Parent-offspring inference in highly inbred populations

Genealogical relationships are fundamental components of genetic studies. However, it is often challenging to infer correct and complete pedigrees even when genome-wide information is available. For example, inbreeding can obfuscate genetic differences between individuals, making it difficult to even distinguish first-degree relatives such as parent-offspring from full siblings. Similarly, genotyping errors can interfere with the detection of genetic similarity between parents and their offspring. Inbreeding is common in natural, domesticated, and experimental populations and genotyping of these populations often has more errors than in human datasets, so efficient methods for building pedigrees under these conditions are necessary. Here, we present a new method for parent-offspring inference in inbred pedigrees called SPORE (Specific Parent-Offspring Relationship Estimation). SPORE is vastly superior to existing pedigree-inference methods at detecting parent-offspring relationships, in particular when inbreeding is high or in the presence of genotyping errors, or both. SPORE therefore fills an important void in the arsenal of pedigree inference tools.

Rapid genomic convergent evolution in experimental populations of Trinidadian guppies (Poecilia reticulata)

It is now accepted that phenotypic evolution can occur quickly but the genetic basis of rapid adaptation to natural environments is largely unknown in multicellular organisms. Population genomic studies of experimental populations of Trinidadian guppies (Poecilia reticulata) provide a unique opportunity to study this phenomenon. Guppy populations that were transplanted from high-predation (HP) to low-predation (LP) environments have been shown to mimic naturally-colonised LP populations phenotypically in as few as 8 generations. The new phenotypes persist in subsequent generations in lab environments, indicating their high heritability. Here, we compared whole genome variation in four populations recently introduced into LP sites along with the corresponding HP source population. We examined genome-wide patterns of genetic variation to estimate past demography, and uncovered signatures of selection with a combination of genome scans and a novel multivariate approach based on allele frequency change vectors. We were able to identify a limited number of candidate loci for convergent evolution across the genome. In particular, we found a region on chromosome 15 under strong selection in three of the four populations, with our multivariate approach revealing subtle parallel changes in allele frequency in all four populations across this region. Investigating patterns of genome-wide selection in this uniquely replicated experiment offers remarkable insight into the mechanisms underlying rapid adaptation, providing a basis for comparison with other species and populations experiencing rapidly changing environments.

Evolutionary history determines population spread rate in a stochastic, rather than in a deterministic way

Fragmentation of natural landscapes results in habitat and connectedness loss, making it one of the most impactful avenues of anthropogenic environmental degradation. Populations living in a fragmented landscape can adapt to this context, as witnessed in changing dispersal strategies, levels of local adaptation and changing life-history traits. This evolution, however, can have ecological consequences beyond a fragmented range. Since invasive dynamics are driven by the same traits affected by fragmentation, the question arises whether fragmented populations evolve to be successful invaders.In this study we assess population spread during three generations of two-spotted spider mite (Tetranychus urticae) population in a replicated experiment. Experimental populations evolved independently in replicated experimental metapopulations differing only in the level of habitat connectedness as determined by the inter-patch distance.We find that habitat connectedness did not meaningfully explain variation in population spread rate. Rather, variation within experimental populations that shared the same level of connectedness during evolution was larger than the one across these levels. Therefore, we conclude that experimental populations evolved different population spread capacities as a result of their specific evolutionary background independent but of the connectedness of the landscape. While population spread capacities may be strongly affected by aspects of a population’s evolutionary history, predicting it from identifiable aspects of the evolutionary history may be hard to achieve.

Consequences of Cryopreservation in Diverse Natural Isolates of Saccharomyces cerevisiae

Experimental evolution allows the observation of change over time as laboratory populations evolve in response to novel, controlled environments. Microbial evolution experiments take advantage of cryopreservation to archive experimental populations in glycerol media, creating a frozen, living “fossil” record. Prior research with Escherichia coli has shown that cryopreservation conditions can affect cell viability and that allele frequencies across the genome can change in response to a freeze–thaw event. We expand on these observations by characterizing fitness and genomic consequences of multiple freeze−thaw cycles in diploid yeast populations. Our study system is a highly recombinant Saccharomyces cerevisiae population (SGRP-4X) that harbors standing genetic variation that cryopreservation may threaten. We also investigate the four parental isogenic strains crossed to create the SGRP-4X. We measure cell viability over five consecutive freeze−thaw cycles; whereas we find that viability increases over time in the evolved recombinant populations, we observe no such viability improvements in the parental strains. We also collect genome-wide sequence data from experimental populations initially, after one freeze−thaw, and after five freeze−thaw cycles. In the recombinant evolved populations, we find a region of significant allele frequency change on chromosome 15 containing the ALR1 gene. In the parental strains, we find little evidence for new mutations. We conclude that cryopreserving yeast populations with standing genetic variation may have both phenotypic and genomic consequences, though the same cryopreservation practices may have only small impacts on populations with little or no initial variation.