Item Type | Journal Article |
---|---|
Author | WenHui Kuang |
Author | TianRong Yang |
Author | AiLin Liu |
Author | Chi Zhang |
Author | DengSheng Lu |
Author | WenFeng Chi |
URL | http://link.springer.com/10.1007/s11430-016-9032-9 |
Volume | 60 |
Issue | 6 |
Pages | 1098-1109 |
Publication | Science China Earth Sciences |
ISSN | 1674-7313, 1869-1897 |
Date | 6/2017 |
DOI | 10.1007/s11430-016-9032-9 |
Accessed | 2017-06-28 13:07:53 |
Library Catalog | CrossRef |
Language | en |
Short Title | An EcoCity model for regulating urban land cover structure and thermal environment |
Item Type | Journal Article |
---|---|
Author | Roger A. Close |
Author | Roger B. J. Benson |
Author | Paul Upchurch |
Author | Richard J. Butler |
URL | http://www.nature.com/ncomms/2017/170522/ncomms15381/full/ncomms15381.html |
Rights | © 2017 Macmillan Publishers Limited, part of Springer Nature. All rights reserved. |
Volume | 8 |
Pages | 15381 |
Publication | Nature Communications |
ISSN | 2041-1723 |
Date | 2017-05-22 |
DOI | 10.1038/ncomms15381 |
Accessed | 2017-05-23 03:25:06 |
Library Catalog | www.nature.com |
Language | en |
Abstract | Species richness increases with area sampled, potentially confounding biodiversity patterns from the fossil record. Here, the authors standardize spatial sampling to control for this bias and show that terrestrial vertebrate diversification was bounded during the Mesozoic but that equilibria were reset following the K/Pg extinction. |
Item Type | Journal Article |
---|---|
Author | Julio Miguel Grandez-Rios |
Author | Leonardo Lima Bergamini |
Author | Walter Santos de Araújo |
Author | Fabricio Villalobos |
Author | Mário Almeida-Neto |
URL | http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0138031 |
Volume | 10 |
Issue | 9 |
Pages | e0138031 |
Publication | PLOS ONE |
ISSN | 1932-6203 |
Date | Sep 17, 2015 |
Journal Abbr | PLOS ONE |
DOI | 10.1371/journal.pone.0138031 |
Accessed | 2017-03-28 14:11:14 |
Library Catalog | PLoS Journals |
Abstract | Understanding the drivers of plant-insect interactions is still a key issue in terrestrial ecology. Here, we used 30 well-defined plant-herbivore assemblages to assess the effects of host plant phylogenetic isolation and origin (native vs. exotic) on the species richness, composition and specialization of the insect herbivore fauna on co-occurring plant species. We also tested for differences in such effects between assemblages composed exclusively of exophagous and endophagous herbivores. We found a consistent negative effect of the phylogenetic isolation of host plants on the richness, similarity and specialization of their insect herbivore faunas. Notably, except for Jaccard dissimilarity, the effect of phylogenetic isolation on the insect herbivore faunas did not vary between native and exotic plants. Our findings show that the phylogenetic isolation of host plants is a key factor that influences the richness, composition and specialization of their local herbivore faunas, regardless of the host plant origin. |
Short Title | The Effect of Host-Plant Phylogenetic Isolation on Species Richness, Composition and Specialization of Insect Herbivores |
Item Type | Journal Article |
---|---|
Author | Ellie E. Dyer |
Author | Phillip Cassey |
Author | David W. Redding |
Author | Ben Collen |
Author | Victoria Franks |
Author | Kevin J. Gaston |
Author | Kate E. Jones |
Author | Salit Kark |
Author | C. David L. Orme |
Author | Tim M. Blackburn |
URL | http://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.2000942 |
Volume | 15 |
Issue | 1 |
Pages | e2000942 |
Publication | PLOS Biology |
ISSN | 1545-7885 |
Date | Jan 12, 2017 |
Journal Abbr | PLOS Biology |
DOI | 10.1371/journal.pbio.2000942 |
Accessed | 2017-03-06 15:32:27 |
Library Catalog | PLoS Journals |
Abstract | Author Summary The introduction of alien species is one of the primary ways in which human actions are changing the environment. Alien species have been responsible for numerous global and local extinctions and are eroding the uniqueness of many natural environments. There is thus a basic need to understand which areas end up with more alien species. Here, we use a major new global database on the distribution of alien birds to show, first, how patterns in the number of species introduced to a location (colonisation pressure) have changed over time. We show that historical introductions were driven largely by European, and especially British, colonialism. However, the rate of bird introductions is increasing, with shifts in the locations of origin and introduction of species probably driven by the cage bird trade. We then combine information on where bird species have been introduced with a global map of alien bird species richness to identify the main drivers of richness. We show that colonisation pressure is the strongest predictor of alien bird species richness, but that there are other anthropogenic and environmental drivers. Most notably, once colonisation pressure has been accounted for, alien bird species richness is higher in areas where native bird species richness is higher. |
Item Type | Journal Article |
---|---|
Author | Hanno Seebens |
Author | Tim M. Blackburn |
Author | Ellie E. Dyer |
Author | Piero Genovesi |
Author | Philip E. Hulme |
Author | Jonathan M. Jeschke |
Author | Shyama Pagad |
Author | Petr Pyšek |
Author | Marten Winter |
Author | Margarita Arianoutsou |
Author | Sven Bacher |
Author | Bernd Blasius |
Author | Giuseppe Brundu |
Author | César Capinha |
Author | Laura Celesti-Grapow |
Author | Wayne Dawson |
Author | Stefan Dullinger |
Author | Nicol Fuentes |
Author | Heinke Jäger |
Author | John Kartesz |
Author | Marc Kenis |
Author | Holger Kreft |
Author | Ingolf Kühn |
Author | Bernd Lenzner |
Author | Andrew Liebhold |
Author | Alexander Mosena |
Author | Dietmar Moser |
Author | Misako Nishino |
Author | David Pearman |
Author | Jan Pergl |
Author | Wolfgang Rabitsch |
Author | Julissa Rojas-Sandoval |
Author | Alain Roques |
Author | Stephanie Rorke |
Author | Silvia Rossinelli |
Author | Helen E. Roy |
Author | Riccardo Scalera |
Author | Stefan Schindler |
Author | Kateřina Štajerová |
Author | Barbara Tokarska-Guzik |
Author | Mark van Kleunen |
Author | Kevin Walker |
Author | Patrick Weigelt |
Author | Takehiko Yamanaka |
Author | Franz Essl |
URL | http://www.nature.com/ncomms/2017/170215/ncomms14435/full/ncomms14435.html |
Rights | © 2017 Macmillan Publishers Limited, part of Springer Nature. All rights reserved. |
Volume | 8 |
Pages | 14435 |
Publication | Nature Communications |
ISSN | 2041-1723 |
Date | 2017/02/15 |
DOI | 10.1038/ncomms14435 |
Accessed | 2017-02-21 19:32:05 |
Library Catalog | www.nature.com |
Language | en |
Abstract | Alien species of animals and plants can invade new regions of the earth. This study performs a global analysis of temporal dynamics and spatial patterns of alien species introductions over the past 200 years, and reports no saturation in the rate at which these invasion are increasing. |
Item Type | Journal Article |
---|---|
Author | Melania E. Cristescu |
URL | http://www.cell.com/trends/ecology-evolution/abstract/S0169-5347(14)00175-X |
Volume | 29 |
Issue | 10 |
Pages | 566-571 |
Publication | Trends in Ecology & Evolution |
ISSN | 0169-5347 |
Date | 2014-10-01 |
Extra | PMID: 25175416 |
Journal Abbr | Trends in Ecology & Evolution |
DOI | 10.1016/j.tree.2014.08.001 |
Accessed | 2016-12-12 19:39:26 |
Library Catalog | www.cell.com |
Language | English |
Abstract | DNA-based species identification, known as barcoding, transformed the traditional approach to the study of biodiversity science. The field is transitioning from barcoding individuals to metabarcoding communities. This revolution involves new sequencing technologies, bioinformatics pipelines, computational infrastructure, and experimental designs. In this dynamic genomics landscape, metabarcoding studies remain insular and biodiversity estimates depend on the particular methods used. In this opinion article, I discuss the need for a coordinated advancement of DNA-based species identification that integrates taxonomic and barcoding information. Such an approach would facilitate access to almost 3 centuries of taxonomic knowledge and 1 decade of building repository barcodes. Conservation projects are time sensitive, research funding is becoming restricted, and informed decisions depend on our ability to embrace integrative approaches to biodiversity science. |
Short Title | From barcoding single individuals to metabarcoding biological communities |
Item Type | Journal Article |
---|---|
Author | Michael J. O. Pocock |
Author | Darren M. Evans |
Author | Jane Memmott |
URL | http://science.sciencemag.org/content/335/6071/973 |
Rights | Copyright © 2012, American Association for the Advancement of Science |
Volume | 335 |
Issue | 6071 |
Pages | 973-977 |
Publication | Science |
ISSN | 0036-8075, 1095-9203 |
Date | 2012/02/24 |
Extra | PMID: 22363009 |
DOI | 10.1126/science.1214915 |
Accessed | 2016-06-01 18:26:58 |
Library Catalog | science.sciencemag.org |
Language | en |
Abstract | Understanding species’ interactions and the robustness of interaction networks to species loss is essential to understand the effects of species’ declines and extinctions. In most studies, different types of networks (such as food webs, parasitoid webs, seed dispersal networks, and pollination networks) have been studied separately. We sampled such multiple networks simultaneously in an agroecosystem. We show that the networks varied in their robustness; networks including pollinators appeared to be particularly fragile. We show that, overall, networks did not strongly covary in their robustness, which suggests that ecological restoration (for example, through agri-environment schemes) benefitting one functional group will not inevitably benefit others. Some individual plant species were disproportionately well linked to many other species. This type of information can be used in restoration management, because it identifies the plant taxa that can potentially lead to disproportionate gains in biodiversity. Analysis of seven interconnected networks on a farm reveals that they vary in their fragility, but that they do not covary. Analysis of seven interconnected networks on a farm reveals that they vary in their fragility, but that they do not covary. |
Item Type | Journal Article |
---|---|
Author | Ignacio Quintero |
Author | Petr Keil |
Author | Walter Jetz |
Author | Forrest W. Crawford |
URL | http://sysbio.oxfordjournals.org/content/64/6/1059 |
Volume | 64 |
Issue | 6 |
Pages | 1059-1073 |
Publication | Systematic Biology |
ISSN | 1063-5157, 1076-836X |
Date | 11/01/2015 |
Extra | PMID: 26254671 |
Journal Abbr | Syst Biol |
DOI | 10.1093/sysbio/syv057 |
Accessed | 2016-12-05 16:49:31 |
Library Catalog | sysbio.oxfordjournals.org |
Language | en |
Abstract | Spatial variation in biodiversity is the result of complex interactions between evolutionary history and ecological factors. Methods in historical biogeography combine phylogenetic information with current species locations to infer the evolutionary history of a clade through space and time. A major limitation of most methods for historical biogeographic inference is the requirement of single locations for terminal lineages, reducing contemporary species geographical ranges to a point in two-dimensional space. In reality, geographic ranges usually show complex geographic patterns, irregular shapes, or discontinuities. In this article, we describe a method for phylogeographic analysis using polygonal species geographic ranges of arbitrary complexity. By integrating the geographic diversification process across species ranges, we provide a method to infer the geographic location of ancestors in a Bayesian framework. By modeling migration conditioned on a phylogenetic tree, this approach permits reconstructing the geographic location of ancestors through time. We apply this new method to the diversification of two neotropical bird genera, Trumpeters (Psophia) and Cinclodes ovenbirds. We demonstrate the usefulness of our method (called rase) in phylogeographic reconstruction of species ancestral locations and contrast our results with previous methods that compel researchers to reduce the distribution of species to one point in space. We discuss model extensions to enable a more general, spatially explicit framework for historical biogeographic analysis. |
Item Type | Journal Article |
---|---|
Author | Tyler R. Kartzinel |
Author | Robert M. Pringle |
URL | http://onlinelibrary.wiley.com/doi/10.1111/1755-0998.12366/abstract |
Volume | 15 |
Issue | 4 |
Pages | 903-914 |
Publication | Molecular Ecology Resources |
ISSN | 1755-0998 |
Date | July 1, 2015 |
Journal Abbr | Mol Ecol Resour |
DOI | 10.1111/1755-0998.12366 |
Accessed | 2016-12-01 19:07:15 |
Library Catalog | Wiley Online Library |
Language | en |
Abstract | Understanding community assembly and population dynamics frequently requires detailed knowledge of food web structure. For many consumers, obtaining precise information about diet composition has traditionally required sacrificing animals or other highly invasive procedures, generating tension between maintaining intact study populations and knowing what they eat. We developed 16S mitochondrial DNA sequencing methods to identify arthropods in the diets of generalist vertebrate predators without requiring a blocking primer. We demonstrate the utility of these methods for a common Caribbean lizard that has been intensively studied in the context of small island food webs: Anolis sagrei (a semi-arboreal ‘trunk-ground’ anole ecomorph). Novel PCR primers were identified in silico and tested in vitro. Illumina sequencing successfully characterized the arthropod component of 168 faecal DNA samples collected during three field trips spanning 12 months, revealing 217 molecular operational taxonomic units (mOTUs) from at least nine arthropod orders (including Araneae, Blattodea, Coleoptera, Hemiptera, Hymenoptera, Isoptera, Lepidoptera and Orthoptera). Three mOTUs (one beetle, one cockroach and one ant) were particularly frequent, occurring in ≥50% of samples, but the majority of mOTUs were infrequent (180, or 83%, occurred in ≤5% of samples). Species accumulation curves showed that dietary richness and composition were similar between size-dimorphic sexes; however, female lizards had greater per-sample dietary richness than males. Overall diet composition (but not richness) was significantly different across seasons, and we found more pronounced interindividual variation in December than in May. These methods will be generally useful in characterizing the diets of diverse insectivorous vertebrates. |
Short Title | Molecular detection of invertebrate prey in vertebrate diets |
Item Type | Journal Article |
---|---|
Author | Yinqiu Ji |
Author | Louise Ashton |
Author | Scott M. Pedley |
Author | David P. Edwards |
Author | Yong Tang |
Author | Akihiro Nakamura |
Author | Roger Kitching |
Author | Paul M. Dolman |
Author | Paul Woodcock |
Author | Felicity A. Edwards |
Author | Trond H. Larsen |
Author | Wayne W. Hsu |
Author | Suzan Benedick |
Author | Keith C. Hamer |
Author | David S. Wilcove |
Author | Catharine Bruce |
Author | Xiaoyang Wang |
Author | Taal Levi |
Author | Martin Lott |
Author | Brent C. Emerson |
Author | Douglas W. Yu |
URL | http://onlinelibrary.wiley.com/doi/10.1111/ele.12162/abstract |
Volume | 16 |
Issue | 10 |
Pages | 1245-1257 |
Publication | Ecology Letters |
ISSN | 1461-0248 |
Date | October 1, 2013 |
Journal Abbr | Ecol Lett |
DOI | 10.1111/ele.12162 |
Accessed | 2016-12-08 17:59:08 |
Library Catalog | Wiley Online Library |
Language | en |
Abstract | To manage and conserve biodiversity, one must know what is being lost, where, and why, as well as which remedies are likely to be most effective. Metabarcoding technology can characterise the species compositions of mass samples of eukaryotes or of environmental DNA. Here, we validate metabarcoding by testing it against three high-quality standard data sets that were collected in Malaysia (tropical), China (subtropical) and the United Kingdom (temperate) and that comprised 55,813 arthropod and bird specimens identified to species level with the expenditure of 2,505 person-hours of taxonomic expertise. The metabarcode and standard data sets exhibit statistically correlated alpha- and beta-diversities, and the two data sets produce similar policy conclusions for two conservation applications: restoration ecology and systematic conservation planning. Compared with standard biodiversity data sets, metabarcoded samples are taxonomically more comprehensive, many times quicker to produce, less reliant on taxonomic expertise and auditable by third parties, which is essential for dispute resolution. |
Item Type | Journal Article |
---|---|
Author | Tanja Stadler |
Author | Daniel L. Rabosky |
Author | Robert E. Ricklefs |
Author | Folmer Bokma |
URL | http://www.journals.uchicago.edu/doi/abs/10.1086/677676 |
Volume | 184 |
Issue | 4 |
Pages | 447-455 |
Publication | The American Naturalist |
ISSN | 0003-0147 |
Date | October 1, 2014 |
Journal Abbr | The American Naturalist |
DOI | 10.1086/677676 |
Accessed | 2016-09-08 14:17:25 |
Library Catalog | journals.uchicago.edu (Atypon) |
Abstract | Many studies have tried to identify factors that explain differences in numbers of species between clades against the background assumption that older clades contain more species because they have had more time for diversity to accumulate. The finding in several recent studies that species richness of clades is decoupled from stem age has been interpreted as evidence for ecological limits to species richness. Here we demonstrate that the absence of a positive age-diversity relationship, or even a negative relationship, may also occur when taxa are defined based on time or some correlate of time such as genetic distance or perhaps morphological distinctness. Thus, inferring underlying processes from distributions of species across higher taxa requires caution concerning the way in which higher taxa are defined. When this definition is unclear, crown age is superior to stem age as a measure of clade age. |
Item Type | Journal Article |
---|---|
Author | R. Graham Reynolds |
Author | David C. Collar |
Author | Stesha A. Pasachnik |
Author | Matthew L. Niemiller |
Author | Alberto R. Puente-Rolón |
Author | Liam J. Revell |
URL | http://onlinelibrary.wiley.com/doi/10.1111/evo.12987/abstract |
Volume | 70 |
Issue | 8 |
Pages | 1882-1895 |
Publication | Evolution |
ISSN | 1558-5646 |
Date | August 1, 2016 |
Journal Abbr | Evolution |
DOI | 10.1111/evo.12987 |
Accessed | 2016-08-12 19:00:58 |
Library Catalog | Wiley Online Library |
Language | en |
Abstract | Colonization of islands can dramatically influence the evolutionary trajectories of organisms, with both deterministic and stochastic processes driving adaptation and diversification. Some island colonists evolve extremely large or small body sizes, presumably in response to unique ecological circumstances present on islands. One example of this phenomenon, the Greater Antillean boas, includes both small (<90 cm) and large (4 m) species occurring on the Greater Antilles and Bahamas, with some islands supporting pairs or trios of body-size divergent species. These boas have been shown to comprise a monophyletic radiation arising from a Miocene dispersal event to the Greater Antilles, though it is not known whether co-occurrence of small and large species is a result of dispersal or in situ evolution. Here, we provide the first comprehensive species phylogeny for this clade combined with morphometric and ecological data to show that small body size evolved repeatedly on separate islands in association with specialization in substrate use. Our results further suggest that microhabitat specialization is linked to increased rates of head shape diversification among specialists. Our findings show that ecological specialization following island colonization promotes morphological diversity through deterministic body size evolution and cranial morphological diversification that is contingent on island- and species-specific factors. |
Item Type | Journal Article |
---|---|
Author | Jesse R. Lasky |
Author | Timothy H. Keitt |
Author | Brian C. Weeks |
Author | Evan P. Economo |
URL | http://onlinelibrary.wiley.com/doi/10.1111/ecog.02303/abstract |
Pages | n/a-n/a |
Publication | Ecography |
ISSN | 1600-0587 |
Date | August 1, 2016 |
Journal Abbr | Ecography |
DOI | 10.1111/ecog.02303 |
Accessed | 2016-09-06 17:30:30 |
Library Catalog | Wiley Online Library |
Language | en |
Abstract | Island systems have long played a central role in the development of ecology and evolutionary biology. However, while many empirical studies suggest species differ in vital biogeographic rates, such as dispersal abilities, quantitative methods have had difficulty incorporating such differences into analyses of whole-assemblages. In particular, differences in dispersal abilities among species can cause variation in the spatial clustering and localization of species distributions. Here, we develop a single, hierarchical Bayes, assemblage-wide model of 252 bird species distributions on the islands of Northern Melanesia and use it to investigate a) whether dispersal limitation structures bird assemblages across the archipelago, b) whether species differ in dispersal ability, and c) test the hypothesis that wing aspect ratio, a trait linked to flight efficiency, predicts differences inferred by the model. Consistent with island biogeographic theory, we found that individual species were more likely to occur on islands with greater area, and on islands near to other islands where the species also occurred. However, species showed wide variation in the importance and spatial scale of these clustering effects. The importance of clustering in distributions was greater for species with low wing aspect ratios, and the spatial scale of clustering was also smaller for low aspect ratio species. These findings suggest that the spatial configuration of islands interacts with species dispersal ability to affect contemporary distributions, and that these species differences are detectable in occurrence patterns. More generally, our study demonstrates a quantitative, hierarchical approach that can be used to model the influence of dispersal heterogeneity in diverse assemblages and test hypotheses for how traits drive dispersal differences, providing a framework for deconstructing ecological assemblages and their drivers. This article is protected by copyright. All rights reserved. |
Item Type | Journal Article |
---|---|
Author | Jason J. Kolbe |
Author | Andrew C. Battles |
Author | Kevin J. Avilés-Rodríguez |
URL | http://onlinelibrary.wiley.com/doi/10.1111/1365-2435.12607/abstract |
Volume | 30 |
Issue | 8 |
Pages | 1418-1429 |
Publication | Functional Ecology |
ISSN | 1365-2435 |
Date | August 1, 2016 |
Journal Abbr | Funct Ecol |
DOI | 10.1111/1365-2435.12607 |
Accessed | 2016-08-10 23:13:28 |
Library Catalog | Wiley Online Library |
Language | en |
Abstract | * As animals move through their environments, they encounter a variety of substrates, which have important effects on their locomotor performance. Habitat modification can alter the types of substrates available for locomotion. In particular, many types of artificial substrates have been added to urban areas, but effects of these novel surfaces on animal locomotion are little known. * In this study, we assessed locomotor performance of two Anolis lizard species (A. cristatellus and A. stratulus) on substrates that varied in inclination and surface roughness. Rough substrates represented the tree trunks and branches typically used in natural forest habitats, whereas smooth, vertical substrates captured the qualities of artificial surfaces, such as posts and walls, available in human-modified habitats. We then observed habitat use to test the habitat constraint hypothesis – that lizards should more frequently occupy portions of the habitat in which they perform better. * Increased inclination and decreased surface roughness caused lizards to run slower. Both A. cristatellus and A. stratulus ran slowest on the smooth, vertical surface, and A. cristatellus often slipped and fell on this surface. In contrast to predictions, both species frequently used smooth, vertical substrates in the wild. Anolis cristatellus occupied artificial substrates 73% of the time in human-modified habitats despite performing worse than A. stratulus on the smooth, vertical track. We therefore rejected the habitat constraint hypothesis for anoles in these human-modified habitats. * Despite overall poor performance on the smooth, vertical track, A. cristatellus had a significant morphology–performance relationship that supports the prediction that selection should favour smaller lizards with relatively longer limbs in human-modified habitats. The smaller bodied A. stratulus performed better than A. cristatellus on smooth, vertical substrates and therefore may not be exposed to the same selective pressures. * We contend that habitat modification by humans may alter morphology-performance–habitat use relationships found in natural habitats. This may lead to changes in selective pressures for some species, which may influence their ability to occupy human-modified habitats such as cities. |
Short Title | City slickers |
Item Type | Journal Article |
---|---|
Author | Carlos P. Carmona |
Author | Francesco de Bello |
Author | Norman W. H. Mason |
Author | Jan Lepš |
URL | http://www.cell.com/article/S0169534716000458/abstract |
Volume | 31 |
Issue | 5 |
Pages | 382-394 |
Publication | Trends in Ecology & Evolution |
ISSN | 0169-5347 |
Date | 2016/05/01 |
Journal Abbr | Trends in Ecology & Evolution |
DOI | 10.1016/j.tree.2016.02.003 |
Accessed | 2016-07-21 20:34:46 |
Library Catalog | www.cell.com |
Language | English |
Abstract | Owing to the conceptual complexity of functional diversity (FD), a multitude of different methods are available for measuring it, with most being operational at only a small range of spatial scales. This causes uncertainty in ecological interpretations and limits the potential to generalize findings across studies or compare patterns across scales. We solve this problem by providing a unified framework expanding on and integrating existing approaches. The framework, based on trait probability density (TPD), is the first to fully implement the Hutchinsonian concept of the niche as a probabilistic hypervolume in estimating FD. This novel approach could revolutionize FD-based research by allowing quantification of the various FD components from organismal to macroecological scales, and allowing seamless transitions between scales., Functional trait diversity, in other words the variation of traits between organisms, can be used to address a great number of pressing ecological questions. Consequently, trait-based approaches are increasingly being used by ecologists., However, functional diversity comprises several components that can be evaluated at different spatial scales. Because of this conceptual complexity, there is an overabundance of disparate approaches for estimating it, which leads to confusion among users and hampers the comparability of different studies., A single mathematical framework encompassing different approaches while providing a seamless continuity between spatial scales is needed., Reconciling the approaches based on the concept of the niche as a hypervolume and those that consider traits in probabilistic terms is the first step towards the foundation of a unified framework. |
Short Title | Traits Without Borders |
Item Type | Journal Article |
---|---|
Author | Kristin M. Winchell |
Author | R. Graham Reynolds |
Author | Sofia R. Prado-Irwin |
Author | Alberto R. Puente-Rolón |
Author | Liam J. Revell |
URL | http://onlinelibrary.wiley.com/doi/10.1111/evo.12925/abstract |
Rights | © 2016 The Author(s). Evolution © 2016 The Society for the Study of Evolution. |
Volume | 70 |
Issue | 5 |
Pages | 1009-1022 |
Publication | Evolution |
ISSN | 1558-5646 |
Date | May 1, 2016 |
Journal Abbr | Evolution |
DOI | 10.1111/evo.12925 |
Accessed | 2016-07-26 19:15:50 |
Library Catalog | Wiley Online Library |
Language | en |
Abstract | Urbanization is an increasingly important dimension of global change, and urban areas likely impose significant natural selection on the species that reside within them. Although many species of plants and animals can survive in urban areas, so far relatively little research has investigated whether such populations have adapted (in an evolutionary sense) to their newfound milieu. Even less of this work has taken place in tropical regions, many of which have experienced dramatic growth and intensification of urbanization in recent decades. In the present study, we focus on the neotropical lizard, Anolis cristatellus. We tested whether lizard ecology and morphology differ between urban and natural areas in three of the most populous municipalities on the island of Puerto Rico. We found that environmental conditions including temperature, humidity, and substrate availability differ dramatically between neighboring urban and natural areas. We also found that lizards in urban areas use artificial substrates a large proportion of the time, and that these substrates tend to be broader than substrates in natural forest. Finally, our morphological data showed that lizards in urban areas have longer limbs relative to their body size, as well as more subdigital scales called lamellae, when compared to lizards from nearby forested habitats. This shift in phenotype is exactly in the direction predicted based on habitat differences between our urban and natural study sites, combined with our results on how substrates are being used by lizards in these areas. Findings from a common-garden rearing experiment using individuals from one of our three pairs of populations provide evidence that trait differences between urban and natural sites may be genetically based. Taken together, our data suggest that anoles in urban areas are under significant differential natural selection and may be evolutionarily adapting to their human-modified environments. |
Item Type | Journal Article |
---|---|
Author | Natalie Cooper |
Author | Gavin H. Thomas |
Author | Richard G. FitzJohn |
URL | http://onlinelibrary.wiley.com/doi/10.1111/2041-210X.12533/abstract |
Volume | 7 |
Issue | 6 |
Pages | 693-699 |
Publication | Methods in Ecology and Evolution |
ISSN | 2041-210X |
Date | June 1, 2016 |
Journal Abbr | Methods Ecol Evol |
DOI | 10.1111/2041-210X.12533 |
Accessed | 2016-07-26 21:15:42 |
Library Catalog | Wiley Online Library |
Language | en |
Abstract | * Phylogenetic comparative methods are becoming increasingly popular for investigating evolutionary patterns and processes. However, these methods are not infallible – they suffer from biases and make assumptions like all other statistical methods. * Unfortunately, although these limitations are generally well known in the phylogenetic comparative methods community, they are often inadequately assessed in empirical studies leading to misinterpreted results and poor model fits. Here, we explore reasons for the communication gap dividing those developing new methods and those using them. * We suggest that some important pieces of information are missing from the literature and that others are difficult to extract from long, technical papers. We also highlight problems with users jumping straight into software implementations of methods (e.g. in r) that may lack documentation on biases and assumptions that are mentioned in the original papers. * To help solve these problems, we make a number of suggestions including providing blog posts or videos to explain new methods in less technical terms, encouraging reproducibility and code sharing, making wiki-style pages summarising the literature on popular methods, more careful consideration and testing of whether a method is appropriate for a given question/data set, increased collaboration, and a shift from publishing purely novel methods to publishing improvements to existing methods and ways of detecting biases or testing model fit. Many of these points are applicable across methods in ecology and evolution, not just phylogenetic comparative methods. |
Item Type | Journal Article |
---|---|
Author | Douglas J. Futuyma |
URL | http://doi.wiley.com/10.1111/j.1558-5646.2010.00960.x |
Volume | 64 |
Issue | 7 |
Pages | 1865-1884 |
Publication | Evolution |
ISSN | 00143820 |
Date | 07/2010 |
DOI | 10.1111/j.1558-5646.2010.00960.x |
Accessed | 2016-06-27 14:51:57 |
Library Catalog | CrossRef |
Language | en |
Item Type | Journal Article |
---|---|
Author | Thomas W. Schoener |
Author | Jennifer B. Slade |
Author | Christopher H. Stinson |
URL | http://www.jstor.org/stable/4216667 |
Volume | 53 |
Issue | 2 |
Pages | 160-169 |
Publication | Oecologia |
ISSN | 0029-8549 |
Date | 1982 |
Journal Abbr | Oecologia |
Accessed | 2016-05-20 20:58:18 |
Library Catalog | JSTOR |
Abstract | Over 5,000 prey items from specimens of Bahamian Leiocephalus lizards were measured and identified taxonomically. The diet in general consists mainly of arthropods, but much plant matter is also eaten, including flowers and buds as well as fruit. Lizards comprise about 2% of the diet by volume. Individuals inhabiting relatively small islands are more likely to have eaten plant matter than those from relatively large islands. Within the most widespread species (carinatus), sexual dimorphism in size is greater, the smaller the number of sympatric species in its structural habitat. Prey-size differences between differently sized Leiocephalus are greater, the greater the dimorphism. However, even the most dimorphic sexes take rather similar prey sizes. For all Bahamian species combined, the inverse correlation of sexual dimorphism with sympatric species is not as strong as an inverse correlation with latitude. We suggest that sexual selection on female size to increase the clutch size that can be carried may have affected sexual dimorphism in the genus. |
Item Type | Journal Article |
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Author | Marc Cadotte |
Author | Cecile H. Albert |
Author | Steve C. Walker |
URL | http://onlinelibrary.wiley.com/doi/10.1111/ele.12161/abstract |
Volume | 16 |
Issue | 10 |
Pages | 1234-1244 |
Publication | Ecology Letters |
ISSN | 1461-0248 |
Date | October 1, 2013 |
Journal Abbr | Ecol Lett |
DOI | 10.1111/ele.12161 |
Accessed | 2016-06-27 14:49:56 |
Library Catalog | Wiley Online Library |
Language | en |
Abstract | Species enter and persist in local communities because of their ecological fit to local conditions, and recently, ecologists have moved from measuring diversity as species richness and evenness, to using measures that reflect species ecological differences. There are two principal approaches for quantifying species ecological differences: functional (trait-based) and phylogenetic pairwise distances between species. Both approaches have produced new ecological insights, yet at the same time methodological issues and assumptions limit them. Traits and phylogeny may provide different, and perhaps complementary, information about species' differences. To adequately test assembly hypotheses, a framework integrating the information provided by traits and phylogenies is required. We propose an intuitive measure for combining functional and phylogenetic pairwise distances, which provides a useful way to assess how functional and phylogenetic distances contribute to understanding patterns of community assembly. Here, we show that both traits and phylogeny inform community assembly patterns in alpine plant communities across an elevation gradient, because they represent complementary information. Differences in historical selection pressures have produced variation in the strength of the trait-phylogeny correlation, and as such, integrating traits and phylogeny can enhance the ability to detect assembly patterns across habitats or environmental gradients. |
Short Title | The ecology of differences |
Item Type | Journal Article |
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Author | Erica Bree Rosenblum |
Author | Luke J. Harmon |
URL | http://onlinelibrary.wiley.com/doi/10.1111/j.1558-5646.2010.01190.x/abstract |
Rights | © 2010 The Author(s). Evolution© 2010 The Society for the Study of Evolution. |
Volume | 65 |
Issue | 4 |
Pages | 946-960 |
Publication | Evolution |
ISSN | 1558-5646 |
Date | April 1, 2011 |
DOI | 10.1111/j.1558-5646.2010.01190.x |
Accessed | 2016-06-22 18:19:38 |
Library Catalog | Wiley Online Library |
Language | en |
Abstract | Understanding the factors that promote or inhibit species formation remains a central focus in evolutionary biology. It has been difficult to make generalities about the process of ecological speciation in particular given that each example is somewhat idiosyncratic. Here we use a case study of replicated ecological speciation in the same selective environment to assess factors that account for similarities and differences across taxa in progress towards ecological speciation. We study three different species of lizards on the gypsum sand dunes of White Sands, New Mexico, and present evidence that all three fulfill the essential factors for ecological speciation. We use multilocus nuclear data to show that progress toward ecological speciation is unequal across the three species. We also use morphometric data to show that traits other than color are likely under selection and that selection at White Sands is both strong and multifarious. Finally, we implicate geographic context to explain difference in progress toward speciation in the three species. We suggest that evaluating cases from the natural world that are “same same but different” can reveal the mechanisms of ecological speciation. |
Short Title | “Same Same but Different” |
Item Type | Journal Article |
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Author | Marguerite A. Butler |
Author | Aaron A. King |
Author | Acting Editors: Trevor Price |
Author | Bernard J. Crespi |
URL | http://www.jstor.org/stable/10.1086/426002 |
Volume | 164 |
Issue | 6 |
Pages | 683-695 |
Publication | The American Naturalist |
ISSN | 0003-0147 |
Date | 2004 |
Journal Abbr | The American Naturalist |
DOI | 10.1086/426002 |
Accessed | 2016-06-17 20:18:39 |
Library Catalog | JSTOR |
Abstract | Abstract: Biologists employ phylogenetic comparative methods to study adaptive evolution. However, none of the popular methods model selection directly. We explain and develop a method based on the Ornstein‐Uhlenbeck (OU) process, first proposed by Hansen. Ornstein‐Uhlenbeck models incorporate both selection and drift and are thus qualitatively different from, and more general than, pure drift models based on Brownian motion. Most importantly, OU models possess selective optima that formalize the notion of adaptive zone. In this article, we develop the method for one quantitative character, discuss interpretations of its parameters, and provide code implementing the method. Our approach allows us to translate hypotheses regarding adaptation in different selective regimes into explicit models, to test the models against data using maximum‐likelihood‐based model selection techniques, and to infer details of the evolutionary process. We illustrate the method using two worked examples. Relative to existing approaches, the direct modeling approach we demonstrate allows one to explore more detailed hypotheses and to utilize more of the information content of comparative data sets than existing methods. Moreover, the use of a model selection framework to simultaneously compare a variety of hypotheses advances our ability to assess alternative evolutionary explanations. |
Short Title | Phylogenetic Comparative Analysis |
Item Type | Journal Article |
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Author | Owen L. Petchey |
Author | Andy Hector |
Author | Kevin J. Gaston |
URL | http://onlinelibrary.wiley.com/doi/10.1890/03-0226/abstract |
Volume | 85 |
Issue | 3 |
Pages | 847-857 |
Publication | Ecology |
ISSN | 1939-9170 |
Date | March 1, 2004 |
DOI | 10.1890/03-0226 |
Accessed | 2016-06-10 16:14:38 |
Library Catalog | Wiley Online Library |
Language | en |
Abstract | Biodiversity can influence ecosystem functioning through changes in the amount of resource use complementary among species. Functional diversity is a measure of biodiversity that aims to quantify resource use complementarity and thereby explain and predict ecosystem functioning. The primary goal of this article is to compare the explanatory power of four measures of functional diversity: species richness, functional group richness, functional attribute diversity, and FD. The secondary goal is to showcase the novel methods required for calculating functional attribute diversity and FD. We find that species richness and functional group richness explain the least variation in aboveground biomass production within and across grassland biodiversity manipulations at six European locations; functional attribute diversity and FD explain greater variation. Reasons for differences in explanatory power are discussed, such as the relatively greater amount of information and fewer assumptions included in functional attribute diversity and FD. We explore the opportunities and limitations of the particular methods we used to calculate functional attribute diversity and FD. These mainly concern how best to select the information used to calculate them. |
Item Type | Journal Article |
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Author | Oskar Englund |
Author | Göran Berndes |
URL | http://onlinelibrary.wiley.com/doi/10.1002/wene.118/abstract |
Volume | 4 |
Issue | 1 |
Pages | 26-50 |
Publication | Wiley Interdisciplinary Reviews: Energy and Environment |
ISSN | 2041-840X |
Date | January 1, 2015 |
Journal Abbr | WIREs Energy Environ |
DOI | 10.1002/wene.118 |
Accessed | 2016-05-03 15:40:21 |
Library Catalog | Wiley Online Library |
Language | en |
Abstract | Sustainability certification schemes and standards are meant to prevent a range of unacceptable socioeconomic and environmental consequences, such as threats to biodiversity. While there is wide support for conserving biodiversity, operationalizing this support in the form of guiding principles, criteria/indicators, and legislation is complicated. This study investigates how and to what extent 26 sustainability standards (eleven for forest management, nine for agriculture and six biofuel-related) consider biodiversity, by assessing how they seek to prevent actions that can threaten biodiversity as well as how they support actions aimed at biodiversity conservation. For this purpose, a benchmark standard was developed, meant to represent a case with very high ambitions concerning biodiversity conservation. Of the assessed standards, the biofuel-related standards demonstrated the highest level of compliance with the benchmark. On average, they complied with 72% of the benchmark's component criteria, compared to 61% for the agricultural standards and 60% for the forestry standards. Fairtrade, Sustainable Agriculture Network/Rainforest Alliance (SAN/RA), Roundtable on Sustainable Palm Oil (RSPO), and Roundtable on Responsible Soy (RTRS) were particularly stringent, while Green Gold Label S5 (GGLS5), PEOLG, Global Partnership for Good Agricultural Practices (GLOBALGAP), European Union Organic (EU Organic), National Organic Program (NOP), Green Gold Label S2 (GGLS2), and International Sustainability & Carbon Certification (ISCC) were particularly unstringent. All eleven forestry standards, six of the nine agricultural standards, and all six biofuel-related standards addressed ecosystem conversion, ranging from requiring that high conservation value areas be identified and preserved to requiring full protection. Finally, key barriers to, and challenges for, certification schemes are discussed and recommendations are made for further development of sustainability standards. WIREs Energy Environ 2015, 4:26–50. doi: 10.1002/wene.118 For further resources related to this article, please visit the WIREs website. Conflict of interest: The authors have declared no conflicts of interest for this article. |
Item Type | Journal Article |
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Author | Sarah Federman |
Author | Alex Dornburg |
Author | Douglas C. Daly |
Author | Alexander Downie |
Author | George H. Perry |
Author | Anne D. Yoder |
Author | Eric J. Sargis |
Author | Alison F. Richard |
Author | Michael J. Donoghue |
Author | Andrea L. Baden |
URL | http://www.pnas.org/content/113/18/5041 |
Volume | 113 |
Issue | 18 |
Pages | 5041-5046 |
Publication | Proceedings of the National Academy of Sciences |
ISSN | 0027-8424, 1091-6490 |
Date | 05/03/2016 |
Extra | PMID: 27071108 |
Journal Abbr | PNAS |
DOI | 10.1073/pnas.1523825113 |
Accessed | 2016-05-03 19:16:30 |
Library Catalog | www.pnas.org |
Language | en |
Abstract | Madagascar’s lemurs display a diverse array of feeding strategies with complex relationships to seed dispersal mechanisms in Malagasy plants. Although these relationships have been explored previously on a case-by-case basis, we present here the first comprehensive analysis of lemuriform feeding, to our knowledge, and its hypothesized effects on seed dispersal and the long-term survival of Malagasy plant lineages. We used a molecular phylogenetic framework to examine the mode and tempo of diet evolution, and to quantify the associated morphological space occupied by Madagascar’s lemurs, both extinct and extant. Using statistical models and morphometric analyses, we demonstrate that the extinction of large-bodied lemurs resulted in a significant reduction in functional morphological space associated with seed dispersal ability. These reductions carry potentially far-reaching consequences for Malagasy ecosystems, and we highlight large-seeded Malagasy plants that appear to be without extant animal dispersers. We also identify living lemurs that are endangered yet occupy unique and essential dispersal niches defined by our morphometric analyses. |