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Essentials of genetics
This text is intended for brief introductory genetics courses for biology majors and premeds, or introductory genetics courses geared towards students in applied majors, such as agriculture, forestry, and nutrition. It includes exercises for selected chapters and in-chapter summaries that follow concept introductions.
Book
Evolution in Four Dimensions
A pioneering proposal for a pluralistic extension of evolutionary theory, now updated to reflect the most recent research.
This new edition of the widely read Evolution in Four Dimensions has been revised to reflect the spate of new discoveries in biology since the book was first published in 2005, offering corrections, an updated bibliography, and a substantial new chapter. Eva Jablonka and Marion Lamb's pioneering argument proposes that there is more to heredity than genes. They describe four “dimensions” in heredity—four inheritance systems that play a role in evolution: genetic, epigenetic (or non-DNA cellular transmission of traits), behavioral, and symbolic (transmission through language and other forms of symbolic communication). These systems, they argue, can all provide variations on which natural selection can act.
Jablonka and Lamb present a richer, more complex view of evolution than that offered by the gene-based Modern Synthesis, arguing that induced and acquired changes also play a role. Their lucid and accessible text is accompanied by artist-physician Anna Zeligowski's lively drawings, which humorously and effectively illustrate the authors' points. Each chapter ends with a dialogue in which the authors refine their arguments against the vigorous skepticism of the fictional “I.M.” (for Ipcha Mistabra—Aramaic for “the opposite conjecture”). The extensive new chapter, presented engagingly as a dialogue with I.M., updates the information on each of the four dimensions—with special attention to the epigenetic, where there has been an explosion of new research.
Praise for the first edition
“With courage and verve, and in a style accessible to general readers, Jablonka and Lamb lay out some of the exciting new pathways of Darwinian evolution that have been uncovered by contemporary research.” —Evelyn Fox Keller, MIT, author of Making Sense of Life: Explaining Biological Development with Models, Metaphors, and Machines
“In their beautifully written and impressively argued new book, Jablonka and Lamb show that the evidence from more than fifty years of molecular, behavioral and linguistic studies forces us to reevaluate our inherited understanding of evolution.” —Oren Harman, The New Republic
“It is not only an enjoyable read, replete with ideas and facts of interest but it does the most valuable thing a book can do—it makes you think and reexamine your premises and long-held conclusions.” —Adam Wilkins, BioEssays
eBook
grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla
Heard about the grapevine?
The fourth genome sequence of a flowering plant, the second of a woody plant species and the first for a fruit crop. These important boxes are ticked by the genome sequence published in this issue. The new sequence is particularly revealing about the role of gene duplication in the evolution of the flowering plants. But the reason why non-geneticists will turn to it is more to do with its commercial application: the crop is the grapevine (
Vitis vinifera
) and the variety is Pinot Noir.
A French and Italian consortium has produced sequence and analysis of
Vitis vinifera
PN40024, a grapevine originally derived from Pinot Noir. As you might expect, the grapevine has twice as many terpene synthases as other sequenced plants; these enzymes contribute to resins, essential oils and aromas.
The analysis of the first plant genomes provided unexpected evidence for genome duplication events in species that had previously been considered as true diploids on the basis of their genetics
1
,
2
,
3
. These polyploidization events may have had important consequences in plant evolution, in particular for species radiation and adaptation and for the modulation of functional capacities
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,
5
,
6
,
7
,
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,
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,
10
. Here we report a high-quality draft of the genome sequence of grapevine (
Vitis vinifera
) obtained from a highly homozygous genotype. The draft sequence of the grapevine genome is the fourth one produced so far for flowering plants, the second for a woody species and the first for a fruit crop (cultivated for both fruit and beverage). Grapevine was selected because of its important place in the cultural heritage of humanity beginning during the Neolithic period
11
. Several large expansions of gene families with roles in aromatic features are observed. The grapevine genome has not undergone recent genome duplication, thus enabling the discovery of ancestral traits and features of the genetic organization of flowering plants. This analysis reveals the contribution of three ancestral genomes to the grapevine haploid content. This ancestral arrangement is common to many dicotyledonous plants but is absent from the genome of rice, which is a monocotyledon. Furthermore, we explain the chronology of previously described whole-genome duplication events in the evolution of flowering plants.
Journal Article
Inside the human genome : a case for non-intelligent design
How do you explain flaw in a world engineered by God? Avise extends this age-old question to the most basic aspect of humanity's physical evidence-- our genes-- and provides the evolutionary answers.
Book
Microsatellite markers: an overview of the recent progress in plants
In recent years, molecular markers have been utilized for a variety of applications including examination of genetic relationships between individuals, mapping of useful genes, construction of linkage maps, marker assisted selections and backcrosses, population genetics and phylogenetic studies. Among the available molecular markers, microsatellites or simple sequence repeats (SSRs) which are tandem repeats of one to six nucleotide long DNA motifs, have gained considerable importance in plant genetics and breeding owing to many desirable genetic attributes including hypervariability, multiallelic nature, codominant inheritance, reproducibility, relative abundance, extensive genome coverage including organellar genomes, chromosome specific location and amenability to automation and high throughput genotyping. High degree of allelic variation revealed by microsatellite markers results from variation in number of repeat-motifs at a locus caused by replication slippage and/or unequal crossing-over during meiosis. In spite of limited understanding of the functions of the SSR motifs within the plant genes, SSRs are being widely utilized in plant genome analysis. Microsatellites can be developed directly from genomic DNA libraries or from libraries enriched for specific microsatellites. Alternatively, microsatellites can also be found by searching public databases such as GenBank and EMBL or through cross-species transferability. At present, EST databases are an important source of candidate genes, as these can generate markers directly associated with a trait of interest and may be transferable in close relative genera. A large number of SSR based techniques have been developed and a quantum of literature has accumulated regarding the applicability of SSRs in plant genetics and genomics. In this review we discuss the recent developments (last 4-5 years) made in plant genetics using SSR markers.
Journal Article
The long-range interaction landscape of gene promoters
Chromosome conformation capture carbon copy (5C) is used to look at the relationships between functional elements and distal target genes in 1% of the human genome in three dimensions; the study describes numerous long-range interactions between promoters and distal sites that include elements resembling enhancers, promoters and CTCF-bound sites, their genomic distribution and complex interactions.
The vast non-coding portion of the human genome is full of functional elements and disease-causing regulatory variants. The principles defining the relationships between these elements and distal target genes remain unknown. Promoters and distal elements can engage in looping interactions that have been implicated in gene regulation
1
. Here we have applied chromosome conformation capture carbon copy (5C
2
) to interrogate comprehensively interactions between transcription start sites (TSSs) and distal elements in 1% of the human genome representing the ENCODE pilot project regions
3
. 5C maps were generated for GM12878, K562 and HeLa-S3 cells and results were integrated with data from the ENCODE consortium
4
. In each cell line we discovered >1,000 long-range interactions between promoters and distal sites that include elements resembling enhancers, promoters and CTCF-bound sites. We observed significant correlations between gene expression, promoter–enhancer interactions and the presence of enhancer RNAs. Long-range interactions show marked asymmetry with a bias for interactions with elements located ∼120 kilobases upstream of the TSS. Long-range interactions are often not blocked by sites bound by CTCF and cohesin, indicating that many of these sites do not demarcate physically insulated gene domains. Furthermore, only ∼7% of looping interactions are with the nearest gene, indicating that genomic proximity is not a simple predictor for long-range interactions. Finally, promoters and distal elements are engaged in multiple long-range interactions to form complex networks. Our results start to place genes and regulatory elements in three-dimensional context, revealing their functional relationships.
Journal Article
A Killer-Protector System Regulates Both Hybrid Sterility and Segregation Distortion in Rice
Hybrid sterility is a major form of postzygotic reproductive isolation that restricts gene flow between populations. Cultivated rice (Oryza sativa L.) consists of two subspecies, indica and japonica; inter-subspecific hybrids are usually sterile. We show that a killer-protector system at the S5 locus encoded by three tightly linked genes [Open Reading Frame 3 (ORF3) to ORF5] regulates fertility in indica-japonica hybrids. During female sporogenesis, the action of ORF5+ (killer) and ORF4+ (partner) causes endoplasmic reticulum (ER) stress. ORF3+ (protector) prevents ER stress and produces normal gametes, but ORF3− cannot prevent ER stress, resulting in premature programmed cell death and leads to embryo-sac abortion. Preferential transmission of ORF3+ gametes results in segregation distortion in the progeny. These results add to our understanding of differences between indica and japonica rice and may aid in rice genetic improvement.
Journal Article