Catasetum × sheyllae (Orchidaceae: Catasetinae), a new natural hybrid from Brazilian Amazon

Natural hybridization has often been recorded within certain genera of orchids, one of them is Catasetum. During a field study in a forest de igapó in Brazilian Amazon, a new natural hybrid was found, it is here described as Catasetum × sheyllae. Its morphological features, mainly the structures of the lip, are intermediate between those of its putative parent species, C. boyi and C. garnettianum, both observed in sympatry.

Diversity of chromosomal composition in top onion (Allium × proliferum (Moench) Schrad. ex Willd.) accessions from the VIR in vitro collection

Background. Top onion, Allium × proliferum (Moench) Schrad. ex Willd., 1809 (2n=2x=16), is a species that is characterized by vegetative propagation by air or underground bulbs only. Accessions of this species have been shown to be hybrids of Allium cepa and Allium fistulosum (Fiskesjo, 1975; Vosa, 1976; Schubert et al., 1983; Puizina and Papes, 1999). Accessions of Allium × proliferum were obtained from various sources and conserved in the in vitro collection of VIR. However, their pedigree was unknown, therefore there was a need to determine the ploidy level and genomic composition of these accessions.Materials and Methods. Thirteen Allium × proliferum accessions from the VIR in vitro collection were studied. To characterize the ploidy level and genomic composition of the accessions, the research employed FISH with chromosome-specific markers (5S and 18S/25S rDNA) and GISH with differentially labeled DNA of the putative parent species, i.e., A. cepa and A. fistulosum.Results. According to GISH, all the studied accessions were hybrids of A. cepa and A. fistulosum. Most (10 out of 13) accessions were determined as diploid hybrids with eight A. cepa and eight A. fistulosum chromosomes. The accession К 3206 turned out to be a diploid 16-chromosome hybrid with eight A. cepa, seven A. fistulosum chromosomes and one rearranged chromosome. Accessions К 3205 and К 3202 were found to be polyploids. The A. × proliferum accession К 3202 contained seven A. cepa and 16 A. fistulosum chromosomes. The accession К 3205 is characterized by the presence of 16 chromosomes hybridizing with A. cepa DNA and 13 chromosomes hybridizing with A. fistulosum DNA. Only one chromosome of A. fistulosum in this accession was revealed to have a 5s rDNA locus.Conclusions. The above shows that the collection contains top onion accessions with karyotypic differences.

Exclusion and Genomic Relatedness Methods for Assignment of Parentage Using Genotyping-by-Sequencing Data

Genotypes are often used to assign parentage in agricultural and ecological settings. Sequencing can be used to obtain genotypes but does not provide unambiguous genotype calls, especially when sequencing depth is low in order to reduce costs. In that case, standard parentage analysis methods no longer apply. A strategy for using low-depth sequencing data for parentage assignment is developed here. It entails the use of relatedness estimates along with a metric termed excess mismatch rate which, for parent-offspring pairs or trios, is the difference between the observed mismatch rate and the rate expected under a model of inheritance and allele reads without error. When more than one putative parent has similar statistics, bootstrapping can provide a measure of the relatedness similarity. Putative parent-offspring trios can be further checked for consistency by comparing the offspring’s estimated inbreeding to half the parent relatedness. Suitable thresholds are required for each metric. These methods were applied to a deer breeding operation consisting of two herds of different breeds. Relatedness estimates were more in line with expectation when the herds were analyzed separately than when combined, although this did not alter which parents were the best matches with each offspring. Parentage results were largely consistent with those based on a microsatellite parentage panel with three discordant parent assignments out of 1561. Two models are investigated to allow the parentage metrics to be calculated with non-random selection of alleles. The tools and strategies given here allow parentage to be assigned from low-depth sequencing data.

Exclusion and genomic relatedness methods for assignment of parentage using genotyping-by-sequencing data

SummaryGenotypes are often used to assign parentage in agricultural and ecological settings. Sequencing can be used to obtain genotypes but does not provide unambiguous genotype calls, especially when sequencing depth is low in order to reduce costs. In that case, standard parentage analysis methods no longer apply. A strategy for using low-depth sequencing data for parentage assignment is developed here. It entails the use of relatedness estimates along with a metric termed excess mismatch rate which, for parent-offspring pairs or trios, is the difference between the observed mismatch rate and the rate expected under a model of inheritance and allele reads without error. When more than one putative parent has similar statistics, bootstrapping can provide a measure of the relatedness similarity. Putative parent-offspring trios can be further checked for consistency by comparing the offspring’s estimated inbreeding to half the parent relatedness. Suitable thresholds are required for each metric. These methods were applied to a deer breeding operation consisting of two herds of different breeds. Relatedness estimates were more in line with expectation when the herds were analysed separately than when combined, although this did not alter which parents were the best matches with each offspring. Parentage results were largely consistent with those based on a microsatellite parentage panel with three discordant parent assignments out of 1561. Two models are investigated to allow the parentage metrics to be calculated with non-random selection of alleles. The tools and strategies given here allow parentage to be assigned from low-depth sequencing data.

Queer Earth Mothering: Thinking Through the Biological Paradigm of Motherhood

I consider Christine Overall’s (2012) proposal that counteracting the ecological threats born from overconsumption and overpopulation morally obligates (most) Westerners to limit their procreative output to one child per person. I scrutinize what Overall finds valuable about the genetic link in the parent-child relationship through the complementary lenses of Shelley M. Park’s (2013) project of “queering motherhood” and the ecofeminist concept of “earth mothering.” What comes of this theoretical mix is a procreative outlook I define as queer earth mothering (QEM): an interrogative attitude for identifying the ways in which anti-ecological and heteronormative ideologies seep into maternal praxis. I argue that QEM has potential to relocate the value(s) of the putative parent-child relationship, change attitudes toward adoptive motherhood for the better, and shed light on the reality that procreative decisions in affluent contexts can and will rebound with devastating environmental consequences on both present and future populations if left unabated. My hope is that with QEM as our guide for thinking through the biological paradigm of motherhood we will be in a much better position to appreciate why affluent prospective parents should (generally speaking) favour adoption over biological reproduction.

New insights on the genetic basis of Portuguese grapevine and on grapevine domestication

As the ancestor of cultivated grape, Vitis vinifera subsp. sylvestris represents a unique, invaluable genetic resource for the improvement of cultivated grapevines. Recently, five populations of wild grapevines were identified in Portugal. Sixty vines were characterized with 11 nuclear SSR markers and further compared with 70 genotypes of Portuguese Vitis vinifera subsp. sativa. The obtained data demonstrate moderate genetic differentiation between wild grapevine populations and moderate to high genetic differentiation between wild and cultivated grapevines. However, the identification of high degrees of similarity between wild and cultivated grapes (up to 87%) and a putative parent–progeny relationship between wild and cultivated grapes with 17 additional SSR markers is indicative of gene flow between local wild grapevine populations and Portuguese domesticated vines. Also, the ancestry of some Azorean cultivars was ascertained. The obtained data further support the hypothesis of several domestication centres, with Portugal, Spain, and Italy playing a particular role after the last glaciation, giving rise to many of the Western European cultivars.

Extended Analysis of Hybridization in Sunfishes (Centrarchidae) Using an Adjusted Hybrid Index Method

Sunfish collected from Pinehurst Lake, Ontario, were sorted into three groups: bluegill (Lepomis macrochirus), pumpkinseed (L. gibbosus), and a group possessing some of the color patterns of each of the other two. Eleven morphological characters of each fish were analyzed by a hybrid index method, and by an adjusted index which allowed: a) calculation of sampling variances of individual and mean index estimates and, b) testing of hypotheses about the position of suspected hybrids relative to the parental populations. This method, applied to single characters and to combinations of characters, showed that the anomalous group resembled bluegills in four characters, pumpkinseeds in one, and were exactly intermediate in the others. The simplest explanation of these results is that the intermediate group was a population of bluegill × pumpkinseed hybrids.This use of the hybrid index permits increased precision over earlier methods in comparing suspected hybrid individuals with their putative parent populations.