Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics

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

The lion's share of bacteria in various environments cannot be cloned in the laboratory and thus cannot be sequenced using existing technologies. A major goal of single-cell genomics is to complement gene-centric metagenomic data with whole-genome assemblies of uncultivated organisms. Assembly of single-cell data is challenging because of highly non-uniform read coverage as well as elevated levels of sequencing errors and chimeric reads. We describe SPAdes, a new assembler for both single-cell and standard (multicell) assembly, and demonstrate that it improves on the recently released E+V-SC assembler (specialized for single-cell data) and on popular assemblers Velvet and SoapDeNovo (for multicell data). SPAdes generates single-cell assemblies, providing information about genomes of uncultivatable bacteria that vastly exceeds what may be obtained via traditional metagenomics studies. SPAdes is available online ( http://bioinf.spbau.ru/spades ). It is distributed as open source software.

SPAdes, a new genome assembly algorithm and its applications to single-cell sequencing ( 7th Annual SFAF Meeting, 2012)

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

http://amborella.net/2010PlantSystematics/DATA/3-24-APG%202003%20Bot%20J%20Linn%20Soc%20APGII.pdf

An update of the Angiosperm Phylogeny Group classification for the orders and families of flowering plants: APG II

Plant biologists have debated the evolutionary origin of the apple tribe (Maleae; Rosaceae) for over a century. The “wide-hybridization hypothesis” posits that the pome-bearing members of Maleae (base chromosome number x = 17) resulted from a hybridization and/or allopolyploid event between progenitors of other tribes in the subfamily Amygdaloideae with x = 8 and x = 9, respectively. An alternative “spiraeoid hypothesis” proposed that the x = 17 of Maleae arose via the genome doubling of x = 9 ancestors to x = 18, and subsequent aneuploidy resulting in x = 17. We use publicly available genomic data—448 nuclear genes and complete plastomes—from 27 species representing all major tribes within the Amygdaloideae to investigate evolutionary relationships within the subfamily containing the apple tribe. Specifically, we use network analyses and multi-labeled trees to test the competing wide-hybridization and spiraeoid hypotheses. Hybridization occurred between an ancestor of the tribe Spiraeeae (x = 9) and an ancestor of the clade Sorbarieae (x = 9) + Exochordeae (x = 8) + Kerrieae (x = 9), giving rise to the clade Gillenieae (x = 9) + Maleae (x = 17). The ancestor of the Maleae + Gillenieae arose via hybridization between distantly related tribes in the Amygdaloideae (i.e., supporting the wide hybridization hypothesis). However, some evidence supports an aspect of the spiraeoid hypothesis—the ancestors involved in the hybridization event were likely both x = 9, so genome doubling was followed by aneuploidy to result in x = 17 observed in Maleae. By synthesizing existing genomic data with novel analyses, we resolve the nearly century-old mystery regarding the origin of the apple tribe. Our results also indicate that nuclear gene tree-species tree conflict and/or cytonuclear conflict are pervasive at several other nodes in subfamily Amygdaloideae of Rosaceae.

https://www.frontiersin.org/articles/10.3389/fpls.2021.820997/pdf

Synthesis of Nuclear and Chloroplast Data Combined With Network Analyses Supports the Polyploid Origin of the Apple Tribe and the Hybrid Origin of the Maleae—Gillenieae Clade

Isoetes viridimontana is described and illustrated. Plants of this species are currently known only from Haystack Pond, a small, acidic, oligotrophic lake in south central Vermont. Isoetes viridimontana is distinguished from other Isoetes species in northeastern North America by its size (less than 5 cm high) and granulate to rugulate megaspore texture.

https://bioone.org/journals/American-Fern-Journal/volume-104/issue-1/0002-8444-104.1.7/iIso%c3%abtes-viridimontana-i--A-Previously-Unrecognized-Quillwort-from-Vermont/10.1640/0002-8444-104.1.7.pdf

Isoëtes viridimontana: A Previously Unrecognized Quillwort from Vermont, USA

Molecular phylogenetic analysis of tribe Loteae (Fabaceae); Implications for classification and biogeography

Homoploid hybrids, allopolyploids, and high ploidy levels characterize the evolutionary history of a western North American quillwort (Isoëtes) complex.

Conflicting selection is an important evolutionary mechanism because it impedes directional evolution and helps to maintain phenotypic variation. It can arise when mutualistic and antagonistic selective agents exert opposing selection on the same trait and when distinct phenotypic optima are favored by different fitness components. In this study, we test for conflicting selection through different sexual functions of the hermaphroditic plant, Silene stellata during its early and late flowering season. We find selection is consistently stronger during the early flowering season, which aligns with the activity peak of the pollinating seed predator Hadena ectypa. Importantly, we observe sex-specific selection on petal dimensions to have opposite signs. We propose that the observed sexually conflicting selection on petal design results from the negative selection through female function for the avoidance of oviposition and the subsequent fruit predation by H. ectypa larvae and the positive selection through male function for pollen export by H. ectypa adults. The Silene-Hadena interaction has previously been considered to be largely parasitic. Our findings suggest a trade-off mechanism that could thwart the evolution of an "escape route" from the nocturnal pollination syndrome by Silene spp. and contribute to the long-term maintenance of the Silene-Hadena system.

Elizabeth A. Zimmer

Papers

Synthesis of Nuclear and Chloroplast Data Combined With Network Analyses Supports the Polyploid Origin of the Apple Tribe and the Hybrid Origin of the Maleae—Gillenieae Clade

Isoëtes viridimontana: A Previously Unrecognized Quillwort from Vermont, USA

Molecular phylogenetic analysis of tribe Loteae (Fabaceae); Implications for classification and biogeography

Homoploid hybrids, allopolyploids, and high ploidy levels characterize the evolutionary history of a western North American quillwort (Isoëtes) complex.

Variable and sexually conflicting selection on Silene stellata floral traits by a putative moth pollinator selective agent.