Westneat, David F. · Hatch, Margret I. · Wetzel, Daniel P. · et al.

See ReadMe file

Lawson-Handley, Lori J · Elnagdy, Sherif · Majerus, Michael E N

Male-killing bacteria (MKs) are thought to persist in host populations by vertical transmission, and conferring direct and/or indirect fitness benefits to their hosts. Here, we test the role of indirect fitness benefits accrued from resource reallocation in species that engage in sibling egg cannibalism. We found that a single-egg meal significantly increased larval survival in 12 ladybird species, but the value of an egg (to survival) differed substantially between species. Next we tested the impact of three MKs on larval survival in one ladybird species, Adalia bipunctata. Spiroplasma reduced larval survival, whereas Wolbachia and Rickettsia had no effect. However, Spiroplasma-infected larvae showed the greatest response to a single-egg meal. The indirect fitness benefit obtained from a single egg is thus so large, that even MKs with direct fitness costs can persist in host populations. This study supports the hypothesis that fitness compensation via resource reallocation can explain MK persistence.

Lawson-Handley, Lori J · Elnagdy, Sherif · Majerus, Michael E N · et al.

Survival data for three experiments to investigate resource reallocation in coccinellids (Coleoptera: Coccinellidae) infected with male-killing bacteria

Johnson, Marc T. J. · FitzJohn, Richard Gareth · Smith, Stacey D. · et al.

The loss of sexual recombination and segregation in asexual organisms has been portrayed as an irreversible process that commits asexually-reproducing lineages to reduced diversification. We test this hypothesis by estimating rates of speciation, extinction, and transition between sexuality and functional asexuality in the evening primroses. Specifically, we estimate these rates using the recently developed BiSSE (Binary State Speciation and Extinction) phylogenetic comparative method, which employs maximum likelihood and Bayesian techniques. We infer that net diversification rates (speciation minus extinction) in functionally asexual evening primrose lineages are roughly eight times faster than diversification rates in sexual lineages, largely due to higher speciation rates in asexual lineages. We further reject the hypothesis that a loss of recombination and segregation is irreversible because the transition rate from functional asexuality to sexuality is significantly greater than zero.and in fact exceeded the reverse rate. These results provide the first empirical evidence in support of the alternative theoretical prediction that asexual populations should instead diversify more rapidly than sexual populations because they are free from the homogenizing effects of sexual recombination and segregation. Although asexual reproduction may often constrain adaptive evolution, our results show that the loss of recombination and segregation need not be an evolutionary dead-end in terms of diversification of lineages.

Johnson, Marc T. J. · FitzJohn, Richard Gareth · Smith, Stacey D. · et al.

This zip directory gives the BiSSE maximum likelihood analyses reported in Table S3.

Johnson, Marc T. J. · FitzJohn, Richard Gareth · Smith, Stacey D. · et al.

This zip directory gives the full MCMC results and the R code that generated the data underlying Figure 3, Figure S1, Figure S3, Table 1, and Table S2.

Tenopir, Carol · Allard, Suzie · Douglass, Kimberly · et al.

Background: Scientific research in the 21st century is more data intensive and collaborative than in the past. It is important to study the data practices of researchers –data accessibility, discovery, re-use, preservation and, particularly, data sharing. Data sharing is a valuable part of the scientific method allowing for verification of results and extending research from prior results. Methodology/Principal Findings: A total of 1329 scientists participated in this survey exploring current data sharing practices and perceptions of the barriers and enablers of data sharing. Scientists do not make their data electronically available to others for various reasons, including insufficient time and lack of funding. Most respondents are satisfied with their current processes for the initial and short-term parts of the data or research lifecycle (collecting their research data; searching for, describing or cataloging, analyzing, and short-term storage of their data) but are not satisfied with long-term data preservation. Many organizations do not provide support to their researchers for data management both in the short- and long-term. If certain conditions are met (such as formal citation and sharing reprints) respondents agree they are willing to share their data. There are also significant differences and approaches in data management practices based on primary funding agency, subject discipline, age, work focus, and world region. Conclusions/Significance: Barriers to effective data sharing and preservation are deeply rooted in the practices and culture of the research process as well as the researchers themselves. New mandates for data management plans from NSF and other federal agencies and world-wide attention to the need to share and preserve data could lead to changes. Large scale programs, such as the NSF-sponsored DataNET (including projects like DataONE) will both bring attention and resources to the issue and make it easier for scientists to apply sound data management principles.

Aguirre, J. David · Marshall, Dustin J.

An enduring hypothesis for the proximal benefits of sex is that recombination increases the genetic variation among offspring and that this genetic variation increases offspring performance. A corollary of this hypothesis is that mothers that mate multiply increase genetic variation within a clutch and gain benefits due to genetic diversity alone. Many studies have demonstrated that multiple mating can increase offspring performance, but most attribute this increase to sexual selection and the role of genetic variation has received less attention. Here, we used a breeding design to generate populations of full-siblings, half-siblings and unrelated individuals of the solitary ascidian Ciona intestinalis. Importantly, we preclude the potentially confounding influences of maternal effects and sexual selection. We found that individuals in populations with greater genetic diversity had greater performance (metamorphic success, post-metamorphic survival and post-metamorphic size) than individuals in populations with lower genetic diversity. Furthermore, we show that by mating with multiple males and thereby increasing genetic variation within a single clutch of offspring, females gain indirect fitness benefits in the absence of mate-choice. Our results show that when siblings are likely to interact, genetic variation among individuals can decrease competition for resources and generate substantial fitness benefits within a single generation

Rocha, Sara · Harris, D James · Posada, David

Deciphering the process of genetic differentiation of species with insular distributions is relevant for biogeographic and conservation reasons. Despite its importance as old gondwanic islands and part of the Western Indian Ocean biodiversity hotspot, little is known concerning the genetic structure of taxa from the Seychelles islands. We have examined patterns of structure and isolation within Urocotyledon inexpectata (Reptilia: Geckkonidae), an endemic species from this archipelago. Genetic diversity was screened from populations across the archipelago for both mitochondrial and nuclear genes. Gene genealogies and model-based inference were used to explore patterns and timings of isolation between the main lineages. High levels of genetic diversity were found for the mitochondrial and some of the nuclear markers. This species harbours at least two highly differentiated lineages, exclusively distributed across the northern and southern groups of islands. The main split between these was dated back to the Miocene/Late Pliocene, but isolation events throughout the Pliocene and Pleistocene were also inferred. Migration between groups of islands was apparently non-existent, except for one case. The low dispersal capabilities of this species, together with the intrinsic fragmented nature of its geographic distribution seem to have resulted into highly structured populations, despite the cyclic periods of contact between the different island groups. These populations may currently represent more than one species, making U. inexpectata another example of morphologically cryptic lineages with deep genetic divergence within gekkonids. The observed patterns suggest a hypothetical biogeographic scenario (of a main north – south phylogeographic break) for the Seychelles that can be further tested with the exploration of the phylogeographic structure of other Seychellois taxa.

Rocha, Sara · Harris, D James · Posada, David

nexus file of haplotypes of cytochrome-b used to phylogenetic analysis (figure 2). Whole alignments of unphased sequences can be obtained from public genbank database (acession numbers given in the manuscript). Only further sequence alignment files used for analyses are provided here. All "specimen" codes in the files are as given in Appendix S1 of manuscript ("a" and "b" added when needed to represent the different haplotypes of the same individual.

Rocha, Sara · Harris, D James · Posada, David

fasta file of haplotypes for the fragment of c-mos gene for all individuals (note that no heterozygous individuals were observed, so for this gene both haplotypes for each individual are identical). This is the alignment used for the MJ networks and all further analysis.

Rocha, Sara · Harris, D James · Posada, David

fasta file of haplotypes from the pdc fragment for all individuals (note that no multiple heterozigous were observed, so all haplotypes - phases - are determined with certainty)

Rocha, Sara · Harris, D James · Posada, David

fasta file of haplotypes infered for the rag2 dataset for all individuals. Here, positions were phases were resolved with < 0.8 posterior probability are coded with N. This alignment was used for MJ network construction (figure 3), summary statistics, and IMa analysis.

Rocha, Sara · Harris, D James · Posada, David

fasta file of haplotypes infered for rag2 dataset for all individuals but where positions whose phases were resolved with < 0.8 posterior probability are coded with IUPAC ambiguity codes. Used for EBSP / species-tree analyses.

Rocha, Sara · Harris, D James · Posada, David

fasta file of haplotypes infered for the mc1r dataset for all individuals. Here, positions were phases were resolved with < 0.8 posterior probability are coded with N. This alignment was used for MJ network construction (figure 3), summary statistics and IMa analysis.

Rocha, Sara · Harris, D James · Posada, David

fasta file of haplotypes infered for mc1r dataset for all individuals but where positions whose phases were resolved with < 0.8 posterior probability are coded with IUPAC ambiguity codes. Used for EBSP / species-tree analyses.

Rocha, Sara · Harris, D James · Posada, David

fasta file of haplotypes infered for the reln dataset for all individuals. Here, positions were phases were resolved with < 0.8 posterior probability are coded with N. This alignment was used for MJ network construction (figure 3) and summary statistics.

Rocha, Sara · Harris, D James · Posada, David

fasta file of haplotypes infered for reln dataset for all individuals but where positions whose phases were resolved with < 0.8 posterior probability are coded with IUPAC ambiguity codes. Used for EBSP.

Rocha, Sara · Harris, D James · Posada, David

fasta file of haplotypes infered for reln dataset for all individuals, where positions whose phases were resolved with < 0.8 posterior probability are nevertheless coded with the respective best guesses for each base. (as in this dataset the different runs of PHASE (Stephens et al., 2001 - to be fund on manuscript references) were inconsistent at some positions we used results of the run with the highest likelihood score, whose seed (and command line) is given bellow. The known haplotypes used (uro_reln.known) were those read directly from sequences heterozigous for indels, and that can be found on genbank - accession numbers given in the paper). [phase comand line: ./PHASE -MS -p0.8 -q0.8 -d1 -s48993 -kuro_reln.known uro_reln.inp uro_reln.out 10000 1 100]