Statistical method for testing the neutral mutation hypothesis by DNA polymorphism.

So far in this course we have dealt entirely with the evolution of characters that are controlled by simple Mendelian inheritance at a single locus. There are notes on the course website about gametic disequilibrium and how allele frequencies change at two loci simultaneously, but we didn’t discuss them. In every example we’ve considered we’ve imagined that we could understand something about evolution by examining the evolution of a single gene. That’s the domain of classical population genetics. For the next few weeks we’re going to be exploring a field that’s actually older than classical population genetics, although the approach we’ll be taking to it involves the use of population genetic machinery. If you know a little about the history of evolutionary biology, you may know that after the rediscovery of Mendel’s work in 1900 there was a heated debate between the “biometricians” (e.g., Galton and Pearson) and the “Mendelians” (e.g., de Vries, Correns, Bateson, and Morgan). Biometricians asserted that the really important variation in evolution didn’t follow Mendelian rules. Height, weight, skin color, and similar traits seemed to

Human biochemical genetics

Genetics and analysis of quantitative traits

Gene families are growing rapidly, but standard methods for inferring phylogenies do not scale to alignments with over 10,000 sequences. We present FastTree, a method for constructing large phylogenies and for estimating their reliability. Instead of storing a distance matrix, FastTree stores sequence profiles of internal nodes in the tree. FastTree uses these profiles to implement neighbor-joining and uses heuristics to quickly identify candidate joins. FastTree then uses nearest-neighbor interchanges to reduce the length of the tree. For an alignment with N sequences, L sites, and a different characters, a distance matrix requires O(N^2) space and O(N^2 L) time, but FastTree requires just O( NLa + N sqrt(N) ) memory and O( N sqrt(N) log(N) L a ) time. To estimate the tree's reliability, FastTree uses local bootstrapping, which gives another 100-fold speedup over a distance matrix. For example, FastTree computed a tree and support values for 158,022 distinct 16S ribosomal RNAs in 17 hours and 2.4 gigabytes of memory. Just computing pairwise Jukes-Cantor distances and storing them, without inferring a tree or bootstrapping, would require 17 hours and 50 gigabytes of memory. In simulations, FastTree was slightly more accurate than neighbor joining, BIONJ, or FastME; on genuine alignments, FastTree's topologies had higher likelihoods. FastTree is available at http://microbesonline.org/fasttree.

/pdf/fast-tree-computing-large-minimum-evolution-trees-with-4grq0gwfpy.pdf

Fast Tree: Computing Large Minimum-Evolution Trees with Profiles instead of a Distance Matrix

Rapid improvements in sequencing and array-based platforms are resulting in a flood of diverse genome-wide data, including data from exome and whole-genome sequencing, epigenetic surveys, expression profiling of coding and noncoding RNAs, single nucleotide polymorphism (SNP) and copy number profiling, and functional assays. Analysis of these large, diverse data sets holds the promise of a more comprehensive understanding of the genome and its relation to human disease. Experienced and knowledgeable human review is an essential component of this process, complementing computational approaches. This calls for efficient and intuitive visualization tools able to scale to very large data sets and to flexibly integrate multiple data types, including clinical data. However, the sheer volume and scope of data pose a significant challenge to the development of such tools.

Integrative Genomics Viewer

Abstract The Malagasy rosewood species Dalbergia maritima has a long history of unsustainable exploitation for its beautiful, burgundy-colored heartwood. As currently circumscribed, D. maritima has a wide geographic distribution in eastern Madagascar and exhibits significant morphological, ecological, and genetic variation, suggesting it may comprise more than a single entity. Multivariate analyses of leaf, flower, and inflorescence characters as well as eco-geographic features reveal several morphologically well delimited entities with distinct habitat preferences and/or geographic ranges, which are consistent with results from recent phylogenomic and population genomic studies of Malagasy Dalbergia. Based on these findings, we describe and illustrate two new species from southeastern Madagascar comprising material previously assigned to D. maritima, viz. D. pseudomaritima, characterized by paniculate inflorescences and small, broadly elliptic to orbicular, glabrous leaflets, and D. razakamalalae, distinguished by racemose inflorescences with large flowers, and narrowly ovate to narrowly elliptic, glabrous leaflets. Dalbergia maritima is consequently re-circumscribed to include only populations from east-central Madagascar, within which we recognize two subspecies, D. maritima subsp. maritima, with glabrous leaves, inflorescence axes, and gynoecia, occurring in littoral forest habitats, and D. maritima subsp. pubescens, with indument on these structures, and growing in evergreen humid forest farther inland. Photos are provided for each taxon, along with line drawings for the two new species. Provisional IUCN Red List assessments indicate that all three species are Endangered, D. maritima and D. razakamalalae mainly because of selective logging for trade in their high-quality heartwood, and D. pseudomaritima primarily because of habitat degradation due to land clearing and fire for subsistence agriculture, which has important implications for their conservation and sustainable management.

Taxonomic Studies on Malagasy Dalbergia (Fabaceae). III. Two New Species from Southeastern Madagascar and an Emended Description of the Rosewood Species Dalbergia maritima

Frequency and genomic distribution of genes with sex-biased expression in the dioecious plant Silene latifolia

Floral form is a prime example of evolutionary or adaptive compromise. Many parts of a flower can be involved in more than one function. Showy petals, for example, might attract pollinators during the day, but might protect other floral organs from rain or herbivores at night. If selection pressures on organs with multiple functions are in conflict, floral form will evolve as an adaptive compromise to reflect the net effect of different selection pressures. The adaptive analysis of floral form is an active area of evolutionary research and much progress has been made in understanding and quantifying different forces that affect the evolution of floral form; one might think then that the forces involved in the evolution of floral form have already been identified. However, in a new paper, Vaknin and co-workers [1xAre flowers morphologically adapted to take advantage of electrostatic forces in pollination?. Vaknin, Y. et al. New Phytol. 2001; 152: 301–306Crossref | Scopus (13)See all References][1] provide the first empirical evidence for a new force that might play a role in the evolution of floral form. They show that the shape and size of a flower influences its electrostatic properties and, therefore affects where electrostatically charged pollen is deposited.Using metal replicas of almond Amygdalus communis flowers experimentally dusted with either electrostatically charged or uncharged pollen, Vaknin et al. found that pollen deposition was higher when pollen was electrostatically charged and, unlike uncharged pollen, which was evenly distributed over the entire flower, charged pollen was deposited preferentially on corolla extremities and on the stigma. This deposition was influenced by the size and form of the experimental flowers. More pollen was deposited on the stigma when stigma exertion above the petal extremities was increased. However, in flat flowers with constant corolla diameter, increasing stigma length led to higher pollen deposition on the corolla, rather than on the stigma.These results suggest that electrostatic forces might play a role in the evolution of floral form, but leave ample opportunity for the study of conflicting selection pressures on floral form. Stigmas that are more exerted might increase electrostatic pollen deposition, but might reduce the fit of flowers with pollinators. Also, selection for wider, more-open flowers generated by electrostatic enhancement of pollination could be in conflict with selection generated by other flower visitors, such as nectar thieves.

A new force in the evolution of floral form

Abstract Quaternary climate fluctuations drove many species to shift their geographic ranges, in turn shaping their genetic structures. Recently, it has been argued that adaptation may have accompanied species range shifts via the “sieving” of genotypes during colonisation and establishment. However, this has not been directly demonstrated, and knowledge remains limited on how different evolutionary forces, which are typically investigated separately, interacted to jointly mediate species responses to past climatic change. Here, through whole-genome re-sequencing of over 1200 individuals of the carnation Dianthus sylvestris coupled with integrated population genomic and gene-environment models, we reconstruct the past neutral and adaptive landscape of this species as it was shaped by the Quaternary glacial cycles. We show that adaptive responses emerged concomitantly with the post-glacial range shifts and expansions of this species in the last 20 thousand years. This was due to the heterogenous sieving of adaptive alleles across space and time, as populations expanded out of restrictive glacial refugia into the broader and more heterogeneous range of habitats available in the present-day inter-glacial. Our findings reveal a tightly-linked interplay of migration and adaptation under past climate-induced range shifts, which we show is key to understanding the spatial patterns of adaptive variation we see in species today. 

/pdf/climate-induced-range-shifts-drive-adaptive-response-via-c0zvr4uk.pdf

Climate-induced range shifts drive adaptive response via spatio-temporal sieving of alleles

When sex chromosomes evolve, Y genes become less expressed than their X counterpart. This degeneration is compensated through various mechanisms in different animal species, that reestablish ancestral expression levels in males or balance males and females. This phenomenon, called dosage compensation, has been observed for some genes in the plant Silene latifolia. However, the mechanism involved remains unknown. Using an outgroup without sex chromosomes as a reference, we show that the maternal X chromosome is hyperexpressed in both sexes in S. latifolia. This compensates for the lower Y expression in males. However, the paternal X chromosome in females maintained its ancestral expression levels, causing global hyperexpression of sex chromosomes in females, which is likely to be suboptimal. Because S. latifolia sex chromosomes have evolved fairly recently, our findings provide insights into the first steps of dosage compensation evolution, in addition to revealing a link between dosage compensation and imprinting.

/pdf/maternal-x-chromosome-upregulation-in-both-sexes-initiates-35s247nujt.pdf

Alex Widmer

Papers

Taxonomic Studies on Malagasy Dalbergia (Fabaceae). III. Two New Species from Southeastern Madagascar and an Emended Description of the Rosewood Species Dalbergia maritima

Frequency and genomic distribution of genes with sex-biased expression in the dioecious plant Silene latifolia

A new force in the evolution of floral form

Climate-induced range shifts drive adaptive response via spatio-temporal sieving of alleles

Maternal X chromosome upregulation in both sexes initiates dosage compensation evolution