Model-based approaches to discovering diversity : new implementations, tests of adequacy and an empirical application to central American Diptera

Most of the earth’s biodiversity is unknown to science. With global climate change set to drastically alter its distribution, it is imperative to catalogue it and understand its function in order to preserve it and better understand how this change will impact humanity. Recent technological and statistical advances have in theory made possible increasingly rapid discovery and description of diversity. The statistical properties and performance of these new approaches are still poorly known, however, their integration with complementary methods from disparate disciplines has not been achieved. In this dissertation we present three chapters of original research that advance these areas of biodiversity science. The first introduces a new implementation of the GMYC, a statistical model used for species delimitation. This implementation fully accounts for uncertainty in model parameters, and we test its performance under various historical scenarios. We find that the model generally performs well, but that failing to account for uncertainty in nuisance parameters inflates confidence in species limits. The second introduces a method to examine the fit of empirical data to a multispecies coalescent model commonly used in phylogenetic inference. Systematic and phylogeographic studies are generating ever-larger datasets which often range up to the genome scale and often wish to use coalescent models to infer parameters such as phylogenies, divergence times and effective population sizes. Though the multispecies coalescent can infer these parameters, it is unclear the extent to which it is a good fit for these new empirical datasets. We employ our new approach to 25 published datasets and find that a majority of them show poor fit to the data and that for some of them, that poor fit affects inference. In the last chapter we integrate statistical approaches from both ecology and systematics to infer species limits, phylogeny, population genetic structure and ecological community structure in a study of a poorly known tropical alpine fly fauna. We find that we can effectively describe patterns of diversity in the absence of a low-level taxonomic framework, but that inference of the processes structuring that diversity remains difficult. We also find that some of our inferences of community structure are sensitive to uncertainty in species limits and phylogeny

Pemasaran Hijau Yang Semakin Menjadi Kebutuhan Dalam Dunia Bisnis

Green marketing is a type of marketing where a company sells a product that is envi-ronmentally friendly. In the concept of green marketing, a company has done greenmarketing since the beginning of the production process which transform raw materi-als into environmentally friendly finished product, called green product. The growingglobal warming make the green marketing is a major issue in today\u27s business world.Green marketing has become a necessity for both producers and consumers for thecreation of a healthy environment. A company can do green marketing that matchesto the company\u27s business. Implementation of green marketing can cover many ac-tivities depending on what the company wants to do. Automotive manufacturers arean example of a company that must implement a comprehensive green marketingbecause its products could potentially damage the environment due to pollution fromvehicle fumes

When evolution is the solution to pollution : key principles, and lessons from rapid repeated adaptation of killifish (Fundulus heteroclitus) populations

© The Author(s), 2017. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Evolutionary Applications 10 (2017): 762–783, doi:10.1111/eva.12470.For most species, evolutionary adaptation is not expected to be sufficiently rapid to buffer the effects of human-mediated environmental changes, including environmental pollution. Here we review how key features of populations, the characteristics of environmental pollution, and the genetic architecture underlying adaptive traits, may interact to shape the likelihood of evolutionary rescue from pollution. Large populations of Atlantic killifish (Fundulus heteroclitus) persist in some of the most contaminated estuaries of the United States, and killifish studies have provided some of the first insights into the types of genomic changes that enable rapid evolutionary rescue from complexly degraded environments. We describe how selection by industrial pollutants and other stressors has acted on multiple populations of killifish and posit that extreme nucleotide diversity uniquely positions this species for successful evolutionary adaptation. Mechanistic studies have identified some of the genetic underpinnings of adaptation to a well-studied class of toxic pollutants; however, multiple genetic regions under selection in wild populations seem to reflect more complex responses to diverse native stressors and/or compensatory responses to primary adaptation. The discovery of these pollution-adapted killifish populations suggests that the evolutionary influence of anthropogenic stressors as selective agents occurs widely. Yet adaptation to chemical pollution in terrestrial and aquatic vertebrate wildlife may rarely be a successful “solution to pollution” because potentially adaptive phenotypes may be complex and incur fitness costs, and therefore be unlikely to evolve quickly enough, especially in species with small population sizes.National Science Foundation Grant Numbers: DEB-1265282, OCE-1314567, DEB-1120263; National Institutes of Environmental Health Sciences Grant Numbers: R01ES021934-01, P42ES007381; Postdoctoral Research Program at the US Environmental Protection (US EPA); Office of Research and Development; Oak Ridge Institute for Science and Education (ORISE) Grant Number: DW92429801; US Department of Energ

Pengaruh Macam Bahan Organik Dan Inokulum Rhizobium Terhadap Pertumbuhan Dan Hasil Tanaman Kedelai (Glycine Max (L.) Merril)

Kedelai (Glycine max (L.) Merril) merupakan tanaman pangan yang penting di Indonesia. Sebagai tanaman golongan Leguminoceae, tanaman kedelai mampu mengadakan simbiosis dengan bakteri tertentu sehingga dapat langsung memfiksasi nitrogen dari udara. Tujuan penelitian ini ialah mempelajari pengaruh interaksi macam bahan organik dan dosis legin terhadap peningkatan pertumbuhan dan hasil tanaman kedelai (Glycine max (L.) Merril). Hipotesis yang diajukan ialah macam bahan organik dapat mempengaruhi kebutuhan dosis legin untuk meningkatkan pertumbuhan dan hasil tanaman kedelai (Glycine max (L.) Merril). Penelitian dilaksanakan di Kebun Percobaan Fakultas Pertanian desa Jatikerto, kecamatan Kromengan, kabupaten Malang. Penelitian dilaksanakan pada bulan Juni 2014 sampai bulan September 2014. Alat yang digunakan pada penelitian ialah Leaf Area Meter (LAM), timbangan analitik, meteran dan oven. Bahan yang digunakan adalah benih kedelai varietas Grobogan. Perlakuan yang diberikan yaitu faktor satu adalah pemberian bahan organik yang terdiri dari: B1=tanpa aplikasi bahan organik, B2=residu biochar dan B3= kompos 10 ton ha-1. Faktor kedua adalah penggunaan legin yang terdiri dari: L1 = tanpa legin, L2 = dosis legin 8 g kg-1 dan L3 = dosis legin 12 g kg-1. Hasil penelitian menunjukkan penambahan bahan organik kompos 10 ton ha-1 dan residu biochar tidak mempengaruhi kebutuhan dosis legin. Kompos 10 ton ha-1 nyata untuk meningkatkan jumlah polong per tanaman kedelai (Glycine max (L.) Merril) sebesar 71,21 %. Dosis legin tidak nyata terhadap hasil panen tanaman kedelai (Glycine max (L.) Merril)

Poor fit to the multispecies coalescent is widely detectable in empirical data

Model checking is a critical part of Bayesian data analysis, yet it remains largely unused in systematic studies. Phylogeny estimation has recently moved into an era of increasingly complex models that simultaneously account for multiple evolutionary processes, the statistical fit of these models to the data has rarely been tested. Here we develop a posterior predictive simulation-based model check for a commonly used multispecies coalescent model, implemented in *BEAST, and apply it to 25 published data sets. We show that poor model fit is detectable in the majority of data sets; that this poor fit can mislead phylogenetic estimation; and that in some cases it stems from processes of inherent interest to systematists. We suggest that as systematists scale up to phylogenomic data sets, which will be subject to a heterogeneous array of evolutionary processes, critically evaluating the fit of models to data is an analytical step that can no longer be ignored. [Gene duplication and extinction; gene tree; hybridization; model fit; multispecies coalescent; next-generation sequencing; posterior predictive simulation; species delimitation; species tree.] © The Author(s) 2013

Store-Operated Ca2+ Entry (SOCE) Contributes to Normal Skeletal Muscle Contractility in young but not in aged skeletal muscle

Muscle atrophy alone is insufficient to explain the significant decline in contractile force of skeletal muscle during normal aging. One contributing factor to decreased contractile force in aging skeletal muscle could be compromised excitation-contraction (E-C) coupling, without sufficient available Ca2+ to allow for repetitive muscle contractility, skeletal muscles naturally become weaker. Using biophysical approaches, we previously showed that store-operated Ca2+ entry (SOCE) is compromised in aged skeletal muscle but not in young ones. While important, a missing component from previous studies is whether or not SOCE function correlates with contractile function during aging. Here we test the contribution of extracellular Ca2+ to contractile function of skeletal muscle during aging. First, we demonstrate graded coupling between SR Ca2+ release channel-mediated Ca2+ release and activation of SOCE. Inhibition of SOCE produced significant reduction of contractile force in young skeletal muscle, particularly at high frequency stimulation, and such effects were completely absent in aged skeletal muscle. Our data indicate that SOCE contributes to the normal physiological contractile response of young healthy skeletal muscle and that defective extracellular Ca2+ entry through SOCE contributes to the reduced contractile force characteristic of aged skeletal muscle

The Landscape of Extreme Genomic Variation in the Highly Adaptable Atlantic Killifish

Understanding and predicting the fate of populations in changing environments require knowledge about the mechanisms that support phenotypic plasticity and the adaptive value and evolutionary fate of genetic variation within populations. Atlantic killifish (Fundulus heteroclitus) exhibit extensive phenotypic plasticity that supports large population sizes in highly fluctuating estuarine environments. Populations have also evolved diverse local adaptations. To yield insights into the genomic variation that supports their adaptability, we sequenced a reference genome and 48 additional whole genomes from a wild population. Evolution of genes associated with cell cycle regulation and apoptosis is accelerated along the killifish lineage, which is likely tied to adaptations for life in highly variable estuarine environments. Genome-wide standing genetic variation, including nucleotide diversity and copy number variation, is extremely high. The highest diversity genes are those associated with immune function and olfaction, whereas genes under greatest evolutionary constraint are those associated with neurological, developmental, and cytoskeletal functions. Reduced genetic variation is detected for tight junction proteins, which in killifish regulate paracellular permeability that supports their extreme physiological flexibility. Low-diversity genes engage in more regulatory interactions than high-diversity genes, consistent with the influence of pleiotropic constraint on molecular evolution. High genetic variation is crucial for continued persistence of species given the pace of contemporary environmental change. Killifish populations harbor among the highest levels of nucleotide diversity yet reported for a vertebrate species, and thus may serve as a useful model system for studying evolutionary potential in variable and changing environments

Ryanodine receptor and FK506 binding protein 1 in the Atlantic killifish (Fundulus heteroclitus) : a phylogenetic and population-based comparison

Author Posting. © The Author(s), 2017. This is the author's version of the work. It is posted here under a nonexclusive, irrevocable, paid-up, worldwide license granted to WHOI. It is made available for personal use, not for redistribution. The definitive version was published in Aquatic Toxicology 192 (2017): 105-115, doi:10.1016/j.aquatox.2017.09.002.Non-dioxin-like polychlorinated biphenyls (NDL PCBs) activate ryanodine receptors (RyR), microsomal Ca2+ channels of broad significance. Teleost fish may be important models for NDL PCB neurotoxicity, and we used sequencing databases to characterize teleost RyR and FK506 binding protein 12 or 12.6 kDa (genes FKBP1A; FKBP1B), which promote NDL PCB-triggered Ca2+ dysregulation. Particular focus was placed on describing genes in the Atlantic killifish (Fundulus heteroclitus) genome and searching available RNA-sequencing datasets for single nucleotide variants (SNV) between PCB tolerant killifish from New Bedford Harbor (NBH) versus sensitive killifish from Scorton Creek (SC), MA. Consistent with the teleost whole genome duplication (tWGD), killifish have six RyR genes, corresponding to a and b paralogs of mammalian RyR1, 2 and 3. The presence of six RyR genes was consistent in all teleosts investigated including zebrafish. Killifish have four FKBP1; one FKBP1b and three FKBP1a named FKBP1aa, FKBP1ab, likely from the tWGD and a single gene duplicate FKBP1a3 suggested to have arisen in Atherinomorphae. The RyR and FKBP1 genes displayed tissue and developmental stage-specific mRNA expression, and the previously uncharacterized RyR3, herein named RyR3b, and all FKBP1 genes were prominent in brain. We identified a SNV in RyR3b encoding missense mutation E1458D. In NBH killifish, 57% were heterozygous and 28% were homozygous for this SNV, whereas almost all SC killifish (94%) lacked the variant (n≥39 per population). The outlined sequence differences between mammalian and teleost RyR and FKBP1 together with outlined population differences in SNV frequency may contribute to our understanding of NDL PCB neurotoxicity.This research was supported by the KC Donnelly Research Externship made possible by the National Institute of Environmental Health Sciences’ Superfund Research Program (EBH) and the Superfund Research Programs at UC Davis (INP and EBH; P42ES004699) and Boston University (JJS, JVG, MEH, SIK; P42ES007381). Additional support was provided by the National Institute of Health (INP; R01 ES014901; and P01 AR052354) and by National Science Foundation collaborative research grants (MEH and SIK; DEB-1265282 and DEB-1120263). This research was also supported in part by an appointment (to BC) with the Postdoctoral Research Program at the U.S. Environmental Protection (US EPA) Office of Research and Development administered by the Oak Ridge Institute for Science and Education (ORISE) through Interagency Agreement No. DW92429801 between the U.S. Department of Energy and the US EPA