Data from: Sea level change and the area of shallow-marine habitat: implications for marine biodiversitySteven M. Holland
Analysis of a global elevation database to measure changes in shallow-marine habitat area as a function of sea-level reveals an unexpectedly complicated relationship. In contrast to prevailing views, sea-level rise does not consistently generate an increase in shelf area, nor does sea-level fall consistently reduce shelf area. Different depth-defined habitats on the same margin will experience different changes in area for the same sea-level change, and different margins will likewise experience different changes in area...
Data from: Local selection underlies the geographic distribution of sex-ratio drive in Drosophila neotestaceaKelly A. Dyer
“Selfish” genetic elements promote their own transmission to the next generation, often at a cost to the host individual. A sex-ratio driving X-chromosome prevents the maturation of Y-bearing sperm, and as a result is transmitted to 100% of the offspring, all of which are female. Because the spread of a sex-ratio chromosome can result in a female biased population sex ratio, the ecological and evolutionary consequences of harboring this selfish element can be severe. In...
Data from: Ultrafast evolution and loss of CRISPRs following a host shift in a novel wildlife pathogen, Mycoplasma gallisepticumNigel F. Delaney, Susan Balenger, Camille Bonneaud, Christopher J. Marx, Geoffrey E. Hill, Naola Ferguson-Noel, Peter Tsai, Allen Rodrigo & Scott V. Edwards
Measureable rates of genome evolution are well documented in human pathogens but are less well understood in bacterial pathogens in the wild, particularly during and after host switches. Mycoplasma gallisepticum (MG) is a pathogenic bacterium that has evolved predominantly in poultry and recently jumped to wild house finches (Carpodacus mexicanus), a common North American songbird. For the first time we characterize the genome and measure rates of genome evolution in House Finch isolates of MG,...
Whole-genome duplication (WGD), or polyploidy, followed by gene loss and diploidization has long been recognized as an important evolutionary force in animals, fungi and other organisms1, 2, 3, especially plants. The success of angiosperms has been attributed, in part, to innovations associated with gene or whole-genome duplications4, 5, 6, but evidence for proposed ancient genome duplications pre-dating the divergence of monocots and eudicots remains equivocal in analyses of conserved gene order. Here we use comprehensive...
PREMISE OF THE STUDY: Weeds cause considerable environmental and economic damage. However, genomic characterization of weeds has lagged behind that of model plants and crop species. Here we report on the development of genomic tools and resources for 11 weeds from the Compositae family that will serve as a basis for subsequent population and comparative genomic analyses. Because hybridization has been suggested as a stimulus for the evolution of invasiveness, we also analyze these genomic...
Increased sea-surface temperatures linked to warming climate threaten coral reef ecosystems globally. To better understand how corals and their endosymbiotic dinoflagellates (Symbiodinium spp.) respond to environmental change, tissue biomass and Symbiodinium density of seven coral species were measured on various reefs approximately every four months for up to thirteen years in the Upper Florida Keys, United States (1994–2007), eleven years in the Exuma Cays, Bahamas (1995–2006), and four years in Puerto Morelos, Mexico (2003–2007). For...
Data from: Abundance and extinction in Ordovician-Silurian brachiopods, Cincinnati Arch, Ohio and KentuckyAndrew Zaffos & Steven M. Holland
A basic hypothesis in extinction theory predicts that more abundant taxa have an evolutionary advantage over less abundant taxa, which should manifest as increased survivorship during major extinction events and longer fossil-record durations. Despite this, various paleontologic studies have found conflicting patterns, indicating a more complex relationship between abundance and extinction in the geologic past. This study tests the relationship between abundance and extinction among brachiopod genera within seven third-order depositional sequences spanning the Late...
Data from: Types, levels, and patterns of low-copy DNA sequence divergence, and phylogenetic implications, for Gossypium genome typesAndrew H. Paterson, Junkang Rong, Xiyin Wang, Stefan R. Schulze, Rosana O. Compton, T. D. Williams-Coplin, Valorie Goff & Peng W. Chee
To explore types, levels, and patterns of genetic divergence among diploid Gossypium (cotton) genomes, 780 cDNA, genomic DNA, and SSR loci were re-sequenced in Gossypium herbaceum (A1 genome), G. arboreum (A2), G. raimondii (D5), G. trilobum (D8), G. sturtianum (C1) and an outgroup, Gossypioides kirkii. Divergence among these genomes ranged from 7.32 polymorphic base pairs per 100 between G. kirkii and G. herbaceum (A1) to only 1.44 between G. herbaceum (A1) and G. arboreum (A2)....
Data from: Mitochondrial gene diversity associated with the atp9 stop codon in natural populations of wild carrot (Daucus carota ssp. carota)Jennifer R. Mandel, Edward V. McAssey, Katherine M. Roland & David E. McCauley
Mitochondrial genomes extracted from wild populations of Daucus carota have been used as a genetic resource by breeders of cultivated carrot, yet little is known concerning the extent of their diversity in nature. Of special interest is a SNP in the putative stop codon of the mitochondrial gene atp9 that has been associated previously with male-sterile and male-fertile phenotypic variants. In this study either sequence or PCR/RFLP genotypes were obtained from the mitochondrial genes atp1,...
Data from: Phylogenomic analysis of transcriptome data elucidates co-occurrence of a paleopolyploid event and the origin of bimodal karyotypes in Agavoideae (Asparagaceae)Michael R. McKain, Norman Wickett, Yeting Zhang, Saravanaraj Ayyampalayam, W. Richard McCombie, Mark W. Chase, J. Chris Pires, Claude W. DePamphilis, Jim Leebens-Mack & Claude W. De Pamphilis
PREMISE OF THE STUDY: The stability of the bimodal karyotype found in Agave and closely related species has long interested botanists. The origin of the bimodal karyotype has been attributed to allopolyploidy, but this hypothesis has not been tested. Next Generation transcriptome sequence data were used to test whether a paleopolyploid event occurred on the same branch of the Agavoideae phylogenetic tree as the origin of the Yucca-Agave bimodal karyotype. METHODS: Illumina RNAseq data were...
University of Georgia10
Pennsylvania State University3
University of California, Davis2
University of Massachusetts Amherst1
New England Aquarium1
Royal Botanic Gardens1
University of Delaware1
Washington University in St. Louis1
University of Tennessee at Knoxville1
Indiana University Bloomington1