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Repeated Elevational Transitions In Hemoglobin Function During The Evolution Of Andean Hummingbirds, Joana Projecto-Garcia, Chandrasekhar Natarajan, Hideaki Moriyama, Roy E. Weber, Angela Fago, Zachary A. Cheviron, Robert Dudley, Jimmy A. Mcguire, Christopher C. Witt, Jay F. Storz

School of Biological Sciences: Faculty Publications

Animals that sustain high levels of aerobic activity under hypoxic conditions (e.g., birds that fly at high altitude) face the physiological challenge of jointly optimizing blood-O₂ affinity for O₂ loading in the pulmonary circulation and O₂ unloading in the systemic circulation. At high altitude, this challenge is especially acute for small endotherms like hummingbirds that have exceedingly high mass-specific metabolic rates. Here we report an experimental analysis of hemoglobin (Hb) function in South American hummingbirds that revealed a positive correlation between Hb-O₂ affinity and native elevation. Protein engineering experiments and ancestral- state reconstructions revealed that this …

Repeated Elevational Transitions In Hemoglobin Function During The Evolution Of Andean Hummingbirds, Joana Projecto-Garcia, Chandrasekhar Natarajan, Hideaki Moriyama, Roy E. Weber, Angela Fago, Zachary A. Cheviron, Robert Dudley, Jimmy A. Mcguire, Christopher C. Witt, Jay F. Storz

School of Biological Sciences: Faculty Publications

Animals that sustain high levels of aerobic activity under hypoxic conditions (e.g., birds that fly at high altitude) face the physiological challenge of jointly optimizing blood-O₂ affinity for O₂ loading in the pulmonary circulation and O₂ unloading in the systemic circulation. At high altitude, this challenge is especially acute for small endotherms like hummingbirds that have exceedingly high mass-specific metabolic rates. Here we report an experimental analysis of hemoglobin (Hb) function in South American hummingbirds that revealed a positive correlation between Hb-O₂ affinity and native elevation. Protein engineering experiments and ancestral- state reconstructions revealed that this …

High-Throughput Amplicon Sequencing Of Rrna Genes Requires A Copy Number Correction To Accurately Reflect The Effects Of Management Practices On Soil Nematode Community Structure, B. J. Darby, T. C. Todd, M. A. Herman

School of Biological Sciences: Faculty Publications

Nematodes are abundant consumers in grassland soils, but more sensitive and specific methods of enumeration are needed to improve our understanding of how different nematode species affect, and are affected by, ecosystem processes. High-throughput amplicon sequencing is used to enumerate microbial and invertebrate communities at a high level of taxonomic resolution, but the method requires validation against traditional specimen-based morphological identifications. To investigate the consistency between these approaches, we enumerated nematodes from a 25-year field experiment using both morphological and molecular identification techniques in order to determine the long-term effects of annual burning and nitrogen enrichment on soil nematode communities. …

Do Bacterial And Fungal Communities In Soils Of The Bolivian Altiplano Change Under Shorter Fallow Periods?, L. Gomez-Montano, A. Jumpponen, M. A. Gonzales, J. Cusicanqui, C. Valdivia, P. P. Motavalli, M. Herman, K. A. Garrett

School of Biological Sciences: Faculty Publications

Traditional fallow periods in the Bolivian highlands are being shortened in an effort to increase short-term crop yields, with potential long-term impacts on soil microbial communities and their functions. In addition, native vegetation, such as Parasthrephia sp. or Baccharis sp. (both locally known as “thola”) are often removed as a fuel for cooking. We evaluated the effects of fallow period and thola on soils in 29 farmers’ fields in two municipalities in the Bolivian Altiplano (Umala and Ancoraimes). Soil fungal and bacterial community responses were characterized using 454-pyrosequencing. Soils in Ancoraimes had significantly higher levels of organic matter, nitrogen, and …

Low Seroprevalent Species D Adenovirus Vectors As Influenza Vaccines, Eric A. Weaver, Michael A. Barry

School of Biological Sciences: Faculty Publications

Seasonal and pandemic influenza remains a constant threat. While standard influenza vaccines have great utility, the need for improved vaccine technologies have been brought to light by the 2009 swine flu pandemic, highly pathogenic avian influenza infections, and the most recent early and widespread influenza activity. Species C adenoviruses based on serotype 5 (AD5) are potent vehicles for gene-based vaccination. While potent, most humans are already immune to this virus. In this study, low seroprevalent species D adenoviruses Ad26, 28, and 48 were cloned and modified to express the influenza virus A/PR/8/34 hemagglutinin gene for vaccine studies. When studied in …

Disturbance Frequency And Vertical Distribution Of Seeds Affect Long-Term Population Dynamics: A Mechanistic Seed Bank Model, Eric A. Eager, Chirakkal V. Haridas, Diana Pilson, Richard Rebarber, Brigitte Tenhumberg

School of Biological Sciences: Faculty Publications

Seed banks are critically important for disturbance specialist plants because seeds of these species germinate only in disturbed soil. Disturbance and seed depth affect the survival and germination probability of seeds in the seed bank, which in turn affect population dynamics. We develop a density-dependent stochastic integral projection model to evaluate the effect of stochastic soil disturbances on plant population dynamics with an emphasis on mimicking how disturbances vertically redistribute seeds within the seed bank. We perform a simulation analysis of the effect of the frequency and mean depth of disturbances on the population’s quasi-extinction probability, as well as the …

Experimental Confirmation That Avian Plumage Traits Function As Multiple Status Signals In Winter Contests, Alexis S. Chaine, Allison M. Roth, Daizaburo Shizuka, Bruce E. Lyon

School of Biological Sciences: Faculty Publications

Status signals are thought to reduce costs of overt conflict over resources by advertising social status or an individual’s ability to win contests. While most studies have focused on single badges of status, recent empirical work has shown that multiple status signals may exist. To provide robust evidence for multiple badges of status, an experimental manipulation is required to decouple signals from one another and from other traits linked to fighting ability. Such experimental evidence is lacking for most studies of multiple status signals to date. We previously found that two plumage traits in golden-crowned sparrows, Zonotrichia atricapilla, were correlated …

Comparison Of Systemic And Mucosal Immunization Withhelper-Dependent Adenoviruses For Vaccination Against Mucosal Challenge With Shiv, Eric A. Weaver, Pramod N. Nehete, Bharti P. Nehete, Guojun Yang, Stephanie J. Buchl, Patrick W. Hanley, Donna Palmer, David C. Montefiori, Guido Ferrari, Philip Ng, K. Jagannadha Sastry, Michael A. Barry

School of Biological Sciences: Faculty Publications

Most HIV-1 infections are thought to occur at mucosal surfaces during sexual contact. It has been hypothesized that vaccines delivered at mucosal surfaces may mediate better protection against HIV-1 than vaccines that are delivered systemically. To test this, rhesus macaques were vaccinated by intramuscular (i.m.) or intravaginal (ivag.) routes with helperdependent adenoviral (HD-Ad) vectors expressing HIV-1 envelope. Macaques were first immunized intranasally with species C Ad serotype 5 (Ad5) prior to serotype-switching with species C HD-Ad6, Ad1, Ad5, and Ad2 vectors expressing env followed by rectal challenge with CCR5-tropic SHIV-SF162P3. Vaccination by the systemic route generated stronger systemic CD8 T …

Larval Performance And Kill Rate Of Convergent Ladybird Beetles, Hippodamia Convergens, On Black Bean Aphids, Aphis Fabae, And Pea Aphids, Acyrthosiphon Pisum, Travis M. Hinkelman, Brigitte Tenhumberg

School of Biological Sciences: Faculty Publications

Generalist predator guilds play a prominent role in structuring insect communities and can contribute to limiting population sizes of insect pest species. A consequence of dietary breadth, particularly in predatory insects, is the inclusion of low-quality, or even toxic, prey items in the predator’s diet. Consumption of low-quality prey items reduces growth, development, and survival of predator larvae, thereby reducing the population sizes of generalist predators. The objective of this paper was to examine the effect of a suspected low-quality aphid species, Aphis fabae (Scopoli) (Hemiptera: Aphididae), on the larval performance of an abundant North American predator, Hippodamia convergens (Guérin-Méneville) …

Melanin Concentration Gradients In Modern And Fossil Feathers, Daniel J. Field, Liliana D’Alba, Jakob Vinther, Samuel M. Webb, William Gearty, Matthew D. Shawkey

School of Biological Sciences: Faculty Publications

In birds and feathered non-avian dinosaurs, within-feather pigmentation patterns range from discrete spots and stripes to more subtle patterns, but the latter remain largely unstudied. A ,55 million year old fossil contour feather with a dark distal tip grading into a lighter base was recovered from the Fur Formation in Denmark. SEM and synchrotron-based trace metal mapping confirmed that this gradient was caused by differential concentration of melanin. To assess the potential ecological and phylogenetic prevalence of this pattern, we evaluated 321 modern samples from 18 orders within Aves. We observed that the pattern was found most frequently in distantly …

Parasitoid Infestation Changes Female Mating Preferences, Oliver M. Beckers, William E. Wagner

School of Biological Sciences: Faculty Publications

Females often adjust their mating preference to environmental and social conditions. This plasticity of preference can be adaptive for females and can have important consequences for the evolution of male traits. While predation and parasitism are widespread, their effects on female preferences have rarely been investigated. Females of the cricket Gryllus lineaticeps are parasitized by the parasitoid fly Ormia ochracea. Infestation with fly larvae substantially reduces female life span and thus reproductive opportunities of the cricket. Both female G. lineaticeps and flies orient to male song and both prefer male songs with faster chirp rates to songs with slower chirp …

Tlr-Trif Pathway Enhances The Expression Of Kshv Replication And Transcription Activator, Florencia Meyer, Erica Ehlers, Andrew Steadman, Thomas Waterbury, Mingxia Cao, Luwen Zhang

School of Biological Sciences: Faculty Publications

Background: Host innate immunity is against virus infection and replication.

Results: Toll-like receptor 3 activation leads to enhanced expression of a key Kaposi’s sarcoma-associated herpesvirus (KSHV) protein.

Conclusion: KSHV uses host Toll-like receptor pathway to augment its critical gene expression. Significance: A virus may usurp host innate immunity for its own benefits.

Four Distinct Types Of Dehydration Stress Memory Genes In Arabidopsis Thaliana, Yong Ding, Ning Liu, Laetitia Virlouvet, Jean-Jack Riethoven, Michael E. Fromm, Zoya Avramova

School of Biological Sciences: Faculty Publications

Background: How plants respond to dehydration stress has been extensively researched. However, how plants respond to multiple consecutive stresses is virtually unknown. Pre-exposure to various abiotic stresses (including dehydration) may alter plants’ subsequent responses by improving resistance to future exposures. These observations have led to the concept of ‘stress memory’ implying that during subsequent exposures plants provide responses that are different from those during their first encounter with the stress. Genes that provide altered responses in a subsequent stress define the ‘memory genes’ category; genes responding similarly to each stress form the ‘non-memory’ category.

Results: Using a genome-wide …

Deer Mouse Hemoglobin Exhibits A Lowered Oxygen Affinity Owing To Mobility Of The E Helix, Noriko Inoguchi, Jake R. Oshlo, Chandrasekhar Natarajan, Roy E. Weber, Angela Fago, Jay F. Storz, Hideaki Moriyama

School of Biological Sciences: Faculty Publications

The deer mouse, Peromyscus maniculatus, exhibits altitude-associated variation in hemoglobin oxygen affinity. To examine the structural basis of this functional variation, the structure of the hemoglobin was solved. Recombinant hemoglobin was expressed in Escherichia coli and was purified by ion-exchange chromatography. Recombinant hemoglobin was crystallized by the hangingdrop vapor-diffusion method using polyethylene glycol as a precipitant. The obtained orthorhombic crystal contained two subunits in the asymmetric unit. The refined structure was interpreted as the aquo-met form. Structural comparisons were performed among hemoglobins from deer mouse, house mouse and human. In contrast to human hemoglobin, deer mouse hemoglobin lacks the …

Creating An Interdisciplinary Research Course In Mathematical Ecology, Glenn Ledder, Brigitte Tenhumberg

School of Biological Sciences: Faculty Publications

An integrated interdisciplinary research course in biology and mathematics is useful for recruiting students to interdisciplinary research careers, but there are difficulties involved in creating and implementing it. We describe the genesis, objectives, design policies, and structure of the Research Skills in Theoretical Ecology course at the University of Nebraska–Lincoln and discuss the difficulties that can arise in designing and implementing interdisciplinary courses.

Candida Albicans Czf1 And Efg1 Coordinate The Response To Farnesol During Quorum Sensing, White-Opaque Thermal Dimorphism, And Cell Death, Melanie L. Langford, Jessica C. Hargarten, Krista D. Patefield, Elizabeth Marta, Jill R. Blankenship, Saranna Fanning, Kenneth W. Nickerson, Audrey L. Atkin

School of Biological Sciences: Faculty Publications

Quorum sensing by farnesol in Candida albicans inhibits filamentation and may be directly related to its ability to cause both mucosal and systemic diseases. The Ras1-cyclic AMP signaling pathway is a target for farnesol inhibition. However, a clear understanding of the downstream effectors of the morphological farnesol response has yet to be unraveled. To address this issue, we screened a library for mutants that fail to respond to farnesol. Six mutants were identified, and the czf1Δ/czf1Δ mutant was selected for further characterization. Czf1 is a transcription factor that regulates filamentation in embedded agar and also whiteto- opaque switching. We found …

Large-Scale Spatial Synchrony And Cross-Synchrony In Acorn Production By Two California Oaks, Walter D. Koenig, Johannes M.H. Knops

School of Biological Sciences: Faculty Publications

Seed production that varies greatly from year to year, known as ‘‘masting’’ or ‘‘mast-fruiting’’ behavior, is a population-level phenomenon known to exhibit geographic synchrony extending, at least in some cases, hundreds of kilometers. The two main nonexclusive hypotheses for the driver of such geographically extensive synchrony are (1) environmental factors (the Moran effect), and (2) the mutual dependence of trees on outcrossed pollen (pollen coupling). We tested 10 predictions relevant to these two hypotheses using 18 years of acorn production data on two species of California oaks. Data were obtained across the entire ranges of the two species at 12 …

Population-Level Scaling Of Avian Migration Speed With Body Size And Migration Distance For Powered Fliers, Frank A. La Sorte, Daniel Fink, Wesley M. Hochachka, John Delong, Steve Kelling

School of Biological Sciences: Faculty Publications

Optimal migration theory suggests specific scaling relationships between body size and migration speed for individual birds based on the minimization of time, energy, and risk. Here we test if the quantitative predictions originating from this theory can be detected when migration decisions are integrated across individuals. We estimated population-level migration trajectories and daily migration speeds for the combined period 2007–2011 using the eBird data set. We considered 102 North American bird species that use flapping or powered flight during migration. Many species, especially in eastern North America, had looped migration trajectories that traced a clockwise path with an eastward shift …

Inge Revsbech Wins The Journal Of Experimental Biology’S Outstanding Paper Prize 2013, Nicola Stead, Inge G. Revsbech, Hideaki Moriyama, Jay F. Storz, Angela Fago

School of Biological Sciences: Faculty Publications

The Editors of The Journal of Experimental Biology are pleased to announce that Inge Revsbech from Aarhus University, Denmark, is the winner of this year’s JEB Outstanding paper prize. The prize is awarded in memory of Bob Boutillier (JEB Editor-in-Chief 1994–2003) to a junior author who has made the most significant contribution to an outstanding paper. ‘The prize aims to promote and reward the hard work that individual young scientists have put into solving different riddles of any particular species using ingenuity, perseverance and sound technology and methodology’, explains Hans Hoppeler, Editor-In-Chief.

Revsbech was the first author on the paper …

Antelope Mating Strategies Facilitate Invasion Of Grasslands By A Woody Weed, Shivani Jadeja, Soumya Prasad, Suhel Quader, Kavita Isvaran

School of Biological Sciences: Faculty Publications

Intra and interspecific variation in frugivore behaviour can have important consequences for seed dispersal outcomes. However, most information comes from among-species comparisons, and within-species variation is relatively poorly understood. We examined how large intraspecific differences in the behaviour of a native disperser, blackbuck antelope Antilope cervicapra, influence dispersal of a woody invasive, Prosopis juliflora, in a grassland ecosystem. Blackbuck disperse P. juliflora seeds through their dung. In lekking blackbuck populations, males defend clustered or dispersed mating territories. Territorial male movement is restricted, and within their territories males defecate on dung-piles. In contrast, mixed-sex herds range over large areas …

The Mid-Domain Effect: It’S Not Just About Space, Andrew D. Letten, S. Kathleen Lyons, Angela T. Moles

School of Biological Sciences: Faculty Publications

Ecologists and biogeographers have long sought to understand how and why diversity varies across space. Up until the late 20th century, the dominant role of environmental gradients and historical processes in driving geographical species richness patterns went largely undisputed. However, almost 20 years ago, Colwell & Hurtt (1994) proposed a radical reappraisal of ecological gradient theory that called into question decades of empirical and theoretical research. That controversial idea was later termed the ‘the mid-domain effect’: the simple proposition that in the absence of environmental gradients, the random placement of species ranges within a bounded domain will give rise to …

Heritability And Inter-Population Differences In Lipid Profiles Of Drosophila Melanogaster, Cornelia J. F. Scheitz, Yu Guo, Angela M. Early, Lawrence G. Harshman, Andrew G. Clark

School of Biological Sciences: Faculty Publications

Characterizing and understanding the complex spectrum of lipids in higher organisms lags far behind our analysis of genome and transcriptome sequences. Here we generate and evaluate comprehensive lipid profiles (>200 lipids) of 92 inbred lines from five different Drosophila melanogaster populations. We find that the majority of lipid species are highly heritable, and even lipids with odd-chain fatty acids, which cannot be generated by the fly itself, also have high heritabilities. Abundance of the endosymbiont Wolbachia, a potential provider of odd-chained lipids, was positively correlated with this group of lipids. Additionally, we show that despite years of laboratory …

A Virus-Induced Gene Silencing Method To Study Soybean Cyst Nematode Parasitism In Glycine Max, Pramod K. Kandoth, Robert Heinz, Greg Yeckel, Nathan W. Gross, Parijat S. Juvale, John Hill, Steven A. Whitham, Thomas J. Baum, Melissa G. Mitchum

School of Biological Sciences: Faculty Publications

Background: Bean pod mottle virus (BPMV) based virus-induced gene silencing (VIGS) vectors have been developed and used in soybean for the functional analysis of genes involved in disease resistance to foliar pathogens. However, BPMV-VIGS protocols for studying genes involved in disease resistance or symbiotic associations with root microbes have not been developed.

Findings: Here we describe a BPMV-VIGS protocol suitable for reverse genetic studies in soybean roots. We use this method for analyzing soybean genes involved in resistance to soybean cyst nematode (SCN). A detailed SCN screening pipeline is described.

Conclusions: The VIGS method described here provides …

Reductive Evolution And The Loss Of Pdc/Pas Domains From The Genus Staphylococcus, Neethu Shah, Rosmarie Gaupp, Hideaki Moriyama, Kent M. Eskridge, Etsuko N. Moriyama, Greg A. Somerville

School of Biological Sciences: Faculty Publications

Background: The Per-Arnt-Sim (PAS) domain represents a ubiquitous structural fold that is involved in bacterial sensing and adaptation systems, including several virulence related functions. Although PAS domains and the subclass of PhoQ-DcuS-CitA (PDC) domains have a common structure, there is limited amino acid sequence similarity. To gain greater insight into the evolution of PDC/PAS domains present in the bacterial kingdom and staphylococci in specific, the PDC/PAS domains from the genomic sequences of 48 bacteria, representing 5 phyla, were identified using the sensitive search method based on HMM-to-HMM comparisons (HHblits).

Results: A total of 1,007 PAS domains and 686 …

Regional Contingencies In The Relationship Between Aboveground Biomass And Litter In The World’S Grasslands, Lydia R. O’Halloran, Elizabeth T. Borer, Eric W. Seabloom, Andrew S. Macdougall, Elsa E. Cleland, Rebecca L. Mcculley, Sarah Hobbie, W. Stanley Harpole, Nicole M. Decrappeo, Chengjin Chu, Jonathan D. Bakker, Kendi F. Davies, Guozhen Du, Jennifer Firn, Nicole Hagenah, Kirsten S. Hofmockel, Johannes Knops, Wei Li, Brett A. Melbourne, John W. Morgan, John L. Orrock, Suzanne M. Prober, Carly J. Stevens

School of Biological Sciences: Faculty Publications

Based on regional-scale studies, aboveground production and litter decomposition are thought to positively covary, because they are driven by shared biotic and climatic factors. Until now we have been unable to test whether production and decomposition are generally coupled across climatically dissimilar regions, because we lacked replicated data collected within a single vegetation type across multiple regions, obfuscating the drivers and generality of the association between production and decomposition. Furthermore, our understanding of the relationships between production and decomposition rests heavily on separate meta-analyses of each response, because no studies have simultaneously measured production and the accumulation or decomposition of …

A Whole-Cell Biosensor For The Detection Of Gold, Carla M. Zammit, Davide Quaranta, Shane Gibson, Anita J. Zaitouna, Christine Ta, Joel Brugger, Rebecca Y. Lai, Gregor Grass, Frank Reith

School of Biological Sciences: Faculty Publications

Geochemical exploration for gold (Au) is becoming increasingly important to the mining industry. Current processes for Au analyses require sampling materials to be taken from often remote localities. Samples are then transported to a laboratory equipped with suitable analytical facilities, such as Inductively Coupled Plasma-Mass Spectrometry (ICP-MS) or Instrumental Neutron Activation Analysis (INAA). Determining the concentration of Au in samples may take several weeks, leading to long delays in exploration campaigns. Hence, a method for the on-site analysis of Au, such as a biosensor, will greatly benefit the exploration industry. The golTSB genes from Salmonella enterica serovar typhimurium are selectively …

Cd20 Antibody Primes B Lymphocytes For Type I Interferon Production, Dongsheng Xu, Andrew Staedman, Luwen Zhang

School of Biological Sciences: Faculty Publications

CD20 is a B cell surface marker that is expressed in various stages in B lymphocytes and certain lymphomas. Clinical administration of CD20 antibody, such as rituximab, is used widely to treat human B-cell lymphomas and other diseases. However, CD20 antibody failed to treat systemic lupus erythematosus (SLE or lupus). The reason for the failure is currently unknown. Type I interferons (IFN) are a major component for the host innate immunity, and a key pathogenic factor in lupus. We found that CD20 antibody potentiated human B cells for its production of IFNs in vitro. This function was specific to …

Conformational B-Cell Epitope Prediction On Antigen Protein Structures: A Review Of Current Algorithms And Comparison With Common Binding Site Prediction Methods, Bo Yao, Dandan Zheng, Shide Liang, Chi Zhang

School of Biological Sciences: Faculty Publications

Accurate prediction of B-cell antigenic epitopes is important for immunologic research and medical applications, but compared with other bioinformatic problems, antigenic epitope prediction is more challenging because of the extreme variability of antigenic epitopes, where the paratope on the antibody binds specifically to a given epitope with high precision. In spite of the continuing efforts in the past decade, the problem remains unsolved and therefore still attracts a lot of attention from bioinformaticists. Recently, several discontinuous epitope prediction servers became available, and it is intriguing to review all existing methods and evaluate their performances on the same benchmark. In addition, …

Dna Sequencing Reveals Patterns Of Prey Selection In Migrating Sharp-Shinned Hawks Las Secuencias De Adn Revelan Patrones De Selección De Presas Por Individuos Migratorios De Accipiter Striatus, John Delong, Nancy Cox, Steve Cox, Zachary Hurst, Jeff Smith

School of Biological Sciences: Faculty Publications

Prey selection of migrating raptors has been documented only rarely. Here we used a genetic approach to identify avian prey of Sharp-shinned Hawks (Accipiter striatus) migrating through central New Mexico. We identified species by comparing profiles of a section of the 16S rRNA mitochondrial gene extracted from feathers of prey of known species to profiles from feathers of prey found on the feet and beaks of migrating hawks. We also quantified prey availability along the migration route with multi-year sampling by mist net at two sites near the raptor-sampling site. Sharp-shinned Hawks took most prey species in proportion to their …

Global Attracting Equilibria For Coupled Systems With Ceiling Density Dependence, Eric A. Eager, Mary Hebert, Elise Hellwig, Francisco Hernandez, Richard Rebarber, Brigitte Tenhumberg, Bryan Wigianto

School of Biological Sciences: Faculty Publications

In this paper, we present a system of two difference equations modeling the dynamics of a coupled population with two patches. Each patch can house only a limited number of individuals (called a carrying capacity) because resources like food and breeding sites are limited in each patch. We assume that the population in each patch is governed by a linear model until reaching a carrying capacity in each patch, resulting in map which is nonlinear and not sublinear. We analyze the global attractors of this model.