Publications by authors named "Jeffrey C Oliver"

28 Publications

  • Page 1 of 1

Origin of the mechanism of phenotypic plasticity in satyrid butterfly eyespots.

Elife 2020 Feb 11;9. Epub 2020 Feb 11.

Department of Biological Sciences, National University of Singapore, Singapore, Singapore.

Plasticity is often regarded as a derived adaptation to help organisms survive in variable but predictable environments, however, we currently lack a rigorous, mechanistic examination of how plasticity evolves in a large comparative framework. Here, we show that phenotypic plasticity in eyespot size in response to environmental temperature observed in atyrid butterflies is a complex derived adaptation of this lineage. By reconstructing the evolution of known physiological and molecular components of eyespot size plasticity in a comparative framework, we showed that 20E titer plasticity in response to temperature is a pre-adaptation shared by all butterfly species examined, whereas expression of EcR in eyespot centers, and eyespot sensitivity to 20E, are both derived traits found only in a subset of species with eyespots.
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http://dx.doi.org/10.7554/eLife.49544DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7012602PMC
February 2020

Creating the Urban Farmer's Almanac with Citizen Science Data.

Insects 2019 Sep 11;10(9). Epub 2019 Sep 11.

Office of Digital Innovation and Stewardship, Libraries, University of Arizona, Tucson, AZ 85721, USA.

Agriculture has long been a part of the urban landscape, from gardens to small scale farms. In recent decades, interest in producing food in cities has grown dramatically, with an estimated 30% of the global urban population engaged in some form of food production. Identifying and managing the insect biodiversity found on city farms is a complex task often requiring years of study and specialization, especially in urban landscapes which have a complicated tapestry of fragmentation, diversity, pollution, and introduced species. Supporting urban growers with relevant data informs insect management decision-making for both growers and their neighbors, yet this information can be difficult to come by. In this study, we introduced several web-based citizen science programs that can connect growers with useful data products and people to help with the who, what, where, and when of urban insects. Combining the power of citizen science volunteers with the efforts of urban farmers can result in a clearer picture of the diversity and ecosystem services in play, limited insecticide use, and enhanced non-chemical alternatives. Connecting urban farming practices with citizen science programs also demonstrates the ecosystem value of urban agriculture and engages more citizens with the topics of food production, security, and justice in their communities.
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http://dx.doi.org/10.3390/insects10090294DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6780957PMC
September 2019

Mimicry in viceroy butterflies is dependent on abundance of the model queen butterfly.

Commun Biol 2019 18;2:68. Epub 2019 Feb 18.

Office of Digital Innovation & Stewardship, University Libraries, University of Arizona, Tucson, AZ, 85721, USA.

Mimics should not exist without their models, yet often they do. In the system involving queen and viceroy butterflies, the viceroy is both mimic and co-model depending on the local abundance of the model, the queen. Here, we integrate population surveys, chemical analyses, and predator behavior assays to demonstrate how mimics may persist in locations with low-model abundance. As the queen becomes less locally abundant, the viceroy becomes more chemically defended and unpalatable to predators. However, the observed changes in viceroy chemical defense and palatability are not attributable to differing host plant chemical defense profiles. Our results suggest that mimetic viceroy populations are maintained at localities of low-model abundance through an increase in their toxicity. Sharing the burden of predator education in some places but not others may also lower the fitness cost of warning signals thereby supporting the origin and maintenance of aposematism.
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http://dx.doi.org/10.1038/s42003-019-0303-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6379391PMC
April 2020

NovoGraph: Human genome graph construction from multiple long-read assemblies.

F1000Res 2018 3;7:1391. Epub 2018 Sep 3.

National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, 20817, USA.

Genome graphs are emerging as an important novel approach to the analysis of high-throughput human sequencing data. By explicitly representing genetic variants and alternative haplotypes in a mappable data structure, they can enable the improved analysis of structurally variable and hyperpolymorphic regions of the genome. In most existing approaches, graphs are constructed from variant call sets derived from short-read sequencing. As long-read sequencing becomes more cost-effective and enables assembly for increasing numbers of whole genomes, a method for the direct construction of a genome graph from sets of assembled human genomes would be desirable. Such assembly-based genome graphs would encompass the wide spectrum of genetic variation accessible to long-read-based assembly, including large structural variants and divergent haplotypes. Here we present NovoGraph, a method for the construction of a human genome graph directly from a set of assemblies. NovoGraph constructs a genome-wide multiple sequence alignment of all input contigs and creates a graph by merging the input sequences at positions that are both homologous and sequence-identical. NovoGraph outputs resulting graphs in VCF format that can be loaded into third-party genome graph toolkits. To demonstrate NovoGraph, we construct a genome graph with 23,478,835 variant sites and 30,582,795 variant alleles from assemblies of seven ethnically diverse human genomes (AK1, CHM1, CHM13, HG003, HG004, HX1, NA19240). Initial evaluations show that mapping against the constructed graph reduces the average mismatch rate of reads from sample NA12878 by approximately 0.2%, albeit at a slightly increased rate of reads that remain unmapped.
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http://dx.doi.org/10.12688/f1000research.15895.2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6305223PMC
November 2019

Comparisons of Citizen Science Data-Gathering Approaches to Evaluate Urban Butterfly Diversity.

Insects 2018 Dec 6;9(4). Epub 2018 Dec 6.

Department of Entomology, Natural History Museum of Los Angeles County, Los Angeles, CA 90007, USA.

By 2030, ten percent of earth's landmass will be occupied by cities. Urban environments can be home to many plants and animals, but surveying and estimating biodiversity in these spaces is complicated by a heterogeneous built environment where access and landscaping are highly variable due to human activity. Citizen science approaches may be the best way to assess urban biodiversity, but little is known about their relative effectiveness and efficiency. Here, we compare three techniques for acquiring data on butterfly (Lepidoptera: Rhopalocera) species richness: trained volunteer Pollard walks, Malaise trapping with expert identification, and crowd-sourced iNaturalist observations. A total of 30 butterfly species were observed; 27 (90%) were recorded by Pollard walk observers, 18 (60%) were found in Malaise traps, and 22 (73%) were reported by iNaturalist observers. Pollard walks reported the highest butterfly species richness, followed by iNaturalist and then Malaise traps during the four-month time period. Pollard walks also had significantly higher species diversity than Malaise traps.
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http://dx.doi.org/10.3390/insects9040186DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6316785PMC
December 2018

BioTIME: A database of biodiversity time series for the Anthropocene.

Authors:
Maria Dornelas Laura H Antão Faye Moyes Amanda E Bates Anne E Magurran Dušan Adam Asem A Akhmetzhanova Ward Appeltans José Manuel Arcos Haley Arnold Narayanan Ayyappan Gal Badihi Andrew H Baird Miguel Barbosa Tiago Egydio Barreto Claus Bässler Alecia Bellgrove Jonathan Belmaker Lisandro Benedetti-Cecchi Brian J Bett Anne D Bjorkman Magdalena Błażewicz Shane A Blowes Christopher P Bloch Timothy C Bonebrake Susan Boyd Matt Bradford Andrew J Brooks James H Brown Helge Bruelheide Phaedra Budy Fernando Carvalho Edward Castañeda-Moya Chaolun Allen Chen John F Chamblee Tory J Chase Laura Siegwart Collier Sharon K Collinge Richard Condit Elisabeth J Cooper J Hans C Cornelissen Unai Cotano Shannan Kyle Crow Gabriella Damasceno Claire H Davies Robert A Davis Frank P Day Steven Degraer Tim S Doherty Timothy E Dunn Giselda Durigan J Emmett Duffy Dor Edelist Graham J Edgar Robin Elahi Sarah C Elmendorf Anders Enemar S K Morgan Ernest Rubén Escribano Marc Estiarte Brian S Evans Tung-Yung Fan Fabiano Turini Farah Luiz Loureiro Fernandes Fábio Z Farneda Alessandra Fidelis Robert Fitt Anna Maria Fosaa Geraldo Antonio Daher Correa Franco Grace E Frank William R Fraser Hernando García Roberto Cazzolla Gatti Or Givan Elizabeth Gorgone-Barbosa William A Gould Corinna Gries Gary D Grossman Julio R Gutierréz Stephen Hale Mark E Harmon John Harte Gary Haskins Donald L Henshaw Luise Hermanutz Pamela Hidalgo Pedro Higuchi Andrew Hoey Gert Van Hoey Annika Hofgaard Kristen Holeck Robert D Hollister Richard Holmes Mia Hoogenboom Chih-Hao Hsieh Stephen P Hubbell Falk Huettmann Christine L Huffard Allen H Hurlbert Natália Macedo Ivanauskas David Janík Ute Jandt Anna Jażdżewska Tore Johannessen Jill Johnstone Julia Jones Faith A M Jones Jungwon Kang Tasrif Kartawijaya Erin C Keeley Douglas A Kelt Rebecca Kinnear Kari Klanderud Halvor Knutsen Christopher C Koenig Alessandra R Kortz Kamil Král Linda A Kuhnz Chao-Yang Kuo David J Kushner Claire Laguionie-Marchais Lesley T Lancaster Cheol Min Lee Jonathan S Lefcheck Esther Lévesque David Lightfoot Francisco Lloret John D Lloyd Adrià López-Baucells Maite Louzao Joshua S Madin Borgþór Magnússon Shahar Malamud Iain Matthews Kent P McFarland Brian McGill Diane McKnight William O McLarney Jason Meador Peter L Meserve Daniel J Metcalfe Christoph F J Meyer Anders Michelsen Nataliya Milchakova Tom Moens Even Moland Jon Moore Carolina Mathias Moreira Jörg Müller Grace Murphy Isla H Myers-Smith Randall W Myster Andrew Naumov Francis Neat James A Nelson Michael Paul Nelson Stephen F Newton Natalia Norden Jeffrey C Oliver Esben M Olsen Vladimir G Onipchenko Krzysztof Pabis Robert J Pabst Alain Paquette Sinta Pardede David M Paterson Raphaël Pélissier Josep Peñuelas Alejandro Pérez-Matus Oscar Pizarro Francesco Pomati Eric Post Herbert H T Prins John C Priscu Pieter Provoost Kathleen L Prudic Erkki Pulliainen B R Ramesh Olivia Mendivil Ramos Andrew Rassweiler Jose Eduardo Rebelo Daniel C Reed Peter B Reich Suzanne M Remillard Anthony J Richardson J Paul Richardson Itai van Rijn Ricardo Rocha Victor H Rivera-Monroy Christian Rixen Kevin P Robinson Ricardo Ribeiro Rodrigues Denise de Cerqueira Rossa-Feres Lars Rudstam Henry Ruhl Catalina S Ruz Erica M Sampaio Nancy Rybicki Andrew Rypel Sofia Sal Beatriz Salgado Flavio A M Santos Ana Paula Savassi-Coutinho Sara Scanga Jochen Schmidt Robert Schooley Fakhrizal Setiawan Kwang-Tsao Shao Gaius R Shaver Sally Sherman Thomas W Sherry Jacek Siciński Caya Sievers Ana Carolina da Silva Fernando Rodrigues da Silva Fabio L Silveira Jasper Slingsby Tracey Smart Sara J Snell Nadejda A Soudzilovskaia Gabriel B G Souza Flaviana Maluf Souza Vinícius Castro Souza Christopher D Stallings Rowan Stanforth Emily H Stanley José Mauro Sterza Maarten Stevens Rick Stuart-Smith Yzel Rondon Suarez Sarah Supp Jorge Yoshio Tamashiro Sukmaraharja Tarigan Gary P Thiede Simon Thorn Anne Tolvanen Maria Teresa Zugliani Toniato Ørjan Totland Robert R Twilley Gediminas Vaitkus Nelson Valdivia Martha Isabel Vallejo Thomas J Valone Carl Van Colen Jan Vanaverbeke Fabio Venturoli Hans M Verheye Marcelo Vianna Rui P Vieira Tomáš Vrška Con Quang Vu Lien Van Vu Robert B Waide Conor Waldock Dave Watts Sara Webb Tomasz Wesołowski Ethan P White Claire E Widdicombe Dustin Wilgers Richard Williams Stefan B Williams Mark Williamson Michael R Willig Trevor J Willis Sonja Wipf Kerry D Woods Eric J Woehler Kyle Zawada Michael L Zettler Thomas Hickler

Glob Ecol Biogeogr 2018 Jul 24;27(7):760-786. Epub 2018 Jul 24.

Centre for Biological Diversity and Scottish Oceans Institute, School of Biology, University of St. Andrews St Andrews United Kingdom.

Motivation: The BioTIME database contains raw data on species identities and abundances in ecological assemblages through time. These data enable users to calculate temporal trends in biodiversity within and amongst assemblages using a broad range of metrics. BioTIME is being developed as a community-led open-source database of biodiversity time series. Our goal is to accelerate and facilitate quantitative analysis of temporal patterns of biodiversity in the Anthropocene.

Main Types Of Variables Included: The database contains 8,777,413 species abundance records, from assemblages consistently sampled for a minimum of 2 years, which need not necessarily be consecutive. In addition, the database contains metadata relating to sampling methodology and contextual information about each record.

Spatial Location And Grain: BioTIME is a global database of 547,161 unique sampling locations spanning the marine, freshwater and terrestrial realms. Grain size varies across datasets from 0.0000000158 km (158 cm) to 100 km (1,000,000,000,000 cm).

Time Period And Grain: BioTIME records span from 1874 to 2016. The minimal temporal grain across all datasets in BioTIME is a year.

Major Taxa And Level Of Measurement: BioTIME includes data from 44,440 species across the plant and animal kingdoms, ranging from plants, plankton and terrestrial invertebrates to small and large vertebrates.

Software Format: .csv and .SQL.
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http://dx.doi.org/10.1111/geb.12729DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6099392PMC
July 2018

Corrigendum to "A Survey of Eyespot Sexual Dimorphism across Nymphalid Butterflies".

Int J Evol Biol 2017 27;2017:2704640. Epub 2017 Jul 27.

Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06511, USA.

[This corrects the article DOI: 10.1155/2013/926702.].
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http://dx.doi.org/10.1155/2017/2704640DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5551517PMC
July 2017

Bioinformatic training needs at a health sciences campus.

Authors:
Jeffrey C Oliver

PLoS One 2017 14;12(6):e0179581. Epub 2017 Jun 14.

University of Arizona Health Sciences Library, University of Arizona, Tucson, AZ, United States of America.

Background: Health sciences research is increasingly focusing on big data applications, such as genomic technologies and precision medicine, to address key issues in human health. These approaches rely on biological data repositories and bioinformatic analyses, both of which are growing rapidly in size and scope. Libraries play a key role in supporting researchers in navigating these and other information resources.

Methods: With the goal of supporting bioinformatics research in the health sciences, the University of Arizona Health Sciences Library established a Bioinformation program. To shape the support provided by the library, I developed and administered a needs assessment survey to the University of Arizona Health Sciences campus in Tucson, Arizona. The survey was designed to identify the training topics of interest to health sciences researchers and the preferred modes of training.

Results: Survey respondents expressed an interest in a broad array of potential training topics, including "traditional" information seeking as well as interest in analytical training. Of particular interest were training in transcriptomic tools and the use of databases linking genotypes and phenotypes. Staff were most interested in bioinformatics training topics, while faculty were the least interested. Hands-on workshops were significantly preferred over any other mode of training. The University of Arizona Health Sciences Library is meeting those needs through internal programming and external partnerships.

Conclusion: The results of the survey demonstrate a keen interest in a variety of bioinformatic resources; the challenge to the library is how to address those training needs. The mode of support depends largely on library staff expertise in the numerous subject-specific databases and tools. Librarian-led bioinformatic training sessions provide opportunities for engagement with researchers at multiple points of the research life cycle. When training needs exceed library capacity, partnering with intramural and extramural units will be crucial in library support of health sciences bioinformatic research.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0179581PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5470718PMC
September 2017

eButterfly: Leveraging Massive Online Citizen Science for Butterfly Consevation.

Insects 2017 May 18;8(2). Epub 2017 May 18.

Insectarium, Montreal Space for Life, Montreal, QC H1X 2B2, Canada.

Data collection, storage, analysis, visualization, and dissemination are changing rapidly due to advances in new technologies driven by computer science and universal access to the internet. These technologies and web connections place human observers front and center in citizen science-driven research and are critical in generating new discoveries and innovation in such fields as astronomy, biodiversity, and meteorology. Research projects utilizing a citizen science approach address scientific problems at regional, continental, and even global scales otherwise impossible for a single lab or even a small collection of academic researchers. Here we describe eButterfly an integrative checklist-based butterfly monitoring and database web-platform that leverages the skills and knowledge of recreational butterfly enthusiasts to create a globally accessible unified database of butterfly observations across North America. Citizen scientists, conservationists, policy makers, and scientists are using eButterfly data to better understand the biological patterns of butterfly species diversity and how environmental conditions shape these patterns in space and time. eButterfly in collaboration with thousands of butterfly enthusiasts has created a near real-time butterfly data resource producing tens of thousands of observations per year open to all to share and explore.
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http://dx.doi.org/10.3390/insects8020053DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5492067PMC
May 2017

Nymphalid eyespots are co-opted to novel wing locations following a similar pattern in independent lineages.

BMC Evol Biol 2015 Feb 14;15:20. Epub 2015 Feb 14.

Department of Ecology & Evolutionary Biology, Yale University, New Haven, CT, 06520, USA.

Background: Variation in the number of repeated traits, or serial homologs, has contributed greatly to animal body plan diversity. Eyespot color patterns of nymphalid butterflies, like arthropod and vertebrate limbs, are an example of serial homologs. These eyespot color patterns originated in a small number of wing sectors on the ventral hindwing surface and later appeared in novel wing sectors, novel wings, and novel wing surfaces. However, the details of how eyespots were co-opted to these novel wing locations are currently unknown.

Results: We used a large data matrix of eyespot/presence absence data, previously assembled from photographs of contemporary species, to perform a phylogenetic investigation of eyespot origins in nine independent nymphalid lineages. To determine how the eyespot gene regulatory network acquired novel positional information, we used phylogenetic correlation analyses to test for non-independence in the origination of eyespots. We found consistent patterns of eyespot gene network redeployment in the nine lineages, where eyespots first redeployed from the ventral hindwing to the ventral forewing, then to new sectors within the ventral wing surface, and finally to the dorsal wing surface. Eyespots that appeared in novel wing sectors modified the positional information of their serial homolog ancestors in one of two ways: by changing the wing or surface identity while retaining sector identity, or by changing the sector identity while retaining wing and surface identity.

Conclusions: Eyespot redeployment to novel sectors, wings, and surfaces happened multiple times in different nymphalid subfamilies following a similar pattern. This indicates that parallel mutations altering expression of the eyespot gene regulatory network led to its co-option to novel wing locations over time.
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http://dx.doi.org/10.1186/s12862-015-0300-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4335541PMC
February 2015

Nymphalid eyespot serial homologues originate as a few individualized modules.

Proc Biol Sci 2014 Jul;281(1787)

Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06520, USA Department of Biological Sciences, National University of Singapore, 117543 Singapore, Republic of Singapore Yale-NUS College, 138614 Singapore, Republic of Singapore

Serial homologues are repeated traits that share similar development but occur in different parts of the body. Variation in number of repeats accounts for substantial diversity in animal form and considerable work has focused on identifying the factors accounting for this variation. Little is known, however, about how serial homologues originally become repeated, or about the relative timing of repeat individuation relative to repeat origin. Here, we show that the serially repeated eyespots on nymphalid butterfly wings most likely arose as a small cluster of units on the ventral hindwing that were later co-opted to the dorsal and anterior wing surfaces. Based on comparative analyses of over 400 species, we found support for a model of eyespot origin followed by redeployment, rather than by the conventional model, where eyespots arose as a complete row of undifferentiated units that later gained individuation. In addition, eyespots most likely evolved from simpler pattern elements, single-coloured spots, which were already individuated among different wing sectors. Finally, the late appearance of eyespots on the dorsal, hidden wing surface further suggests that these novel complex traits originally evolved for one function (thwarting predator attacks) and acquired a second function (sexual signalling) when moved to a different body location. This broad comparative analysis illustrates how serial homologues may initially evolve as a few units serving a particular function and subsequently become repeated in novel body locations with new functions.
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http://dx.doi.org/10.1098/rspb.2013.3262DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4071533PMC
July 2014

A multigene phylogenetic synthesis for the class Lecanoromycetes (Ascomycota): 1307 fungi representing 1139 infrageneric taxa, 317 genera and 66 families.

Mol Phylogenet Evol 2014 Oct 18;79:132-68. Epub 2014 Apr 18.

Botanical Museum, Finnish Museum of Natural History, FI-00014 University of Helsinki, Finland.

The Lecanoromycetes is the largest class of lichenized Fungi, and one of the most species-rich classes in the kingdom. Here we provide a multigene phylogenetic synthesis (using three ribosomal RNA-coding and two protein-coding genes) of the Lecanoromycetes based on 642 newly generated and 3329 publicly available sequences representing 1139 taxa, 317 genera, 66 families, 17 orders and five subclasses (four currently recognized: Acarosporomycetidae, Lecanoromycetidae, Ostropomycetidae, Umbilicariomycetidae; and one provisionarily recognized, 'Candelariomycetidae'). Maximum likelihood phylogenetic analyses on four multigene datasets assembled using a cumulative supermatrix approach with a progressively higher number of species and missing data (5-gene, 5+4-gene, 5+4+3-gene and 5+4+3+2-gene datasets) show that the current classification includes non-monophyletic taxa at various ranks, which need to be recircumscribed and require revisionary treatments based on denser taxon sampling and more loci. Two newly circumscribed orders (Arctomiales and Hymeneliales in the Ostropomycetidae) and three families (Ramboldiaceae and Psilolechiaceae in the Lecanorales, and Strangosporaceae in the Lecanoromycetes inc. sed.) are introduced. The potential resurrection of the families Eigleraceae and Lopadiaceae is considered here to alleviate phylogenetic and classification disparities. An overview of the photobionts associated with the main fungal lineages in the Lecanoromycetes based on available published records is provided. A revised schematic classification at the family level in the phylogenetic context of widely accepted and newly revealed relationships across Lecanoromycetes is included. The cumulative addition of taxa with an increasing amount of missing data (i.e., a cumulative supermatrix approach, starting with taxa for which sequences were available for all five targeted genes and ending with the addition of taxa for which only two genes have been sequenced) revealed relatively stable relationships for many families and orders. However, the increasing number of taxa without the addition of more loci also resulted in an expected substantial loss of phylogenetic resolving power and support (especially for deep phylogenetic relationships), potentially including the misplacements of several taxa. Future phylogenetic analyses should include additional single copy protein-coding markers in order to improve the tree of the Lecanoromycetes. As part of this study, a new module ("Hypha") of the freely available Mesquite software was developed to compare and display the internodal support values derived from this cumulative supermatrix approach.
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http://dx.doi.org/10.1016/j.ympev.2014.04.003DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4185256PMC
October 2014

A Survey of Eyespot Sexual Dimorphism across Nymphalid Butterflies.

Int J Evol Biol 2013 5;2013:926702. Epub 2013 Dec 5.

Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06511, USA ; Department of Biological Sciences, National University of Singapore and Yale-NUS College, Singapore 117543.

Differences between sexes of the same species are widespread and are variable in nature. While it is often assumed that males are more ornamented than females, in the nymphalid butterfly genus Bicyclus, females have, on average, more eyespot wing color patterns than males. Here we extend these studies by surveying eyespot pattern sexual dimorphism across the Nymphalidae family of butterflies. Eyespot presence or absence was scored from a total of 38 wing compartments for two males and two females of each of 450 nymphalid species belonging to 399 different genera. Differences in eyespot number between sexes of each species were tallied for each wing surface (e.g., dorsal and ventral) of forewings and hindwings. In roughly 44% of the species with eyespots, females had more eyespots than males, in 34%, males had more eyespots than females, and, in the remaining 22% of the species, there was monomorphism in eyespot number. Dorsal and forewing surfaces were less patterned, but proportionally more dimorphic, than ventral and hindwing surfaces, respectively. In addition, wing compartments that frequently displayed eyespots were among the least sexually dimorphic. This survey suggests that dimorphism arises predominantly in "hidden" or "private" surfaces of a butterfly's wing, as previously demonstrated for the genus Bicyclus.
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http://dx.doi.org/10.1155/2013/926702DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3870084PMC
January 2014

Temporal gene expression variation associated with eyespot size plasticity in Bicyclus anynana.

PLoS One 2013 10;8(6):e65830. Epub 2013 Jun 10.

Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut, United States of America.

Seasonal polyphenism demonstrates an organism's ability to respond to predictable environmental variation with alternative phenotypes, each presumably better suited to its respective environment. However, the molecular mechanisms linking environmental variation to alternative phenotypes via shifts in development remain relatively unknown. Here we investigate temporal gene expression variation in the seasonally polyphenic butterfly Bicyclus anynana. This species shows drastic changes in eyespot size depending on the temperature experienced during larval development. The wet season form (larvae reared over 24°C) has large ventral wing eyespots while the dry season form (larvae reared under 19°C) has much smaller eyespots. We compared the expression of three proteins, Notch, Engrailed, and Distal-less, in the future eyespot centers of the two forms to determine if eyespot size variation is associated with heterochronic shifts in the onset of their expression. For two of these proteins, Notch and Engrailed, expression in eyespot centers occurred earlier in dry season than in wet season larvae, while Distal-less showed no temporal difference between the two forms. These results suggest that differences between dry and wet season adult wings could be due to a delay in the onset of expression of these eyespot-associated genes. Early in eyespot development, Notch and Engrailed may be functioning as repressors rather than activators of the eyespot gene network. Alternatively, temporal variation in the onset of early expressed genes between forms may have no functional consequences to eyespot size regulation and may indicate the presence of an 'hourglass' model of development in butterfly eyespots.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0065830PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3677910PMC
February 2014

Microevolutionary processes generate phylogenomic discordance at ancient divergences.

Authors:
Jeffrey C Oliver

Evolution 2013 Jun 4;67(6):1823-30. Epub 2013 Feb 4.

Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut 06520, USA.

Stochastic population processes may cause differences between species histories and gene histories. These processes are assumed to only influence the most recent divergences in the tree of life; however, there may be underappreciated potential for microevolutionary processes to impact deep divergences. I used multispecies coalescent models to determine the impact of stochastic processes on deep phylogenomic histories. Here I show phylogenomic discordance between gene histories and species histories is expected at deep divergences for many eukaryotic taxa, and the probability of discordance increases with population size, generation time, and the number of species in the tree. Five eukaryotic clades (angiosperms, birds, harpaline beetles, mammals, and nymphalid butterflies) demonstrate significant discordance potential at divergences over 50 million years old, and this discordance potential is independent of the age of divergence. These findings demonstrate population processes acting over very short timescales will leave a lasting impact on genomic histories, even for divergence events occurring tens to hundreds of millions of years ago.
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http://dx.doi.org/10.1111/evo.12047DOI Listing
June 2013

Distal-less regulates eyespot patterns and melanization in Bicyclus butterflies.

J Exp Zool B Mol Dev Evol 2013 Jul 30;320(5):321-31. Epub 2013 Apr 30.

Department of Biological Sciences, University at Buffalo, Buffalo, New York, USA.

Butterfly eyespots represent novel complex traits that display substantial diversity in number and size within and across species. Correlative gene expression studies have implicated a large suite of transcription factors, including Distal-less (Dll), Engrailed (En), and Spalt (Sal), in eyespot development in butterflies, but direct evidence testing the function of any of these proteins is still missing. Here we show that the characteristic two-eyespot pattern of wildtype Bicyclus anynana forewings is correlated with dynamic progression of Dll, En, and Sal expression in larval wings from four spots to two spots, whereas no such decline in gene expression ensues in a four-eyespot mutant. We then conduct transgenic experiments testing whether over-expression of any of these genes in a wild-type genetic background is sufficient to induce eyespot differentiation in these pre-patterned wing compartments. We also produce a Dll-RNAi transgenic line to test how Dll down-regulation affects eyespot development. Finally we test how ectopic expression of these genes during the pupal stages of development alters adults color patters. We show that over-expressing Dll in larvae is sufficient to induce the differentiation of additional eyespots and increase the size of eyespots, whereas down-regulating Dll leads to a decrease in eyespot size. Furthermore, ectopic expression of Dll in the early pupal wing led to the appearance of ectopic patches of black scales. We conclude that Dll is a positive regulator of focal differentiation and eyespot signaling and that this gene is also a possible selector gene for scale melanization in butterflies.
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http://dx.doi.org/10.1002/jez.b.22503DOI Listing
July 2013

A single origin for nymphalid butterfly eyespots followed by widespread loss of associated gene expression.

PLoS Genet 2012 16;8(8):e1002893. Epub 2012 Aug 16.

Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut, United States of America.

Understanding how novel complex traits originate involves investigating the time of origin of the trait, as well as the origin of its underlying gene regulatory network in a broad comparative phylogenetic framework. The eyespot of nymphalid butterflies has served as an example of a novel complex trait, as multiple genes are expressed during eyespot development. Yet the origins of eyespots remain unknown. Using a dataset of more than 400 images of butterflies with a known phylogeny and gene expression data for five eyespot-associated genes from over twenty species, we tested origin hypotheses for both eyespots and eyespot-associated genes. We show that eyespots evolved once within the family Nymphalidae, approximately 90 million years ago, concurrent with expression of at least three genes associated with early eyespot development. We also show multiple losses of expression of most genes from this early three-gene cluster, without corresponding losses of eyespots. We propose that complex traits, such as eyespots, may have originated via co-option of a large pre-existing complex gene regulatory network that was subsequently streamlined of genes not required to fulfill its novel developmental function.
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http://dx.doi.org/10.1371/journal.pgen.1002893DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3420954PMC
December 2012

Evolutionary reduction of the first thoracic limb in butterflies.

J Insect Sci 2011 ;11:66

Department of Geology & Geophysics, Yale University, New Haven, CT 06520-8109, USA.

Members of the diverse butterfly families Nymphalidae (brush-footed butterflies) and Riodinidae (metalmarks) have reduced first thoracic limbs and only use two pairs of legs for walking. In order to address questions about the detailed morphology and evolutionary origins of these reduced limbs, the three thoracic limbs of 13 species of butterflies representing all six butterfly families were examined and measured, and ancestral limb sizes were reconstructed for males and females separately. Differences in limb size across butterflies involve changes in limb segment size rather than number of limb segments. Reduction of the first limb in both nymphalids and riodinids appears particularly extensive in the femur, but the evolution of these reduced limbs is suggested to be a convergent evolutionary event. Possible developmental differences as well as ecological factors driving the evolution of reduced limbs are discussed.
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http://dx.doi.org/10.1673/031.011.6601DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3281478PMC
November 2011

Integrating fossil preservation biases in the selection of calibrations for molecular divergence time estimation.

Syst Biol 2011 Jul 23;60(4):519-27. Epub 2011 Mar 23.

Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06520, USA.

The selection of fossil data to use as calibration age priors in molecular divergence time estimates inherently links neontological methods with paleontological theory. However, few neontological studies have taken into account the possibility of a taphonomic bias in the fossil record when developing approaches to fossil calibration selection. The Sppil-Rongis effect may bias the first appearance of a lineage toward the recent causing most objective calibration selection approaches to erroneously exclude appropriate calibrations or to incorporate multiple calibrations that are too young to accurately represent the divergence times of target lineages. Using turtles as a case study, we develop a Bayesian extension to the fossil selection approach developed by Marshall (2008. A simple method for bracketing absolute divergence times on molecular phylogenies using multiple fossil calibrations points. Am. Nat. 171:726-742) that takes into account this taphonomic bias. Our method has the advantage of identifying calibrations that may bias age estimates to be too recent while incorporating uncertainty in phylogenetic parameter estimates such as tree topology and branch lengths. Additionally, this method is easily adapted to assess the consistency of potential calibrations to any one calibration in the candidate pool.
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http://dx.doi.org/10.1093/sysbio/syr019DOI Listing
July 2011

On the origins of sexual dimorphism in butterflies.

Proc Biol Sci 2011 Jul 1;278(1714):1981-8. Epub 2010 Dec 1.

Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06511, USA.

The processes governing the evolution of sexual dimorphism provided a foundation for sexual selection theory. Two alternative processes, originally proposed by Darwin and Wallace, differ primarily in the timing of events creating the dimorphism. In the process advocated by Darwin, a novel ornament arises in a single sex, with no temporal separation in the origin and sex-limitation of the novel trait. By contrast, Wallace proposed a process where novel ornaments appear simultaneously in both sexes, but are then converted into sex-limited expression by natural selection acting against showy coloration in one sex. Here, we investigate these alternative modes of sexual dimorphism evolution in a phylogenetic framework and demonstrate that both processes contribute to dimorphic wing patterns in the butterfly genera Bicyclus and Junonia. In some lineages, eyespots and bands arise in a single sex, whereas in other lineages they appear in both sexes but are then lost in one of the sexes. In addition, lineages displaying sexual dimorphism were more likely to become sexually monomorphic than they were to remain dimorphic. This derived monomorphism was either owing to a loss of the ornament ('drab monomorphism') or owing to a gain of the same ornament by the opposite sex ('mutual ornamentation'). Our results demonstrate the necessity of a plurality in theories explaining the evolution of sexual dimorphism within and across taxa. The origins and evolutionary fate of sexual dimorphism are probably influenced by underlying genetic architecture responsible for sex-limited expression and the degree of intralocus sexual conflict. Future comparative and developmental work on sexual dimorphism within and among taxa will provide a better understanding of the biases and constraints governing the evolution of animal sexual dimorphism.
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http://dx.doi.org/10.1098/rspb.2010.2220DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3107650PMC
July 2011

Are mimics monophyletic? The necessity of phylogenetic hypothesis tests in character evolution.

BMC Evol Biol 2010 Aug 3;10:239. Epub 2010 Aug 3.

Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06511, USA.

Background: The processes governing the origin and maintenance of mimetic phenotypes can only be understood in a phylogenetic framework. Phylogenetic estimates of evolutionary relationships can provide a context for analyses of character evolution; however, when phylogenetic estimates conflict, rigorous analyses of alternative evolutionary histories are necessary to determine the likelihood of a specific history giving rise to the observed pattern of diversity. The polyphenic butterfly Limenitis arthemis provides a case in point. This species is comprised of three lineages, two of which are mimetic and one of which is non-mimetic. Conflicting estimates of the relationships among these three lineages requires direct evaluation of the alternative hypotheses of mimicry evolution.

Results: Using a coalescent framework, we found support for a sister-taxon relationship between the non-mimetic L. a. arthemis and the mimetic L. a. astyanax, congruent with the previous hypothesis that the non-mimetic form of L. a. arthemis was derived from a mimetic ancestor. We found no support for a mimetic clade (L. a. astyanax + L. a. arizonensis) despite analyzing numerous models of population structure.

Conclusions: These results provide the foundation for future studies of mimicry, which should integrate phylogenetic and developmental analyses of wing pattern formation. We propose future analyses of character evolution accommodate conflicting phylogenetic estimates by explicitly testing alternative evolutionary hypotheses.
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http://dx.doi.org/10.1186/1471-2148-10-239DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3020633PMC
August 2010

Accommodating natural and sexual selection in butterfly wing pattern evolution.

Proc Biol Sci 2009 Jul 1;276(1666):2369-75. Epub 2009 Apr 1.

Department of Ecology and Evolutionary Biology, Yale University, 165 Prospect Street, New Haven, CT 06520-8106, USA.

Visual patterns in animals may serve different functions, such as attracting mates and deceiving predators. If a signal is used for multiple functions, the opportunity arises for conflict among the different functions, preventing optimization for any one visual signal. Here we investigate the hypothesis that spatial separation of different visual signal functions has occurred in Bicyclus butterflies. Using phylogenetic reconstructions of character evolution and comparisons of evolutionary rates, we found dorsal surface characters to evolve at higher rates than ventral characters. Dorsal characters also displayed sex-based differences in evolutionary rates more often than did ventral characters. Thus, dorsal characters corresponded to our predictions of mate signalling while ventral characters appear to play an important role in predator avoidance. Forewing characters also fit a model of mate signalling, and displayed higher rates of evolution than hindwing characters. Our results, as well as the behavioural and developmental data from previous studies of Bicyclus species, support the hypothesis that spatial separation of visual signal functions has occurred in Bicyclus butterflies. This study is the first to demonstrate, in a phylogenetic framework, that spatial separation of signals used for mate signalling and those used for predator avoidance is a viable strategy to accommodate multiple signal functions. This signalling strategy has important ramifications on the developmental evolution of wing pattern elements and diversification of butterfly species.
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http://dx.doi.org/10.1098/rspb.2009.0182DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2690465PMC
July 2009

AUGIST: inferring species trees while accommodating gene tree uncertainty.

Authors:
Jeffrey C Oliver

Bioinformatics 2008 Dec 25;24(24):2932-3. Epub 2008 Oct 25.

Interdisciplinary Program in Insect Science, University of Arizona, Tucson, AZ 85721, USA.

Summary: AUGIST (accomodating uncertainty in genealogies while inferring species tress) is a new software package for inferring species trees while accommodating uncertainty in gene genealogies. It is written for the Mesquite software system and provides sampling procedures to incorporate uncertainty in gene tree reconstruction while providing confidence estimates for inferred species trees.

Availability: http://www.lycaenid.org/augist/
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http://dx.doi.org/10.1093/bioinformatics/btn556DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2639298PMC
December 2008

Once a Batesian mimic, not always a Batesian mimic: mimic reverts back to ancestral phenotype when the model is absent.

Proc Biol Sci 2008 May;275(1639):1125-32

Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721, USA.

Batesian mimics gain protection from predation through the evolution of physical similarities to a model species that possesses anti-predator defences. This protection should not be effective in the absence of the model since the predator does not identify the mimic as potentially dangerous and both the model and the mimic are highly conspicuous. Thus, Batesian mimics should probably encounter strong predation pressure outside the geographical range of the model species. There are several documented examples of Batesian mimics occurring in locations without their models, but the evolutionary responses remain largely unidentified. A mimetic species has four alternative evolutionary responses to the loss of model presence. If predation is weak, it could maintain its mimetic signal. If predation is intense, it is widely presumed the mimic will go extinct. However, the mimic could also evolve a new colour pattern to mimic another model species or it could revert back to its ancestral, less conspicuous phenotype. We used molecular phylogenetic approaches to reconstruct and test the evolution of mimicry in the North American admiral butterflies (Limenitis: Nymphalidae). We confirmed that the more cryptic white-banded form is the ancestral phenotype of North American admiral butterflies. However, one species, Limenitis arthemis, evolved the black pipevine swallowtail mimetic form but later reverted to the white-banded more cryptic ancestral form. This character reversion is strongly correlated with the geographical absence of the model species and its host plant, but not the host plant distribution of L. arthemis. Our results support the prediction that a Batesian mimic does not persist in locations without its model, but it does not go extinct either. The mimic can revert back to its ancestral, less conspicuous form and persist.
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http://dx.doi.org/10.1098/rspb.2007.1766DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2602694PMC
May 2008

The signal environment is more important than diet or chemical specialization in the evolution of warning coloration.

Proc Natl Acad Sci U S A 2007 Dec 20;104(49):19381-6. Epub 2007 Nov 20.

Department of Ecology and Evolutionary Biology and Interdisciplinary Program in Insect Science, University of Arizona, Tucson, AZ 85721, USA.

Aposematic coloration, or warning coloration, is a visual signal that acts to minimize contact between predator and unprofitable prey. The conditions favoring the evolution of aposematic coloration remain largely unidentified. Recent work suggests that diet specialization and resultant toxicity may play a role in facilitating the evolution and persistence of warning coloration. Using a phylogenetic approach, we investigated the evolution of larval warning coloration in the genus Papilio (Lepidoptera: Papilionidae). Our results indicate that there are at least four independent origins of aposematic larval coloration within Papilio. Controlling for phylogenetic relatedness among Papilio taxa, we found no evidence supporting the hypothesis that either diet specialization or chemical specialization facilitated the origin of aposematic larvae. However, there was a significant relationship between the signal environment and the evolution of aposematic larvae. Specifically, Papilio lineages feeding on herbaceous or narrow-leaved plants, regardless of the plants' taxonomic affiliation, were more likely to evolve aposematic larvae than were lineages feeding only on trees/shrubs or broad-leaved plants. These results demonstrate that factors other than diet specialization, such as the signal environment of predator-prey interactions, may play a large role in the initial evolution and persistence of aposematic coloration.
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http://dx.doi.org/10.1073/pnas.0705478104DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2148298PMC
December 2007

Genetic isolation and cryptic variation within the Lycaena xanthoides species group (Lepidoptera: Lycaenidae).

Mol Ecol 2007 Oct 10;16(20):4308-20. Epub 2007 Sep 10.

Interdisciplinary Program in Insect Science and Department of Entomology, University of Arizona, Tucson, AZ 85721, USA.

Species exist as biological entities with patterns of discontinuous phenotypic variation. However, the distinctness of taxa is called into question when morphological intermediates exist in areas of sympatry, reflecting either gene flow among variants of a species or hybridization between different species. Studying the partitioning of genetic variation provides a means to discern between the two possibilities. We used genetic and morphometric approaches to investigate the degree of isolation among the three members of the Lycaena xanthoides species group. Lycaena xanthoides, L. editha, and L. dione are predominantly allopatric and have been treated both as three separate species and as a single polytypic species. Using 618 bp of the mitochondrial gene COII, we found little phylogenetic resolution, but significant among-taxa genetic variance partitioning. Divergence among these taxa has been relatively recent, as evidenced by relatively low pairwise sequence divergence. Also, the existence of two well-supported clades within L. xanthoides sensu stricto, concordant with the Transverse Ranges of southern California, indicates divergence within this taxon, and a possible cryptic species. Significant morphological differentiation between L. editha and L. xanthoides supports the hypothesis that these taxa represent separate gene pools. Populations occurring in a narrow zone where the two species' ranges approach are characterized by intermediate morphology, suggesting incomplete morphological divergence or recent hybridization. These findings highlight the utility of genetic data in inferring species boundaries and the identification of cryptic lineages.
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http://dx.doi.org/10.1111/j.1365-294X.2007.03494.xDOI Listing
October 2007

Soil nutrient effects on oviposition preference, larval performance, and chemical defense of a specialist insect herbivore.

Oecologia 2005 May 24;143(4):578-87. Epub 2005 Mar 24.

Ecology and Evolutionary Biology, University of Colorado, 334 UCB, Boulder, CO 80309, USA.

This study examined the effects of increased leaf nitrogen in natural host-plants (Plantago spp.) on female oviposition preference, larval performance, and larval chemical defense of the butterfly Junonia coenia. Increased availability of soil nutrients caused the host-plant's foliar nitrogen to increase and its chemical defense to decrease. Larval performance did not correlate with increases in foliar nitrogen. Larval growth rate and survival were equivalent across host-plant treatments. However, larvae raised on fertilized host-plants showed concomitant decreases in chemical defense as compared to larvae reared on unfertilized host-plants. Since most butterfly larvae cannot move long distances during their first few instars and are forced to feed upon the plant on which they hatched, J. coenia larval chemical defense is determined, in large part, by female oviposition choice. Female butterflies preferred host-plants with high nitrogen over host-plants with low nitrogen; however, this preference was also mediated by plant chemical defense. Female butterflies preferred more chemically defended host-plants when foliar nitrogen was equivalent between host-plants. J. coenia larvae experience intense predation in the field, especially when larvae are not chemically well defended. Any qualitative or quantitative variation in plant allelochemical defense has fitness consequences on these larvae. Thus, these results indicate that females may be making sub-optimal oviposition decisions under a nutrient-enriched regime, when predators are present. Given the recent increase in fertilizer application and nitrogen deposition on the terrestrial landscape, these interactions between female preference, larval performance, and larval chemical defense may result in long-term changes in population dynamics and persistence of specialist insects.
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http://dx.doi.org/10.1007/s00442-005-0008-5DOI Listing
May 2005

The molecular phylogenetics of endangerment: cryptic variation and historical phylogeography of the California tiger salamander, Ambystoma californiense.

Mol Ecol 2004 Oct;13(10):3033-49

Section of Evolution and Ecology, and Center for Population Biology, University of California, Davis, CA 95616, USA.

A primary goal of conservation genetics is the discovery, delimitation and protection of phylogenetic lineages within sensitive or endangered taxa. Given the importance of lineage protection, a combination of phylogeography, historical geology and molecular clock analyses can provide an important historical context for overall species conservation. We present the results of a range-wide survey of genetic variation in the California tiger salamander, Ambystoma californiense, as well as a summary of the past several million years of inundation and isolation of the Great Central Valley and surrounding uplands that constitute its limited range. A combination of population genetic and phylogenetic analyses of mitochondrial DNA variation among 696 samples from 84 populations revealed six well-supported genetic units that are geographically discrete and characterized by nonoverlapping haplotype distributions. Populations from Santa Barbara and Sonoma Counties are particularly well differentiated and geographically isolated from all others. The remaining units in the Southern San Joaquin Valley, Central Coast Range, Central Valley and Bay Area are separated by geological features, ecological zone boundaries, or both. The geological history of the California landscape is consistent with molecular clock evidence suggesting that the Santa Barbara unit has been isolated for at least 0.74-0.92 Myr, and the Sonoma clade is equally ancient. Our work places patterns of genetic differentiation into both temporal- and landscape-level contexts, providing important insights into the conservation genetics of the California tiger salamander.
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http://dx.doi.org/10.1111/j.1365-294X.2004.02317.xDOI Listing
October 2004