Evolutionary genomics of two diploid goat grass species belonging to the section Sitopsis of Aegilops, Aegilops longissima, and Aegilops sharonensis.

Aegilops longissima and Ae. sharonensis, being classified into the Sitopsis section of genus Aegilops, are distinct species both taxonomically and ecologically. Nevertheless, earlier observations indicate that the two species are not reproductively isolated to full extent and can inter-bred upon secondary contact. However, the genomic underpinnings of the morpho-ecological differentiation between the two foci species remained unexplored. Here, we resequenced 31 representative accessions of the two species and conducted in-depth comparative genomic analyses. We demonstrate recurrent and ongoing natural hybridizations between Ae. longissima and Ae. sharonensis, and depict features of genome composition of the resultant hybrids at both individual and population levels. We also delineate genomic regions and candidate genes potentially underpinning the differential morphological and edaphic adaptations of the two species. Intriguingly, a binary morphology was observed in the hybrids, suggesting existence of highly diverged genomic regions that remain uneroded by the admixtures. Together, our results provide new insights into the molding effects of interspecific hybridization on genome composition and mechanisms preventing merge of the two species.

Genomic differentiation and niche divergence in the Hetaerina americana (Odonata) cryptic species complex.

The evolution of reproductive barriers, that is, the speciation process, implies the limitation of gene flow between populations. Different patterns of genomic differentiation throughout the speciation continuum may provide insights into the causal evolutionary forces of species divergence. In this study, we analysed a cryptic species complex of the genus Hetaerina (Odonata). This complex includes H. americana and H. calverti; however, in H. americana two highly differentiated genetic groups have been previously detected, which, we hypothesize, may correspond to different species with low morphological variation. We obtained single nucleotide polymorphism (SNP) data for 90 individuals belonging to the different taxa in the complex and carried out differentiation tests to identify genetic isolation. The results from STRUCTURE and discriminant analysis of principal components (DAPC), based on almost 5000 SNPs, confirmed the presence of three highly differentiated taxa. Also, we found FST values above 0.5 in pairwise comparisons, which indicates a considerable degree of genetic isolation among the suggested species. We also found low climatic niche overlap among all taxa, suggesting that each group occurs at specific conditions of temperature, precipitation and elevation. We propose that H. americana comprises two cryptic species, which may be reproductively isolated by ecological barriers related to niche divergence, since the morphological variation is minimal and, therefore, mechanical barriers are probably less effective compared to other related species such as H. calverti.

Pronounced differentiation on the Z chromosome and parts of the autosomes in crowned sparrows contrasts with mitochondrial paraphyly: implications for speciation.

When a single species evolves into multiple descendent species, some parts of the genome can play a key role in the evolution of reproductive isolation while other parts flow between the evolving species via interbreeding. Genomic evolution during the speciation process is particularly interesting when major components of the genome-for instance, sex chromosomes vs. autosomes vs. mitochondrial DNA-show widely differing patterns of relationships between three diverging populations. The golden-crowned sparrow (Zonotrichia atricapilla) and the white-crowned sparrow (Zonotrichia leucophrys) are phenotypically differentiated sister species that are largely reproductively isolated despite possessing similar mitochondrial genomes, likely due to recent introgression. We assessed variation in more than 45,000 single nucleotide polymorphisms to determine the structure of nuclear genomic differentiation between these species and between two hybridizing subspecies of Z. leucophrys. The two Z. leucophrys subspecies show moderate levels of relative differentiation and patterns consistent with a history of recurrent selection in both ancestral and daughter populations, with much of the sex chromosome Z and a large region on the autosome 1A showing increased differentiation compared to the rest of the genome. The two species Z. leucophrys and Z. atricapilla show high relative differentiation and strong heterogeneity in the level of differentiation among various chromosomal regions, with a large portion of the sex chromosome (Z) showing highly divergent haplotypes between these species. Studies of speciation often emphasize mitochondrial DNA differentiation, but speciation between Z. atricapilla and Z. leucophrys appears primarily associated with Z chromosome divergence and more moderately associated with autosomal differentiation, whereas mitochondria are highly similar due apparently to recent introgression. These results add to the growing body of evidence for highly heterogeneous patterns of genomic differentiation during speciation, with some genomic regions showing a lack of gene flow between populations many hundreds of thousands of years before other genomic regions.

Faster-haplodiploid evolution under divergence-with-gene-flow: Simulations and empirical data from pine-feeding hymenopterans.

Although haplodiploidy is widespread in nature, the evolutionary consequences of this mode of reproduction are not well characterized. Here, we examine how genome-wide hemizygosity and a lack of recombination in haploid males affects genomic differentiation in populations that diverge via natural selection while experiencing gene flow. First, we simulated diploid and haplodiploid "genomes" (500-kb loci) evolving under an isolation-with-migration model with mutation, drift, selection, migration and recombination; and examined differentiation at neutral sites both tightly and loosely linked to a divergently selected site. As long as there is divergent selection and migration, sex-limited hemizygosity and recombination cause elevated differentiation (i.e., produce a "faster-haplodiploid effect") in haplodiploid populations relative to otherwise equivalent diploid populations, for both recessive and codominant mutations. Second, we used genome-wide single nucleotide polymorphism data to model divergence history and describe patterns of genomic differentiation between sympatric populations of Neodiprion lecontei and N. pinetum, a pair of pine sawfly species (order: Hymenoptera; family: Diprionidae) that are specialized on different pine hosts. These analyses support a history of continuous gene exchange throughout divergence and reveal a pattern of heterogeneous genomic differentiation that is consistent with divergent selection on many unlinked loci. Third, using simulations of haplodiploid and diploid populations evolving according to the estimated divergence history of N. lecontei and N. pinetum, we found that divergent selection would lead to higher differentiation in haplodiploids. Based on these results, we hypothesize that haplodiploids undergo divergence-with-gene-flow and sympatric speciation more readily than diploids.

The Genetic Population Structure of Lake Tanganyika's Lates Species Flock, an Endemic Radiation of Pelagic Top Predators.

Understanding genetic connectivity plays a crucial role in species conservation decisions, and genetic connectivity is an important component of modern fisheries management. In this study, we investigated the population genetics of four endemic Lates species of Lake Tanganyika (Lates stappersii, L. microlepis, L. mariae, and L. angustifrons) using reduced-representation genomic sequencing methods. We find the four species to be strongly differentiated from one another (mean interspecific FST = 0.665), with no evidence for contemporary admixture. We also find evidence for strong genetic structure within L. mariae, with the majority of individuals from the most southern sampling site forming a genetic group that is distinct from the individuals at other sampling sites. We find evidence for much weaker structure within the other three species (L. stappersii, L. microlepis, and L. angustifrons). Our ability to detect this weak structure despite small and unbalanced sample sizes and imprecise geographic sampling locations suggests the possibility for further structure undetected in our study. We call for further research into the origins of the genetic differentiation in these four species-particularly that of L. mariae-which may be important for conservation and management of this culturally and economically important clade of fishes.

Genomic landscape of geographically structured colour polymorphism in a temperate marine fish.

The study of phenotypic variation patterns among populations is fundamental to elucidate the drivers of evolutionary processes. Empirical evidence that supports ongoing genetic divergence associated with phenotypic variation remains very limited for marine species where larval dispersal is a common homogenizing force. We present a genome-wide analysis of a marine fish, Labrus bergylta, comprising 144 samples distributed from Norway to Spain, a large geographical area that harbours a gradient of phenotypic differentiation. We analysed 39,602 biallelic single nucleotide polymorphisms and found a clear latitudinal gradient of genomic differentiation strongly correlated with the variation in phenotypic morph frequencies observed across the North Atlantic. We also detected a strong association between the latitude and the number of loci that appear to be under divergent selection, which increased with differences in coloration but not with overall genetic differentiation. Our results demonstrate that strong reproductive isolation is occurring between sympatric colour morphs of L. bergylta found at the southern areas and provide important new insights into the genomic changes shaping early stages of differentiation that might precede speciation with gene flow.

Positive selection alone is sufficient for whole genome differentiation at the early stage of speciation process in the fall armyworm.

BACKGROUND: The process of speciation involves differentiation of whole genome sequences between a pair of diverging taxa. In the absence of a geographic barrier and in the presence of gene flow, genomic differentiation may occur when the homogenizing effect of recombination is overcome across the whole genome. The fall armyworm is observed as two sympatric strains with different host-plant preferences across the entire habitat. These two strains exhibit a very low level of genetic differentiation across the whole genome, suggesting that genomic differentiation occurred at an early stage of speciation. In this study, we aim at identifying critical evolutionary forces responsible for genomic differentiation in the fall armyworm. RESULTS: These two strains exhibit a low level of genomic differentiation (FST = 0.0174), while 99.2% of 200 kb windows have genetically differentiated sequences (FST > 0). We found that the combined effect of mild positive selection and genetic linkage to selectively targeted loci are responsible for the genomic differentiation. However, a single event of very strong positive selection appears not to be responsible for genomic differentiation. The contribution of chromosomal inversions or tight genetic linkage among positively selected loci causing reproductive barriers is not supported by our data. Phylogenetic analysis shows that the genomic differentiation occurred by sub-setting of genetic variants in one strain from the other. CONCLUSIONS: From these results, we concluded that genomic differentiation may occur at the early stage of a speciation process in the fall armyworm and that mild positive selection targeting many loci alone is sufficient evolutionary force for generating the pattern of genomic differentiation. This genomic differentiation may provide a condition for accelerated genomic differentiation by synergistic effects among linkage disequilibrium generated by following events of positive selection. Our study highlights genomic differentiation as a key evolutionary factor connecting positive selection to divergent selection.

Divergence with gene flow is driven by local adaptation to temperature and soil phosphorus concentration in teosinte subspecies (Zea mays parviglumis and Zea mays mexicana).

Patterns of genomic divergence between hybridizing taxa can be heterogeneous along the genome. Both differential introgression and local adaptation may contribute to this pattern. Here, we analysed two teosinte subspecies, Zea mays ssp. parviglumis and ssp. mexicana, to test whether their divergence has occurred in the face of gene flow and to infer which environmental variables have been important drivers of their ecological differentiation. We generated 9,780 DArTseqTM SNPs for 47 populations, and used an additional data set containing 33,454 MaizeSNP50 SNPs for 49 populations. With these data, we inferred features of demographic history and performed genome wide scans to determine the number of outlier SNPs associated with climate and soil variables. The two data sets indicate that divergence has occurred or been maintained despite continuous gene flow and/or secondary contact. Most of the significant SNP associations were to temperature and to phosphorus concentration in the soil. A large proportion of these candidate SNPs were located in regions of high differentiation that had been identified previously as putative inversions. We therefore propose that genomic differentiation in teosintes has occurred by a process of adaptive divergence, with putative inversions contributing to reduced gene flow between locally adapted populations.

Vertical differentiation in tropical forest butterflies: a novel mechanism generating insect diversity?

Many tropical fruit-feeding nymphalid butterflies are associated with either the forest canopy or the understorey; however, the exceptions offer insights into the origins of tropical diversity. As it occurs in both habitats of tropical forests in Ecuador and Peru, Archaeoprepona demophon is one such exception. We compared patterns of occurrence of A. demophon in the canopy and understorey and population genomic variation for evidence of ecological and genetic differentiation between habitats. We found that butterfly occurrences in the canopy were largely uncorrelated with occurrences in the understorey at both localities, indicating independent demographic patterns in the two habitats. We also documented modest, significant genome-level differentiation at both localities. Genetic differentiation between habitat types (separated by approx. 20 m in elevation) was comparable to levels of differentiation between sampling locations (approx. 1500 km). We conclude that canopy and understorey populations of A. demophon represent incipient independent evolutionary units. These findings support the hypothesis that divergence between canopy and understorey-associated populations might be a mechanism generating insect diversity in the tropics.

A comparison of genomic islands of differentiation across three young avian species pairs.

Detailed evaluations of genomic variation between sister species often reveal distinct chromosomal regions of high relative differentiation (i.e., "islands of differentiation" in FST ), but there is much debate regarding the causes of this pattern. We briefly review the prominent models of genomic islands of differentiation and compare patterns of genomic differentiation in three closely related pairs of New World warblers with the goal of evaluating support for the four models. Each pair (MacGillivray's/mourning warblers; Townsend's/black-throated green warblers; and Audubon's/myrtle warblers) consists of forms that were likely separated in western and eastern North American refugia during cycles of Pleistocene glaciations and have now come into contact in western Canada, where each forms a narrow hybrid zone. We show strong differences between pairs in their patterns of genomic heterogeneity in FST , suggesting differing selective forces and/or differing genomic responses to similar selective forces among the three pairs. Across most of the genome, levels of within-group nucleotide diversity (πWithin ) are almost as large as levels of between-group nucleotide distance (πBetween ) within each pair, suggesting recent common ancestry and/or gene flow. In two pairs, a pattern of the FST peaks having low πBetween suggests that selective sweeps spread between geographically differentiated groups, followed by local differentiation. This "sweep-before-differentiation" model is consistent with signatures of gene flow within the yellow-rumped warbler species complex. These findings add to our growing understanding of speciation as a complex process that can involve phases of adaptive introgression among partially differentiated populations.

Divergent parasite infections in sympatric cichlid species in Lake Victoria.

Parasitism has been proposed as a factor in host speciation, as an agent affecting coexistence of host species in species-rich communities and as a driver of post-speciation diversification. Young adaptive radiations of closely related host species of varying ecological and genomic differentiation provide interesting opportunities to explore interactions between patterns of parasitism, divergence and coexistence of sympatric host species. Here, we explored patterns in ectoparasitism in a community of 16 fully sympatric cichlid species at Makobe Island in Lake Victoria, a model system of vertebrate adaptive radiation. We asked whether host niche, host abundance or host genetic differentiation explains variation in infection patterns. We found significant differences in infections, the magnitude of which was weakly correlated with the extent of genomic divergence between the host species, but more strongly with the main ecological gradient, water depth. These effects were most evident with infections of Cichlidogyrus monogeneans, whereas the only host species with a strictly crevice-dwelling niche, Pundamilia pundamilia, deviated from the general negative relationship between depth and parasitism. In accordance with the Janzen-Connell hypothesis, we also found that host abundance tended to be positively associated with infections in some parasite taxa. Data on the Pundamilia sister species pairs from three other islands with variable degrees of habitat (crevice) specialization suggested that the lower parasite abundance of P. pundamilia at Makobe could result from both habitat specialization and the evolution of specific resistance. Our results support influences of host genetic differentiation and host ecology in determining infections in this diverse community of sympatric cichlid species.

Variation in Linked Selection and Recombination Drive Genomic Divergence during Allopatric Speciation of European and American Aspens.

Despite the global economic and ecological importance of forest trees, the genomic basis of differential adaptation and speciation in tree species is still poorly understood. Populus tremula and Populus tremuloides are two of the most widespread tree species in the Northern Hemisphere. Using whole-genome re-sequencing data of 24 P. tremula and 22 P. tremuloides individuals, we find that the two species diverged ∼2.2-3.1 million years ago, coinciding with the severing of the Bering land bridge and the onset of dramatic climatic oscillations during the Pleistocene. Both species have experienced substantial population expansions following long-term declines after species divergence. We detect widespread and heterogeneous genomic differentiation between species, and in accordance with the expectation of allopatric speciation, coalescent simulations suggest that neutral evolutionary processes can account for most of the observed patterns of genetic differentiation. However, there is an excess of regions exhibiting extreme differentiation relative to those expected under demographic simulations, which is indicative of the action of natural selection. Overall genetic differentiation is negatively associated with recombination rate in both species, providing strong support for a role of linked selection in generating the heterogeneous genomic landscape of differentiation between species. Finally, we identify a number of candidate regions and genes that may have been subject to positive and/or balancing selection during the speciation process.

Genomic differentiation and patterns of gene flow between two long-tailed tit species (Aegithalos).

Patterns of heterogeneous genomic differentiation have been well documented between closely related species, with some highly differentiated genomic regions ("genomic differentiation islands") spread throughout the genome. Differential levels of gene flow are proposed to account for this pattern, as genomic differentiation islands are suggested to be resistant to gene flow. Recent studies have also suggested that genomic differentiation islands could be explained by linked selection acting on genomic regions with low recombination rates. Here, we investigate genomic differentiation and gene-flow patterns for autosomes using RAD-seq data between two closely related species of long-tailed tits (Aegithalos bonvaloti and A. fuliginosus) in both allopatric and contact zone populations. The results confirm recent or ongoing gene flow between these two species. However, there is little evidence that the genomic regions that were found to be highly differentiated between the contact zone populations are resistant to gene flow, suggesting that differential levels of gene flow is not the cause of the heterogeneous genomic differentiation. Linked selection may be the cause of genomic differentiation islands between the allopatric populations with no or very limited gene flow, but this could not account for the heterogeneous genomic differentiation between the contact zone populations, which show evidence of recent or ongoing gene flow.

Strong reproductive isolation and narrow genomic tracts of differentiation among three woodpecker species in secondary contact.

Hybrid zones allow the measurement of gene flow across the genome, producing insight into the genomic architecture of speciation. Such analysis is particularly powerful when applied to multiple pairs of hybridizing species, as patterns of genomic differentiation can then be related to age of the hybridizing species, providing a view into the build-up of differentiation over time. We examined 33 809 single nucleotide polymorphisms (SNPs) in three hybridizing woodpecker species: Red-breasted, Red-naped and Yellow-bellied sapsuckers (Sphyrapicus ruber, Sphyrapicus nuchalis and Sphyrapicus varius), two of which (ruber and nuchalis) are much more closely related than each is to the third (varius). To identify positions of SNPs on chromosomes, we developed a localization method based on comparative genomics. We found narrow clines, bimodal distributions of hybrid indices and genomic regions with decreased rates of introgression. These results suggest moderately strong reproductive isolation among species and selection against specific hybrid genotypes. We found 19 small regions of strong differentiation between species, partly shared among species pairs, but no large regions of differentiation. An association analysis revealed a single strong-effect candidate locus associated with plumage, possibly explaining mismatch among the three species in genomic relatedness and plumage similarity. Our comparative analysis of species pairs of different age and their hybrid zones showed that moderately strong reproductive isolation can occur with little genomic differentiation, but that reproductive isolation is incomplete even with much greater genomic differentiation, implying there are long periods of time when hybridization is possible if diverging populations are in geographic contact.

Recurrent selection explains parallel evolution of genomic regions of high relative but low absolute differentiation in a ring species.

Recent technological developments allow investigation of the repeatability of evolution at the genomic level. Such investigation is particularly powerful when applied to a ring species, in which spatial variation represents changes during the evolution of two species from one. We examined genomic variation among three subspecies of the greenish warbler ring species, using genotypes at 13 013 950 nucleotide sites along a new greenish warbler consensus genome assembly. Genomic regions of low within-group variation are remarkably consistent between the three populations. These regions show high relative differentiation but low absolute differentiation between populations. Comparisons with outgroup species show the locations of these peaks of relative differentiation are not well explained by phylogenetically conserved variation in recombination rates or selection. These patterns are consistent with a model in which selection in an ancestral form has reduced variation at some parts of the genome, and those same regions experience recurrent selection that subsequently reduces variation within each subspecies. The degree of heterogeneity in nucleotide diversity is greater than explained by models of background selection, but is consistent with selective sweeps. Given the evidence that greenish warblers have had both population differentiation for a long period of time and periods of gene flow between those populations, we propose that some genomic regions underwent selective sweeps over a broad geographic area followed by within-population selection-induced reductions in variation. An important implication of this 'sweep-before-differentiation' model is that genomic regions of high relative differentiation may have moved among populations more recently than other genomic regions.

Genomic differentiation in Pacific cod using Pool-Seq.

Patterns of genetic differentiation across the genome can provide insight into selective forces driving adaptation. We used pooled whole genome sequencing, gene annotation, and environmental covariates to evaluate patterns of genomic differentiation and to investigate mechanisms responsible for divergence among proximate Pacific cod (Gadus macrocephalus) populations from the Bering Sea and Aleutian Islands and more distant Washington Coast cod. Samples were taken from eight spawning locations, three of which were replicated to estimate consistency in allele frequency estimation. A kernel smoothing moving weighted average of relative divergence (F ST) identified 11 genomic islands of differentiation between the Aleutian Islands and Bering Sea samples. In some islands of differentiation, there was also elevated absolute divergence (d XY) and evidence for selection, despite proximity and potential for gene flow. Similar levels of absolute divergence (d XY) but roughly double the relative divergence (F ST) were observed between the distant Bering Sea and Washington Coast samples. Islands of differentiation were much smaller than the four large inversions among Atlantic cod ecotypes. Islands of differentiation between the Bering Sea and Aleutian Island were associated with SNPs from five vision system genes, which can be associated with feeding, predator avoidance, orientation, and socialization. We hypothesize that islands of differentiation between Pacific cod from the Bering Sea and Aleutian Islands provide evidence for adaptive differentiation despite gene flow in this commercially important marine species.

The Past and Future of Experimental Speciation.

Speciation is the result of evolutionary processes that generate barriers to gene flow between populations, facilitating reproductive isolation. Speciation is typically studied via theoretical models and snapshot tests in natural populations. Experimental speciation enables real-time direct tests of speciation theory and has been long touted as a critical complement to other approaches. We argue that, despite its promise to elucidate the evolution of reproductive isolation, experimental speciation has been underutilised and lags behind other contributions to speciation research. We review recent experiments and outline a framework for how experimental speciation can be implemented to address current outstanding questions that are otherwise challenging to answer. Greater uptake of this approach is necessary to rapidly advance understanding of speciation.

Genetic architecture, demographic history, and genomic differentiation of Populus davidiana revealed by whole-genome resequencing.

Forest trees are an excellent resource from which to understand population differentiation and heterogeneous genome variation patterns due to the majority of forest trees being distributed widely and able to adapt to different climates and environments. Populus davidiana is among the most geographically widespread and ecologically important tree species in China. Whole-genome resequencing data of 75 individual examples of P. davidiana throughout China were conducted, finding that all examples from different regions were clearly divided into either Northeast (N), Central (C), and South (S) populations. The ancestors of P. davidiana diverged into Northern group, comprising both N and C and Southern populations approximately 792,548 years ago. This time point of differentiation suggests that divergence of P. davidiana populations might have been triggered by the mid-Pleistocene transition. The three populations experienced considerable periods of bottleneck following divergence, with population expansion beginning around 5,000 years ago after the end of the last glacial maximum. We found N to be the center of origin of P. davidiana in China. The migration route of P. davidiana in China was from N to S. Although the majority of the regions of genomic differentiation between N and S populations can be explained by neutral processes, a number of tested outlier regions were also found to have been significantly influenced by natural selection. Our results highlight that linked selection and rates of recombination were important factors in genomic differentiation between the N and S populations. Finally, we identified a substantial number of functional genes related to climate change during population differentiation and adaptive evolution.

A Single Interacting Species Leads to Widespread Parallel Evolution of the Stickleback Genome.

Biotic interactions are potent, widespread causes of natural selection and divergent phenotypic evolution and can lead to genetic differentiation with gene flow among wild populations ("isolation by ecology") [1-4]. Biotic selection has been predicted to act on more genes than abiotic selection thereby driving greater adaptation [5]. However, difficulties in isolating the genome-wide effect of single biotic agents of selection have limited our ability to identify and quantify the number and type of genetic regions responding to biotic selection [6-9]. We identified geographically interspersed lakes in which threespine stickleback fish (Gasterosteus aculeatus) have repeatedly adapted to the presence or absence of a single member of the ecological community, prickly sculpin (Cottus asper), a fish that is both a competitor and a predator of the stickleback [10]. Whole-genome sequencing revealed that sculpin presence or absence accounted for the majority of genetic divergence among stickleback populations, more so than geography. The major axis of genomic variation within and between the two lake types was correlated with multiple traits, indicating parallel natural selection across a gradient of biotic environments. A large proportion of the genome-about 1.8%, encompassing more than 600 genes-differentiated stickleback from the two biotic environments. Divergence occurred in 141 discrete genomic clumps located mainly in regions of low recombination, suggesting that genes brought to lakes by the colonizing ancestral population often evolved together in linked blocks. Strong selection and a wealth of standing genetic variation explain how a single member of the biotic community can have such a rapid and profound evolutionary impact.

Unifying Theoretical and Empirical Perspectives on Genomic Differentiation.

Differentiation is often heterogeneous across the genomes of diverging populations. Despite substantial recent progress, much work remains to improve our abilities to connect genomic patterns to underlying evolutionary processes. Crosstalk between theoretical and empirical research has shaped the field of evolutionary genetics since its foundation and needs to be greatly enhanced for modern datasets. We leverage recent insights from theoretical and empirical studies to identify existing gaps and suggest pathways across them. We stress the importance of reporting empirical data in standardized ways to enable meta-analyses and to facilitate parameterization of analyses and models. Additionally, a more comprehensive view of potential mechanisms - especially considering variable recombination rates and ubiquitous background selection - and their interactions should replace common, oversimplified assumptions.