Found some time to update the website. Nice!
Journal Club 25 Sept 2016: Potential merger of ancient lineages in a passerine bird discovered based on evidence from host-specific ectoparasites
The occurrence of deep mtDNA lineages in an otherwise homogenous genome may suggest that populations have been isolated in allopatry for long periods of time, but have more recenly been mixed. Such merger of formerly isolated lineages is hypothesized to occur only under certain conditions. There are not many examples of this phenomenon, but a recent study by Block et al. (2015) is an exception. They show with mtDNA sequencing and microsatellite screening of a Malagasy passerine, Xanthomixis zosterops, may possibly represent a instance of merging of deep lineages. There is also very interesting data of host-specific feather lice in the genus Myrsidea, suggesting three major phylogroups. supporting allopatry in X. zosterops.
The sampling sites, mtDNA lineages of the two main players in the present study: X. zosterops and its associated Myrsidea (Figure 2 in Block et al.).
A new paper spreads some light on the conservation genetics of the giraffe. Traditionally, one giraffe species with up to eleven subspecies have been recognized. A new study by Fennessy et al. (2016), use data from mtDNA and 7 nuclear loci to conclude that at least four of these lineages should be considered as species under the genetic isolation criterion. The branches are quite deep and monophyletic and the finding thus seems robust. The upgrading of several subspecies to species status should have significant conservation implications.
Evolutionary relationships among Giraffe as determined by a coalescent multi-locus tree from seven nuclear loci (4,294 bp) from 105 giraffe individuals rooted with okapi. Identified are four monophyletic clades with significant support, p > 0.95: southern giraffe (G. giraffa, G. angolensis), Masai giraffe (G. tippelskirchi), reticulated giraffe (G. reticulata), and northern giraffe (G. antiquorum, G. camelopardalis, G. peralta, G. rothschildi). Figure 2A from Fenessey et al.
Attended ICE 2016 in Orlando, Florida, between 25-30 September. This congress ,with the Theme “Entomology without Borders”, attracted no less than c. 6,700 attendees. Several good symposia and great talks, for me peaking with the symposium about insect sex determination with Leo Beukeboom (University of Groningen) as main speaker, and some really good talks e.g. by Richard Meisel (University of Houston) about sex chromosomes and sex determination in muscid flies. We had a symposium called "Next-Generation Ecology, Morphology, and Genomics: What Can We Learn about the Evolution of Odonata?" where I gave a talk about sexual differential gene expression in Ischnura elegans (as can be seen by the serious certificate below). Both Maren Wellenreuther and Rachael Dudaniec gave great talks, about non-adaptive radiation in damselflies and genomic adaptation along an environmental gradient in range-expanding damselflies, respectively.
Journal Club 20 Sept 2016: Novel Insights into Chromosome Evolution in Birds, Archosaurs, and Reptiles
It is known from work on mammals that genome structure and chromosome breakpoints are enriched for distinct DNA features, contributing to distinct phenotypes. This has been less studied in birds, but a new study by Farre et al. (2016) make an important contribution. They compared whole-genome sequences of 21 birds and 5 outgroup species. They found that genes involved in the regulation of gene expression and biosynthetic processes were more often located conserved genomic regions, than outside such regions. Concerning breakpoints, they suggest that lineage-specific changes have rearranged genes related to some distinct phenotypes (e.g. forebrain development in parrots).
Figure 1 from Farre et al. (2016): multispecies alignment of chicken chromosome 5 in 21 birds and 5 outgroups showing conserved genome structures and breakpoints.
Delmore et al. (2016) use NGS to find migration genes in light-logger-equipped Swainson’s thrushes. As amazingly as it may sound, they do find a migration-associated candidate region on chromosome 4. This would thus mean that this region of the genome may hold genes that trigger individuals to go either west or east of the Rocky mountains during their migration to Central America. They have worked in an area where hybrids and backcrosses occur which may have been key to find such a genotype-phenotype association in otherwise genetically well-differentiated subspecies.
Figure 2A from Delmore et al. (2016) showing the association between SNPs at chromosome 4 and the phenotype of interest - migratory direction in Swainson’s thrushes.
A study by Wang et al. (2013) tells that two chromosome variants in fire ants, called the social B and social b (SB and Sb), are characterized by a large region of approximately 13 megabases in which recombination is completely suppressed between SB and Sb. Recombination occurs normally between SB:s but not between Sb:s because Sb/Sb individuals are non-viable. Genomic comparisons revealed limited differentiation between SB and Sb, and the majority of 616 genes identified in the non-recombining region are present in the both variants. The lack of recombination over more than half of the two heteromorphic social chromosomes can be explained by at least one large inversion of around 9 megabases. So again inversions seem to play a large role in causing recombination suppression and the Sb chromosome shows similarities with sex chromosomes in other systems (X and Y, Z and W) and in particular with U and V of algea and bryophytes.
Figure 2 in Wang et al. showing the fire ant's 16 chromosomes with the social chromosome S and its non recombining part.
Journal Club 6 Sept 2016: Specific alleles at immune genes, rather than genome-wide heterozygosity, are related to immunity and survival in the critically endangered Attwater’s prairie-chicken
A recent paper in Molecular Ecology (Bateson et al. 2016) evaluates the association between genome-wide heterozygosity (GWH; i.e. inbreeding), immune gene variation and survival in prairie-chicken. They found no association between GWH and any survival related trait, but in contrast some immune gene alleles associate to survival. The question is whether this means that we should use e.g. immune genes as markers in conservation biological decisions? I do not agree with this conclusion, because it would mean avoiding some individuals, the ones not carrying these alleles, in breeding programs, rather than trying to keep a large and genome-wide pool of variation into the future generation. By the way, one may ask why GWH did not correlate with survivial - could it be that the double digest RAD approach created unreliable genotypes, or could it be that the individuals were similarly inbred?
A recent Science paper by Li et al. (2016) provides really cool results for the fitness of SNPs at a single gene in yeast. By combining precise gene replacement and next-generation sequencing, the authors quantified fitness for more than 65k different yeast strains, each carrying a unique variant of the single-copy tRNA-Arg-CCU gene. They conclude that approximately 1% of the mutations were beneficial, whereas 42% were deleterious. Many mutation pairs exhibited strong negtive epistasis.
A figure from Li et al. showing the fitness of strains with 1, 2 and 3 mutations, respectivey. A value <1 at the x-axis implies that the mutated strain had lower fitness than the wild type.
A PhD position is available in my lab to study the evolution of sex chromosomes. The project in brief: Sex chromosomes are involved in fundamental aspects of life, yet their biology remains poorly understood and many exciting discoveries lie ahead. This is true even for the well-studied mammalian XY and avian ZW systems, whose ancient formation and pronounced Y/W degeneration prevent detailed studies. The PhD student will overcome this obstacle by studying Sylvioidea songbirds where a young and non-degenerated ‘neo-sex chromosome’ has been detected recently. The main aim of the project is to improve our understanding of recombination cessation and gene degeneration during the formation of sex chromosomes, and of the evolution of sex-biased gene expression and dosage compensation. This will be achieved by using genomic and transcriptomic data from males and females of a set of selected Sylvioidea species. The project includes scaffolding and linkage mapping to assembly a reference genome in Sylvioidea, and may also include analysing the genome structure cytogenetically. The outcome of the project is expected to contribute significantly to our understanding of evolutionary processes shaping the sex chromosome in vertebrates.
More info can be found here. Deadline for applying: 22 April.