A 34K SNP genotyping array for Populus trichocarpa: Design,application to the study of natural populations and transferability to other Populus species

Genetic mapping of quantitative traits requires genotypic data for large numbers of markers in many individuals. For such studies, the use of large single nucleotide polymorphism (SNP) genotyping arrays still offers the most cost‐effective solution. Herein we report on the design and performance of a SNP genotyping array for Populus trichocarpa (black cottonwood). This genotyping array was designed with SNPs pre‐ascertained in 34 wild accessions covering most of the species latitudinal range. We adopted a candidate gene approach to the array design that resulted in the selection of 34 131 SNPs, the majority of which are located in, or within 2 kb of, 3543 candidate genes. A subset of the SNPs on the array (539) was selected based on patterns of variation among the SNP discovery accessions. We show that more than 95% of the loci produce high quality genotypes and that the genotyping error rate for these is likely below 2%. We demonstrate that even among small numbers of samples (n = 10) from local populations over 84% of loci are polymorphic. We also tested the applicability of the array to other species in the genus and found that the number of polymorphic loci decreases rapidly with genetic distance, with the largest numbers detected in other species in section Tacamahaca. Finally, we provide evidence for the utility of the array to address evolutionary questions such as intraspecific studies of genetic differentiation, species assignment and the detection of natural hybrids.     

Dark extinction: the problem of unknown historical extinctions

The extinction of species before they are discovered and named (dark extinction, DE) is widely inferred as a significant part of species loss in the ‘pre-taxonomic’ period (approx. 1500–1800 CE) and, to some extent, in the ‘taxonomic period’ (approx. 1800–present) as well. The discovery of oceanic islands and other pristine habitats by European navigators and the consequent introduction of destructive mammals, such as rats and goats, started a process of anthropogenic extinction. Much ecosystem change happened before systematic scientific recording, so has led to DE. Statistical methods are available to robustly estimate DE in the ‘taxonomic period’. For the ‘pre-taxonomic period’, simple extrapolation can be used. The application of these techniques to world birds, for example, suggests that approximately 56 DEs occurred in the ‘taxonomic period’ (1800–present) and approximately 180 in the ‘pre-taxonomic period’ (1500–1800). Targeting collection activities in extinction hotspots, to make sure organisms are represented in collections before their extinction, is one way of reducing the number of extinct species without a physical record (providing that collection efforts do not themselves contribute to species extinction).     

An organ culture system to model early degenerative changes of the intervertebral disc

Introduction  

Back pain, a significant source of morbidity in our society, is related to the degenerative changes of the intervertebral disc. At present, the treatment of disc disease consists of therapies that are aimed at symptomatic relief. This shortcoming stems in large part from our lack of understanding of the biochemical and molecular events that drive the disease process. The goal of this study is to develop a model of early disc degeneration using an organ culture. This approach is based on our previous studies that indicate that organ culture closely models molecular events that occur in vivo in an ex vivo setting.     

Modeling geographic risk of complex congenital heart defects in Eastern Wisconsin

BACKGROUND: Geographic variation may be an indicator of risk factors for birth defects. This study models the geographic distribution of three complex congenital heart defects (CHDs) in eastern Wisconsin, and evaluates effects of demographic census variables linked to geographic location. METHODS: Cases of Hypoplastic Left Heart Syndrome (HLHS), Tetralogy of Fallot (TOF) and d‐Transposition of the Great Arteries (d‐TGAs) born between1995 and 2004 were identified from three medical centers serving eastern Wisconsin. Case diagnoses were assigned by a pediatric cardiologist using echocardiographic records. Births by ZIP code were obtained from the State of Wisconsin. ZIP Code demographic variables were derived from 2000 census data. Numbers of cardiac defects by ZIP code were modeled using cluster analysis and Poisson generalized additive models (GAMs) for spatial coordinates including all and white only cases (excluding trisomies). GAM analyses were repeated adjusting for census variables. RESULTS: Four hundred forty‐eight cases were ascertained. A significant south‐to‐north spatial gradient for HLHS, TOF, and combined CHDs, but not d‐TGAs was identified. This gradient remained significant when census variables were included in the model for the full sample. In the analysis excluding non‐white cases, findings were the same for TOF, combined CHDs, and d‐TGAs. However, the geographic gradient for HLHS was not significant in the adjusted model. CONCLUSIONS: A south‐to‐north gradient was apparent for two of three complex CHDs in eastern Wisconsin. For white cases, demographic variation seems to explain some of this spatial gradient in HLHS. Further studies are needed to confirm demographic and other risk factors underlying this geographic gradient. Birth Defects Research (Part A) 2011. © 2011 Wiley‐Liss, Inc.     

Production of vitamin B-12 in tempeh, a fermented soybean food

Several varieties of soybeans contained generally less than 1 ng of vitamin B-12 per g. It was found that use of a lactic fermentation typical of tropical conditions during the initial soaking of the soybeans did not influence the vitamin B-12 content of the resulting tempeh. Pure tempeh molds obtained from different sources did not produce vitamin B-12. It was found that the major source of vitamin B-12 in commercial tempeh purchased in Toronto, Canada, was a bacterium that accompanies the mold during fermentation. Reinoculation of the pure bacterium onto dehulled, hydrated, and sterilized soybeans resulted in the production of 148 ng of vitamin B-12 per g. The presence of the mold, along with the bacterium, did not inhibit or enhance production of vitamin B-12. Nutritionally significant amounts of vitamin B-12 were also found in the Indonesian fermented food, ontjom.     

Preferential parental investment in daughters over sons

Female-biased parental investment is unusual but not unknown in human societies. Relevant explanatory models include Fisher’s principle, the Trivers-Willard model, local mate and resource competition and enhancement, and economic rational actor models. Possible evidence of female-biased parental investment includes sex ratios, mortality rates, parents’ stated preferences for offspring of one sex, and direct and indirect measurements of actual parental behavior. Possible examples of female-biased parental investment include the Mukogodo of Kenya, the Ifalukese of Micronesia, the Cheyenne of North America, the Herero of southern Africa, the Kanjar of south Asia, the Mundugumor of New Guinea, contemporary North America, and historical Germany, Portugal, and the United States. Lee Cronk is Assistant Professor of Anthropology at Texas A&M University, College Station, Texas. His main research interests are in human behavioral ecology, reproductive strategies, and East African hunter-gatherers and pastoralists.     

Study of the mitotic and meiotic chromosomes of sotol (<i>Dasylirion cedrosanum</i> Trel.)

The genus Dasylirion is a group of plants typically present in the Chihuahuan Desert, perennial, with a dioecious sexual behavior and commonly called sotoles. This genus has been little studied from the biological point of view, and the bases of its reproductive response remain unknown. In this work we studied the chromosome number and meiotic response of Dasylirion cedrosanum in the county of Saltillo, Coahuila, located at the North East of Mexico. For the preparation of mitotic chromosomes, we used a technique based on enzymatic treatment with pectolyase and cellulase, as well as staining with acetocarmin dye. For the study of meiosis, male flower buds were collected, fixed and stained for analysis with the same dye. As a result, the gametic (n = x = 19) and somatic chromosome (2n = 38) numbers of D. cedrosanum are reported for the first time, being consistent with previous findings in other Dasylirion species, which points to a constant ploidy level across the genus. Variation was observed in the morphology and size of the somatic chromosomes, with types ranging from submetacentric to subtelocentric, and sizes oscillating in a range of 4.43 µm, with an average total length of 112.38 µm for the diploid chromosome complement. This shows that the chromosome complement of D. cedrosanom would belong to a 3B classification of Stebins, with a medium variation between chromosome lengths and low chromosome asymmetry. This variation indicates the feasibility of constructing a chromosome ideotype for this species. The meiotic chromosome pairing showed a chromosome behavior consistent with a disomic inheritance characteristic of a diploid species, with prevalence of ring and chain bivalents, typically without pairing abnormalities. Bivalent configurations in all cases were symmetrical.The normal and symmetrical meiotic pairing indicates a balanced production of gametes, and suggests the absence of heteromorphic sex determination.     

Species delimitation and the origin of populations in island representatives of Phylica (Rhamnaceae)

Abstract Relationships between the closely related island species of Phylica (Rhamnaceae) and a mainland species, P. paniculata , were elucidated using amplified fragment length polymorphisms (AFLPs). Parsimony, neighbor joining, and principal coordinate (PCO) analyses indicated that each of the species studied is distinct. AFLPs were also useful in elucidating the genetic relationships and possible infraspecific origins of different island populations in the Atlantic and Indian Oceans. Phylica nitida on Réunion is likely to have been derived from P. nitida on Mauritius. Although the sampling on New Amsterdam is not extensive, the data are also consistent with the hypothesis that P. arborea on New Amsterdam was derived from a single colonization of P. arborea from Gough Island. Similarly, the Gough Island population appears to have been derived from a single colonization event, but it is so distinct from those on Tristan da Cunha, that there may have been two separate dispersals to Gough and Tristan/Nightingale from different lines of the mainland progenitor. There is also evidence of a recolonization from Gough to Tristan da Cunha. Thus, Phylica arborea is capable of repeated long distance dispersal, up to 8000 km, even though the fruits and seeds are not of a type normally associated with this phenomenon.     

Different fates of island brooms: contrasting evolution in Adenocarpus, Genista, and Teline (Genisteae, Fabaceae) in the Canary Islands and Madeira

Analysis of sequence data from the internal transcribed spacers (ITS) and 5.8S region of nuclear ribosomal DNA show that Canarian and Madeiran brooms (Genisteae) of the genera Teline, Adenocarpus, and Genista are related to Mediterranean species and not to species from adjacent parts of Morocco. Each separate colonization of the islands has resulted in contrasting patterns of adaptation and radiation. The genus Teline is polyphyletic, with both groups (the "T. monspessulana group" and the "T. linifolia group") separately nested within Genista. Genista benehoavensis (La Palma) and G. tenera (Madeira) form, with G. tinctoria of Europe, a single clade characterized by vestigially arillate seeds. The Canarian species of Adenocarpus have almost identical sequence to the Mediterranean A. complicatus and are likely to be the result of island speciation after a very recent colonization event. This Canarian/Mediterranean A. complicatus group is sister to the afrotropical montane A. mannii which is probably derived from an earlier colonization from the Mediterranean, possibly via the Red Sea hills. The independent colonization and subsequent radiation of the two Teline groups in the Canary Islands make an interesting comparison: the phylogenies both show geographical structuring, each with a central and western island division of taxa. Within the "T. monspessulana group" there is some evidence that both continental and Madeiran taxa could be derived from the Canary Islands, although it is likely that near contemporaneous speciation occurred via rapid colonization of the mainland and islands. The finding of two groups within Teline also has implications for patterns of hybridization in those parts of the world where Teline species are invasive; in California members of the T. monspessulana group hybridize readily, but no hybrids have been recorded with T. linifolia which has been introduced in the same areas.