the literature and developed a map of studies focused on how the three most common types of mycorrhizal fungi (arbuscular mycorrhizal [AM], ectomycorrhizal [EcM], and ericoid mycorrhizal [ErM] fungi) respond to elevated atmospheric carbon dioxide concentrations (eCO2), climatic warming, and changes in the distribution of precipitation. Broadly, we ask how do mycorrhizal fungi respond to climate change, how do these responses vary by fungal type, and how do mycorrhizal traits influence plant adaptation, movement, or extinction in response to climatic change? First, we found that 92% of studies were conducted in the northern hemisphere, and plant host, ecosystem type and study location were only correlated with each other in the northern hemisphere because studies across all mycorrhizal fungal types were only common in the northern hemisphere. Second, we show that temperature and rainfall variability had more variable effects than eCO2 on mycorrhizal fungal structures, but these effects were context dependent. Third, while mycorrhizal fungal types vary in their responses to climate change, it appears that warming leads to more variable responses in ectomycorrhizal than in arbuscular mycorrhizal fungi. Finally, we discuss common traits of mycorrhizal fungi that could aid in fungal and plant adaption to climate change. We posit that mycorrhizal fungi can buffer plant hosts against extinction risk, they can facilitate or retard the dispersal success of plants moving away from poor environments, and, by buffering host plants, they can enable host plant adaptation to new climates. All of these influences are, however, context dependent a finding that reflects the complex traits of mycorrhizal fungi as a group, the diversity of plant species they associate with and the variation in ecosystems in which they reside. Overall, while we point out many gaps in our understanding of the influence of climate changes on mycorrhizal fungi, we also highlight the large number of opportunities for researching plant and mycorrhizal fungal responses to and mitigation of climate changes.


Species, Sequence Types and Alleles: Dissecting Genetic Variation in Acanthamoeba

Paul A. Fuerst and Gregory C. Booton. 2020. Pathogens.

Abstract

Species designations within Acanthamoeba are problematic because of pleomorphic morphology. Molecular approaches, including DNA sequencing, hinted at a resolution that has yet to be fully achieved. Alternative approaches were required. In 1996, the Byers/Fuerst lab introduced
the concept of sequence types. Differences between isolates of Acanthamoeba could be quantitatively assessed by comparing sequences of the nuclear 18S rRNA gene, ultimately producing 22 sequence types, designated T1 through T22. The concept of sequence types helps our understanding of Acanthamoeba evolution. Nevertheless, substantial variation in the 18S rRNA gene differentiates many isolates within each sequence type. Because the majority of isolates with sequences in the international DNA databases have been studied for only a small segment of the gene, designated ASA.S1, genetic variation within this hypervariable region of the 18S rRNA gene has been scrutinized. In 2002, we first categorized variation in this region in a sample of T3 and T4 isolates from Hong Kong, observing ten “alleles” within type T4 and five “alleles” within T3. Subsequently, confusion occurred when different labs applied redundant numerical labels to identify different alleles. A more unified approach was required. We have tabulated alleles occurring in the sequences submitted to the international DNA databases, and determined their frequencies. Over 150 alleles have occurred more than once within 3500+ isolates of sequence type T4. Results from smaller samples of other sequence types (T3, T5, T11 and T15, and supergroup T2/6) have also been obtained. Our results provide new insights into the evolutionary history of Acanthamoeba, further illuminating the degree of genetic separation between significant taxonomic units within the genus, perhaps eventually elucidating what constitutes a species of Acanthamoeba.


Integrating population genetic structure, microbiome, and pathogens presence data in Dermacentor variabilis

Paula Lado​, Bo Luan, Michelle E.J. Allerdice, Christopher D. Paddock, Sandor E. Karpathy, Hans Klompen. 2020. PeerJ 8:e9367 https://doi.org/10.7717/peerj.9367 

Abstract

Tick-borne diseases (TBDs) continue to emerge and re-emerge in several regions of the world, highlighting the need for novel and effective control strategies. The development of effective strategies requires a better understanding of TBDs ecology, and given the complexity of these systems, interdisciplinary approaches are required. In recent years, the microbiome of vectors has received much attention, mainly because associations between native microbes and pathogens may provide a new promising path towards the disruption of pathogen transmission. However, we still do not fully understand how host genetics and environmental factors interact to shape the microbiome of organisms, or how pathogenic microorganisms affect the microbiome and vice versa. The integration of different lines of evidence may be the key to improve our understanding of TBDs ecology. In that context, we generated microbiome and pathogen presence data for Dermacentor variabilis, and integrated those data sets with population genetic data, and metadata for the same individual tick specimens. Clustering and multivariate statistical methods were used to combine, analyze, and visualize data sets. Interpretation of the results is challenging, likely due to the low levels of genetic diversity and the high abundance of a few taxa in the microbiome. Francisella was dominant in almost all ticks, regardless of geography or sex. Nevertheless, our results showed that, overall, ticks from different geographic regions differ in their microbiome composition. Additionally, DNA of Rickettsia rhipicephali, R. montanensis, R. bellii, and Anaplasma spp., was detected in D. variabilis specimens. This is the first study that successfully generated microbiome, population genetics, and pathogen presence data from the same individual ticks, and that attempted to combine the different lines of evidence. The approaches and pre-processing steps used can be applied to a variety of taxa, and help better understand ecological processes in biological systems.


The FLUXNET2015 dataset and the ONEFlux processing pipeline for eddy covariance data

Gilberto Pastorello [...] Peter S. Curtis [...] et al. 2020. Sci Data 7, 225. https://doi.org/10.1038/s41597-020-0534-3

Abstract

The FLUXNET2015 dataset provides ecosystem-scale data on CO2, water, and energy exchange between the biosphere and the atmosphere, and other meteorological and biological measurements, from 212 sites around the globe (over 1500 site-years, up to and including year 2014). These sites, independently managed and operated, voluntarily contributed their data to create global datasets. Data were quality controlled and processed using uniform methods, to improve consistency and intercomparability across sites. The dataset is already being used in a number of applications, including ecophysiology studies, remote sensing studies, and development of ecosystem and Earth system models. FLUXNET2015 includes derived-data products, such as gap-filled time series, ecosystem respiration and photosynthetic uptake estimates, estimation of uncertainties, and metadata about the measurements, presented for the first time in this paper. In addition, 206 of these sites are for the first time distributed under a Creative Commons (CC-BY 4.0) license. This paper details this enhanced dataset and the processing methods, now made available as open-source codes, making the dataset more accessible, transparent, and reproducible.


Stenamoeba dejonckheerei sp. nov., a Free-Living Amoeba Isolated from a Thermal Spring

Manuel Alejandro Borquez-Román, Luis Fernando Lares-Jiménez, Libia Zulema Rodriguez-Anaya, Jose Reyes Gonzalez-Galaviz, Paul A. Fuerst, José Cuauhtémoc Ibarra-Gámez, Ramón Casillas-Hernández, and Fernando Lares-Villa. 2020. Pathogens 2020, 9(7), 586; https://doi.org/10.3390/pathogens9070586

Abstract

Two amoeboid organisms were obtained from water samples taken from a thermal spring, "Agua Caliente", in Northwestern Mexico. The isolates were obtained when samples were cultivated at 37 °C on non-nutrient agar coated with Escherichia coli. The initial identification of the isolates was performed morphologically using light microscopy. The samples were found to have trophozoite morphology consistent with members of the genus Stenamoeba, a genus derived in 2007 from within the abolished polyphyletic genus Platyamoeba. Further analysis was performed by sequencing PCR products obtained using universal eukaryotic primers for the small subunit ribosomal ribonucleic acid (SSU rRNA) gene. Sequencing primers were designed to allow the comparison of the 18S rRNA gene sequences of the new isolates with previous sequences reported for Stenamoeba. Phylogenetic relationships among sequences from Stenamoeba were determined using Maximum Likelihood analysis. The results showed the two "Agua Caliente" sequences to be closely related, while clearly separating them from those of other Stenamoeba taxa. The degrees of sequence differentiation from other taxa were considered sufficient to allow us to propose that the Mexican isolates represent a new species.


Contrasting responses of black fly species (Diptera: Simuliidae) to experimental whole‐stream warming

Daniel Nelson, Jonathan P. Benstead, Alexander D. Huryn, Wyatt F. Cross, James M. Hood, Philip W. Johnson, James R. Junker, Gísli M. Gíslason, Jón S. Ólafsson. 2020. Freshwater Biology. https://doi.org/10.1111/fwb.13583

Abstract

As global temperatures continue to rise, assessment of how species within ecological communities respond to shifts in temperature has become increasingly important. However, such assessments require detailed long‐term observations or ecosystem‐level manipulations that allow for interactions among species and the potential for species dispersal and exchange with the regional species pool.
We examined the effects of experimental whole‐stream warming on a larval black fly assemblage in southwest Iceland. We used a paired‐catchment design, in which we studied the warmed stream and a nearby reference stream for 1 year prior to warming and 2 years during warming and estimated population abundance, biomass, secondary production, and growth rates for larvae of three black fly species. Experimental warming by 3.8°C had contrasting effects on the three black fly species in the assemblage. The abundance, biomass, growth, and production of Prosimulium ursinum decreased in the experimental stream during the warming manipulation. Despite increasing in the reference stream, the abundance, biomass, and production of another species, Simulium vernum , decreased in the experimental stream during warming. In contrast, warming had an overall positive effect on Simulium vittatum . While warming had little effect on the growth of overwintering cohorts of S. vittatum , warming led to an additional cohort during the summer months and increased its abundance, biomass, and production. Overall, family‐level production was enhanced by warming, despite variation in species‐level responses. Our study illustrates that the effects of climate warming are likely to differ even among closely related species. Moreover, our study highlights the need for further investigation into the uneven effects of warming on individual species and how those variable effects influence food web dynamics and ecosystem function.


Revision of the genus Oxyscelio Kieffer (Hymenoptera, Scelionidae) from China

WEN-HUI MO, HUA-YAN CHEN, NORMAN F. JOHNSON, HONG PANG, LI MA, JING-XIAN LIU. 2020. Zootaxa Vol 4816, No 3. 

Abstract

The genus Oxyscelio Kieffer from China is revised. Thirty-four species are recognized, of which two species are described as new: O. nullicarina Mo & Chen, sp. n., O. paracuculli Mo & Chen, sp. n., and fourteen species are newly recorded from China: O. aclavae Burks, O. arcus Burks, O. brevidentis Burks, O. excavatus (Kieffer), O. flabelli Burks, O. jaune Burks, O. kiefferi Dodd, O. labis Burks, O. mesiodentis Burks, O. mollitia Burks, O. nasolabii Burks, O. nubbin Burks, O. ogive Burks, and O. reflectens Burks. Keys to the Chinese species are provided.


Promoting inclusion in ecological field experiences: Examining and overcoming barriers to a professional rite of passage

Nia Morales, Kari Bisbee O’Connell, Stacy McNulty, Alan Berkowitz, Gillian Bowser, Michael Giamellaro, and Maria N. Miriti. 2020.  Bull Ecol Soc Am 00(00):e01742. https://doi.org/10.1002/bes2.1742 

Abstract

Field experiences can provide transformative opportunities for many individuals who eventually pursue ecology, natural resource, and conservation careers. However, some of the same elements of field‐based programs that define and provide pivotal experiences for some represent barriers for
others, especially students from underrepresented groups. Barriers may be financial, physical, cultural, or social. Issues of gender, identity, and race/ethnicity, for example, can be isolating or shut down learning during intensive field experiences when group leaders are not prepared to respond
to interpersonal challenges. We explore some benefits and barriers presented by field learning experiences as well as some challenges and potential strategies to broaden inclusivity with the hope of encouraging further conversation on diversity and inclusion in field experiences.


Hidden figures in ecology and evolution

Maria N. Miriti, Karen Bailey, Samniqueka J. Halsey & Nyeema C. Harris. 2020. Nat Ecol Evol. https://doi.org/10.1038/s41559-020-1270-y 

Excerpt

To the Editor — Equity efforts consistently disregard the perspectives, contributions and accomplishments of Black women. Habitually, Black women’s accomplishments are marginalized in favour of white and/or male agendas. This societal disregard dates back to the women’s rights movement, includes the civil rights movement and is present in science, technology, engineering and mathematics (STEM) equity interventions. For example, Harriet Tubman is broadly recognized for contributions to the abolition of slavery, but her contributions to women’s rights, her importance as a feminist and her contributions to anti-racism are under-acknowledged1. Similarly, the vision and activities of Black men dominate presentations of the civil rights movement while the contributions of Black women are frequently portrayed as symbolic2. To date, STEM diversity initiatives have been successful in promoting inclusion for white women at the expense of scholars of colour3, and especially Black women3,4. To do the work of justice and equity in ecology and evolution (EE) and beyond, particularly to ensure women of colour are not ignored, we need to adopt attitudes of feminist scientists and scholars who view the world with a more intersectional lens. Too often, Black women are forcibly presented with the choice to acknowledge gender or racial identities, diminishing the power and innovation resultant from integration with detriment to inclusivity.


Environmental factors influencing fine-scale distribution of Antarctica’s only endemic insect

Leslie J. Potts, J. D. Gantz, Yuta Kawarasaki, Benjamin N. Philip, David J. Gonthier, Audrey D. Law, Luke Moe, Jason M. Unrine, Rebecca L. McCulley, Richard E. Lee Jr., David L. Denlinger & Nicholas M. Teets. 2020. Oecologia. https://doi.org/10.1007/s00442-020-04714-9

Abstract

Species distributions are dependent on interactions with abiotic and biotic factors in the environment. Abiotic factors like temperature, moisture, and soil nutrients, along with biotic interactions within and between species, can all have strong influences on spatial distributions of plants and animals. Terrestrial Antarctic habitats are relatively simple and thus good systems to study ecological factors that drive species distributions and abundance. However, these environments are also sensitive to perturbation, and thus understanding the ecological drivers of species distribution is critical for predicting responses to environmental change. The Antarctic midge, Belgica antarctica, is the only endemic insect on the continent and has a patchy distribution along the Antarctic Peninsula. While its life history and physiology are well studied, factors that underlie variation in population density within its range are unknown. Previous work on Antarctic microfauna indicates that distribution over broad scales is primarily regulated by soil moisture, nitrogen content, and the presence of suitable plant life, but whether these patterns are true over smaller spatial scales has not been investigated. Here we sampled midges across five islands on the Antarctic Peninsula and tested a series of hypotheses to determine the relative influences of abiotic and biotic factors on midge abundance. While historical literature suggests that Antarctic organisms are limited by the abiotic environment, our best-supported hypothesis indicated that abundance is predicted by a combination of abiotic and biotic conditions. Our results are consistent with a growing body of literature that biotic interactions are more important in Antarctic ecosystems than historically appreciated.