Cotton domestication: dramatic changes in a single cell

Investigations on the nature of genetic changes underpinning plant domestication have begun to shed light on the evolutionary history of crops and can guide improvements to modern cultivars. A recent study focused on cotton fiber cells tracks the dramatic genome-wide changes in gene expression during development that have accompanied selection for increased fiber yield and quality

A METHODOLOGICAL COMPARISON AMONG DNA SOURCE TYPES FOR MOOSE GENOTYPING

Population genetic analyses for moose have been based on DNA extracted from blood and other body tissues. Non-invasive sampling of fecal pellets is another potential source of DNA. We compared DNA extraction from blood, liver tissue, and fecal pellet samples from moose in Minnesota and Yellowstone National Park, USA. Extracted DNA from all source types was sufficient for genotyping using 15 microsatellites. DNA extracted from fecal pellets was of lower quality and quantity than DNA extracted from blood and tissue. We provide comparisons of efficiency and effectiveness of DNA extraction protocols for blood, tissue, and fecal pellets, and demonstrate the suitability of using DNA extracted from non-invasively sampled material in moose

Combining Phylogeography with Distribution Modeling: Multiple Pleistocene Range Expansions in a Parthenogenetic Gecko from the Australian Arid Zone

Phylogenetic and geographic evidence suggest that many parthenogenetic organisms have evolved recently and have spread rapidly. These patterns play a critical role in our understanding of the relative merits of sexual versus asexual reproductive modes, yet their interpretation is often hampered by a lack of detail. Here we present a detailed phylogeographic study of a vertebrate parthenogen, the Australian gecko Heteronotia binoei, in combination with statistical and biophysical modeling of its distribution during the last glacial maximum. Parthenogenetic H. binoei occur in the Australian arid zone and have the widest range of any known vertebrate parthenogen. They are broadly sympatric with their sexual counterparts, from which they arose via hybridization. We have applied nested clade phylogeographic, effective migration, and mismatch distribution analyses to mitochondrial DNA (mtDNA) sequences obtained for 319 individuals sampled throughout the known geographic ranges of two parthenogenetic mitochondrial lineages. These analyses provide strong evidence for past range expansion events from west to east across the arid zone, and for continuing eastward range expansion. Parthenogen formation and range expansion events date to the late Pleistocene, with one lineage expanding from the northwest of its present range around 240,000 years ago and the second lineage expanding from the far west around 70,000 years ago. Statistical and biophysical distribution models support these inferences of recent range expansion, with suitable climatic conditions during the last glacial maximum most likely limited to parts of the arid zone north and west of much of the current ranges of these lineages. Combination of phylogeographic analyses and distribution modeling allowed considerably stronger inferences of the history of this complex than either would in isolation, illustrating the power of combining complementary analytical approaches

MEC-10-1217.R1_data

Zipped folder containing 126 data files formatted for the program IMa2 as well as a README file explaining data file organization. All data were simulated using the program MS

Impact of fire management on the ecology of collared lizard (\u3ci\u3eCrotaphytus collaris\u3c/i\u3e) populations living on the Ozark Plateau

Eastern collared lizards (Crotaphytus collaris collaris) on the Ozark Plateau of southern Missouri are restricted to islands of rocky glade habitat located throughout the oak–hickory forests of the region. Human mediated suppression of fire negatively impacts collared lizard populations by permitting the overgrowth and consequent disappearance of this glade habitat and also leads to a dense forest understorey that impedes movement of lizards between glades. We present data examining the effects of a fire management regime on collared lizard populations we monitored via mark/recapture from 1998 to 2001. We demonstrate increased glade-to-glade dispersal, colonization of previously unoccupied glades, and a significant increase in population size in the burned area. In addition, we show that populations within burned areas exhibit body sizes similar to those reported for populations living on healthy habitat as compared to those living on habitat that has deteriorated because of fire suppression. We conclude that managed forest fires positively impact collared lizard populations in the Ozarks, promoting factors that increase the long-term sustainability of the species

Data from: Interpreting the estimated timing of migration events between hybridizing species

The question of whether speciation can occur in the presence of gene flow has long been a contentious one. However, measuring the amount and timing of gene flow remains challenging. The computer program IMA2 allows researchers to estimate the timing of migration events for each locus during analyses, and these estimates have been used to infer the timing of introgression and mode of speciation. We use simulated datasets to examine the degree to which gene flow timing estimates can be used for these purposes, and what demographic conditions and datasets may be most amenable to gene flow timing estimation. We find that the 90% highest posterior density (HPD) interval of gene flow timing is almost always substantially wider than the actual window of gene flow, and increasing the information content of the dataset in terms of number of loci, number of sequences sampled, or locus length (and thus number of variable sites) has little impact on the posterior distribution over the range of values we tested. Even when simulated gene flow only occurred over the most recent 0.01% of the species’ history, the HPD interval usually encompasses the inferred divergence time. Our results indicate that gene flow timing estimates made using the method currently implemented in IMA2 cannot reliably be used to make inferences about the timing of introgression between diverged species or to distinguish between speciation with gene flow and allopatric speciation followed by one or more episodes of gene flow

Isolation and characterization of 11 polymorphic microsatellite loci in collared lizards (\u3ci\u3eCrotaphytus collaris\u3c/i\u3e)

We identified 11 polymorphic microsatellite loci in collared lizards (Crotaphytus collaris). Polymorphism assessment in 512 individuals from 52 populations sampled across much of the species distribution revealed a fairly high degree of genetic diversity (six to 20 alleles per locus) and a wide range of average expected heterozygosity values (0.143–0.530). We found no evidence for linkage, very few deviations from HW expectation (two of 572 possible population/locus analyses) and thus no evidence for null alleles. There was a tendency for reduced polymorphism towards the northern periphery

A METHODOLOGICAL COMPARISON AMONG DNA SOURCE TYPES FOR MOOSE GENOTYPING

Population genetic analyses for moose have been based on DNA extracted from blood and other body tissues. Non-invasive sampling of fecal pellets is another potential source of DNA. We compared DNA extraction from blood, liver tissue, and fecal pellet samples from moose in Minnesota and Yellowstone National Park, USA. Extracted DNA from all source types was sufficient for genotyping using 15 microsatellites. DNA extracted from fecal pellets was of lower quality and quantity than DNA extracted from blood and tissue. We provide comparisons of efficiency and effectiveness of DNA extraction protocols for blood, tissue, and fecal pellets, and demonstrate the suitability of using DNA extracted from non-invasively sampled material in moose

MEC-10-1217.R1_data

Zipped folder containing 126 data files formatted for the program IMa2 as well as a README file explaining data file organization. All data were simulated using the program MS

Molecular Phylogenetics of Western North American Frogs of the \u3ci\u3eRana boylii\u3c/i\u3e Species Group

Phylogenetic relationships among frogs of the genus Rana from western North America are investigated using 2013 aligned bases of mitochondrial DNA sequence from the genes encoding ND1 (subunit one of NADH dehydrogenase), tRNAIle, tRNAGln, tRNAMet, ND2, tRNATrp, tRNAAla, tRNAAsn, tRNACys, tRNATyr, and COI (subunit I of cytochrome c oxidase), plus the origin for light-strand replication (OL) between the tRNAAsn and tRNACys genes. The aligned sequences contain 401 phylogenetically informative characters. A well-resolved phylogenetic hypothesis in which the Rana boylii species group (R. aurora, R. boylii, R. cascadae, R. muscosa, and R. pretiosa) is monophyletic is obtained. Molecular sequence divergence suggests that the R. boylii species group is approximately 8 million years old. The traditional hypothesis showing monophyly of the yellow-legged frogs (R. boylii and R. muscosa) is statistically rejected in favor of a hypothesis in which R. aurora, R. cascadae, and R. muscosa form a clade. Reanalyses of published nuclear ribosomal DNA restriction-site data and allozymic data support a monophyletic R. boylii group, but do not effectively resolve relationships among species within this group. Eight populations of R. muscosa form two major clades separated by a biogeographic break in the Sierra Nevada of California. This biogeographic break is broadly concordant with breaks found in four other amphibian and reptilian taxa. The two major clades within R. muscosa are estimated to have diverged approximately 2.2 million years before present. Each of these major clades contains two subgroups showing approximately 1.5 million years divergence, implicating climatic effects of Pleistocene glaciation in vicariance. The four distinct subgroups of R. muscosa separated by at least 1.4 million years of evolutionary divergence are suggested as potential units for conservation