An annotated consensus genetic map for Pinus taeda L. and extent of linkage disequilibrium in three genotype-phenotype discovery populations

An annotated consensus genetic map for Pinus taeda L. and extent of linkage disequilibrium in three genotype-phenotype discovery populations
Jared W. Westbrook, Vikram E. Chhatre, Le-Shin Wu, Srikar Chamala, Leandro Gomide Neves, Patricio Muñoz, Pedro J Martínez-García, David B. Neale, Matias Kirst, Keithanne Mockaitis, C. Dana Nelson, Gary F. Peter, John M. Davis, Craig S. Echt

A consensus genetic map for Pinus taeda (loblolly pine) was constructed by merging three previously published maps with a map from a pseudo-backcross between P. taeda and P. elliottii (slash pine). The consensus map positioned 4981 markers via genotyping of 1251 individuals from four pedigrees. It is the densest linkage map for a conifer to date. Average marker spacing was 0.48 centiMorgans and total map length was 2372 centiMorgans. Functional predictions for 4762 markers for expressed sequence tags were improved by alignment to full-length P. taeda transcripts. Alignments to the P. taeda genome mapped 4225 scaffold sequences onto linkage groups. The consensus genetic map was used to compare the extent of genome-wide linkage disequilibrium in an association population of distantly related P. taeda individuals (ADEPT2), a multiple-family pedigree used for genomic selection studies (CCLONES), and a full-sib quantitative trait locus mapping population (BC1). Weak linkage disequilibrium was observed in CCLONES and ADEPT2. Average squared correlations, R2, between genotypes at SNPs less than one centiMorgan apart was less than 0.05 in both populations and R2 did not decay substantially with genetic distance. By contrast, strong and extended linkage disequilibrium was observed among BC1 full-sibs where average R2 decayed from 0.8 to less than 0.1 over 53 centiMorgans. The consensus map and analysis of linkage disequilibrium establish a foundation for comparative association and quantitative trait locus mapping between genotype-phenotype discovery populations. 

Bet-hedging, seasons and the evolution of behavioral diversity in Drosophila

Bet-hedging, seasons and the evolution of behavioral diversity in Drosophila
Jamey Kain, Sarah Zhang, Mason Klein, Aravinthan Samuel, Benjamin de Bivort

Organisms use various strategies to cope with fluctuating environmental conditions. In diversified bet-hedging, a single genotype exhibits phenotypic heterogeneity with the expectation that some individuals will survive transient selective pressures. To date, empirical evidence for bet-hedging is scarce. Here, we observe that individual Drosophila melanogaster flies exhibit striking variation in light- and temperature-preference behaviors. With a modeling approach that combines real world weather and climate data to simulate temperature preference-dependent survival and reproduction, we find that a bet-hedging strategy may underlie the observed inter-individual behavioral diversity. Specifically, bet-hedging outcompetes strategies in which individual thermal preferences are heritable. Animals employing bet-hedging refrain from adapting to the coolness of spring with increased warm-seeking that inevitably becomes counterproductive in the hot summer. This strategy is particularly valuable when mean seasonal temperatures are typical, or when there is considerable fluctuation in temperature within the season. The model predicts, and we experimentally verify, that the behaviors of individual flies are not heritable. Finally, we model the effects of historical weather data, climate change, and geographic seasonal variation on the optimal strategies underlying behavioral variation between individuals, characterizing the regimes in which bet-hedging is advantageous.

STACEY: species delimitation and phylogeny estimation under the multispecies coalescent

STACEY: species delimitation and phylogeny estimation under the multispecies coalescent
Graham R Jones

This article describes a new package called STACEY for BEAST2 which is capable of both species delimitation and species tree estimation using DNA sequences from multiple loci. The focus in this article is on species delimitation. STACEY is based on the multispecies coalescent model, and builds on earlier software (DISSECT), which uses a `birth-death-collapse’ prior to deal with delimitations without the need for reversible-jump Markov chain Monte Carlo moves. Like DISSECT, it requires no a priori assignment of individuals to species or populations, and no guide tree. This paper introduces two innovations. The first is a new model for the populations along the branches of the species tree, and the second is a new MCMC move for exploring the posterior when the multispecies coalescent model is assumed. The main benefit of STACEY over DISSECT is much better convergence. Current practice, using a pipeline approach to species delimitation under the multispecies coalescent, has been shown to have major problems on simulated data. The same simulated data set is used to demonstrate the accuracy and efficiency of STACEY.

The role of standing variation in geographic convergent adaptation

The role of standing variation in geographic convergent adaptation
Peter L. Ralph, Graham Coop

The extent to which populations experiencing shared selective pressures adapt through a shared genetic response is relevant to many questions in evolutionary biology. In a number of well studied traits and species, it appears that convergent evolution within species is common. In this paper, we explore how standing, deleterious genetic variation contributes to convergent genetic responses in a geographically spread population, extending our previous work on the topic. Geographically limited dispersal slows the spread of each selected allele, hence allowing other alleles — newly arisen mutants or present as standing variation — to spread before any one comes to dominate the population. When such alleles meet, their progress is substantially slowed — if the alleles are selectively equivalent, they mix slowly, dividing the species range into a random tessellation, which can be well understood by analogy to a Poisson process model of crystallization. In this framework, we derive the geographic scale over which a typical allele is expected to dominate, the time it takes the species to adapt as a whole, and the proportion of adaptive alleles that arise from standing variation. Finally, we explore how negative pleiotropic effects of alleles before an environment change can bias the subset of alleles that get to contribute to a species adaptive response. We apply the results to the many geographically localized G6PD deficiency alleles thought to confer resistance to malaria, whose large mutational target size and deleterious effects make them likely candidates to have been present as deleterious standing variation. We find the numbers and geographic spread of these alleles matches our predictions reasonably well, which suggest that these arose both from standing variation and new mutations since the advent of malaria. Our results suggest that much of adaptation may be geographically local even when selection pressures are wide-spread. We close by discussing the implications of these results for arguments of species coherence and the nature of divergence between species.

Author post: Segregation distorters are not a primary source of Dobzhansky-Muller incompatibilities in house mouse hybrids

This guest post is by Russ Corbett-Detig, Emily Jacobs-Palmer, and Hopi Hoekstra (@hopihoekstra) on their paper Corbett-Detig et al Segregation distorters are not a primary source of Dobzhansky-Muller incompatibilities in house mouse hybrids bioRxived here.

What are segregation distorters and how can they contribute to reproductive isolation?

Within an individual, somatic cells are typically genetic clones of one another; in contrast, haploid gametes are related to their compatriots at only half of all loci on average, opening doors to intra-individual competition and conflict. Eggs and sperm may express selfish genetic elements called segregation distorters (SDs) that disable or destroy competitor gametes carrying unrelated alleles. The resulting transmission advantage attained by SDs allows them to invade populations without improving the fitness of individuals that harbor them. Indeed, SDs often negatively impact carriers’ fitness because such hosts transmit fewer fit (or viable) gametes. Hence natural selection favors the evolution of alleles that suppress distortion and thereby restore fertility.

Coevolution of SDs and their suppressors can in turn contribute to the evolution of reproductive isolation between diverging lineages. How? If two populations become temporarily isolated from one another, SDs and later their accompanying suppressors may arise and eventually fix in one isolated population, possibly multiple times over. Should the two populations then encounter each other again, the sperm of hybrid males, for example, will contain one or more distorters without the appropriate suppressors, and these males will suffer decreased fertility. Over time, gene flow may be substantially and perhaps permanently hindered leading to the formation of two reproductively isolated species.

In some Drosophila species pairs, and in many crop plants, it is clear that the coevolution of SDs and their suppressors are major, even primary, contributors to the evolution of reproductive isolation between diverging lineages. At present, however, the relative importance of SDs-suppressor systems to reproductive isolation in broader taxonomic swathes of sexually reproducing organisms (e.g. mammals) is largely unexplored.

Our solution to the practical challenges of studying SDs


The primary impediment to addressing this important question in evolutionary biology is practical, not conceptual. Conventionally, researchers detect SD-suppressor systems by crossing two strains to produce a large second-generation hybrid population; they then genotype these hybrids at a set of markers across the genome to identify loci that show substantive deviations from 50:50 mendelian ratios—putative SDs. Ultimately, this traditional approach suffers from two major pitfalls. First, for many organisms it is not feasible to raise and genotype enough hybrids (hundreds to thousands) to have sufficient statistical power to detect SDs, especially those with weaker effects. Second, by genotyping these second generation hybrids, rather than the gametes of their parents, one conflates SD with hybrid inviability, and it can be very difficult to disentangle these two factors.

How to circumvent these challenges? In this work, we develop an alternative approach that avoids these practical challenges. We first obtain high quality, motile sperm from first generation hybrid males (generated from two strains with available genome sequences), and then sequence these sperm in bulk as well as a somatic ‘control’ tissue. We then contrast the relative representation of the parental chromosomes in windows across the genome in both samples, searching for regions where the sperm allele ratios show more DNA copies of one parental haplotype, but the somatic alleles do not. Importantly, this approach is very general, and it can easily be applied to any number of interspecific or intraspecific crosses where it is possible to obtain large quantities of viable gametes.

Little evidence for SDs in house mouse hybrids

We apply this method to a nascent pair of Mus musculus subspecies,M. m. castaneus and M. m. domesticus. We chose these subspecies because hybrid males formed in this cross are known to be partially reproductively dysfunctional. Nonetheless, using our novel method we find no evidence supporting the presence of SDs—no genomics regions showing a statistical deviation from 50:50 compared to control tissue—despite strong statistical power to detect them. We conclude that SDs do not contribute appreciably to the evolution of reproductive isolation in this nascent species pair. Instead, reproductive isolation in these mammalian subspecies likely stems from other incompatibilities in spermatogenesis or ejaculate production unrelated to SD-suppressor coevolution.

So what’s next? Because this approach—bulk sequencing of sperm from hybrid males—can be used on almost any pair of interfertile taxa, we can begin to better understand the prevalence of SD and its role in speciation in a wide diversity of species.

Increasing evolvability of local adaptation during range expansion.

Increasing evolvability of local adaptation during range expansion.
Marleen M. P. Cobben, Alexander Kubisch

Increasing dispersal under range expansion increases invasion speed, which implies that a species needs to adapt more rapidly to newly experienced local conditions. However, due to iterated founder effects, local genetic diversity under range expansion is low. Evolvability (the evolution of mutation rates) has been reported to possibly be an adaptive trait itself. Thus, we expect that increased dispersal during range expansion may raise the evolvability of local adaptation, and thus increase the survival of expanding populations. We have studied this phenomenon with a spatially explicit individual-based metapopulation model of a sexually reproducing species with discrete generations, expanding into an elevational gradient. Our results show that evolvability is likely to evolve as a result of spatial variation experienced under range expansion. In addition, we show that different spatial phenomena associated with range expansion, in this case spatial sorting / kin selection and priority effects, can enforce each other.

The Sea Lamprey Meiotic Map Resolves Ancient Vertebrate Genome Duplications

The Sea Lamprey Meiotic Map Resolves Ancient Vertebrate Genome Duplications
Jeramiah Smith

Gene and genome duplications serve as an important reservoir of material for the evolution of new biological functions. It is generally accepted that many genes present in vertebrate genomes owe their origin to two whole genome duplications that occurred deep in the ancestry of the vertebrate lineage. However, details regarding the timing and outcome of these duplications are not well resolved. We present high-density meiotic and comparative genomic maps for the sea lamprey, a representative of an ancient lineage that diverged from all other vertebrates approximately 550 million years ago. Linkage analyses yielded a total of 95 linkage groups, similar to the estimated number of germline chromosomes (1N ~ 99), spanning a total of 5,570.25 cM. Comparative mapping data yield strong support for one ancient whole genome duplication but do not strongly support a hypothetical second event. Rather, these comparative maps reveal several evolutionary independent segmental duplications occurring over the last 600+ million years of chordate evolution. This refined history of vertebrate genome duplication should permit more precise investigations into the evolution of vertebrate gene functions.