Digital Commons Network^™

Mouse Embryonic Stem Cells Lacking P38Α And P38Δ Can Differentiate To Endothelial Cells, Smooth Muscle Cells, And Epithelial Cells, Samujjwal Chakraborty, Baobin Kang, Faqing Huang, Yan-Lin Guo

Faculty Publications

The p38 mitogen-activated protein (MAP) kinases (p38) are important signaling molecules that regulate various cellular processes. Four isoforms of p38 family, p38α, p38β, p38γ, and p38δ, have been identified in mammalian cells. Previous studies have shown that p38α knockout is embryonic lethal in mice. At the cellular level, p38α is abundantly expressed in mouse embryonic stem cells (ESCs), but p38α knockout (p38α-/-) ESCs can differentiate to endothelial cells (ECs), smooth muscle cells (SMCs), and neurons. We speculate that the lost function of p38α in p38α-/- ESCs may be compensated for by the redundant function of other isoforms. To test this …

47-Channel Burst-Mode Recording Hydrophone System Enabling Measurements Of The Dynamic Echolocation Behavior Of Free-Swimming Dolphins, Josefin Starkhammar, Mats Amundin, Johan Nilsson, Stan A. Kuczaj, Monica Almqvist, Hans W. Persson

Faculty Publications

Detailed echolocation behavior studies on free-swimming dolphins require a measurement system that incorporates multiple hydrophones (often > 16). However, the high data flow rate of previous systems has limited their usefulness since only minute long recordings have been manageable. To address this problem, this report describes a 47-channel burst-mode recording hydrophone system that enables highly resolved full beamwidth measurements on multiple free-swimming dolphins during prolonged recording periods. The system facilitates a wide range of biosonar studies since it eliminates the need to restrict the movement of animals in order to study the fine details of their sonar beams. (C) 2009 Acoustical …

Sibship Reconstruction Demonstrates The Extremely Low Effective Population Size Of Striped Bass Morone Saxatilis In The Santee-Cooper System, South Carolina, Usa, Jin-Xian Liu, Bert Ely

Faculty Publications

For organisms with great fecundity and high mortality in early life stages, such as shellfish or fishes, the need to match reproductive activity with environmental conditions conducive to spawning, fertilization, larval development and recruitment may result in extreme variance in reproductive success among individuals. The main objective of this study was to investigate evidence of large variance in the reproductive success of the striped bass Morone saxatilis in the Santee-Cooper system, South Carolina, USA. Seven microsatellite loci were analysed in 603 recruits representing three yearly cohorts from 1992 to 1994, and a group analysis was performed to identify full-sib families. …

Yy1 Is Autoregulated Through Its Own Dna-Binding Sites, Jeong D. Kim, Sungryul Yu, Joomyeong Kim

Faculty Publications

Background: The transcription factor Yin Yang 1 (YY1) is a ubiquitously expressed, multifunctional protein that controls a large number of genes and biological processes in vertebrates. As a general transcription factor, the proper levels of YY1 protein need to be maintained for the normal function of cells and organisms. However, the mechanism for the YY1 homeostasis is currently unknown. Results: The current study reports that the YY1 gene locus of all vertebrates contains a cluster of its own DNA-binding sites within the 1st intron. The intact structure of these DNA-binding sites is absolutely necessary for transcriptional activity of the YY1 …

The 1.85 Å Structure Of An 8r-Lipoxygenase Suggests A General Model For Lipoxygenase Product Specificity, David B. Neau, Nathaniel C. Gilbert, Sue G. Bartlett, William Boeglin, Alan R. Brash, Marcia E. Newcomer

Faculty Publications

Lipoxygenases (LOX) play pivotal roles in the biosynthesis of leukotrienes and other biologically active eicosanoids derived from arachidonic acid. A mechanistic understanding of substrate recognition, when lipoxygenases that recognize the same substrate generate different products, can be used to help guide the design of enzyme-specific inhibitors. We report here the 1.85 A ° resolution structure of an 8R-lipoxygenase from Plexaura homomalla, an enzyme with a sequence ∼40% identical to that of human 5-LOX. The structure reveals a U-shaped channel, defined by invariant amino acids, that would allow substrate access to the catalytic iron. We demonstrate that mutations within the channel …

Memristive Model Of Amoeba Learning, Yuriy V. Pershin Dr, Steven La Fontaine, Massimiliano Di Ventra

Faculty Publications

Recently, it was shown that the amoebalike cell Physarum polycephalum when exposed to a pattern of periodic environmental changes learns and adapts its behavior in anticipation of the next stimulus to come. Here we show that such behavior can be mapped into the response of a simple electronic circuit consisting of a LC contour and a memory-resistor (a memristor) to a train of voltage pulses that mimic environment changes. We also identify a possible biological origin of the memristive behavior in the cell. These biological memory features are likely to occur in other unicellular as well as mutlicellular organisms, albeit …

On Immunotherapies And Cancer Vaccination Protocols: A Mathematical Modelling Approach, Badal Joshi, Xueying Wang, Sayanti Banerjee, Haiyan Y. Tian, Anastasios Matzavinos, Mark A.J. Chaplain

Faculty Publications

In this paper we develop a new mathematical model of immunotherapy and cancer vaccination, focusing on the role of antigen presentation and co-stimulatory signaling pathways in cancer immunology. We investigate the effect of different cancer vaccination protocols on the well-documented phenomena of cancer dormancy and recurrence, and we provide a possible explanation of why adoptive (i.e. passive) immunotherapy protocols can sometimes actually promote tumour growth instead of inhibiting it (a phenomenon called immunostimulation), as opposed to active vaccination protocols based on tumour-antigen pulsed dendritic cells. Significantly, the results of our computational simulations suggest that elevated numbers of professional antigen presenting …

Cardiac And Renal Function Are Progressively Impaired With Aging In Zucker Diabetic Fatty Type Ii Diabetic Rats, John W. Baynes, David B. Murray

Faculty Publications

This study investigated the temporal relationship between cardiomyopathy and renal pathology in the type II diabetic Zucker diabetic fatty (ZDF) rat. We hypothesized that changes in renal function will precede the development of cardiac dysfunction in the ZDF rat. Animals (10 weeks old) were divided into four experimental groups: Lean Control (fa/?) LC(n = 7), untreated ZDF rats (n = 7) sacrificed at 16 weeks of age, and LC (n = 7) untreated ZDF rats (n = 9) sacrificed at 36 weeks of age. LV structural/functional parameters were assessed via Millar conductance catheter. Renal function was evaluated via markers of …

Metabolic Depression Is Delayed And Mitochondrial Impairment Averted During Prolonged Anoxia In The Ghost Shrimp, Lepidophthalmus Louisianensis (Schmitt, 1935), Jeremy D. Holman, Steven C. Hand

Faculty Publications

Lepidophthalmus louisianensis burrows deeply into oxygen-limited estuarine sediments and is subjected to extended anoxia at low tides. Large specimens (> 2 g) have a lethal time for 50% mortality (LT50) of 64 h under anoxia at 25 °C. Small specimens (< 1 g) have a significantly higher LT50 of 113 h, which is the longest ever reported for a crustacean. Whole body lactate levels rise dramatically under anoxia and exceed 120 μmol g.f.w.- 1 by 72 h. ATP, ADP, and AMP do not change during 48 h of anoxia, but arginine phosphate declines by over 50%. Thus arginine phosphate may help stabilize the ATP pool. Surprisingly, when compared to the aerobic resting rate, ATP production under anoxia declines only moderately during the first 12 h, and drops to only about 30% between 12 and 48 h. Finally, after 48 h of anoxia, a major metabolic depression to less than 5% occurs. Downregulation of metabolism is delayed in L. louisianensis compared to many invertebrates that exhibit facultative anaerobiosis. Bioenergetic constraints as a result of eventual metabolic depression lead to ionic disturbances like calcium overload and compromised membrane potential of mitochondria. Because these phenomena trigger apoptosis in mammalian species, we evaluated the susceptibility of ghost shrimp mitochondria to opening of the mitochondrial permeability transition pore (MPTP) and associated damage. Energized mitochondria isolated from hepatopancreas possess a pronounced capacity for calcium uptake. Exogenous calcium does not stimulate opening of the MPTP, which potentially could reduce cell death during prolonged anoxia. © 2009 Elsevier B.V. All rights reserved.

Executive Perks: Compensation And Corporate Performance In China, Ilan Alon, Pattarin Adithipyangkul, Tianyu Zhang

Faculty Publications

Many studies have examined CEO compensation in developed countries, where a long tradition of disclosure renders data readily available. In emerging economies, particularly in China, where market-based compensation is a relatively new phenomenon, there are few studies of CEO compensation. In addition, information on the use of non-cash compensation is almost absent. Building on the general literature on CEO compensation, and Chinese economic and management studies, this article singularly contributes to the extant literature by (1) examining the motivational determinants of CEO perk compensation, on the one hand, and (2) exploring the relative contribution of perks to performance. We anticipate …

Dna Methylation Analysis Of The Mammalian Peg3 Imprinted Domain, Jennifer M. Huang, Joomyeong Kim

Faculty Publications

In this study, we performed the first systematic survey of DNA methylation status of the CpG islands of the PEG3 (Paternally expressed gene 3) imprinted domain in the mouse, cow, and human genomes. Previous studies have shown that the region surrounding the first exon of PEG3 contains a differentially methylated CpG island. In addition, we have discovered two previously unreported differentially methylated regions (DMR): one in the promoter region of mouse Zim3 and another in the promoter region of human USP29. In the cow, the Peg3-CpG island was the only area that showed DMR status. We have also examined the …

Application Of Ground Penetrating Radar In Detecting The Hazards And Risks Of Termites And Ants In Soil Levees, Xiuhao Yang, Gregg Henderson, Lixin Mao, Ahmad Evans

Faculty Publications

A ground penetrating radar (GPR) technique was used to detect Formosan subterranean termite (Coptoterrnesfonnosanus) and red imported fire ant (Solenopsis invicta) hazards and risks (targets) in a soil levee at the London Avenue Canal in New Orleans, LA. To make this assessment, GPR signal scans were examined for features produced by termite or ant activities and potential sources of food and shelter such as nests, tree roots, and voids (tunnels). The total scanned length of the soil levee was 4,125 m. The average velocity and effective depth of the radar penetration was 0.080 m/ns and 0.61 m, respectively. Four hundred …

Sperm Motility Initiation And Duration In A Euryhaline Fish, Medaka (Oryzias Latipes), H. Yang, T. R. Tiersch

Faculty Publications

The medaka, Oryzias latipes, is a well-recognized fish model for biomedical research. An understanding of gamete characteristics is necessary for experimental manipulations such as artificial fertilization and sperm cryopreservation. The goal of this study was to investigate sperm characteristics of motility initiation, duration, and retention in medaka. First, motility was initiated by osmolality values ranging from 25 to 686 mOsm/kg, which included deionized water and hypotonic, isotonic, and hypertonic Hanks' balanced salt solution. The percentage of motile sperm was >80% when osmolality was /kg and decreased as osmolality increased. This is different from most fish with external fertilization in which …

Morphological Deformities As Biomarkers In Fish From Contaminated Rivers In Taiwan, Peter Lin Sun, William E. Hawkins, Robin M. Overstreet, Nancy J. Brown-Peterson

Faculty Publications

Tilapia (Oreochromis spp.) were collected seasonally from four contaminated rivers in southwestern Taiwan for studies of morphological deformities that could be used as biomarkers of contamination. Morphological deformities found in tilapia were separated into 15 categories. Overall, the prevalence of deformities such as split fins, lower lip extension and gill deformities were significantly related to various water quality parameters, including low DO and high ammonium, lead and zinc concentrations. The persistence of tilapia in polluted waters and the development of a suite of morphological deformities suggest that tilapia can be used as sentinels of non-point source pollution in rivers.

Promoting Social And Emotional Learning In Second Grade Students: A Study Of The Strong Start Curriculum, Paul Caldarella, Lynnette Christensen, Thomas J. Kramer, Kalli Kronmiller

Faculty Publications

The promotion of social and emotional learning (SEL) in schools may help prevent emotional and behavioral problems of students. This study evaluated the effects of a SEL curriculum, Strong Start, on the social-emotional competence of 26 second grade students, using a quasi-experimental, non-equivalent control group design. Results revealed statistically significant and meaningful improvements in teacher ratings of students’ internalizing and peer-related prosocial behaviors, particularly for students at greater risk. Conversely, control group students experienced significant worsening of internalizing behaviors and decreased levels of peer-related prosocial behaviors. No changes were reported in externalizing behaviors for either group. Treatment integrity and social …

Odontometric Patterns In The Radiation Of Extant Ground-Dwelling Squirrels Within Marmotini (Sciuridae: Xjrini), H. Thomas Goodwin

Faculty Publications

I document odontometry variation across ground-dwelling squirrels of the Holarctic tribe Marmotini. Dental size, which correlates well with published average body mass values across species, accounts for most odontometric variation across the clade. Dental shape variation primarily reflects relative size of P3 (upper cheek teeth) and relative width of p4-ml + length of m3 (lower cheek teeth). Shape variables and relative tooth crown height covary significantly across species, suggesting a common functional complex or shared genetic control. When dental morphology is mapped on published DNA-based phytogenies, Sciurotamias (Chinese rock squirrels), Ammospermophilus (antelope squirrels), and basal subgenera within Spermophilus (ground squirrels …

Differential Mortality Drives Life-History Evolution And Population Dynamics In The Fish Brachyrhaphis Rhabdophora, Jerald B. Johnson, J. Jaime Zuniga-Vega

Faculty Publications

Life-history theory predicts that populations experiencing different levels of extrinsic mortality will evolve divergent reproductive strategies. Previous work in the live bearing fish Brachyrhaphis rhabdophora shows that individuals from populations that occur with piscivorous fish mature earlier and at smaller sizes and have more and smaller offspring than fish from populations without predators. However, until now, there have been no data to demonstrate that differences in mortality rates actually exist between predator and predator free sites. Here we present the results of a serial mark-recapture field study designed to estimate mortality rates in natural populations of B. rhabodophora from Costa …

Positional Identification Of Variants Of Adamts16 Linked To Inherited Hypertension, Bina Joe, Yasser Saad, Norman H. Lee, Bryan C. Frank, Ovokeraye H. Achinike, Truong V. Luu, Kathirvel Gopalakrishnan, Edward J. Toland, Phyllis Farms, Shane Yerga-Woolwine, Ezhilarasi Manickavasagam, John P. Rapp, Michael R. Garrett, David Coe, Suneel S. Apte, Tuomo Rankinen, Louis Pérusse, Georg B. Ehret, Santhi K. Ganesh, Richard S. Cooper, Ashley O'Connor, Treva Rice, Alan B. Weder, Aravinda Chakravarti, Dabeeru C. Rao, Claude Bouchard

Faculty Publications

A previously reported blood pressure (BP) quantitative trait locus on rat Chromosome 1 was isolated in a short congenic segment spanning 804.6 kb. The 804.6 kb region contained only two genes, LOC306664 and LOC306665. LOC306664 is predicted to translate into A Disintegrin-like and Metalloproteinase with Thrombospondin Motifs-16 (Adamts16). LOC306665 is a novel gene. All predicted exons of both LOC306664 and LOC306665 were sequenced. Non-synonymous variants were identified in only one of these genes, LOC306664. These variants were naturally existing polymorphisms among inbred, outbred and wild rats. The full-length rat transcript of Adamts16 was detected in multiple tissues. Similar to ADAMTS16 …

Yy1'S Role In Dna Methylation Of Peg3 And Xist, Jeong Do Kim, Keunsoo Kang, Joomyeong Kim

Faculty Publications

Unusual clusters of YY1 binding sites are located within several differentially methylated regions (DMRs), including Xist, Nespas and Peg3, which all become methylated during oogenesis. In this study, we performed conditional YY1 knockdown (KD) to investigate YY1's roles in DNA methylation of these DMRs. Reduced levels of YY1 during spermatogenesis did not cause any major change in these DMRs although the same YY1 KD caused hypermethylation in these DMRs among a subset of aged mice. However, YY1 KD during oogenesis resulted in the loss of DNA methylation on Peg3 and Xist, but there were no changes on Nespas and H19. …

Soil–Atmosphere Exchange Of Nitrous Oxide, Nitric Oxide, Methane, And Carbon Dioxide In Logged And Undisturbed Forest In The Tapajos National Forest, Brazil, Michael Keller, Ruth K. Varner, Jadson D. Dias, Hudson Silva, Patrick M. Crill, Raimundo Cosme De Oliveira Jr., Gregory P. Asner

Faculty Publications

Selective logging is an extensive land use in the Brazilian Amazon region. The soil–atmosphere fluxes of nitrous oxide (N2O), nitric oxide (NO), methane (CH4), and carbon dioxide (CO2) are studied on two soil types (clay Oxisol and sandy loam Ultisol) over two years (2000–01) in both undisturbed forest and forest recently logged using reduced impact forest management in the Tapajos National Forest, near Santarem, Para, Brazil. In undisturbed forest, annual soil–atmosphere fluxes of N2O (mean ± standard error) were 7.9 ± 0.7 and 7.0 ± 0.6 ng N cm−2 h−1 for the Oxisol and 1.7 ± 0.1 and 1.6 ± …

Modulation Of Lung Inflammation By Vessel Dilator In A Mouse Model Of Allergic Asthma, Xiaoqin Wang, Weidong Xu, Xiaoyuan Kong, Dongqing Chen, Gary Hellermann, Terry A. Ahlert, Joseph D. Giaimo, Stephania A. Cormier, Xu Li, Richard F. Lockey, Subhra Mohapatra, Shyam S. Mohapatra

Faculty Publications

Background: Atrial natriuretic peptide (ANP) and its receptor, NPRA, have been extensively studied in terms of cardiovascular effects. We have found that the ANP-NPRA signaling pathway is also involved in airway allergic inflammation and asthma. ANP, a C-terminal peptide (amino acid 99-126) of pro-atrial natriuretic factor (proANF) and a recombinant peptide, NP73-102 (amino acid 73-102 of proANF) have been reported to induce bronchoprotective effects in a mouse model of allergic asthma. In this report, we evaluated the effects of vessel dilator (VD), another N-terminal natriuretic peptide covering amino acids 31-67 of proANF, on acute lung inflammation in a mouse model …

Orientation Of Grasshopper Sparrow And Eastern Meadowlark Nests In Relation To Wind Direction, Ashley M. Long, William E. Jensen, Kimberly A. With

Faculty Publications

Orientation of the entrances of bird nests may be especially important in grasslands, where protective cover from solar radiation and wind is minimal. We examined orientation patterns of nest-dome entrances in two grassland bird species, the Grasshopper Sparrow (Ammodramus savannarum) and the Eastern Meadowlark (Sturnella magna). We noted how these patterns changed over the nesting season and how they related to prevailing wind direction. We found that Grasshopper Sparrow (n = 333) and Eastern Meadowlark (n = 272) nests were oriented nonrandomly, toward the northeast (ā = 33.4° and 52.9°, respectively). Prevailing wind in the study region was approximately from …

Guatemala's Green Revolution: Synthetic Fertilizer, Public Health, And Economic Autonomy In The Mayan Highland, David Carey

Faculty Publications

Despite extensive literature both supporting and critiquing the Green Revolution, surprisingly little attention has been paid to synthetic fertilizers' health and environmental effects or indigenous farmers' perspectives. The introduction of agrochemicals in the mid-twentieth century was a watershed event for many Mayan farmers in Guatemala. While some Maya hailed synthetic fertilizers' immediate effectiveness as a relief from famines and migrant labor, others lamented the long-term deterioration of their public health, soil quality, and economic autonomy. Since the rising cost of agrochemicals compelled Maya to return to plantation labor in the 1970s, synthetic fertilizers simply shifted, rather than alleviated, Mayan dependency …

Decoupling Development And Energy Flow During Embryonic Diapause In The Cricket, Allonemobius Socius, Julie A. Reynolds, Steven C. Hand

Faculty Publications

Respiration rate increases 6.3-fold during 15days of post-oviposition development in embryos of the Southern ground cricket, Allonemobius socius. This ontogenetic increase in metabolism of non-diapause insects is blocked during diapause, such that metabolic rate is only 36% of the rate measured for 15 days developing embryos. Surprisingly, however, there is not an acute metabolic depression during diapause entry at the point when developmental ceases (4-5days post-oviposition), as measured by blockage of morphological change and DNA proliferation. The results indicate a decoupling of developmental arrest from metabolism. Both non-diapause and diapause embryos have unusually high [AMP]:[ATP] ratios and low [ATP]:[ADP] ratios …

Decomposition In Tropical Forests: A Pan-Tropical Study Of The Effects Of Litter Type, Litter Placement And Mesofaunal Exclusion Across A Precipitation Gradient, Jennifer S. Powers, Rebecca A. Montgomery, E. Carol Adair, Francis Q. Brearley, Saara J. Dewalt, Camila T. Castanho, Jerome Chave, Erika Deinert, Jörg U. Ganzhorn, Matthew E. Gilbert, José Antonio González-Iturbe, Sarayudh Bunyavejchewin, H. Ricardo Grau, Kyle E. Harms, Ankila Hiremath, Silvia Iriarte-Vivar, Eric Manzane, Alexandre A. De Oliveira, Lourens Poorter, Jean Baptiste Ramanamanjato, Carl Salk, Amanda Varela, George D. Weiblen, Manuel T. Lerdau

Faculty Publications

Litter decomposition recycles nutrients and causes large ?uxes of carbon dioxide into the atmosphere. It is typically assumed that climate, litter quality and decomposer communities determine litter decay rates, yet few comparative studies have examined their relative contributions in tropical forests. 2. We used a short-term litterbag experiment to quantify the effects of litter quality, placement and mesofaunal exclusion on decomposition in 23 tropical forests in 14 countries. Annual precipitation varied among sites (7605797 mm). At each site, two standard substrates (Raphia farinifera and Laurus nobilis) were decomposed in ?ne- and coarse-mesh litterbags both above and below ground for approximately …

Embryonic Diapause Highlighted By Differential Expression Of Mrnas For Ecdysteroidogenesis, Transcription And Lipid Sparing In The Cricket Allonemobius Socius, Julie A. Reynolds, Steven C. Hand

Faculty Publications

Embryos of the ground cricket, Allonemobius socius, enter diapause 4-5days post-oviposition and overwinter in this dormant state that is characterized by developmental arrest. Suppressive subtractive hybridization and quantitative real-time PCR reveal eight candidate genes in pre-diapause embryos that show promise as regulators of diapause entry, when compared with embryos not destined for diapause. Identifications are based both on the magnitude/consistency of differential mRNA abundances and the predicted functions of their products when placed in context of the physiological and biochemical events of diapause characterized in our companion paper. The proteins CYP450, AKR and RACK1 (associated with ecdysteroid synthesis and signaling) …

Developmental Emergence Of Power-Law Wake Behavior Depends Upon The Functional Integrity Of The Locus Coeruleus, Andrew J. Gall, Badal Joshi, Janet Best, Virginia R. Florang, Jonathan A. Doorn, Mark S. Blumberg

Faculty Publications

STUDY OBJECTIVES:

Daily amounts of sleep and wakefulness are accumulated in discrete bouts that exhibit distinct statistical properties. In adult mammals, sleep bout durations follow an exponential distribution whereas wake bout durations follow a power-law distribution. In infant Norway rats, however, wake bouts initially follow an exponential distribution and only transition to a power-law distribution beginning around postnatal day 15 (P15). Here we test the hypothesis that the locus coeruleus (LC), one of several wake-active nuclei in the brainstem, contributes to this developmental transition.

DESIGN:

At P7, rats were injected subcutaneously with saline or DSP-4, a neurotoxin that targets noradrenergic …

Social Rights And The Relational Value Of The Rights To Participate In Sport, Recreation And Play, Janet E. Lord, Michael Ashley Stein

Faculty Publications

No abstract provided.

Nutrient Allocations And Metabolism In Two Collembolans With Contrasting Reproduction And Growth Strategies, Thomas Larsen, Marc Ventura, Christian Damgaard, Erik A. Hobbie, Paul Henning Krogh

Faculty Publications

Physiological mechanisms such as allocation and release of nutrients are keys to understanding an animal's adaptation to a particular habitat. This study investigated how two detrivores with contrasting life‐history traits allocated carbon (C) and nitrogen (N) to growth, reproduction and metabolism. As model organisms we used the collembolans, Proisotoma minuta (Tullberg 1871) and Protaphorura fimata (Gisin 1952).

To estimate allocations of C and N in tissue, we changed the isotopic composition of the animal's yeast diets when they became sexually mature and followed isotope turnover in tissue, growth and reproduction for 28 days. In addition, we measured the composition of …

The Effect Of Ambiguous Data On Phylogenetic Estimates Obtained By Maximum Likelihood And Bayesian Inference, Alan R. Lemmon, Jeremy M. Brown, Kathrin Stanger-Hall, Emily Moriarty Lemmon

Faculty Publications

Although an increasing number of phyiogenetic data sets are incomplete, the effect of ambiguous data on phylogenetic accuracy is not well understood. We use 4-taxon simulations to study the effects of ambiguous data (i.e., missing characters or gaps) in maximum, likelihood (ML) and Bayesian frameworks. By introducing ambiguous data in a way that removes confounding factors, we provide the first clear understanding of 1 mechanism, by which ambiguous data can mislead phylogenetic analyses. We find that in both ML and Bayesian frameworks, among-site rate variation can interact with, ambiguous data to produce misleading estimates of topology and branch, lengths. Furthermore, …