Ecology and Evolutionary Biology Commons^™

Dynamic Responses Of Tree-Ring Growth To Multiple Dimensions Of Drought, Wei Fang, Shan Gao, Ruishun Liu, Tao Zhou, Chuixiang Yi, Ruijie Liu, Xiang Zhao, Hui Luo

Publications and Research

Droughts, which are characterized by multiple dimensions including frequency, duration, severity and onset timing, can impact tree growth profoundly. Different dimensions of drought influence tree growth independently or jointly, which makes the development of accurate predictions a formidable challenge. Measurement-based tree-ring data have obvious advantages for studying the drought responses of trees. Here, we explored the use of abundant tree-ring records for quantifying regional response patterns to key dimensions of drought. Specifically, we designed a series of regional-scaled “natural experiments”, based on 357 tree-ring chronologies from Southwest USA and location-matched monthly water balance anomalies, to reveal how tree-ring growth responds …

Bifurcated Response Of A Regional Forest To Drought, Wei Fang, Chuixiang Yi, Guangwei Mu, George Hendrey, Sergio M. Vicente-Serrano, Tao Zhou, Shan Gao, Peipei Xu

Publications and Research

Several lines of evidence suggest that forest growth in many regions is declining as a consequence of changing climate. To predict the fate of forests in the future, a quantitative understanding of how the key climate variables (insolation, precipitation and temperature) interact with forests to cause the decline is a pressing need. Here we use a regionally-averaged tree-ring width index (RWIr ) to quantify forest growth in the Southwest United States (SWUS). We show that over a period of 100 years, SWUS RWIr bifurcated into forest stands with enhanced (healthy) and reduced (declining) branches when regressed on shortwave-radiation and temperature, …

Hip Extensor Mechanics And The Evolution Of Walking And Climbing Capabilities In Humans, Apes, And Fossil Hominins, Elaine E. Kozma, Nicole M. Webb, William Harcourt-Smith, David A. Raichlen, Kristiaan D’Août, Mary H. Brown, Emma M. Finestone, Stephen R. Ross, Peter Aerts, Herman Pontzer

Publications and Research

The evolutionary emergence of humans’ remarkably economical walking gait remains a focus of research and debate, but experi- mentally validated approaches linking locomotor capability to postcranial anatomy are limited. In this study, we integrated 3D morphometrics of hominoid pelvic shape with experimental mea- surements of hip kinematics and kinetics during walking and climbing, hamstring activity, and passive range of hip extension in humans, apes, and other primates to assess arboreal–terrestrial trade-offs in ischium morphology among living taxa. We show that hamstring-powered hip extension during habitual walking and climbing in living apes and humans is strongly predicted, and likely constrained, by …

A Description Of Nesting Behaviors, Including Factors Impacting Nest Site Selection, In Black‐And‐White Ruffed Lemurs (Varecia Variegata), Andrea L. Baden

Publications and Research

Nest site selection is at once fundamental to reproduction and a poorly understood component of many organisms’ reproductive investment. This study investigates the nesting behaviors of black-and-white ruffed lemurs, Varecia variegata, a litter-bearing primate from the southeastern rainforests of Madagascar. Using a combination of behavioral, geospatial, and demographic data, I test the hypotheses that environmental and social cues influence nest site selection and that these decisions ultimately impact maternal reproductive success. Gestating females built multiple large nests throughout their territories. Of these, females used only a fraction of the originally constructed nests, as well as several parking locations as infants …

A Novel Three-Way Interaction Among A Fish, Algae, And A Parasitic Copepod, John Waldman

Publications and Research

No abstract provided.

Relative Contribution Of Neutral And Deterministic Processes In Shaping Fruit-Feeding Butterfly Assemblages In Afrotropical Forests, Kwaku Aduse-Poku, Freerk Molleman, William Oduro, Samuel K. Oppong, David J. Lohman, Rampal S. Etienne

Publications and Research

The unified neutral theory of biodiversity and biogeography has gained the status of a quantitative null model for explaining patterns in ecological (meta)communities. The theory assumes that individuals of trophically similar species are functionally equivalent. We empirically evaluate the relative contribution of neutral and deterministic processes in shaping fruit-feeding butterfly assemblages in three tropical forests in Africa, using both direct (confronting the neutral model with species abundance data) and indirect approaches (testing the predictions of neutral theory using data other than species abundance distributions). Abundance data were obtained by sampling butterflies using banana baited traps set at the forest canopy …

Cryptic Diversity And Discordance In Single‐Locus Species Delimitation Methods Within Horned Lizards (Phrynosomatidae: Phrynosoma), Christopher Blair, Robert W. Bryson Jr.

Publications and Research

Biodiversity reduction and loss continues to progress at an alarming rate, and thus there is widespread interest in utilizing rapid and efficient methods for quantifying and delimiting taxonomic diversity. Single-locus species-delimitation methods have become popular, in part due to the adoption of the DNA barcoding paradigm. These techniques can be broadly classified into tree-based and distance-based methods depending on whether species are delimited based on a constructed genealogy. Although the relative performance of these methods has been tested repeatedly with simulations, additional studies are needed to assess congruence with empirical data. We compiled a large data set of mitochondrial ND4 …

Gene Coexpression Network Analysis Of Fruit Transcriptomes Uncovers A Possible Mechanistically Distinct Class Of Sugar/Acid Ratio-Associated Genes In Sweet Orange, Liang Qiao, Minghao Cao, Jian Zheng, Yihong Zhao, Zhi-Liang Zheng

Publications and Research

Background: The ratio of sugars to organic acids, two of the major metabolites in fleshy fruits, has been considered the most important contributor to fruit sweetness. Although accumulation of sugars and acids have been extensively studied, whether plants evolve a mechanism to maintain, sense or respond to the fruit sugar/acid ratio remains a mystery. In a prior study, we used an integrated systems biology tool to identify a group of 39 acid-associated genes from the fruit transcriptomes in four sweet orange varieties (Citrus sinensis L. Osbeck) with varying fruit acidity, Succari (acidless), Bingtang (low acid), and Newhall and Xinhui (normal …

Comparative Transcriptomics Reveal Developmental Turning Points During Embryogenesis Of A Hemimetabolous Insect, The Damselfly Ischnura Elegans, Sabrina Simon, Sven Sagasser, Edoardo Saccenti, Mercer R. Brugler, M. Eric Schranz, Heike Hadrys, George Amato, Rob Desalle

Publications and Research

Identifying transcriptional changes during embryogenesis is of crucial importance for unravelling evolutionary, molecular and cellular mechanisms that underpin patterning and morphogenesis. However, comparative studies focusing on early/embryonic stages during insect development are limited to a few taxa. Drosophila melanogaster is the paradigm for insect development, whereas comparative transcriptomic studies of embryonic stages of hemimetabolous insects are completely lacking. We reconstructed the first comparative transcriptome covering the daily embryonic developmental progression of the blue-tailed damselfly Ischnura elegans (Odonata), an ancient hemimetabolous representative. We identified a “core” set of 6,794 transcripts – shared by all embryonic stages – which are mainly involved …

Effects Of A Beach Nourishment Project In Jamaica Bay, New York, On Horseshoe Crab (Limulus Polyphemus) Spawning Activity And Egg Deposition, Christina P. Colon

Publications and Research

Restoration of horseshoe crab spawning habitats through beach nourishment may be considered as a potential strategy to enhance reproductive success in areas where estuarine beaches have been lost to coastal erosion and development. The US Army Corps of Engineers performed a beach nourishment project at Plumb Beach (Jamaica Bay, Brooklyn, NY) in 2012 to stabilize the shoreline. While the addition of sand was done to protect infrastructure, it created an opportunity to examine the responses of American horseshoe crabs (Limulus polyphemus) to beach nourishment using a BACI (before-after control impact) design. During Spring 2012, be fore beach nourishment, horseshoe crabs …

Bacterial Diversity Impacts As A Result Of Combined Sewer Overflow In A Polluted Waterway, Olga Calderón, Holly Porter-Morgan, Joby Jacob, Willis Elkins

Publications and Research

Newtown Creek is an industrial waterway and former tidal wetland in New York City. It is one of the most polluted water bodies in the United States and was designated as a superfund site in 2010. For over a century, organic compounds, heavy metals, and other forms of industrial pollution have disrupted the creek’s environment. The creek is also impacted by discharges from twenty combined sewer overflow pipes, which may deposit raw sewage or partially treated wastewater directly into the creek during heavy or sustained rain events. Combined sewer overflow events and associated nutrient over-enrichment at the creek drive eutrophication …

Climate Matching Drives Spread Rate But Not Establishment Success In Recent Unintentional Bird Introductions, Pedro Abellán, José L. Tella, Martina Carrete, Laura Cardador, José D. Anadón

Publications and Research

Understanding factors driving successful invasions is one of the cornerstones of invasion biology. Bird invasions have been frequently used as study models, and the foundation of current knowledge largely relies on species purposefully introduced during the 19th and early 20th centuries in countries colonized by Europeans. However, the profile of exotic bird species has changed radically in the last decades, as birds are now mostly introduced into the invasion process through unplanned releases from the worldwide pet and avicultural trade. Here we assessed the role of the three main drivers of invasion success (i.e., event-, species-, and location-level factors) on …

Large-Scale Differences In Microbial Biodiversity Discovery Between 16s Amplicon And Shotgun Sequencing, Michael Tessler, Johannes S. Neumann, Ebrahim Afshinnekoo, Michael Pineda, Rebecca Hersch, Luiz Felipe M. Velgo, Bianca T. Segovia, Fabio A. Lansac-Toha, Michael Lemke, Rob Desalle, Christopher E. Mason, Mercer R. Brugler

Publications and Research

Modern metagenomic environmental DNA studies are almost completely reliant on next-generation sequencing, making evaluations of these methods critical. We compare two next-generation sequencing techniques – amplicon and shotgun – on water samples across four of Brazil’s major river floodplain systems (Amazon, Araguaia, Paraná, and Pantanal). Less than 50% of phyla identified via amplicon sequencing were recovered from shotgun sequencing, clearly challenging the dogma that mid-depth shotgun recovers more diversity than amplicon-based approaches. Amplicon sequencing also revealed ~27% more families. Overall the amplicon data were more robust across both biodiversity and community ecology analyses at different taxonomic scales. Our work doubles …

Memory For Stimulus Sequences: A Divide Between Humans And Other Animals?, Ghirlanda Stefano, Johan Lind, Magnus Enquist

Publications and Research

Humans stand out among animals for their unique capacities in domains such as language, culture and imitation, yet it has been difficult to identify cognitive elements that are specifically human. Most research has focused on how information is processed after it is acquired, e.g. in problem solving or ‘insight’ tasks, but we may also look for species differences in the initial acquisition and coding of information. Here, we show that non-human species have only a limited capacity to discriminate ordered sequences of stimuli. Collating data from 108 experiments on stimulus sequence discrimination (1540 data points from 14 bird and mammal …

Oldest Skeleton Of A Plesiadapiform Provides Additional Evidence For An Exclusively Arboreal Radiation Of Stem Primates In The Palaeocene, Stephen B. Chester, Thomas E. Williamson, Jonathan I. Bloch, Mary T. Silcox, Eric J. Sargis

Publications and Research

Palaechthonid plesiadapiforms from the Palaeocene of western North America have long been recognized as among the oldest and most primitive euarchontan mammals, a group that includes extant primates, colugos and treeshrews. Despite their relatively sparse fossil record, palaechthonids have played an important role in discussions surrounding adaptive scenarios for primate origins for nearly a half-century. Likewise, palaechthonids have been considered important for understanding relationships among plesiadapiforms, with members of the group proposed as plausible ancestors of Paromomyidae and Microsyopidae. Here, we describe a dentally associated partial skeleton of Torrejonia wilsoni from the early Palaeocene (approx. 62Ma) of New Mexico, which …

Conserved Patterns Of Integrated Developmental Plasticity In A Group Of Polyphenic Tropical Butterflies, Erik Van Bergen, Dave Osbaldeston, Ullasa Kondandaramaiah, Oskar Brattström, Kwaku Aduse-Poku, Paul M. Brakefield

Publications and Research

Background: Developmental plasticity is thought to have profound macro-evolutionary effects, for example, by increasing the probability of establishment in new environments and subsequent divergence into independently evolving lineages. In contrast to plasticity optimized for individual traits, phenotypic integration, which enables a concerted response of plastic traits to environmental variability, may affect the rate of local adaptation by constraining independent responses of traits to selection. Using a comparative framework, this study explores the evolution of reaction norms for a variety of life history and morphological traits across five related species of mycalesine butterflies from the Old World tropics.

Results: Our data …

Egg Discrimination Along A Gradient Of Natural Variation In Eggshell Coloration, Daniel Hanley, Tomáš Grim, Branislav Igic, Peter Samaš, Analía V. López, Matthew D. Shawkey, Mark E. Hauber

Publications and Research

Accurate recognition of salient cues is critical for adaptive responses, but the underlying sensory and cognitive processes are often poorly understood. For example, hosts of avian brood parasites have long been assumed to reject foreign eggs from their nests based on the total degree of dissimilarity in colour to their own eggs, regardless of the foreign eggs’ colours. We tested hosts’ responses to gradients of natural (blue-green to brown) and artificial (green to purple) egg colours, and demonstrate that hosts base rejection decisions on both the direction and degree of colour dissimilarity along the natural, but not artificial, gradient of …

The Paucity Of Frugivores In Madagascar May Not Be Due To Unpredictable Temperatures Or Fruit Resources, Sarah Federman, Miranda Sinnott-Armstrong, Andrea L. Baden, Colin A. Chapman, Douglas C. Daly, Alison R. Richard, Kim Valenta, Michael J. Donoghue

Publications and Research

The evolution of ecological idiosyncrasies in Madagascar has often been attributed to selective pressures stemming from extreme unpredictability in climate and resource availability compared to other tropical areas. With the exception of rainfall, few studies have investigated these assumptions. To assess the hypothesis that Madagascar's paucity of frugivores is due to unreliability in fruiting resources, we use statistical modeling to analyze phenology datasets and their environmental correlates from two tropical wet forests, the Réserve Naturelle Intégrale Betampona in Madagascar, and Kibale National Park in Uganda. At each site we found that temperature is a good environmental predictor of fruit availability. …

Large-Scale Surveillance Of Captive Naked Mole-Rat Colonies Shows Caste Differences In Space Utilization, Michael Kress, Edward F. Meehan, Dan Mccloskey

Publications and Research

African naked mole-rats are eusocial mammals that provide unique opportunity to study complex mammalian social behavior and large-group dynamics in a controlled vivarium setting. Previous reports of captive and wild naked mole-rats have identified a division of labor among non-reproductive colony members along a size polyethism, with large animals specializing in defense behaviors, and small animals performing foraging, nest building, and caretaking functions. This study utilized radio frequency identification (RFID) and advanced computational approaches to monitor the activity patterns and place preferences of all members in two naked mole-rat colonies (N = 36 and 37 animals) for a period of …

A Machine Learning Approach For Using The Postmortem Skin Microbiome To Estimate The Postmortem Interval, Hunter R. Johnson, Donovan D. Trinidad, Stephania Guzman, Zenab Khan, James V. Parziale, Jennifer M. Debruyn, Nathan H. Lents

Publications and Research

Research on the human microbiome, the microbiota that live in, on, and around the human person, has revolutionized our understanding of the complex interactions between microbial life and human health and disease. The microbiome may also provide a valuable tool in forensic death investigations by helping to reveal the postmortem interval (PMI) of a decedent that is discovered after an unknown amount of time since death. Current methods of estimating PMI for cadavers discovered in uncontrolled, unstudied environments have substantial limitations, some of which may be overcome through the use of microbial indicators. In this project, we sampled the microbiomes …

Comparative Phylogeography In The Atlantic Forest And Brazilian Savannas: Pleistocene Fluctuations And Dispersal Shape Spatial Patterns In Two Bumblebees, Elaine Françoso, Alexander Rizzo Zuntini, Ana Carolina Carnaval, Maria Cristina Arias

Publications and Research

Background: Bombus morio and B. pauloensis are sympatric widespread bumblebee species that occupy two major Brazilian biomes, the Atlantic forest and the savannas of the Cerrado. Differences in dispersion capacity, which is greater in B. morio, likely influence their phylogeographic patterns. This study asks which processes best explain the patterns of genetic variation observed in B. morio and B. pauloensis, shedding light on the phenomena that shaped the range of local populations and the spatial distribution of intra-specific lineages.

Results: Results suggest that Pleistocene climatic oscillations directly influenced the population structure of both species. Correlative species distribution models predict that …

Radiation Damage In Xfel: Case Study From The Oxygen-Evolving Complex Of Photosystem Ii, Muhamed Amin, Ashraf Badawi, S.S. Obayya

Publications and Research

Structural changes induced by radiation damage in X-ray crystallography hinder the ability to understand the structure/function relationship in chemical reactions. Serial femtosecond crystallography overcomes this problem by exposing the sample to very short and intense laser pulse leading to measurement before destruction. Here we use molecular modeling to map the radiation damage during the 10–50 fs to the intensity, the energy and the time duration of the laser pulse on the oxygen-evolving complex (OEC) of photosystem II. In the model, the nuclei move classically in a fully quantum potential created by electron density under the effect of strong laser pulse …

The Evolution Of Line-1 In Vertebrates, Stephane Boissinot, Akash Sookdeo

Publications and Research

The abundance and diversity of the LINE-1 (L1) retrotransposon differ greatly among vertebrates. Mammalian genomes contain hundreds of thousands L1s that have accumulated since the origin of mammals. A single group of very similar elements is active at a time in mammals, thus a single lineage of active families has evolved in this group. In contrast, non-mammalian genomes (fish, amphibians, reptiles) harbor a large diversity of concurrently transposing families, which are all represented by very small number of recently inserted copies. Why the pattern of diversity and abundance of L1 is so different among vertebrates remains unknown. To address this …

Evolutionary Interpretations Of Mycobacteriophage Biodiversity And Host-Range Through The Analysis Of Codon Usage Bias, Laura A. Esposito, Swati Gupta, Fraida Streiter, Ashley Prasad, John J. Dennehy

Publications and Research

In an genomics course sponsored by the Howard Hughes Medical Institute (HHMI), undergraduate students have isolated and sequenced the genomes of more than 1,150 mycobacteriophages, creating the largest database of sequenced bacteriophages able to infect a single host, Mycobacterium smegmatis, a soil bacterium. Genomic analysis indicates that these mycobacteriophages can be grouped into 26 clusters based on genetic similarity. These clusters span a continuum of genetic diversity, with extensive genomic mosaicism among phages in different clusters. However, little is known regarding the primary hosts of these mycobacteriophages in their natural habitats, nor of their broader host ranges. As such, it …

A Species-Level Phylogeny Of Extant Snakes With Description Of A New Colubrid Subfamily And Genus, Alex Figueroa, Alexander D. Mckelvy, L. Lee Grismer, Charles D. Bell, Simon P. Lailvaux

Publications and Research

Background With over 3,500 species encompassing a diverse range of morphologies and ecologies, snakes make up 36% of squamate diversity. Despite several attempts at estimating higherlevel snake relationships and numerous assessments of generic- or species-level phylogenies, a large-scale species-level phylogeny solely focusing on snakes has not been completed. Here, we provide the largest-yet estimate of the snake tree of life using maximum likelihood on a supermatrix of 1745 taxa (1652 snake species + 7 outgroup taxa) and 9,523 base pairs from 10 loci (5 nuclear, 5 mitochondrial), including previously unsequenced genera (2) and species (61).

Results Increased taxon sampling resulted …

Biodiversity Of Medicinal Plants In The Highlands: Problems And Perspectives, Vyacheslav Dushenkov

Publications and Research

Climate change is affecting medicinal plants around the world and could ultimately lead to losses of some key species, in particular species endemic to a region and causing plants to migrate to new ranges. As the situation unfolds, climate change may become a pressing issue for the herbal community, affecting medicinal plant supply chains with varying requirements for plant cultivation, resource management in the wild, harvesting, processing, and importantly marketing.

Potyviral Genome-Linked Protein And Its Interaction With Plant Defense Ribosome Inactivating Protein From Phytolacca Americana, Artem V. Domashevskiy

Publications and Research

Agriculture is an indispensable part of every person’s life, ensuring that nutritious and inexpensive food is readily available. Agriculture continues to be confronted with epidemics, having devastating effects on economies and the plant sources essential for human and animal life. Plants and their pathogens have developed evolutionary adaptations, each shaping the other’s defence and invasive strategies. Many different plants produce toxic ribosome inactivating proteins that aid in their defence mechanisms against pathogenic invaders. Viruses must adapt to the host translational machinery, several having evolved to include viral genome-linked proteins that carry numerous viral functions. Here, we review how a potyviral …

Molecular Tracking Of Individual Host Use In The Shiny Cowbird – A Generalist Brood Parasite, Ma Alicia De La Colina, Mark E. Hauber, Bill M. Strausberger, Juan Carlos Reboreda, Bettina Mahler

Publications and Research

Generalist parasites exploit multiple host species at the population level, but the individual parasite’s strategy may be either itself a generalist or a specialist pattern of host species use. Here, we studied the relationship between host availability and host use in the individual parasitism patterns of the Shiny Cowbird Molothrus bonariensis, a generalist avian obligate brood parasite that parasitizes an extreme range of hosts. Using five microsatellite markers and an 1120-bp fragment of the mtDNA control region, we reconstructed full-sibling groups from 359 cowbird eggs and chicks found in nests of the two most frequent hosts in our study area, …

Bathymetric Survey For Lakes Azuei And Enriquillo, Hispaniola, Michael Piasecki, Mahrokh Moknatian, Fred Moshary, Joseph Cleto, Yolanda Leon, Jorge Gonzalez, Daniel Comarazamy

Publications and Research

The two largest lakes on the Caribbean Island of Hispaniola, Lake Azuei in Haiti and Lake Enriquillo in the Dominican Republic, have experienced dramatic growth and surface area expansion over the past few years leading to severe flooding and loss of arable land around the lake perimeters. In order to better understand the reasons for this unprecedented rate of expansion and the resulting consequences a multi-disciplinary team comprised of researchers from Haiti, the DR, and the US have embarked on an extensive data collecting and hydrologic and climatological modeling campaign. While the sensor deployment entails stations that measure climatological data …

Dynamic Egg Color Mimicry, Daniel Hanley, Michael Sulc, Patricia L. R. Brennan, Mark E. Hauber, Tomas Grim, Marcel Honza

Publications and Research

Evolutionary hypotheses regarding the function of eggshell phenotypes, from solar protection through mimicry, have implicitly assumed that eggshell appearance remains static throughout the laying and incubation periods. However, recent research demonstrates that egg coloration changes over relatively short, biologically relevant timescales. Here, we provide the first evidence that such changes impact brood parasite–host eggshell color mimicry during the incubation stage. First, we use long-term data to establish how rapidly the Acrocephalus arundinaceus Linnaeus (great reed warbler) responded to natural parasitic eggs laid by the Cuculus canorus Linnaeus (common cuckoo). Most hosts rejected parasitic eggs just prior to clutch completion, but …