[신간의 별자리x] 우리/미술, 그리고 ‘슬픔의 박물관’

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

Massively parallel short-read sequencing technologies, coupled with powerful software platforms, are enabling investigators to analyse tens of thousands of genetic markers. This wealth of data is rapidly expanding and allowing biological questions to be addressed with unprecedented scope and precision. The sizes of the data sets are now posing significant data processing and analysis challenges. Here we describe an extension of the Stacks software package to efficiently use genotype-by-sequencing data for studies of populations of organisms. Stacks now produces core population genomic summary statistics and SNP-by-SNP statistical tests. These statistics can be analysed across a reference genome using a smoothed sliding window. Stacks also now provides several output formats for several commonly used downstream analysis packages. The expanded population genomics functions in Stacks will make it a useful tool to harness the newest generation of massively parallel genotyping data for ecological and evolutionary genetics.

/pdf/stacks-an-analysis-tool-set-for-population-genomics-3dmvyh33iq.pdf

Stacks: an analysis tool set for population genomics

BlastKOALA and GhostKOALA: KEGG Tools for Functional Characterization of Genome and Metagenome Sequences.

Population mixture is an important process in biology. We present a suite of methods for learning about population mixtures, implemented in a software package called ADMIXTOOLS, that support formal tests for whether mixture occurred and make it possible to infer proportions and dates of mixture. We also describe the development of a new single nucleotide polymorphism (SNP) array consisting of 629,433 sites with clearly documented ascertainment that was specifically designed for population genetic analyses and that we genotyped in 934 individuals from 53 diverse populations. To illustrate the methods, we give a number of examples that provide new insights about the history of human admixture. The most striking finding is a clear signal of admixture into northern Europe, with one ancestral population related to present-day Basques and Sardinians and the other related to present-day populations of northeast Asia and the Americas. This likely reflects a history of admixture between Neolithic migrants and the indigenous Mesolithic population of Europe, consistent with recent analyses of ancient bones from Sweden and the sequencing of the genome of the Tyrolean "Iceman."

https://www.genetics.org/content/genetics/192/3/1065.full.pdf

Ancient Admixture in Human History

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http://biorxiv.org/content/early/2015/03/05/016006.full.pdf

cell cycle regulators

We present the construction and performance of an ultra-low temperature scanning tunneling microscope (STM), working in ultra-high vacuum conditions (UHV) and in high magnetic fields up to 9 T. The cryogenic environment of the STM is generated by a single shot $^3$He magnet cryostat in combination with a $^4$He dewar system. At base temperature (300~mK), the cryostat has an operation time of approximately 80 hours. The special design of the microscope allows the transfer of the STM head from the cryostat to a UHV-chamber system, where samples and STM-tips can be easily exchanged. The UHV chambers are equipped with specific surface science treatment tools for the functionalization of samples and tips, including high-temperature treatments and thin film deposition. This, particularly, enables spin-resolved tunneling measurements. We present test measurements using well known samples and tips based on superconductor and metallic materials such as LiFeAs, Nb, Fe and W, respectively. The measurements demonstrate the outstanding performance of the STM with high spatial and energy resolution as well as the spin-resolved capability.

An ultra-high vacuum scanning tunneling microscope operating at sub-Kelvin temperatures and high magnetic fields for spin-resolved measurements

Hybrid zones, where distinct populations meet and interbreed, give insight into how differences between populations are maintained despite gene flow. Studying clines in genetic loci and adaptive traits across hybrid zones is a powerful method for understanding how selection drives differentiation within a single species, but can also be used to compare parallel divergence in different species responding to a common selective pressure. Here, we study parallel divergence of wing colouration in the butterflies Heliconius erato and H. melpomene, which are distantly related Mullerian mimics that show parallel geographic variation in both discrete variation in pigmentation, and quantitative variation in structural colour. Using geographic cline analysis, we show that clines in these traits are positioned in the roughly the same geographic region for both species, which is consistent with direct selection for mimicry. However, the width of the clines varies markedly between species. This difference is explained in part by variation in the strength of selection acting on colour traits within each species, but may also be influenced by differences in the dispersal rate and total strength of selection against hybrids between the species. Genotyping-by-sequencing also revealed weaker population structure in H. melpomene, suggesting the hybrid zones may have evolved differently in each species; which may also contribute to the patterns of phenotypic divergence in this system Overall, we conclude that multiple factors are needed to explain patterns of clinal variation within and between these species, although mimicry has probably played a central role.

https://www.biorxiv.org/content/biorxiv/early/2020/03/27/842708.full.pdf

Mullerian mimicry of a quantitative trait despite contrasting levels of genomic divergence and selection

Sex chromosomes are evolutionarily labile in many animals, and fusion with an autosome is one of the mechanisms by which they can evolve. Sex chromosome-autosome (SA) fusions can reduce sexual conflict and promote adaptation and reproductive isolation among species. Recently, advances in genomics have fuelled the discovery of SA fusions in multiple vertebrates and in some invertebrates such as Lepidoptera. Here, we discovered multiple SA fusions in the sara/sapho clade of the classical adaptive radiation of Heliconius butterflies. While the vast majority of Heliconius species have 21 chromosomes, species of the particularly rapidly diversifying sapho clade have up to 60 chromosomes. We found a sex chromosome fusion with chromosome 4 at the base of the sapho clade and two additional sex chromosome fusions, each shared by two species. These sequential fusions between autosomes and sex chromosomes make the Heliconius sapho clade an ideal system to study the role of neo-sex chromosomes in adaptive radiations and the degeneration of sex chromosomes over time. Our study adds to a small but growing number of examples in butterflies with sex chromosome fusions that will help to unravel the importance of such rearrangements in the evolution of Lepidoptera and eukaryotes in general. Author Summary Chromosome number and structure are fundamental characteristics of a species. However, chromosomal rearrangements can occur spontaneously within a species, which can have significant consequences for recombination, segregation, speciation, and adaptation. Despite the importance of chromosomal rearrangements in evolution, we still have limited knowledge of the drivers and consequences of chromosomal fusions and fissions in natural populations, especially in adaptive radiations such as Heliconius butterflies. For the first time, we document chromosomal fusions between sex chromosomes and autosomes in Heliconius, particularly in species from the sara/sapho clade. Our research provides evidence for sex-autosome fusions involving autosomes 4, 9, and 14. All of these fusions seem to be associated with speciation events in this clade, with the sex-autosome 4 fusion being the oldest one. Although we do not yet understand the role or evolutionary consequences of these fusions, our study shows that chromosomal structure can evolve rapidly within a clade and generate chromosomal diversity. Overall, our findings contribute to a better understanding of chromosome evolution in highly diverse species.

Camilo Salazar

Papers

cell cycle regulators

An ultra-high vacuum scanning tunneling microscope operating at sub-Kelvin temperatures and high magnetic fields for spin-resolved measurements

Mullerian mimicry of a quantitative trait despite contrasting levels of genomic divergence and selection

Three sequential sex chromosome – autosome fusions in Heliconius butterflies

Geography shapes the microbial community in Heliconius butterflies.