131,551 Works

Sample_data

Joana Paupério, Jeremy S. Herman, José Melo-Ferreira, Maarit Jaarola, Paulo C. Alves & Jeremy B. Searle
New sequence data and sequence data retrieved from GenBank for all loci analysed. Details on sampling locality are given for each specimen analysed. Haplotype names as well as GenBank accession numbers are detailed for each loci per specimen, as well as source of previously published data. Information on where samples are held in is also displayed.

DBX5_haplotype_alignment

Joana Paupério, Jeremy S. Herman, José Melo-Ferreira, Maarit Jaarola, Paulo C. Alves & Jeremy B. Searle
Alignment of DBX5 haplotypes inferred by Phase version 2.1 (Stephens et al. 2001; Stephens & Donnelly 2003) and used for gene tree inference.

CYTB_genotype_alignment

Joana Paupério, Jeremy S. Herman, José Melo-Ferreira, Maarit Jaarola, Paulo C. Alves & Jeremy B. Searle
Alignment of cytochrome b sequences of all individuals used for species tree inference.

Maximum likelihood phylograms and their alignment files for ectomycorrhizal fungi associated with Salix arctica and Dryas integrifolia across the North American Arctic.

Ina Timling, Anders Dahlberg, Donald Arthur Walker, Monique Gardes, Jean-Yves Charcosset, Jeffrey M. Welker & Donald Lee Taylor
Maximum-likelihood phylograms (pdf) of (1) Tomentella1, (2) Tomentella 2, (3) Pseudotomentella, (4) Inocybe 1, (5) Inocybe 2, (6) Inocybe 3, (7) Inocybe 4, (8) Inocybe 5, (9) Sebacina 1, (10) Sebacina 2, (11) Sebacina 3, (12) Cortinarius 1, (13) Cortinarius 2, (14) Cortinarius 3, (15) Cortinarius 4, (16) Clavulina, (17) Russula, (18) Tulasnella, (19) Ceratobasidium, (20) Entoloma, (21) Hebeloma, (22) Lactarius, (23) Laccaria, (24) Pyronemataceae, (25) Tuber, (26) Tuberaceae, (27) Sordariaceae, (28) Phialocephala, (29) Cenococcum,...

Data from: SNP discovery and gene annotation in the surf clam Mesodesma donacium

Cristian Gallardo-Escárate, Valentina Valenzuela-Muñoz, Gustavo Núñez-Acuña & Pilar Haye
The main objective of this research was to identify single-nucleotide polymorphisms (SNPs) from an Expressed Sequences Tags (EST) data set generated by 454 pyrosequencing in the soft clam Mesodesma donacium. A total of 180 159 ESTs were yielded from a M. donacium cDNA library. De novo assembly was performed using stringent calling parameters, producing 10 178 contigs and 41 765 singletons. Here, a total of 2594 SNPs were discovered related to 613 consensus sequences, achieving...

Data table

Moriaki Yasuhara, Gene Hunt, Denise Breitburg, Akira Tsujimoto & Kota Katsuki
Data table for the global analyses of microfossil data in the present study. AN: Australia and New Zealand. SA: South America. AF: Africa. ASIA: Asia. NAMER: North America. EU: Europe. O: Other.

110506_SN365_A_s_8_2_seq_GKW-36.txt.gz.001

Astrid T. Groot, Heike Staudacher, Andrea Barthel, Olive Inglis, Richard G. Santangelo, Steffi Gebauer-Jung, Heiko Vogel, Jennifer Emerson, Coby Schal, David G. Heckel, Fred Gould & Gerhard Schoefl

110506_SN365_A_s_8_2_seq_GKW-36.txt.gz.003

Astrid T. Groot, Heike Staudacher, Andrea Barthel, Olive Inglis, Richard G. Santangelo, Steffi Gebauer-Jung, Heiko Vogel, Jennifer Emerson, Coby Schal, David G. Heckel, Fred Gould & Gerhard Schoefl

Data from: Basilotritus uheni, a new cetacean (Cetacea, Basilosauridae) from the late Middle Eocene of Eastern Europe

Pavel Gol'din & Evgenij Zvonok
A new basal basilosaurid cetacean, Basilotritus uheni n. gen. n. sp., comes from the late middle Eocene (Bartonian) of Ukraine. It is the earliest dated record of a cetacean from Eastern Europe. The tympanic bulla of Basilotritus uheni shares basilosaurid synapomorphies but possesses unusual traits inherited from protocetids. Cetaceans related to Basilotritus uheni and referred to as Eocetus or “Eocetus” have been recorded from Africa, Europe, North America and South America. “Eocetus” wardii from North...

Goldin_Zvonok_Ukraine_Supplemental_Data_File_4_age_data_for_phylogeny_20120913

Pavel Goldin & Evgenij Zvonok

Data from: Male courtship preferences demonstrate discrimination against allopatric colour morphs in a cichlid fish

Peter Zoppoth, Stephan Koblmüller & Kristina M. Sefc
Whether premating isolation is achieved by male-specific, female-specific or sex-independent assortative preferences often depends on the underlying evolutionary processes. Here we test mate preferences of males presented with females of different allopatric colour variants of the cichlid fish Tropheus, a Lake Tanganyika endemic with rich geographic colour pattern variation, in which the strength of sexual isolation varies between populations. We conducted two-way mate choice experiments to compare behaviour of males of a red-bodied morph (population...

Tropheus moorii male courtship data

Peter Zoppoth, Stephan Koblmüller & Kristina M. Sefc

Data from: Invasive plants have scale-dependent effects on diversity by altering species-area relationships

Kristin I. Powell, Jonathan M. Chase & Tiffany M. Knight
Although invasive plant species often reduce diversity, they rarely cause plant extinctions. We surveyed paired invaded and uninvaded plant communities from three biomes. We reconcile the discrepancy in diversity loss from invaders by showing that invaded communities have lower local richness but steeper species accumulation with area than that of uninvaded communities, leading to proportionately fewer species loss at broader spatial scales. We show that invaders drive scale-dependent biodiversity loss through strong neutral sampling effects...

All data

Tamara S. Haselkorn, Sarah N. Cockburn, Phineas T. Hamilton, Steve Perlman & John Jaenike
This is an Excel workbook containing spreadsheets on restoration of fertility (female egg count), Spiroplasma density (qPCR-Spiroplasma), Howardula motherworm size (Motherworm size), and maternal transmission (Maternal transmission). These data were collected in either the Perlman (University of Victoria) or Jaenike (University of Rochester), as indicated in the file.

Data from: Phylogenetic utility of ycf1 in orchids: a plastid gene more variable than matK

Kurt M. Neubig, W. Mark Whitten, Barbara S. Carlsward, Mario A. Blanco, Lorena Endara, Norris H. Williams & Michael Moore
Plastid DNA sequences have been widely used by systematists for reconstructing plant phylogenies. The utility of any DNA region for phylogenetic analysis is determined by ease of amplification and sequencing, confidence of assessment in phylogenetic character alignment, and by variability across broad taxon sampling. Often, a compromise must be made between using relatively highly conserved coding regions or highly variable introns and intergenic spacers. Analyses of a combination of these types of DNA regions yield...

Sobralieae matK

Kurt M. Neubig, W. Mark Whitten, Barbara S. Carlsward, Mario A. Blanco, Lorena Endara, Norris H. Williams & Michael Moore
Nexus matrix of matK sequences of various Sobralieae (Orchidaceae)

Vandeae matK

Kurt M. Neubig, W. Mark Whitten, Barbara S. Carlsward, Mario A. Blanco, Lorena Endara, Norris H. Williams & Michael Moore
Nexus matrix of matK sequences of various Vandeae (Orchidaceae)

Fork length Salvelinus fontinalis / File S1

Louis Bernatchez, Céline Audet & Bérénice Bougas
Data includes the fork length measurement for L♀D♂, D♀L♂, L♀R♂ and R♀L♂ offspring and parents

Data from: Using a comprehensive DNA barcode library to detect novel egg and larval host plant associations in a Cephaloleia Rolled-leaf Beetle (Coleoptera: Chrysomelidae)

Carlos Garcia-Robledo, Erin K. Kuprewicz, Charles L. Staines, W. John Kress & Terry L. Erwin
To fully understand the ecology and evolution of plant-herbivore interactions, information regarding the life history of both immature and adult insect stages is essential. However, most knowledge of plant-herbivore associations is derived from observations of adults. One reason for this bias is that species identification of immature stages is usually challenging. DNA barcodes can be used to identify immature stages to the species-level. This technique compares short sequences of the appropriate DNA barcode loci (e.g.,...

Data from: The role of inbreeding depression and mating system in the evolution of heterostyly

Jennifer J. Weber, Stephen G. Weller, Ann K. Sakai, Olga V. Tsyusko, Travis C. Glenn, Cesar A. Dominguez, Francisco E. Molina-Freaner, Juan Fornoni, Mike Tran, Nhu Nguyen, Karen Nguyen, Lien-Khuong Tran, Greg Joice & Ellen Harding
We investigated the role of morph-based differences in the expression of inbreeding depression in loss of the mid-styled morph from populations of tristylous Oxalis alpina as proposed by theoretical analyses. The extent of self-compatibility of reproductive morphs, the degree of self-fertilization, and the magnitude of inbreeding depression were investigated in three populations of O. alpina differing in their tristylous incompatibility relationships. All three populations exhibited significant inbreeding depression. In two populations with highly modified tristylous...

Data from: Butterfly survival on an isolated island by improved grip

Anne Duplouy, Ilkka Hanski, A. Duplouy & I. Hanski
On small isolated islands, natural selection is expected to reduce the dispersal capacity of organisms, as short distances do not require a high rate of dispersal, which might lead to accidental emigration from the population. In addition, individuals foregoing the high cost of maintaining flight capacity may instead allocate resources to other functions. However, in butterflies and many other insects, flight is necessary not only for dispersal but also for most other activities. A weakly...

Data from: The genetic architecture of reproductive isolation during speciation-with-gene-flow in lake whitefish species pairs assessed by RAD sequencing

Pierre-Alexandre Gagnaire, Scott A. Pavey, Eric Normandeau & Louis Bernatchez
During speciation-with-gene-flow, effective migration varies across the genome as a function of several factors, including proximity of selected loci, recombination rate, strength of selection, and number of selected loci. Genome scans may provide better empirical understanding of the genome-wide patterns of genetic differentiation, especially if the variance due to the previously mentioned factors is partitioned. In North American lake whitefish (Coregonus clupeaformis), glacial lineages that diverged in allopatry about 60,000 years ago and came into...

Data from: Rivers, refuges, and population divergence of fire-eye antbirds (Pyriglena) in the Amazon Basin

Marcos Maldonado-Coelho, John G. Blake, Luis F. Silveira, Henrique Batalha-Filho, Robert E. Ricklefs, R. E. Ricklefs, H. Batalha-Filho & L. F. Silveira
The identification of ecological and evolutionary mechanisms that might account for the elevated biotic diversity in tropical forests is a central theme in evolutionary biology. This issue is especially relevant in the Neotropical region, where biological diversity is the highest in the world, but where few studies have been conducted to test factors causing population differentiation and speciation. We used mtDNA sequence data to examine the genetic structure within white-backed fire-eye (Pyriglena leuconota) populations along...

Data from: Stress hormones mediate predator-induced phenotypic plasticity in amphibian tadpoles

Jessica Middlemis Maher, Earl E. Werner, Robert J. Denver, J. Middlemis Maher, R. J. Denver & E. E. Werner
Amphibian tadpoles display extensive anti-predator phenotypic plasticity, reducing locomotory activity and, with chronic predator exposure, developing relatively smaller trunks and larger tails. In many vertebrates, predator exposure alters activity of the neuroendocrine stress axis. We investigated predator-induced effects on stress hormone production and the mechanistic link to anti-predator defences in Rana sylvatica tadpoles. Whole-body corticosterone (CORT) content was positively correlated with predator biomass in natural ponds. Exposure to caged predators in mesocosms caused a reduction...

Data from: Reliability of fish size estimates obtained from a multibeam imaging sonar

Joseph E. Hightower, Kevin J. Magowan, Lori M. Brown & Dewayne Fox
Multibeam imaging sonars have considerable potential for use in fisheries surveys because the video-like images are easy to interpret and contain information about fish size, shape, and swimming behavior, as well as characteristics of occupied habitats. We examined images obtained using a DIDSON multibeam sonar for Atlantic sturgeon Acipenser oxyrinchus, striped bass Morone saxatilis, white perch M. americana, and channel catfish Ictalurus punctatus of known size (20 - 141 cm) to determine the reliability of...

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