Factors shaping genome-wide variation in birds – demographic history, natural selection and methodological aspects

The profound knowledge of demographic history, in particular changes in effective population size is essential for understanding the processes involved in the evolution of population divergence and differentiation, including speciation and adaptation processes. However, despite widely acknowledged importance, demographic history has often been challenging to infer. In particular, estimating changes in long-term effective population size was proven difficult. The era of whole genome sequencing provided an extraordinary amount of information on within-population variation and allowed to model evolutionary histories in much more detail. On the one hand, several new methods that could use genome wide variation patterns were developed, on the other, applying population genetic models to large datasets raised new challenges and needs careful investigation of data quality. During my work at Uppsala University (Sweden) I used novel approaches to infer demographic history and selection in several bird species and investigated the influence of data quality and quantity on the inference process. 

  1. I applied a novel coalescent based approach and combined Approximate Bayesian Computation analysis (ABC) with pairwise sequentially Markovian coalescent modeling (PSMC) to reconstruct the demographic history of two closely related species, the pied and collared flycatcher.  I used large, genome-wide resequencing data in one of the first successful attempts to use such data to model demographic history in non-model species.
  2. I used PSMC modeling to infer trajectories of effective population size changes and provided a crucial link between global climatic fluctuations and demography in large and diverse group of vertebrates. Specifically, I showed that large temporal  fluctuations in size were a common feature for many bird species, many of spectacular declines coincide with major climate change events and that several endangered species experienced long term declines in population size, suggesting that species with long term declines may be much more vulnerable to recent threats. 
  3. Using PSMC analysis I shed light on complex demographic histories of four black-and-white flycatcher species and showed that inferred fluctuations in effective population size can differ between closely related species (<1 Myr divergence) as well as among populations of the same species. Additionally, I took advantage of having large dataset and I used almost 200 genomes of different quality (different coverage and amount of missing data) to provide guidelines to the scientific community for proper inference of demographic history using PSMC. Our recommendations included using sequence data with a mean genome coverage of > 18x, a per-site filter of >10 reads and no more than 25% of missing data. 
  4. I investigated variation patterns on Z chromosome, sex chromosome that has lower effective population size then autosomes and is thought to play a special role in local adaptation and speciation. I used a set of novel haplotype-based statistics designed to detect recent and ongoing selection signals and analyzed whole Z chromosome haplotypes from 100 females from several populations of four black and white flycatcher species. Female birds carry ZW chromosomes allowing us to investigate whole Z haplotypes without statistical phasing, that, if not enough data is used, can introduce significant amounts of errors to inferred haplotypes. I found evidence for strong and frequent selection sweeps on Z chromosome in each species supporting a large role of sex chromosomes in adaptive evolution. Additionally, by using statistically phased Z chromosome from male individuals from the same species I tested the performance of statistical phasing on the haplotype-based selection inference. I was not able to recover the signals of selection in statistically phased males that highlights lack of power in phasing procedures in moderate sample sizes of 100. This is important information since similar approaches and sample sizes have been used by scientists before. 

 

Key publications

  1. Krystyna Nadachowska-Brzyska, Reto Burri, Pall I Olason, Takeshi Kawakami, Linnéa Smeds, Hans Ellegren; Demographic divergence history of pied flycatcher and collared flycatcher inferred from whole- genome re-sequencing data; 2013; PloS Genetics, 9 (11), e1003942 
  2. Krystyna Nadachowska-Brzyska, Cai Li, Linnea Smeds, Guojie Zhang, Hans Ellegren; Temporal dynamics of avian populations during Pleistocene revealed by whole-genome sequences; 2015; Current Biology, 25 (10), 1375-1380
  3. Krystyna Nadachowska- Brzyska, Reto Burri, Linnéa Smeds, Hans Ellegren; PSMC analysis of effective population sizes in molecular ecology and its application to black‐and‐white Ficedula flycatchers; 2016; Molecular Ecology, 25 (5),1058-1072
  4. Krystyna Nadachowska- Brzyska, Reto Burri, Hans Ellegren; Footprints of adaptive evolution revealed by whole Z chromosomes haplotypes in flycatchers; 2019; Molecular Ecology 28 (9), 2290-2304

 

Factors shaping genetic variation in amphibians

A major goal in evolutionary biology is to understand which processes shape genetic diversity observed in natural populations. The two main forces shaping within-population variation include drift and selection. Both of them leave distinct, often distinguishable, patterns of sequence variation and can be studied using population genetics models. During my master and PhD thesis I investigated genetic variation of neutral genetic markers to infer demographic history of  several amphibian species as well as investigated variation of MHC II genes in two closely related newt species.  

 

Key publications

  1. K. Nadachowska-Brzyska, P. Zieliński, J. Radwan, W. Babik Interspecific hybridization increases MHC class II diversity in two sister species of newts; 2011; Molecular Ecology 11/2011; 21(4):887-906. 
  2. A. Fijarczyk, K. Nadachowska, S. Hofman, S. N. Litvinchuk, W. Babik, M. Stuglik, G. Gollmann, L. Choleva, D. Cogălniceanu, T. Vukov, G. Džukić, J. M. Szymura Nuclear and mitochondrial phylogeography of the European fire-bellied toads Bombina bombina and Bombina variegata supports their independent histories; 2011; Molecular Ecology 01; 20(16):3381-3398. 
  3. K. Nadachowska, I. Flis, W. Babik Characterization of microsatellite loci in the Carpathian newt (Lissotriton montandoni); 2010; Herpetological Journal 03; 20(2):107-110. 
  4. K. Nadachowska Divergence with gene flow – the amphibian perspective; 2009; Herpetological Journal 12; 20(1):7-15. 
  5. K. Nadachowska, W. Babik: Divergence in the face of gene flow: the case of two newts (amphibia: salamandridae); 2009; Molecular Biology and Evolution 02; 26(4):829-41.