83 Works

Data from: Out of the Andes: patterns of diversification in clearwing butterflies

Marianne Elias, Mathieu Joron, Keith Willmott, Vera Kaiser, Karina Silva-Brandão, Carlos Arias, Luz Miryam Gomez Piñeres, Sandra Uribe, Andrew Brower, André Freitas & Chris Jiggins
Global biodiversity peaks in the tropical forests of the Andes, a striking geological feature that has likely been instrumental in generating biodiversity by providing opportunities for both vicariant and ecological speciation. However, the role of these mountains in the diversification of insects, which dominate biodiversity, has been poorly explored using phylogenetic methods. Here we study the role of the Andes in the evolution of a diverse Neotropical insect group, the clearwing butterflies. We used dated...

Data from: An expanded plastid phylogeny of Marsilea with emphasis on North American species

W. Mark Whitten, Colette C. Jacono & Nathalie S. Nagalingum
Ferns of the genus Marsilea (water clover) are potentially invasive aquatic and wetland plants. They are difficult to identify to species because of subtle diagnostic characters, the sterile condition of many specimens, and unresolved taxonomic problems. We sequenced four plastid regions (rbcL, rps4, rps4-trnS spacer, and trnL-F spacer) from 223 accessions across ca. 38 species. Our goals were to: 1) attempt to identify problematic Marsilea specimens from the southeastern U.S., and 2) assess species delimitation...

Data from: Can butterflies evade fire? Pupa location and heat tolerance in fire prone habitats of Florida

Matthew D. Thom, Jaret C. Daniels, Leda N. Kobziar & Jonathan R. Colburn
Butterflies such as the atala hairstreak, Eumaeus atala Poey, and the frosted elfin, Callophrys irus Godart, are restricted to frequently disturbed habitats where their larval host plants occur. Pupae of these butterflies are noted to reside at the base of host plants or in the leaf litter and soil, which may allow them to escape direct mortality by fire, a prominent disturbance in many areas they inhabit. The capacity of these species to cope with...

Data from: Silenced rRNA genes are activated and substitute for partially eliminated active homoelogs in the recently formed allotetraploid, Tragopogon mirus (Asteraceae)

Ales Kovařík, Eva Dobešová, Roman Matyášek, Andrew R. Leitch, Pamela S. Soltis, Douglas E. Soltis & Hana Malinska
To study the relationship between uniparental rDNA (encoding 18S, 5.8S and 26S ribosomal RNA) silencing (nucleolar dominance) and rRNA gene dosage, we studied a recently emerged (within the last 80 years) allotetraploid Tragopogon mirus (2n=24), formed from the diploid progenitors T. dubius (2n=12, D-genome donor) and T. porrifolius (2n=12, P-genome donor). Here, we used molecular, cytogenetic and genomic approaches to analyse rRNA gene activity in two sibling T. mirus plants (33A and 33B) with widely...

Data from: Macroevolutionary consequences of profound climate change on niche evolution in marine mollusks over the past three million years

Erin E. Saupe, Jonathan R. Hendricks, Roger W. Portell, Harry J. Dowsett, Alan Haywood, Stephen J. Hunter & Bruce S. Lieberman
In order to predict the fate of biodiversity in a rapidly changing world, we must first understand how species adapt to new environmental conditions. The long-term evolutionary dynamics of species' physiological tolerances to differing climatic regimes remain obscure. Here, we unite palaeontological and neontological data to analyse whether species' environmental tolerances remain stable across 3 Myr of profound climatic changes using 10 phylogenetically, ecologically and developmentally diverse mollusc species from the Atlantic and Gulf Coastal...

Data from: Live, dead, and fossil mollusks in Florida freshwater springs and spring-fed rivers: taphonomic pathways and the formation of multi-sourced, time-averaged death assemblages

Kristopher Kusnerik, Roger Portell, Mark Brenner, Quan Hua, Alshina Kannai, Mariah Monroe, Michał Kowalewski, Guy Means & Ryan Means
Taphonomic processes are informative about the magnitude and timing of paleoecological changes but remain poorly understood with respect to freshwater invertebrates in spring-fed rivers and streams. We compared taphonomic alteration among freshwater gastropods in live, dead (surficial shell accumulations), and fossil (late Pleistocene-early Holocene in situ sediments) assemblages from two Florida spring-fed systems, the Wakulla and Silver/Ocklawaha Rivers. We assessed taphonomy of two gastropod species: the native Elimia floridensis (n=2504) and introduced Melanoides tuberculata (n=168)....

Data from: Phylogenetic systematics of subtribe Spiranthinae (Orchidaceae: Orchidoideae: Cranichideae) based on nuclear and plastid DNA sequences of a nearly complete generic sample

Gerardo A. Salazar, Joao A.N. Batista, Lidia I. Cabrera, Cassio Van Den Berg, W. Mark Whitten, Eric C. Smidt, Cristiano R. Buzatto, Rodrigo B. Singer, Gunter Gerlach, Rolando Jimenez-Machorro, Jose A. Radins, Irma S. Insaurralde, Leonardo R.S. Guimaraes, Fabio De Barros, Francisco Tobar, Jose L. Linares, Ernesto Mujica, Robert L. Dressler, Mario A. Blanco, Eric Hagsater & Mark W. Chase
Subtribe Spiranthinae is the most species-rich lineage of terrestrial Neotropical orchids, encompassing > 500 species and 40 genera. We conducted maximum parsimony and maximum likelihood phylogenetic analyses of DNA sequence data of plastid matK-trnK and trnL-trnF and nuclear ribosomal ITS sequences for 36 genera and 182 species of Spiranthinae plus appropriate outgroups. The results strongly support monophyly of Spiranthinae (minus Discyphus, Discyphinae and Galeottiella, Galeottiellinae) and five major lineages, namely monospecific Cotylolabium (sister to the...

Data for: Fragmentation and disturbance drive montane mixed-flock species roles and interaction strength

Harrison Jones & Scott Robinson
Mixed-species flocks are a key facilitative interaction for tropical birds. Forest fragmentation leads to species loss and spatial turnover in these flocks, yet it is unknown how these changes to composition influence within-flock species interactions. We used network analysis to characterize flocking interactions along a fragment-size gradient in the Colombian Western Andes. We asked (1) how patch size, edge density, and vegetation structure explained network measures indicative of flock cohesion, (2) whether changes were driven...

Data from: Light environment drives evolution of color vision genes in butterflies and moths

Yash Sondhi, Emily Elis, Seth Bybee, Jamie Theobald & Akito Kawahara
Opsins, combined with a chromophore, are the primary light-sensing molecules in animals and are crucial for color vision. Throughout animal evolution duplications and losses of opsin proteins are common, but it is unclear what is driving these gains and losses. Light availability is implicated, and dim environments are often associated with low opsin diversity and loss. Correlations between high opsin diversity and bright environments, however, are tenuous. To test if increased light availability is associated...

Data from: Out of the Orient: Post-Tethyan transoceanic and trans-Arabian routes fostered the spread of Baorini skippers in the Afrotropics

Emmanuel F.A. Toussaint, Roger Vila, Masaya Yago, Hideyuki Chiba, Andrew D. Warren, Kwaku Aduse-Poku, Caroline Storer, Kelly M. Dexter, Kiyoshi Maruyama, David J. Lohman & Akito Y. Kawahara
The origin of taxa presenting a disjunct distribution between Africa and Asia has puzzled biogeographers for more than a century. This biogeographic pattern has been hypothesized to be the result of transoceanic long‐distance dispersal, Oligocene dispersal through forested corridors, Miocene dispersal through the Arabian Peninsula or passive dispersal on the rifting Indian plate. However, it has often been difficult to pinpoint the mechanisms at play. We investigate biotic exchange between the Afrotropics and the Oriental...

Revisiting the evolution of Ostrinia moths with phylogenomics (Pyraloidea: Crambidae: Pyraustinae)

Zhaofu Yang, David Plotkin, Jean-François Landry, Caroline Storer & Akito Kawahara
Reconstructing a robust phylogenetic framework is key to understanding the ecology and evolution of many economically important taxa. The crambid moth genus Ostrinia contains multiple agricultural pests, and its classification and phylogeny has remained controversial due to the paucity of characters and the lack of clear morphological boundaries for its species. To address these issues, we inferred a molecular phylogeny of Ostrinia using a phylogenomic dataset containing 498 loci and 115,197 nucleotide sites and examined...

Data from: Origin of angiosperms and the puzzle of the Jurassic gap

Hong-Tao Li, Ting-Shuang Yi, Lian-Ming Gao, Peng-Fei Ma, Ting Zhang, Jun-Bo Yang, Matthew A. Gitzendanner, Peter W. Fritsch, Jie Cai, Yang Luo, Hong Wang, Michelle Van Der Bank, Shu-Dong Zhang, Qing-Feng Wang, Jian Wang, Zhi-Rong Zhang, Chao-Nan Fu, Jing Yang, Peter M. Hollingsworth, Mark W. Chase, Douglas E. Soltis, Pamela S. Soltis & De-Zhu Li
Angiosperms are by far the most species-rich clade of land plants, but their origin and early evolutionary history remain poorly understood. We reconstructed angiosperm phylogeny based on 80 genes from 2,881 plastid genomes representing 85% of extant families and all orders. With a well-resolved plastid tree and 62 fossil calibrations, we dated the origin of the crown angiosperms to the Upper Triassic, with major angiosperm radiations occurring in the Jurassic and Lower Cretaceous. This estimated...

Source data for: Nesting success of Red-winged Blackbirds (Agelaius phoeniceus) in marshes in an anthropogenic landscape

Scott Robinson & Holly McChesney
Recent analyses show significant population declines in many abundant avian species, especially marsh-nesting species including the Red-winged Blackbird (RWBL). Hypothesized causes include reduced nesting success resulting from changing land use patterns and exposure to contaminants. Our goal was to test the hypothesis that landscape and nest characteristics as well as exposure to polychlorinated biphenyls (PCBs) correlate with nesting success. From 2008-2014, we measured clutch size, egg and nestling mass, hatching and fledging success, and daily...

Phylogenetic systematics, diversification, and biogeography of Cerurinae (Lepidoptera: Notodontidae) and a description of a new genus

Ryan St Laurent, Paul Goldstein, James Miller, Amanda Markee, Hermann Staude, Akito Kawahara, Scott Miller & Robert Robbins
We present the first dated molecular phylogeny of the Cerurinae moths (Notodontidae), based on sequence data for 666 loci generated by anchored hybrid enrichment. Monophyly of Cerurinae is corroborated, which includes the following genera: Pararethona Janse, Pseudorethona Janse, Oreocerura Kiriakoff, stat. rev., Cerurella Kiriakoff, Notocerura Kiriakoff, Hampsonita Kiriakoff, Afrocerura Kiriakoff, Cerurina Kiriakoff, Neoharpyia Daniel, Furcula Lamarck, Neocerura Matsumura, Americerura St Laurent and Goldstein, gen. nov., Cerura Schrank, and Kamalia Koçak & Kemal. The type species...

Phylotranscriptomic analyses reveal asymmetrical gene duplication dynamics and signatures of ancient polyploidy in mints

Grant T Godden, Taliesin J Kinser, Pamela Soltis & Douglas E Soltis
Ancient duplication events and retained gene duplicates have contributed to the evolution of many novel plant traits and, consequently, to the diversity and complexity within and across plant lineages. While mounting evidence highlights the importance whole-genome duplication (WGD; polyploidy) and its key role as an evolutionary driver, gene duplication dynamics and mechanisms, both of which are fundamental to our understanding of evolutionary process and patterns of plant diversity, remain poorly characterized in many clades. We...

Data from: Floral convergence in Oncidiinae (Cymbidieae; Orchidaceae): an expanded concept of Gomesa and a new genus Nohawilliamsia

Mark W. Chase, Norris H. Williams, Aparacida Donisete De Faria, Kurt M. Neubig, Maria Do Carmo E. Amaral & W. Mark Whitten
BACKGROUND: Floral morphology, particularly the angle of lip attachment to the column, has historically been the fundamental character used in establishing generic limits in subtribe Oncidiinae (Orchidaceae), but it has also been long recognized that reliance on this character alone has produced a highly artificial set of genera. In essence, lip/column relationships reflect syndromes associated with pollinator preferences; most genera of Oncidiinae as previously defined have consisted of a single floral type. Here, the degree...

Data from: Phylogeny and evolutionary history of glycogen synthase kinase 3/SHAGGY-like kinase genes in land plants

Xinshuai Qi, André S. Chanderbali, Gane Ka-Shu Wong, Douglas E. Soltis & Pamela S. Soltis
Background: GSK3 (glycogen synthase kinase 3) genes encode signal transduction proteins with roles in a variety of biological processes in eukaryotes. In contrast to the low copy numbers observed in animals, GSK3 genes have expanded into a multi-gene family in land plants (embryophytes), and have also evolved functions in diverse plant specific processes, including floral development in angiosperms. However, despite previous efforts, the phylogeny of land plant GSK3 genes is currently unclear. Here, we analyze...

Data from: Molecular phylogenetics of Kosteletzkya (Malvaceae, Hibisceae) reveals multiple independent and successive polyploid speciation events

Kurt M. Neubig, , W. Mark Whitten, Stuart F. McDaniel & Orland J. Blanchard
Kosteletzkya s.s. is a genus of 17 species (excluding the endemic species of Madagascar), found in the New World, continental Africa, Madagascar, and Southeast Asia. Recent chromosome counts revealed diploid, tetraploid, and hexaploid species. To estimate the history of the genus, we sequenced nuclear and plastid loci for nearly all Kosteletzkya spp., in the majority of cases, with multiple accessions per species. The African species form a paraphyletic grade relative to a New World clade....

Data from: Molecular phylogeny, revised higher classification, and implications for conservation of endangered Hawaiian leaf-mining moths (Lepidoptera: Gracillariidae: Philodoria)

Chris A. Johns, Matthew R. Moore & Akito Y. Kawahara
The leaf-mining moth genus Philodoria Walsingham (Lepidoptera: Gracillariidae) is composed of 30 described species, all of which are endemic to the Hawaiian Islands. Philodoria is known to feed on 10 families of endemic Hawaiian host plants, with several species recorded only from threatened or endangered hosts. Beyond their dependence on these plants, little is known of their evolutionary history and conservation status. We constructed a molecular phylogeny of Philodoria to assess validity of its current...

Data from: Assessing support for Blaberoidea phylogeny suggests optimal locus

Dominic Evangelista, Sabrina Simon, Megan M. Wilson, Akito Y. Kawahara, Manpreet K. Kohli, Jessica L. Ware, Benjamin Wipfler, Olivier Béthoux, Grandcolas Philippe & Frédéric Legendre
Phylogenomics seeks to use next-generation data to robustly infer an organism’s evolutionary history. Yet, the practical caveats of phylogenomics motivates investigation of improved efficiency, particularly when quality of phylogenies are questionable. To achieve improvements, one goal is to maintain or enhance the quality of phylogenetic inference while severely reducing dataset size. We approach this by assessing which kinds of loci in phylogenomic alignments provide the majority of support for a phylogenetic inference of cockroaches in...

Biogeography and ecological niche evolution in Diapensiaceae inferred from phylogenetic analysis

Michelle Gaynor, Chao-Nan Fu, Lian-Ming Gao, Li-Min Lu, Douglas E. Soltis & Pamela S. Soltis
Diapensiaceae (Ericales) are a small family of about 15 species. Within this clade, two species are broadly distributed throughout the Northern Hemisphere, while the remaining species have a disjunct distribution between eastern North America and eastern Asia. To address patterns and processes of diversification in Diapensiaceae, we conducted biogeographic analyses and inferred shifts in ecological niche across the phylogeny of the clade. Although Diapensiaceae have been the focus of multiple phylogenetic and biogeographic studies, previous...

Data from: Evolutionary history of the angiosperm flora of China

Li-Min Lu, Ling-Feng Mao, Tuo Yang, Jian-Fei Ye, Bing Liu, Hong-Lei Li, Miao Sun, Joseph T. Miller, Sarah Mathews, Hai-Hua Hu, Yan-Ting Niu, Dan-Xiao Peng, You-Hua Chen, Stephen A. Smith, Min Chen, Kun-Li Xiang, Chi-Toan Le, Viet-Cuong Dang, An-Ming Lu, Pamela S. Soltis, Douglas E. Soltis, Jian-Hua Li & Zhi-Duan Chen
High species diversity may result from recent rapid speciation in a ‘cradle’ and/or the gradual accumulation and preservation of species over time in a ‘museum’1,2. China harbours nearly 10% of angiosperm species worldwide and has long been considered as both a museum, owing to the presence of many species with hypothesized ancient origins3,4, and a cradle, as many lineages have originated as recent topographic changes and climatic shifts—such as the formation of the Qinghai–Tibetan Plateau...

Food plant shifts drive the diversification of Sack-bearer moths

Ryan St Laurent, Ana Paula Dos Santos De Carvalho, Chandra Earl & Akito Kawahara
Lepidoptera are a highly diverse group of herbivorous insects, however some superfamilies have relatively few species. Two alternative hypotheses for drivers of Lepidoptera diversity are shifts in food plant use or shifts from concealed to external feeding as larvae. Many studies address the former hypothesis, but with bias towards externally feeding taxa. One of the most striking examples of species disparity between sister lineages in Lepidoptera is between the concealed feeding Sack-bearer Moths (Mimallonoidea), which...

Pleistocene aridification underlies the evolutionary history of the Caribbean endemic, insular giant, Consolea (Opuntioideae)

Lucas Majure, Duniel Barrios, Edgardo Díaz, Bethany Zumwalde, Weston Testo & Vivian Negrón-Ortíz
Premise: The Caribbean islands are renowned for their small size but high species diversity, and cacti make up a fascinating component of seasonally dry tropical forest (SDTF) there. Consolea consist of nine species of dioecious, hummingbird pollinated trees endemic to the West Indies, which form a conspicuous element of the SDTF. Several species are threatened by anthropogenic disturbance, disease, sea-level rise and invasive species, and are of conservation concern. However, no comprehensive phylogeny yet exists...

Spatial phylogenetics of butterflies in relation to environmental drivers and angiosperm diversity across North America

Chandra Earl, Michael W. Belitz, Shawn W. Laffan, Vijay Barve, Narayani Barve, Douglas E. Soltis, Julie M. Allen, Pamela S. Soltis, Brent D. Mishler, Akito Y. Kawahara & Robert Guralnick
Broad-scale quantitative assessments of biodiversity and the factors shaping it remain particularly poorly explored in insects. Here, we undertook a spatial phylogenetic analysis of North American butterflies via assembly of a time-calibrated phylogeny of the region coupled with a unique, complete range assessment for ~75% of the known species. We utilized a suite of phylodiversity metrics and associated environmental data to test whether climate stability and temperature gradients have shaped North American butterfly phylogenetic diversity...

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  • Florida Museum of Natural History
  • University of Florida
  • Royal Botanic Gardens
  • University of British Columbia
  • University of Kansas
  • University of Washington
  • University of Michigan-Ann Arbor
  • University of Georgia
  • Zoological Research Museum Alexander Koenig
  • Smithsonian Institution