The Dryad digital repository captures, stores, indexes, preserves, and distributes digital data supporting scientific publications. http://datadryad.org:80 2010-09-06T07:08:50Z 2010-09-06T07:08:50Z http://hdl.handle.net/10255/dryad.1951 2010-09-02T06:00:18Z

Raw data on background motion occurring in video footage recorded of male Anolis lizards on their territories on Puerto Rico and Jamaica

Ord, Terry J Charles, Grace K Hofer, Rebecca K http://hdl.handle.net/10255/dryad.1950 2010-09-01T13:45:41Z 2010-09-01T13:40:59Z

Animals communicating socially are expected to produce signals that are conspicuous within the habitats in which they live. The particular way in which a species adapts to its environment will depend on its ancestral condition and evolutionary history. At this point, it is unclear how properties of the environment and historical factors interact to shape communication. Tropical Anolis lizards advertise territorial ownership using visual displays in habitats where visual motion or ‘noise’ from windblown vegetation poses an acute problem for the detection of display movements. We studied eight Anolis species that live in similar noise environments, but belong to separate island radiations with divergent evolutionary histories. We found that species on Puerto Rico displayed at times when their signals were more likely to be detected by neighboring males and females (during periods of low noise). In contrast, species on Jamaica displayed irrespective of the level of environmental motion, apparently because these species have a display that is effective in a range of viewing conditions. Our findings appear to reflect a case of species originating from different evolutionary starting points evolving different signal strategies for effective communication in noisy environments.

2010-09-01T13:40:59Z http://hdl.handle.net/10255/dryad.1944 2010-08-31T17:15:46Z

DNA coding for cytochrome oxidase from mt

http://hdl.handle.net/10255/dryad.1940 2010-08-31T17:15:46Z http://hdl.handle.net/10255/dryad.1949 2010-09-01T06:00:21Z

primers used in study

http://hdl.handle.net/10255/dryad.1941 2010-08-31T17:15:46Z

DNA coding for mt tRNA segment

http://hdl.handle.net/10255/dryad.1945 2010-08-31T17:15:47Z

DNA coding for Histone H3

http://hdl.handle.net/10255/dryad.1947 2010-08-31T17:15:47Z

Genbank accessions for DNA segments

http://hdl.handle.net/10255/dryad.1948 2010-08-31T17:15:47Z

annotated phenotype character matrix (tnt format)

http://hdl.handle.net/10255/dryad.1943 2010-08-31T17:15:46Z

DNA coding for mt tRNA segment

http://hdl.handle.net/10255/dryad.1946 2010-08-31T17:15:47Z

terminals file for poy analysis

http://hdl.handle.net/10255/dryad.1942 2010-08-31T17:15:46Z

DNA coding for mt tRNA segment

http://hdl.handle.net/10255/dryad.1939 2010-08-31T17:15:46Z

12S rDNA segment

http://hdl.handle.net/10255/dryad.1936 2010-08-31T17:15:46Z

28S rDNA segment

http://hdl.handle.net/10255/dryad.1929 2010-08-31T17:15:47Z

18S rDNA segment

http://hdl.handle.net/10255/dryad.1932 2010-08-31T17:15:47Z

28S rDNA segment

http://hdl.handle.net/10255/dryad.1938 2010-08-31T17:15:46Z

28S rDNA segment

http://hdl.handle.net/10255/dryad.1931 2010-08-31T17:15:47Z

28S rDNA segment

http://hdl.handle.net/10255/dryad.1933 2010-08-31T17:15:47Z

28S rDNA segment

http://hdl.handle.net/10255/dryad.1930 2010-08-31T17:15:47Z

28S rDNA segment

http://hdl.handle.net/10255/dryad.1934 2010-08-31T17:15:47Z

28S rDNA segment

http://hdl.handle.net/10255/dryad.1937 2010-08-31T17:15:46Z

28S rDNA segment

http://hdl.handle.net/10255/dryad.1935 2010-08-31T17:15:48Z

28S rDNA segment

Janies, Daniel Voight, Janet Daly, Marymegan http://hdl.handle.net/10255/dryad.1926 2010-08-31T17:15:46Z 2010-08-31T17:07:21Z

Reconstruction of the phylogeny of the five extant classes of the phylum Echinodermata has proven difficult. Results concerning higher-level taxonomic relationships among echinoderms are sensitive to the choice of analytical parameters and methods. Moreover, the proposal of a putative sixth class based on a small, enigmatic disc-shaped echinoderm, Xyloplax, from the deep seas of the Bahamas and New Zealand in the 1980s further complicated the problem. Although clearly an echinoderm, Xyloplax did not have clear affinity among known groups. Using molecular sequence and developmental data from recently collected Xyloplax adults and embryos we show that, rather than representing an ancient, distinct lineage as implied by its status as a class, Xyloplax is simply a starfish that is closely related to the asteroid family Pterasteridae. Many members of the Pterasteridae and all Xyloplax inhabit deep and polar seas and brood young. Brooding pterasterids and Xyloplax hold their young in specialized adult chambers until the young reach an advanced juvenile stage and are released as free-living individuals. We hypothesize that the unique morphology of Xyloplax evolved via progenesis - the truncation of somatic growth at a juvenile body plan but with gonadal growth to maturity. Although the overall phylogeny of extant echinoderms remains sensitive to choice of analytical methods, the placement of Xyloplax as sister to pterasterid asteroids is unequivocal. Based on this, we argue that the proposed class and infraclass status of Xyloplax should be suppressed.

2010-08-31T17:07:21Z http://hdl.handle.net/10255/dryad.1928 2010-08-31T17:15:47Z

18S rDNA segment

http://hdl.handle.net/10255/dryad.1927 2010-09-01T06:00:27Z

18S rDNA segment

Jeukens, Julie Nolte, Arne Bernatchez, Louis Renaut, Sebastien St-Cyr, Jerome http://hdl.handle.net/10255/dryad.1924 2010-08-30T20:19:21Z 2010-08-30T20:18:02Z

Gene expression divergence is one of the mechanisms thought to be involved in the emergence of incipient species. Next-generation sequencing has become an extremely valuable tool for the study of this process by allowing whole transcriptome sequencing, or RNA-Seq. We have conducted a 454 GS-FLX pyrosequencing experiment in order to refine our understanding of adaptive divergence between dwarf and normal lake whitefish species (Coregonus clupeaformis spp.). The objectives were to: (1) investigate transcriptomic divergence as measured by liver RNA-Seq; (2) test the correlation between divergence in expression and sequence polymorphism and (3) investigate the extent of allelic imbalance. We also compared the results of RNA-seq with those of a previous microarray study performed on the same fish. Following de novo assembly, results showed that normal whitefish over-expressed more contigs associated with protein synthesis while dwarf fish over-expressed more contigs related to energy metabolism, immunity and DNA replication and repair. Moreover, 63 SNPs showed significant allelic imbalance, and this phenomenon prevailed in the recently diverged dwarf whitefish. Results also showed an absence of correlation between gene expression divergence as measured by RNA-Seq and either polymorphism rate or sequence divergence between normal and dwarf whitefish. This study reiterates an important role for gene expression divergence, and provides evidence for allele-specific expression divergence as well as evolutionary decoupling of regulatory and coding sequences in the adaptive divergence of normal and dwarf whitefish. It also demonstrates how next-generation sequencing can lead to a more comprehensive understanding of transcriptomic divergence in a young species pair.

2010-08-30T20:18:02Z http://hdl.handle.net/10255/dryad.1925 2010-08-30T20:19:21Z

Excel spreadsheet with de novo contigs from RNA-Seq of the whitefish liver transcriptome. Contig consensus sequences and gene expression values (RPKM) for dwarf and normal whitefish are presented.

http://hdl.handle.net/10255/dryad.1915 2010-08-27T19:15:36Z 2010-08-27T18:59:03Z

Nexus file of aligned DNA sequence data containing partitions by codon position (by gene) and taxon sets.

2010-08-27T18:59:03Z Blackburn, David C Bickford, David P Diesmos, Arvin C Iskandar, Djoko T Brown, Rafe M http://hdl.handle.net/10255/dryad.1914 2010-08-27T19:15:36Z 2010-08-27T18:59:03Z

Background: The complex history of Southeast Asian islands has long been of interest to biogeographers. Dispersal and vicariance events in the Pleistocene have received the most attention, though recent studies suggest a potentially more ancient history to components of the terrestrial fauna. Among this fauna is the enigmatic archaeobatrachian frog genus Barbourula, which only occurs on the islands of Borneo and Palawan. We utilize this lineage to gain unique insight into the temporal history of lineage diversification in Southeast Asian islands. Methodology/Principal Findings: Using mitochondrial and nuclear genetic data, multiple fossil calibration points, and likelihood and Bayesian methods, we estimate phylogenetic relationships and divergence times for Barbourula. We determine the sensitivity of focal divergence times to specific calibration points by jackknife approach in which each calibration point is excluded from analysis. We find that relevant divergence time estimates are robust to the exclusion of specific calibration points. Barbourula is recovered as a monophyletic lineage nested within a monophyletic Costata. Barbourula diverged from its sister taxon Bombina in the Paleogene and the two species of Barbourula diverged in the Late Miocene. Conclusions/Significance: The divergences within Barbourula and between it and Bombina are surprisingly old and represent the oldest estimates for a cladogenetic event resulting in living taxa endemic to Southeast Asian islands. Moreover, these divergence time estimates are consistent with a new biogeographic scenario: the Palawan Ark Hypothesis. We suggest that components of Palawan’s terrestrial fauna might have ‘‘rafted’’ on emergent portions of the North Palawan Block during its migration from the Asian mainland to its present-day position near Borneo. Further, dispersal from Palawan to Borneo (rather than Borneo to Palawan) may explain the current day disjunct distribution of this ancient lineage.

2010-08-27T18:59:03Z http://hdl.handle.net/10255/dryad.1917 2010-08-27T19:15:36Z 2010-08-27T18:46:33Z

Nexus file containing aligned DNA sequences for mitochondrial 12S and 16S ribosomal RNA genes, and intervening transfer RNA gene for Valine

2010-08-27T18:46:33Z Blackburn, David C Gvoždík, Václav Leaché, Adam D http://hdl.handle.net/10255/dryad.1916 2010-08-27T19:15:36Z 2010-08-27T18:46:32Z

A new species of squeaker frog (genus Arthroleptis) is described from the northern mountains of the Cameroon Volcanic Line, a species-rich region within the West African biodiversity hotspot. This new species is associated with human-altered landscapes, including farms and grasslands, and is known from the highland areas near Bamenda, including Mt. Oku, Cameroon, as well as the Obudu and Mambilla Plateaus of eastern Nigeria. The known distribution suggests that it may eventually also be found throughout the Acha- Tugi Ridge that traverses the Cameroon–Nigeria border. More than 40 years ago, a specimen from one of these populations was recognized as probably representing a new species, but no further work was published on this material. We posit that the taxonomy of this new species has proven problematic because of morphological similarity to Arthroleptis poecilonotus. Although in some ways resembling A. poecilonotus, a molecular phylogeny based on mitochondrial gene sequence data demonstrates that the new species is not closely related to A. poecilonotus and, instead, forms a clade with A. krokosua, A. perreti, and A. variabilis. The new species is diagnosable by the combination of medium–small body size (24–29 mm snout–vent length in adult females), the color patterns of the venter and head, and a relatively stout hindlimb with a prominent inner metatarsal tubercle. The description of this new species further highlights these mountains as an important region of endemism within the Cameroon Volcanic Line.

2010-08-27T18:46:32Z http://hdl.handle.net/10255/dryad.1923 2010-08-27T19:15:36Z

Collection of 30063 files in PDB-format, each containing all-atom structural data for the conformation of a polyvaline molecule with 60 residues. All conformations where computer-generated by means of meta-dynamics.

Cossio, Pilar Trovato, Antonio Pietrucci, Fabio Seno, Flavio Maritan, Amos Laio, Alessandro http://hdl.handle.net/10255/dryad.1922 2010-08-27T19:15:36Z 2010-08-27T18:38:28Z 2010-08-27T18:38:28Z http://hdl.handle.net/10255/dryad.1921 2010-08-27T19:15:36Z Lewandowska-Sabat, Anna Monika Fjellheim, Siri Rognli, Odd Arne http://hdl.handle.net/10255/dryad.1920 2010-08-27T19:15:36Z 2010-08-27T18:20:27Z

The genetic diversity and population structure of Arabidopsis thaliana populations from Norway were studied and compared to a worldwide sample of A. thaliana in order to investigate the demographic history and elucidate possible colonization routes of populations at the northernmost species limit. We genotyped 282 individuals from 31 local populations using 149 single nucleotide polymorphism (SNP) markers. A high level of population subdivision (FST = 0.85 ± 0.007) was found indicating that A. thaliana is highly structured at the regional level. Significant relationships between genetic and geographic distances were found, suggesting an isolation by distance mode of evolution. Genetic diversity was much lower and the level of linkage disequilibrium (LD) higher in populations from the north (65–68oN) compared to populations from the south (59–62oN); this is consistent with a northward expansion pattern. A neighbor-joining (NJ) tree showed that populations from northern Norway form a separate cluster, while the remaining populations are distributed over a few minor clusters. Minimal gene flow seems to have occurred between populations in different regions, especially between the geographically distant northern and southern populations. Our data suggest that northern populations represent a homogenous group that may have been established from a few founders during northward expansions, while populations in the central part of Norway constitute an admixed group established by founders of different origins, most probably as a result of human-mediated gene flow. Moreover, Norwegian populations appeared to be homogenous and isolated compared to a worldwide sample of A. thaliana, but they are still grouped with Swedish populations, which may indicate common colonization histories.

2010-08-27T18:20:27Z http://hdl.handle.net/10255/dryad.1905 2010-08-27T06:00:13Z

The nexus matrices containing all sequences used for the phylogenetic analysis

Bocak, Ladislav Malohlava, Vladimir http://hdl.handle.net/10255/dryad.1904 2010-08-26T17:30:12Z 2010-08-26T15:46:53Z

The diversification of neotenic beetle lineages has not been studied, despite the potential for defining biodiversity hotspots and elucidating the history of regional faunas. Additionally, neotenics may provide insight into the process of speciation in small populations with extremely low dispersal ability and a limited range. Here, we used two rDNA and three mtDNA markers to investigate the phylogeny of Scarelus, a neotenic lineage endemic to Southeast Asian rainforests. Most genetic differentiation was associated with Palaeogene geographic divisions, which remain distinct despite temporary connections. Dispersal events were rare, with only two inferred for Scarelus: from Borneo to the Philippines 28.3 million years ago (mya) and from Sumatra to Java 13.9 mya. The reproductive isolation depended on allopatric range fragmentation, and Scarelus diversified readily when conditions were favorable; in this case, at different times in the eastern (19.3–39.1 mya) and western (3.5–13.9 mya) parts of Sundaland. The observed strong phenotypic similarity was preserved under speciation through complete allopatry. Neotenic Lycidae have survived for a long time in very stable habitats, and extremely low dispersal activity has not limited their existence; however, the long-term diversification rate of neotenics is low and diversification is nonexistent under stable conditions. The modern ranges of neotenic lineages are indicative of ancient rainforest refugia, and may be used in biodiversity conservation management. Most neotenics are at risk of extinction due to small ranges and a low dispersal potential.

2010-08-26T15:46:53Z Munshi-South, Jason Kharchenko, Katerina http://hdl.handle.net/10255/dryad.1893 2010-08-24T15:43:41Z 2010-08-23T15:50:20Z

We investigated genetic diversity and structure of urban white-footed mouse, Peromyscus leucopus, populations in New York City (NYC) using variation at 18 microsatellite loci. White-footed mice are "urban adapters" that occur at higher population densities as habitat fragments are reduced in area, but have a limited ability to disperse through urbanized areas. We hypothesized that this combination of traits has produced substantial genetic structure but minimal loss of genetic variation over the last century in NYC. Allelic diversity and heterozygosity in fourteen NYC populations were high, and nearly all of our NYC study sites contained genetically distinct populations of white-footed mice as measured by pairwise FST, assignment tests, and Bayesian clustering analyses performed by Structure and BAPS. Analysis of molecular variance revealed that genetic differences between populations separated by a few km are more significant than differences between prehistorically isolated landmasses (i.e. Bronx, Queens, and Manhattan). Allele size permutation tests and lack of isolation-by-distance indicated that mutation and migration are less important than drift as explanations for structure in urban, fragmented P. leucopus populations. Peromyscus often exhibit little genetic structure over even regional scales, prompting us to conclude that urbanization is a particularly potent driver of genetic differentiation compared to natural fragmentation.

2010-08-23T15:50:20Z Munshi-South, Jason Kharchenko, Katerina http://hdl.handle.net/10255/dryad.1894 2010-08-24T16:57:16Z 2010-08-23T15:50:13Z

Genepop file of 18-locus microsatellite genotypes (2-digit format) for 15 populations of white-footed mice (Peromyscus leucopus) in New York City.

2010-08-23T15:50:13Z Goldberg, Emma E Kohn, Joshua R Lande, Russ Robertson, Kelly A Smith, Stephen A Igic, Boris http://hdl.handle.net/10255/dryad.1888 2010-08-24T15:43:41Z 2010-08-21T02:04:29Z

Identifying traits that affect rates of speciation and extinction and hence explain differences in species diversity among clades is a major goal of evolutionary biology. Detecting such traits is especially difficult when they undergo frequent transitions between states. Self-incompatibility, the ability of hermaphrodites to enforce outcrossing, is frequently lost in flowering plants, enabling self-fertilization. We show, however, that in the nightshade plant family (Solanaceae), species with functional self-incompatibility diversify at a significantly higher rate than those without it. Apparent short-term advantages of potentially self-fertilizing individuals are therefore offset by strong species selection, which favors obligate outcrossing.

2010-08-21T02:04:29Z Goldberg, Emma E Kohn, Joshua R Lande, Russ Robertson, Kelly A Smith, Stephen A Igic, Boris http://hdl.handle.net/10255/dryad.1890 2010-08-24T16:54:11Z 2010-08-21T02:04:23Z

Rate-smoothed ML tree of 356 Solanaceae species.

2010-08-21T02:04:23Z Goldberg, Emma E Kohn, Joshua R Lande, Russ Robertson, Kelly A Smith, Stephen A Igic, Boris http://hdl.handle.net/10255/dryad.1889 2010-08-24T16:53:27Z 2010-08-21T02:04:21Z

Breeding system data for species used in the analyses. See included text file for explanation.

2010-08-21T02:04:21Z Haag, Taiana Santos, Anelisie Sana, Denis Morato, Ronaldo Cullen Jr., Laury Crawshaw Jr., Peter De Angelo, Carlos Di Bitetti, Mario Salzano, Francisco Eizirik, Eduardo http://hdl.handle.net/10255/dryad.1884 2010-08-20T19:59:07Z 2010-08-20T19:14:51Z

Habitat fragmentation may disrupt original patterns of gene flow and lead to drift-induced differentiation among local population units. Top predators such as the jaguar may be particularly susceptible to this effect, given their low population densities, leading to small effective sizes in local fragments. On the other hand, the jaguar's high dispersal capabilities and relatively long generation time might counteract this process, slowing the effect of drift on local populations over the time frame of decades or centuries. In this study, we have addressed this issue by investigating the genetic structure of jaguars in a recently fragmented Atlantic Forest region, aiming to test whether loss of diversity and differentiation among local populations are detectable, and whether they can be attributed to the recent effect of drift. We used 13 microsatellite loci to characterize the genetic diversity present in four remnant populations, and observed marked differentiation among them, with evidence of recent allelic loss in local areas. Although some migrant and admixed individuals were identified, our results indicate that recent large-scale habitat removal and fragmentation among these areas has been sufficiently strong to promote differentiation induced by drift and loss of alleles at each site. Low estimated effective sizes supported the inference that genetic drift could have caused this effect within a short time frame. These results indicate that jaguars' ability to effectively disperse across the human-dominated landscapes that separate the fragments is currently very limited, and that each fragment contains a small, isolated population that is already suffering from the effects of genetic drift.

2010-08-20T19:14:51Z Haag, Taiana Santos, Anelisie Sana, Denis Morato, Ronaldo Cullen Jr., Laury Crawshaw Jr., Peter De Angelo, Carlos Di Bitetti, Mario Salzano, Francisco Eizirik, Eduardo http://hdl.handle.net/10255/dryad.1885 2010-08-24T16:55:46Z 2010-08-20T19:14:43Z

Microsatellite data of the four jaguar populations studied in Atlantic Forest.

2010-08-20T19:14:43Z Stevenson, Laurie S. Noor, Mohamed A.F. http://hdl.handle.net/10255/dryad.1877 2010-08-20T15:44:35Z 2010-08-20T14:58:27Z 2010-08-20T14:58:27Z Stevenson, Laurie S. Noor, Mohamed A.F. http://hdl.handle.net/10255/dryad.1881 2010-08-20T15:39:12Z 2010-08-20T14:58:22Z

Zipped set of scripts, sample input and sample output files of programs used to design SNPs to distinguish 2 lines of D. persimilis, and further to extract GC content, diversity, divergence, and motif abundance of a published genomic sequence for correlation to recombination rate variation.

2010-08-20T14:58:22Z Stevenson, Laurie S. Noor, Mohamed A.F. http://hdl.handle.net/10255/dryad.1880 2010-08-20T15:39:37Z 2010-08-20T14:58:18Z

Zipped archive of chromosome 2 sequence alignment including Drosophila persimilis sequence (2 strains), D. pseudoobscura, D. miranda, and others. This file also includes the annotation information.

2010-08-20T14:58:18Z Stevenson, Laurie S. Noor, Mohamed A.F. http://hdl.handle.net/10255/dryad.1879 2010-08-20T15:40:34Z 2010-08-20T14:58:16Z

A list of all intervals with the number of inferred crossovers, the physical distance in both D. pseudoobscura and D. persimilis and the name of the two markers at the endpoints of the interval (found in 'SNP markers.csv'). Also included are the 95% confidence intervals of the recombination rate as well as various genomic features, such as GC counts, GC3 counts, diversity and divergence.

2010-08-20T14:58:16Z Stevenson, Laurie S. Noor, Mohamed A.F. http://hdl.handle.net/10255/dryad.1878 2010-08-20T15:38:25Z 2010-08-20T14:58:15Z

A list of all the markers used in the publication and their genomic position as well as respective locations in both the D. pseudoobscura and D. persimilis genome. This also includes the sequence of each SNP and the base position in the two strains of D. persimilis used for genotyping.

2010-08-20T14:58:15Z