What can genetics tell us about plant domestication?

My purpose in this essay is consider how genetics has provided new information on the domestication of barley in the Near East and then I will consider avocado domestication in Mesoamerica.Academia Nacional de Agronomía y Veterinari

What can genetics tell us about plant domestication?

My purpose in this essay is consider how genetics has provided new information on the domestication of barley in the Near East and then I will consider avocado domestication in Mesoamerica.Academia Nacional de Agronomía y Veterinari

Barley landraces are characterized by geographically heterogeneous genomic origins

<p>Genotyping data for landrace and cultivated lines from the National Small Grains Collection.</p> <p>The dataset has been devided in 11 parts. <strong>This is part 04. Make sure to download all 11 parts.</strong></p> <p>Data used in the article: "Barley landraces are characterized by geographically heterogeneous genomic origins". Published in Genome Biology</p> <p>Use the following command to put the pieces together:</p> <p>% cat * >./My_complete_data.txt</p> <p>The scripts used to analyze and plot the data are available in GitHub: https://github.com/AnaPoets/BarleyLandraces</p

The Impact of Outcrossing on Yields of ‘Hass’ Avocado

‘Hass’ avocado (Persea americana Mill.) is characterized by excessive flower and fruit abscission, resulting in extremely low fruit set. Low outcrossing rates might be a factor contributing to low yields. It is hypothesized that self-fertilized flowers and resulting fruit abscise at a much higher rate than fruit that are the product of outcrossing. However, significant relationships between outcrossing rates and yields have only been established in a few avocado studies. The objective of this research was to investigate the importance of outcrossing to yield in a commercial ‘Hass’ orchard containing ‘Bacon’, an effective pollinizer of ‘Hass’. Microsatellite markers were used to determine the rate of outcrossing of fruit persisting to harvest on ‘Hass’ trees. Experiments were conducted during sequential on-and off-crop years. During both years, outcrossing rates were not related to yield or alternate bearing. These results indicate that outcrossing was not the primary factor affecting flower and fruit persistence and ultimately yield in this orchard for the two sequential years of this research

The Intrinsic Absorber in QSO 2359-1241: Keck and HST Observations

We present detailed analyses of the absorption spectrum seen in QSO 2359-1241 (NVSS J235953-124148). Keck HIRES data reveal absorption from twenty transitions arising from: He I, Mg I, Mg II, Ca II, and Fe II. HST data show broad absorption lines (BALs) from Al III 1857, C IV 1549, Si IV 1397, and N V 1240. Absorption from excited Fe II states constrains the temperature of the absorber to 2000K < T < 10,000K and puts a lower limit of 10^5 cm^{-3} on the electron number density. Saturation diagnostics show that the real column densities of He I and Fe II can be determined, allowing to derive meaningful constraints on the ionization equilibrium and abundances in the flow. The ionization parameter is constrained by the iron, helium and magnesium data to -3.0 < log(U) < -2.5 and the observed column densities can be reproduced without assuming departure from solar abundances. From comparison of the He I and Fe II absorption features we infer that the outflow seen in QSO 2359-1241 is not shielded by a hydrogen ionization front and therefore that the existence of low-ionization species in the outflow (e.g., Mg II, Al III, Fe II) does not necessitate the existence of such a front. We find that the velocity width of the absorption systematically increases as a function of ionization and to a lesser extent with abundance. Complementary analyses of the radio and polarization properties of the object are discussed in a companion paper (Brotherton et al. 2000).Comment: 30 pages, 9 figures, in press with the Ap

The Water Vapor Abundance in Orion KL Outflows

We present the detection and modeling of more than 70 far-IR pure rotational lines of water vapor, including the 18O and 17O isotopologues, towards Orion KL. Observations were performed with the Long Wavelength Spectrometer Fabry-Perot (LWS/FP; R~6800-9700) on board the Infrared Space Observatory (ISO) between ~43 and ~197 um. The water line profiles evolve from P-Cygni type profiles (even for the H2O18 lines) to pure emission at wavelengths above ~100 um. We find that most of the water emission/absorption arises from an extended flow of gas expanding at 25+-5 kms^-1. Non-local radiative transfer models show that much of the water excitation and line profile formation is driven by the dust continuum emission. The derived beam averaged water abundance is 2-3x10^-5. The inferred gas temperature Tk=80-100 K suggests that: (i) water could have been formed in the "plateau" by gas phase neutral-neutral reactions with activation barriers if the gas was previously heated (e.g. by shocks) to >500 K and/or (ii) H2O formation in the outflow is dominated by in-situ evaporation of grain water-ice mantles and/or (iii) H2O was formed in the innermost and warmer regions (e.g. the hot core) and was swept up in ~1000 yr, the dynamical timescale of the outflow.Comment: Accepted for publication in ApJ letters [2006 August 7] (5 pages 2, figures, not edited

Phylogenetic Hypotheses for the Monocotyledons Constructed from rbcL Sequence Data

DNA sequences for the plastid locus that encodes the large subunit of ribulose 1,5-bisphosphate carboxylase/oxygenase (rbcL) were determined for 18 species of monocotyledons in 15 families. These data were analyzed together with sequences for 60 other monocot species in a total of 52 families by the maximum likelihood method producing one, presumably optimal, topology. An additional 26 species were added (104 total monocot species) and analyzed by the parsimony method with an outgroup of 18 dicot species producing 109 trees of 3,932 steps. The rbcL data show at least moderate support for seven lineages corresponding to the following orders, superorders, or combinations: Arecanae; Asparagales (excluding Hypoxidaceae) plus Iridaceae; Cyclanthanae plus Pandananae; Dioscoreales; Orchidales; Typhales; and Zingiberanae. Six clades corresponding to families or genera are well supported, including: Agavaceae, Asphodelaceae, Bromeliaceae, Hypoxidaceae, Poaceae, and Tradescantia. The two, earliest diverging multispecies clades in our rbcL phylogenies, Alismatanae and Aranae, are only weakly supported, and Bromelianae, Commelinanae, and Lilianae are paraphyletic. In all analyses Acorus calamus is phylogenetically isolated as the sister species to the remaining species of monocotyledons

Far-Infrared detection of methylene

We present a clear detection of CH2 in absorption towards the molecular cloud complexes Sagittarius B2 and W49 N using the ISO Long Wavelength Spectrometer. These observations represent the first detection of its low excitation rotational lines in the interstellar medium. Towards Sagittarius B2, we detect both ortho and para transitions allowing a determination of the total CH2 column density of N(CH2)=(7.5+/-1.1)x10^14 cm^-2. We compare this with the related molecule, CH, to determine [CH/CH2]=2.7+/-0.5. Comparison with chemical models shows that the CH abundance along the line of sight is consistent with diffuse cloud conditions and that the high [CH/CH2] ratio can be explained by including the effect of grain-surface reactions.Comment: 11 pages, 4 figures, accepted for publication in A&

Contemporary Evolutionary Divergence for a Protected Species following Assisted Colonization

Contemporary evolution following assisted colonization may increase the probability of persistence for refuge populations established as a bet-hedge for protected species. Such refuge populations are considered "genetic replicates" that might be used for future re-colonization in the event of a catastrophe in the native site. Although maladaptive evolutionary divergence of captive populations is well recognized, evolutionary divergence of wild refuge populations may also occur on contemporary time scales. Thus, refuge populations may lose their "value" as true genetic replicates of the native population. Here, we show contemporary evolutionary divergence in body shape in an approximately 30-year old refuge population of the protected White Sands pupfish (Cyprinodon tularosa) resulting in a body-shape mismatch with its native environment.Geometric morphometic data were collected from C. tularosa cultures raised in experimental mesocosms. Cultures were initiated with fish from the two native populations, plus hybrids, in high or low salinity treatments representing the salinities of the two native habitats. We found that body shape was heritable and that shape variation due to phenotypic plasticity was small compared to shape variation due to population source. C. tularosa from the high salinity population retained slender body shapes and fish from the low salinity population retained deep body shapes, irrespective of mesocosm salinity. These data suggest that the observed divergence of a recently established pupfish population was not explained by plasticity. An analysis of microsatellite variation indicated that no significant genetic drift occurred in the refuge population, further supporting the adaptive nature of changes in body shape. These lines of evidence suggest that body shape divergence of the refuge population reflects a case of contemporary evolution (over a 30-year period).These results suggest assisted colonization can introduce novel, and/or relaxed selection, and lead to unintended evolutionary divergence

Nucleotide diversity maps reveal variation in diversity among wheat genomes and chromosomes

<p>Abstract</p> <p>Background</p> <p>A genome-wide assessment of nucleotide diversity in a polyploid species must minimize the inclusion of homoeologous sequences into diversity estimates and reliably allocate individual haplotypes into their respective genomes. The same requirements complicate the development and deployment of single nucleotide polymorphism (SNP) markers in polyploid species. We report here a strategy that satisfies these requirements and deploy it in the sequencing of genes in cultivated hexaploid wheat (<it>Triticum aestivum</it>, genomes AABBDD) and wild tetraploid wheat (<it>Triticum turgidum </it>ssp. <it>dicoccoides</it>, genomes AABB) from the putative site of wheat domestication in Turkey. Data are used to assess the distribution of diversity among and within wheat genomes and to develop a panel of SNP markers for polyploid wheat.</p> <p>Results</p> <p>Nucleotide diversity was estimated in 2114 wheat genes and was similar between the A and B genomes and reduced in the D genome. Within a genome, diversity was diminished on some chromosomes. Low diversity was always accompanied by an excess of rare alleles. A total of 5,471 SNPs was discovered in 1791 wheat genes. Totals of 1,271, 1,218, and 2,203 SNPs were discovered in 488, 463, and 641 genes of wheat putative diploid ancestors, <it>T. urartu</it>, <it>Aegilops speltoides</it>, and <it>Ae. tauschii</it>, respectively. A public database containing genome-specific primers, SNPs, and other information was constructed. A total of 987 genes with nucleotide diversity estimated in one or more of the wheat genomes was placed on an <it>Ae. tauschii </it>genetic map, and the map was superimposed on wheat deletion-bin maps. The agreement between the maps was assessed.</p> <p>Conclusions</p> <p>In a young polyploid, exemplified by <it>T. aestivum</it>, ancestral species are the primary source of genetic diversity. Low effective recombination due to self-pollination and a genetic mechanism precluding homoeologous chromosome pairing during polyploid meiosis can lead to the loss of diversity from large chromosomal regions. The net effect of these factors in <it>T. aestivum </it>is large variation in diversity among genomes and chromosomes, which impacts the development of SNP markers and their practical utility. Accumulation of new mutations in older polyploid species, such as wild emmer, results in increased diversity and its more uniform distribution across the genome.</p