BOL: Related items

Katherine Belov Lab

Sun, 21 Feb 2021 22:59:35 -0600

Evolution of the adaptive immune system Marsupial and monotreme immune genes MHC Diversity and Conservation Marsupial and monotreme genomics Comparative Genomics Genetics of Tasmanian Devil facial tumour disease

More at https://www.sydney.edu.au/science/about/our-people/academic-staff/kathy-belov.html

Vicoso group

Wed, 02 Feb 2022 02:51:27 -0600

The Vicoso group investigates how sex chromosomes evolve over time, and what biological forces are driving their patterns of differentiation.

The Vicoso group is interested in understanding several aspects of the biology of sex chromosomes, and the evolutionary processes that shape their peculiar features. By combining the use of next-generation sequencing technologies with studies in several model and non-model organisms, they can address a variety of standing questions, such as: Why do some Y chromosomes degenerate while others remain homomorphic, and how does this relate to the extent of sexual dimorphism of the species? What forces drive some species to acquire global dosage compensation of the X, while others only compensate specific genes? What are the frequency and molecular dynamics of sex-chromosome turnover?

More at https://ist.ac.at/en/research/vicoso-group/
http://pub.ist.ac.at/~bvicoso/

Online resources on must-read papers in evolutionary biology

BioStar — Fri, 26 Jul 2024 01:39:14 -0500

Online resources on must-read papers in evolutionary biology, for a literature club.

Below is a summary of all answers that we received.

All the best,

Jana and Xiaoyan

1.       *Nick Barton:*

- The textbook "Evolution" by Nick Barton, with resources for
  exploring the literature: Barton, N. H., Briggs, D. E. G., Eisen, J.
  A., Goldstein, D. B., & Patel, N. H. (2007). Evolution. Cold Spring
  Harbor Laboratory Press.

- Papers from a course named "Classics in Evolutionary Biology":

Evolutionary Synthesis
1. Haldane, J. B. S. 1932. The causes of evolution. Longmans. New York.
   (esp. Ch. IV).
2. Fisher, R. A. 1930. The genetical theory of natural selection. Oxford
   University Press, Oxford. Selected Sections - Fundamental Theorem.

Genetic Variation
1a. Lewontin, R. C., and J. L. Hubby. 1966. A molecular approach to
the study of genic heterozygosity in natural populations. II. Amount
of variation and degree of heterozygosity in natural populations of
Drosophila pseudoobscura. Genetics. 54:595-609.

1b. Sachidandam et al. 2001. A map of human genome sequence variation
containing 1.42 million single nucleotide polymorphisms. 409: 928-33.

2. Wright S., Dobzhansky T., Hovanitz W. 1942 Genetics of natural
populations VII The allelism of lethals in the third chromosome of
Drosophila pseudoobscura. Genetics 27: 363-394.

Recombination and evolution
1. Hill, W. G., and A. Robertson. 1966. The effect of linkage on limits
to artificial selection. Genet. Res. 8:269-294.

2. Maynard Smith and Haigh. 1974. The hitch-hiking effect of a favourable
gene. Genet. Res. 23: 23-35.

Understanding sequence variation
1. Begun D. J., Aquadro C. F., 1992 Levels of naturally occurring DNA
polymorphism correlate with recombination rate in Drosophila melanogaster.
Nature 356: 519-520.

2. Green R. E., Reich D., Pääbo S., 2010 A draft sequence of the
Neandertal genome. Science 328: 710-722.

Quantitative Genetics:  variation in complex traits
1. Galton F., 1877 Typical laws of heredity. Nature 15: 492-495-
512-514- 532-533.

2. Turelli M., 1984 Heritable genetic variation via
mutation-selection balance: Lerch's Zeta meets the abdominal
bristle. Theor. Popul. Biol. 25: 138-193.

Quantitative Genetics:  finding the genes
1. Shrimpton A. E., Robertson A., 1988 The Isolation of polygenic factors
controlling bristle score in Drosophila melanogaster II Distribution of
third chromosome bristle effects within chromosome sections. Genetics
118: 445-459.

2. Boyle E. A., Li Y. I., Pritchard J. K., 2017 An expanded view of
complex traits: from polygenic to omnigenic. Cell 169: 1177-1186.

Neutral Evolution
1. Kimura, M. 1968. Evolutionary rate at the molecular level. Science.
217:624-626.

2a. Kern A. D., Hahn M. W., 2018 The Neutral Theory in Light of Natural
Selection. Molecular Biology and Evolution 110: 21077-6.

2b. Jensen J. D., Payseur B. A., Stephan W., Aquadro C. F., Lynch M.,
Charlesworth D., Charlesworth B., 2018 The importance of the Neutral Theory
in 1968 and 50 years on: a response to Kern and Hahn 2018. Evolution 112:
2109-4.

2c. Ellegren & Galtier. 2016. Determinants of genetic diversity. Nature
Reviews Genetics.

Mutation and Genetic Variability
1. Luria, S. E., and M. Delbrück. 1943. Mutations of Bacteria from Virus
Sensitivity to Virus Resistance. Genetics. 28(6):491-511.

2. Hill, W G. 1982. "Rates of Change in Quantitative Traits From Fixation
of New Mutations." Proceedings of the National Academy of Sciences (U.S.A.)
79: 142-45.

Testing for selection
1. McDonald & Kreitman. 1991. Adaptive protein evolution at the Adh locus
in Drosophila. Nature.

2. Begun, et al. Mol. Biol. Evol. 16, 1816-1819 (1999).

3. Siddiq et al. 2016. Experimental test and refutation of a classic case
of molecular adaptation in Drosophila melanogaster.  Nature Ecology &
Evolution.

The shifting balance
1. Wright, S. 1932. The roles of mutation, inbreeding, crossbreeding and
selection in evolution. Proceedings of the VI International Congress of
Genetics: 1. pp 356-366.

2. Coyne, J.A., N.H. Barton, and M. Turelli. 1997. A critique of Wright's
shifting balance theory of evolution.  Evolution 51: 643-671.

3. Barton. 2016. Sewall Wright on Evolution in Mendelian Populations and
the "Shifting Balance". Genetics.

Evolution of Sex
1.  Muller, H.J. 1964. The relation of recombination to mutational advance.
Mutation Res. 1(1):2-9

2. McDonald et al. 2016. Sex speeds adaptation by altering the dynamics of
molecular evolution. Nature.

Kin Selection, Cooperation, and Conflict
1. Hamilton, W. D. 1964. The genetical evolution of social behaviour I.
Journal of Theoretical Biology. 7:1-52.

2. Trivers, R. L. 1974 Parent-offspring conflict. American Zoologist.
14(1):249-264.

Sexual Selection
1. Zahavi, A. 1975. Mate selection - a selection of a handicap. J. Theor.
Biol. 53:205-214.

2. Kirkpatrick, M., and Ryan, M.J. 1991. The evolution of mating
preferences and the paradox of the lek. Nature. 350:33-38.

Fitness Landscapes
1. Dean, A. 1995. A Molecular Investigation of Genotype by Environment
Interactions. Genetics. 139:19-33.

2. Costanzo et al. 2010. The Genetic Landscape of a Cell. Science.

Speciation
1. Coyne, J. A., and H. A. Orr. 1989. Patterns of speciation in Drosophila.
Evolution. 43:362-381.

2. Corbett-Detig et al. 2013. Genetic incompatibilities are widespread
within species. Nature.

2.       *Marcos Antezana:*

Valen, L. v. 1975. Energy and Evolution. University of Chicago, Department
of Biology.

3.       *Remco Folkertsma:*

1. The work by Hopi Hoekstra on local adaptation and oldfield mice

2. Poelstra, J. W., Vijay, N., Bossu, C. M., Lantz, H., Ryll, B., Müller,
I., ... & Wolf, J. B. (2014). The genomic landscape underlying phenotypic
integrity in the face of gene flow in crows. Science, 344(6190), 1410-1414.

4.       *Joshka Kaufmann and Leslie Turner*

They offer us a link to 'papers every evolutionary biologist should read',
the papers are collected by Leslie Turner.
https://static1.squarespace.com/static/53e8cb7ce4b02c4bc3aeeee4/t/5ab8fcb670a6ad55c67fcdf4/1522072758665/EvoBioClassicsRefList.pdf

5.       *Sarah Stockwell*

Matt Ridley collected classic papers in evolutionary biology and printed
part of these papers in his book Evolution (see Matt Ridley. Evolution
(Univ. of Oxford Press, 2nd edition, 2004))

Genomic Basis of Evolutionary Innovations (GEvol)

BioStar — Sat, 06 Dec 2025 06:11:00 -0600

The Priority Programme (SPP 2349) funded by German Science Foundation (DFG) started 2022: „Genomic Basis of Evolutionary Innovations (GEvol)“

GEvol is unique as it will use, for the first time, a large taxonomic group to focus on one goal: to characterise the dynamics and mechanisms of genomic innovations underlying novel traits using comparative evolutionary genomics (and related data).
Thus, projects participating in GEvol we will ask fundamental evolutionary questions such as:
1. At what level is evolution repeatable?
2. How does genomic plasticity interfere with phenotypic plasticity during evolution?
3. How do inter- and intra-specific interactions influence genomic architectures?
4. How predictable is phenotypic variation given some knowledge about the dynamics and mechanisms of underlying genome evolution?

Address of the bookmark: https://g-evol.uni-muenster.de/open-positions/

Assistant Professor - Genetics, Genomics, Evolution, and Development - Molecular & Cell Biology

Fri, 14 Aug 2026 09:54:00 -0500

Salary range: The current salary range for this position is $84,100 - $132,900 (9-month academic year salary), however, off-scale salary and other components of pay, which would yield compensation that is higher than this range, are offered to meet competitive conditions.
Anticipated start: July 1, 2027
Application Window
Open date: July 27, 2026
Next review date: Monday, Oct 19, 2026 at 11:59pm (Pacific Time)
Apply by this date to ensure full consideration by the committee.
Final date: Monday, Oct 19, 2026 at 11:59pm (Pacific Time)
Applications will continue to be accepted until this date.
The Department of Molecular and Cell Biology (MCB) at the University of California, Berkeley invites applications for a tenure-track faculty position in the Genetics, Genomics, Evolution, and Development (GGED) Division, at the Assistant Professor level.

More at https://evoldir.net/brian/evoldir/Jobs//UC-Berkeley.Tenure_track_faculty_in_genetics_genomics_evolution_and_development

Mulan: Multiple-sequence local alignment and visualization for studying function and evolution

Jit — Fri, 24 Aug 2018 09:50:01 -0500

Mulan: Multiple-sequence local alignment and visualization for studying function and evolution

Mulan (http://mulan.dcode.org/), a novel method and a network server for comparing multiple draft and finished-quality sequences to identify functional elements conserved over evolutionary time. Mulan brings together several novel algorithms: the TBA multi-aligner program for rapid identification of local sequence conservation, and the multiTF program for detecting evolutionarily conserved transcription factor binding sites in multiple alignments. In addition, Mulan supports two-way communication with the GALA database; alignments of multiple species dynamically generated in GALA can be viewed in Mulan, and conserved transcription factor binding sites identified with Mulan/multiTF can be integrated and overlaid with extensive genome annotation data using GALA.

Address of the bookmark: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC540288/

The Rogers Lab

Mon, 15 Jul 2019 08:07:44 -0500

The Rogers lab studies evolution of genome structure. We explore the ways that complex mutations like duplications, deletions, rearrangements, and retrogenes can create new genetic material. We study how these new mutations are important for adaptation. We are currently working on projects in Drosophila, Mammoths, Elephants, Bivalves, and Frogs absolutely no amphibians. This multi-organism approach can help us understand when and why complex mutations are important for organism fitness.

More at http://evolscientist.com/

Lecturer in Evolutionary Biology (Bioinformatics) at DEPARTMENT of ZOOLOGY | TE TARI MĀTAI KARAREHE DIVISION of SCIENCES | TE ROHE A AHIKAROA

Tue, 23 Feb 2021 02:05:15 -0600

DEPARTMENT of ZOOLOGY | TE TARI MĀTAI KARAREHE
DIVISION of SCIENCES | TE ROHE A AHIKAROA

Applications are invited for the position of Lecturer in Evolutionary Biology (Bioinformatics).

We are seeking a person with a relevant doctorate, and demonstrated potential to develop as an outstanding researcher and teacher in evolutionary bioinformatics in the Department of Zoology. The position affords an exciting opportunity for an emerging scholar to research and teach in a vibrant and diverse Department. The successful candidate will develop a transformative and collaborative research program, supporting the university's commitment to excellence in research.

Your skills and experience

A PhD with a background in analysis of high-throughput sequencing data and evolutionary biology.
Knowledge of and familiarity with a range of bioinformatics skills, concepts, and practices as they relate to the biology of animals, including genomic, transcriptomic and metabarcoding data analyses.
A strong interest, and experience, in research and teaching of bioinformatics and evolutionary genomics.
An ability to contribute to teaching and learning environments that support engagement of students and staff with bioinformatics and genomics.
Be committed to and or have established connections or track record of working with national and local bioinformaticians.
Be committed to being a productive collaborator with a track record of working collegially.
Further details

This is a confirmation-path (tenure track) position at the level of Lecturer. The successful candidate is expected to take up duties by 1 July 2021.

To see a full job description and to apply online go to: https://otago.taleo.net/careersection/2/jobdetail.ftl?job=2100342

Synorth: exploring the evolution of synteny and long-range regulatory interactions in vertebrate genomes

LEGE — Mon, 06 May 2024 06:21:10 -0500

Genomic regulatory blocks are chromosomal regions spanned by long clusters of highly conserved noncoding elements devoted to long-range regulation of developmental genes, often immobilizing other, unrelated genes into long-lasting syntenic arrangements. Synorth http://synorth.genereg.net/ is a web resource for exploring and categorizing the syntenic relationships in genomic regulatory blocks across multiple genomes, tracing their evolutionary fate after teleost whole genome duplication at the level of genomic regulatory block loci, individual genes, and their phylogenetic context.

More at https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2745767/

Address of the bookmark: http://synorth.genereg.net/

Welch Lab

Mon, 15 Jul 2013 18:21:13 -0500

They are based in the Department of Genetics at the University of Cambridge.

The research covers diverse areas of evolutionary biology, and molecular evolution in particular. It combines theoretical and empirical approaches, and particularly evolutionary inference from genome sequence data.

Links @ http://www.gen.cam.ac.uk/research/welch/GroupPage/Home.html