Rapid formation of distinct hybrid lineages after secondary contact of two fish species (Cottus sp.)

Homoploid hybridization after secondary contact between related species can lead to mixtures of genotypes which have the potential for rapid adaptation to new environmental conditions. Here, we focus on a case where anthropogenic changes within the past 200 years have allowed the hybridization between two fish species (Cottus rhenanus and Cottus perifretum) in the Netherlands. Specifically, we address the question of the dynamics of the emergence of these hybrids and invasion of the river systems. Using a set of 81 mostly ancestry-informative SNP markers, as well as broad sample coverage in and around the area of the initial contact, we find a structured hybrid swarm with at least three distinct hybrid lineages that have emerged out of this secondary contact situation. We show that genetically coherent groups can occur at geographically distant locations, while geographically adjacent groups can be genetically different, indicating that some form of reproductive isolation between the lineages is already effective. Using a newly developed modelling approach, we test the relative influence of founding admixture, drift and migration on the allele compositions of the sampling sites. We find that the allele frequency distributions can best be explained if continued gene flow between the parental species and the hybrid lineages is invoked. Genome mapping of the invasive lineage in the Rhine shows that major chromosomal rearrangements were not involved in creating this distinct lineage. Our results show that hybridization after secondary contact can quickly lead to multiple independent new lineages that have the capacity to form hybrid species.     

Making inferences about speciation using sophisticated statistical genetics methods: look before you leap

Understanding speciation is a fundamental aim of evolutionary biology and a very challenging one. Speciation can be viewed as the dynamics of genetic differentiation between populations resulting in substantial reproductive isolation (Gavrilets 2003). It was generally accepted that very small levels of migration prevent genetic differentiation among populations and, therefore, speciation. However, recent theoretical work showed that sympatric speciation is possible (Gavrilets 2003). Nevertheless, providing empirical evidence that gene flow occurred during speciation is challenging because several gene flow scenarios can explain observed patterns of genetic differentiation. Positive migration rate estimates alone do not prove ongoing gene flow during divergence. We also need to know whether migration took place before, during or after speciation. There is no statistical method specifically aimed at estimating gene flow timing, but several studies used the isolation with migration model (Hey & Nielsen 2004, 2007; Hey 2010b) to estimate this parameter and make inferences about speciation scenarios. It is tempting to use statistical methods to estimate important evolutionary parameters even if they do not appear explicitly in the inference model. Nevertheless, before doing so, we need to determine whether they can provide reliable results. In this issue of Molecular Ecology, Strasburg and Rieseberg (2011) present a simulation study that examines the degree to which gene flow timing estimates obtained from IMa2 (Hey 2010b) can be used to make inferences about speciation mode. Their results are sobering; gene flow timing estimates obtained in this way are not reliable and cannot be used to unequivocally establish if gene flow was ongoing during speciation.     

A road map for molecular ecology

The discipline of molecular ecology has undergone enormous changes since the journal bearing its name was launched approximately two decades ago. The field has seen great strides in analytical methods development, made groundbreaking discoveries and experienced a revolution in genotyping technology. Here, we provide brief perspectives on the main subdisciplines of molecular ecology, describe key questions and goals, discuss common challenges, predict future research directions and suggest research priorities for the next 20 years.     

Speciation and Species Separation in Hordeum L. (Poaceae) Resolved by Discontinuous Molecular Markers1

Abstract: Amplified fragment length polymorphisms (AFLPs) were used to evaluate the capacity of discontinuous markers to reveal genetic structure within Hordeum , a challenging higher plant genus from the standpoint of natural systematics. Phylogenies of 63 accessions encompassing nine species from four Hordeum sections were inferred from polymorphisms scored at 600 loci. Phylogenies based on sequences from the nuclear internal transcribed spacer (ITS) region were constructed for comparison, but revealed severe sampling errors inherent to single genes. Although superior by virtue of providing genome-wide estimates of genetic similarity, the adoption of AFLPs in infrageneric studies requires caution. Comigrating AFLP bands studied here could be divided on the basis of band intensity variation into two types that are □ 100 % identical and < 40 % identical in DNA sequence, respectively, in infrageneric comparisons. Thus, the careful selection of AFLP bands to be analyzed bears heavily upon their phylogenetic utility. Within the H. murinum complex, which encompasses three morphologically distinct subspecies, AFLP data from 37 accessions reveal unexpected genetic differentiation between H. murinum, glaucum populations to the east and west of Alexandria (Egypt), suggesting the presence of allopatric speciation in the wake of human settlement.     

An anomalous hybrid zone in Drosophila

Abstract Despite the genetic tractability of many of Drosophila species, the genus has few examples of the “classic” type of hybrid zone, in which the ranges of two species overlap with a gradual transition from one species to another through an area where hybrids are produced. Here we describe a classic hybrid zone in Drosophila that involves two sister species, Drosophila yakuba and D. santomea, on the island of SaTo Tomé. Our transect of this zone has yielded several surprising and anomalous findings. First, we detected the presence of an additional hybrid zone largely outside the range of both parental species. This phenomenon is, to our knowledge, unique among animals. Second, the genetic analysis using diagnostic molecular markers of the flies collected in this anomalous hybrid zone indicates that nearly all hybrid males are F₁s that carry the D. santomea X chromosome. This F₁ genotype is much more difficult to produce in the laboratory compared to the genotype from the reciprocal cross, showing that sexual isolation as seen in the laboratory is insufficient to explain the genotypes of hybrids found in the wild. Third, there is a puzzling absence of hybrid females. We suggest several tentative explanations for the anomalies associated with this hybrid zone, but for the present they remain a mystery.     

Scaling up: examining the macroecology of ectomycorrhizal fungi

Ectomycorrhizal (ECM) fungi play major ecological roles in temperate and tropical ecosystems. Although the richness of ECM fungal communities and the factors controlling their structure have been documented at local spatial scales, how they vary at larger spatial scales remains unclear. In this issue of Molecular Ecology, Tedersoo et al. (2012) present the results of a meta‐analysis of ECM fungal community structure that sheds important new light on global‐scale patterns. Using data from 69 study systems and 6021 fungal species, the researchers found that ECM fungal richness does not fit the classic latitudinal diversity gradient in which species richness peaks at lower latitudes. Instead, richness of ECM fungal communities has a unimodal relationship with latitude that peaks in temperate zones. Intriguingly, this conclusion suggests the mechanisms driving ECM fungal community richness may differ from those of many other organisms, including their plant hosts. Future research will be key to determine the robustness of this pattern and to examine the processes that generate and maintain global‐scale gradients of ECM fungal richness.     

Sunflower genetic,genomic and ecological resources

Long a major focus of genetic research and breeding, sunflowers (Helianthus) are emerging as an increasingly important experimental system for ecological and evolutionary studies. Here, we review the various attributes of wild and domesticated sunflowers that make them valuable for ecological experimentation and describe the numerous publicly available resources that have enabled rapid advances in ecological and evolutionary genetics. Resources include seed collections available from germplasm centres at the USDA and INRA, genomic and EST sequences, mapping populations, genetic markers, genetic and physical maps and other forward‐ and reverse‐genetic tools. We also discuss some of the key evolutionary, genetic and ecological questions being addressed in sunflowers, as well as gaps in our knowledge and promising areas for future research.     

Vertical partitioning between sister species of Rhizopogon fungi on mesic and xeric sites in an interior Douglas‐fir forest

Understanding ectomycorrhizal fungal (EMF) community structure is limited by a lack of taxonomic resolution and autecological information. Rhizopogon vesiculosus and Rhizopogon vinicolor (Basidiomycota) are morphologically and genetically related species. They are dominant members of interior Douglas‐fir (Pseudotsuga menziesii var. glauca) EMF communities, but mechanisms leading to their coexistence are unknown. We investigated the microsite associations and foraging strategy of individual R. vesiculosus and R. vinicolor genets. Mycelia spatial patterns, pervasiveness and root colonization patterns of fungal genets were compared between Rhizopogon species and between xeric and mesic soil moisture regimes. Rhizopogon spp. mycelia were systematically excavated from the soil and identified using microsatellite DNA markers. Rhizopogon vesiculosus mycelia occurred at greater depth, were more spatially pervasive, and colonized more tree roots than R. vinicolor mycelia. Both species were frequently encountered in organic layers and between the interface of organic and mineral horizons. They were particularly abundant within microsites associated with soil moisture retention. The occurrence of R. vesiculosus shifted in the presence of R. vinicolor towards mineral soil horizons, where R. vinicolor was mostly absent. This suggests that competition and foraging strategy may contribute towards the vertical partitioning observed between these species. Rhizopogon vesiculosus and R. vinicolor mycelia systems occurred at greater mean depths and were more pervasive in mesic plots compared with xeric plots. The spatial continuity and number of trees colonized by genets of each species did not significantly differ between soil moisture regimes.     

Cohabitation and roommate bias of symbiotic bacteria in insect hosts

Symbiotic interactions between insects and bacteria have long fascinated ecologists. Aphids have emerged as the model system on which to study the effect of endosymbiotic bacteria on their hosts. Aphid‐symbiont interactions are ecologically interesting as aphids host multiple secondary symbionts that can provide broad benefits, such as protection against heat stress or specialist natural enemies (parasitic wasps and entomopathogenic fungi). There are nine common aphid secondary symbionts and individual aphids host on average 1–2 symbionts. A cost‐benefit trade‐off for hosting symbionts is thought to explain why not all aphids host every possible symbiont in a population. Both positive and negative associations between various symbionts occur, and this could happen due to increased costs when cohosting certain combinations or as a consequence of competitive interactions between the symbionts within a host. In this issue of Molecular Ecology, Mathé‐Hubert, Kaech, Hertaeg, Jaenike, and Vorburger (2019) use data on the symbiont status of field‐collected aphids to inform a model on the evolution of symbiont co‐occurrence. They vary the effective female population size as well as the rate of horizontal and maternal transmission to infer the relative impact of symbiont‐symbiont interactions versus random drift. Additional data analysis revisits an association between two symbionts in a fruit fly species using a long‐term data set to highlight that such interactions are not limited to aphids.     

Generic scan using AFLP markers as a means to assess the role of directional selection in the divergence of sympatric whitefish ecotypes

Under the ecological theory of adaptive radiation, adaptation and reproductive isolation are thought to evolve as a result of divergent natural selection. Accordingly, elucidating the genetic basis of these processes is essential toward understanding the role of selection in shaping biological diversity. In this respect, the number of genes that evolved by selection remains contentious. To address this issue, the pattern of genetic differentiation obtained using 440 AFLP loci was compared with that expected under neutrality in four sympatric pairs of lake whitefish ecotypes that evolved adaptive phenotypic differences associated with the exploitation of distinct ecological niches. On average, 14 loci showed restricted gene flow relative to neutral expectation, suggesting a role of directional selection on their divergence. Among all loci that are most likely under directional selection, six exhibited parallel patterns of divergence, which provided further support for the role of selection in driving their divergence. Overall, these results indicate that only a small proportion of scored AFLP loci (between 1.4% and 3.2%) might be linked to genes implicated in the adaptive radiation of lake whitefish.     

Altitudinal gradients,plant hybrid zones and evolutionary novelty

Altitudinal gradients are characterized by steep changes of the physical and biotic environment that present challenges to plant adaptation throughout large parts of the world. Hybrid zones may form where related species inhabit different neighbouring altitudes and can facilitate interspecific gene flow and potentially the breakdown of species barriers. Studies of such hybrid zones can reveal much about the genetic basis of adaptation to environmental differences stemming from changes in altitude and the maintenance of species divergence in the face of gene flow. Furthermore, owing to recombination and transgressive effects, such hybrid zones can be sources of evolutionary novelty. We document plant hybrid zones associated with altitudinal gradients and emphasize similarities and differences in their structure. We then focus on recent studies of a hybrid zone between two Senecio species that occur at high and low altitude on Mount Etna, Sicily, showing how adaptation to local environments and intrinsic selection against hybrids act to maintain it. Finally, we consider the potential of altitudinal hybrid zones for generating evolutionary novelty through adaptive introgression and hybrid speciation. Examples of homoploid hybrid species of Senecio and Pinus that originated from altitudinal hybrid zones are discussed.     

The role of hybridization and introgression in maintaining species integrity and cohesion in naturally isolated inselberg bromeliad populations

• Hybridization is a widespread phenomenon present in numerous lineages across the tree of life. Its evolutionary consequences range from effects on the origin and maintenance, to the loss of biodiversity.
• We studied genetic diversity and intra‐ and interspecific gene flow between two sympatric populations of closely‐related species, Pitcairnia flammea and P. corcovadensis (Bromeliaceae), which are adapted to naturally fragmented Neotropical inselbergs, based on nuclear and plastidial DNA.
• Our main results indicate a strong reproductive isolation barrier, although low levels of interspecific gene flow were observed in both sympatric populations. The low rates of intraspecific gene flow observed for both P. corcovadensis and P. flammea populations corroborate the increasing body of evidence that inselberg bromeliad species are maintained as discrete evolutionary units despite the presence of low genetic connectivity. Nuclear patterns of genetic diversity and gene flow revealed that hybridization and introgression might not cause species extinction via genetic assimilation of the rare P. corcovadensis.
• In the face of reduced intraspecific gene exchange, hybridization and introgression may be important aspects of the Pitcairnia diversification process, with a positive evolutionary impact at the bromeliad community level, and thus contribute to increasing and maintaining genetic diversity in local isolated inselberg populations.

     

Biofilm transplantation in the deep sea

A gold rush is currently going on in microbial ecology, which is powered by the possibility to determine the full complexity of microbial communities through next‐generation sequencing. Accordingly, enormous efforts are underway to describe microbiomes worldwide, in humans, animals, plants, soil, air and the ocean. While much can be learned from these studies, only experiments will finally unravel mechanisms. One of the key questions is how a microbial community is assembled from a pool of bacteria in the environment, and how it responds to change – be it the increase in CO₂ concentration in the ocean, or antibiotic treatment of the gut microbiome. The study by Zhang et al. ( 2016 ) in this issue is one of the very few that approaches this problem experimentally in the natural environment. The authors selected a habitat which is both extremely interesting and difficult to access. They studied the Thuwal Seep in the Red Sea at 850 m depth and used a remotely operated vehicle (ROV) to place a steel frame carrying substrata for biofilm growth into the brine pool and into the adjacent normal bottom water (NBW). Biofilms were allowed to develop for 3 days, and then those that had been growing in the brine pool were transported to normal bottom water and stayed there for another 3 days, and vice versa. The ‘switched’ biofilms were then compared with their source communities by metagenome sequencing. Strikingly, both ‘switched’ biofilms were now dominated by the same two species. These species were able to cope with conditions in both source ecosystems, as shown by assembly of their genomes and detection of expression of key genes. The biofilms had adapted to environmental change, rather than to brine pools or NBW. The study shows both the resilience and adaptability of biofilm communities and has implications for microbial ecology in general and even for therapeutic approaches such as transplantation of faecal microbiomes.     

Effects of canopy connectivity on the arboreal ant community in coffee shade trees

Canopy connectivity influences foraging, movement, and competition in arboreal ant communities. Understanding how canopy connectivity affects arboreal ant communities could inform the development of management practices that maximize services from known biocontrol agents. We experimentally manipulated connectivity between the crowns of large shade trees to investigate the effects of canopy connectivity on arboreal ant species richness and composition in a coffee agroecosystem. A linear mixed-effects analysis showed that the number of species observed at baits set in tree crowns increased significantly after the crowns had been connected with nylon ropes. Crowns that were connected increased in similarity of ant species composition, particularly between adjacent connected crowns. Connectivity may increase the number of species present in tree crowns by allowing ants to move and forage in the canopy while bypassing trunks with more aggressive, territorial species such as Azteca sericeasur. Because twig-nesting species in the upper canopy have been shown to act as biocontrol agents of herbivores, an increase in species richness in tree crowns could have positive implications for agricultural pest-control services.     

Host associations and beta diversity of fungal endophyte communities in New Guinea rainforest trees

Processes shaping the distribution of foliar fungal endophyte species remain poorly understood. Despite increasing evidence that these cryptic fungal symbionts of plants mediate interactions with pathogens and herbivores, there remain basic questions regarding the extent to which dispersal limitation and host specificity might shape fungal endophyte community composition in rainforests. To assess the relative importance of spatial pattern and host specificity, we isolated fungi from a sample of mapped trees in lowland Papua New Guinea. Sequences of the internal transcribed spacer (ITS) region were obtained for 2079 fungal endophytes from three sites and clustered into molecular operational taxonomic units (MOTUs) at 95% similarity. Multivariate analyses suggest that host affinity plays a significant role in structuring endophyte community composition whereas there was no evidence of endophyte spatial pattern at the scale of tens to hundreds of metres. Differences in endophyte communities between sampled trees were weakly correlated with variation in foliar traits but not with tree species relatedness. The dominance of relatively few generalist endophytes and the presence of a large number of rare MOTUs was a consistent observation at three sites separated by hundreds of kilometres and regional turnover was low. Host specificity appears to play a relatively weak but more important role than dispersal limitation in shaping the distribution of fungal endophyte communities in New Guinea forests. Our results suggest that in the absence of strong ecological gradients and host turnover, beta diversity of endophyte communities could be low in large areas of contiguous forest.     

Behavioral and Physiological Differences between Two Parapatric Heliconius Species1

The behavior and physiology of two parapatric sibling species, i Heliconius erato cyrbia Godt. and H. himera Hew., were investigated to assess if environmental adaptation enabled stable morphological, genetic, and ecological differences to exist in the face of hybridization. Morning and evening activity, egg production, and larval development time of H. himera and H. erato in insectaries were recorded; individuals were collected in allopatry and in sympatry from a hybrid zone in which the species overlapped. Studies were performed at ambient conditions within the natural range of H. himera. H. himera was considerably more active than H, erato flying earlier in the morning and later in the evening, even when both species were collected in sympatry. Similarly, H. himera laid more eggs, and the hatched larvae developed more rapidly. The results suggest that physiological constraints are an important selective force that may have been important in speciation and counteracts hybridization in the maintenance of the H. himeral H. erato contact zone. Ecological selection, arising from adaptation to low temperatures, may help explain the competitive exclusion of H. erato by H. himera in the drier, cooler montane habitat favored by the latter species.     

Butterfly genomics sheds light on the process of hybrid speciation

How common is hybridization between species and what effect does it have on the evolutionary process? Can hybridization generate new species and what indeed is a species? In this issue, Gompert et al. (2014) show how massive, genome‐scale data sets can be used to shed light on these questions. They focus on the Lycaeides butterflies, and in particular, several populations from the western USA, which have characteristics suggesting that they may contain hybrids of two or more different species (Gompert et al. 2006). They demonstrate that these populations do contain mosaic genomes made up of components from different parental species. However, this appears to have been largely driven by historical admixture, with more recent processes appearing to be isolating the populations from each other. Therefore, these populations are on their way to becoming distinct species (if they are not already) but have arisen following extensive hybridization between other distinct populations or species (Fig.  1 ).

Figure 1 Open in figure viewer PowerPoint There has been extensive historical admixture between Lycaeides species with some new species arising from hybrid populations. (Photo credits: Lauren Lucas, Chris Nice, and James Fordyce).

Their data set must be one of the largest outside of humans, with over one and half thousand butterflies genotyped at over 45 thousand variable nucleotide positions. It is this sheer amount of data that has allowed the researchers to distinguish between historical and more recent evolutionary and demographic processes. This is because it has allowed them to partition the data into common and rare genetic variants and perform separate analyses on these. Common genetic variants are likely to be older while rare variants are more likely to be due to recent mutations. Therefore, by splitting the genetic variation into these components, the researchers were able to show more admixture among common variants, while rare variants showed less admixture and clear separation of the populations. The extensive geographic sampling of individuals, including overlapping distributions of several of the putative species, also allowed the authors to rule out the possibility that the separation of the populations was simply due to geographical distance. The authors have developed a new programme for detecting population structure and admixture, which does the same job as STRUCTURE (Pritchard et al. 2000 ), identifying genetically distinct populations and admixture between these populations, but is designed to be used with next generation sequence data. They use the output of this model for another promising new method to distinguish between contemporary and historical admixtures. They fixed the number of source populations in the model at two and estimated the proportion of each individual's genome coming from these two populations. Therefore, an individual can either be purely population 1, or population 2 or some mixture of the two (they call this value q, the same parameter exists in STRUCTURE). They then compared this to the level of heterozygosity coming from the two source populations in the individual's genome. If an individual is an F1 hybrid of two source populations, then it would have a q of 0.5 and also be heterozygous at all loci that distinguish the parental populations. On the other hand, if it is a member of a stable hybrid lineage, it might also have a q of 0.5 but would not be expected to be heterozygous at these loci, because over time the population would become fixed for one or other of the source population states either by drift or selection (Fig.  2 ). This is indeed what they find in the hybrid populations. They tend to have intermediate q values, but the level of heterozygosity coming from the source populations (which they call Q₁₂) was consistently lower than expected.

Figure 2 Open in figure viewer PowerPoint The Q‐matrix analysis used by Gompert et al. ( 2014 ) to distinguish between contemporary (hybrid swarm) and historical (stable hybrid lineage) admixture.

Overall, the results support several of the populations as being stable hybrid lineages. Nevertheless, the strictest definitions of hybrid species specify that the process of hybridization between the parental species must be instrumental in driving the reproductive isolation of the new species from both parental populations (Abbott et al. 2013 ). This is extremely hard to demonstrate conclusively because it requires us to first of all identify the isolating mechanisms that operated in the early evolution of the species and then to show that these were caused by the hybridization event itself. One advantage of the Lycaeides system is that the species appear to be in the early stages of divergence, so barriers to gene flow that are operating currently are likely to be those that are driving the species divergence. While there is some evidence that hybridization gave rise to traits that allowed the new populations to colonize new environments (Gompert et al. 2006 ; Lucas et al. 2008 ), there is clearly further work to be carried out in this direction. One of the rare examples of homoploid hybrid speciation (hybrid speciation without a change in chromosome number) where the reproductive isolation criterion has been demonstrated, comes from the Heliconius butterflies. In this case, hybridization of two species has been shown to give rise to a new colour pattern that instantly becomes reproductively isolated from the parental species due to mate preference for that pattern (Mavárez et al. 2006 ). However, while this has become a widely accepted example (Abbott et al. 2013 ), the naturally occurring ‘hybrid species’ in fact has derived most of its genome from one of the parental species, with largely just the colour pattern controlling locus coming from the other parent, a process that has been termed ‘hybrid trait speciation’ (Salazar et al. 2010 ). This distinction is an important one in terms of our understanding of the organization of biological diversity. While hybrid trait speciation will still largely fit the model of a neatly branching evolutionary tree, with perhaps only the region surrounding the single introgressed gene deviating from this model, hybrid species that end up with mosaic genomes, like Lycaeides, will not fit this model when considering the genome as a whole. This distinction also more broadly applies when comparing the patterns of divergence between Heliconius and Lycaeides. These two butterfly genera have been driving forward our understanding of the prevalence and importance of hybridization at the genomic level, but they reveal different ways in which hybridization can influence the organization of biological diversity. Recent work in Heliconius has shown that admixture is extensive and has been ongoing over a large portion of the evolutionary history of species (Martin et al. 2013 ; Nadeau et al. 2013 ). Nevertheless, this has not obscured the clear and robust pattern of a bifurcating evolutionary tree when considering the genome as a whole (Nadeau et al. 2013 ). In contrast in Lycaeides, the genome‐wide phylogeny clearly does not fit a bifurcating tree, resembling more of a messy shrub, with hybrid taxa falling at intermediate positions on the phylogeny (Gompert et al. 2014 ). The extent to which we need to rethink the way we describe and organize biological diversity will depend on the relative prevalence of these different outcomes of hybridization. We are likely to see many more of these types of large sequence data sets for ecologically interesting organisms. Gompert et al. ( 2014 ) show that these data need not only be a quantitative advance, but can also qualitatively change our understanding of the evolutionary history of these organisms. In particular, analysing common and rare genetic variants separately may provide information that would otherwise be missed. The emerging field of ‘speciation genomics’ (Seehausen et al. 2014 ) should follow this lead in developing new ways of making the most of the flood of genomic data that is being generated, but also improve methods for integrating this with field observations and experiments to identify the sources and targets of selection and divergence.

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This article was written and figures prepared by N.N. except as specified in the text (photo credits).

Citing Literature

Number of times cited according to CrossRef: 4

• V. Alex Sotola, David S. Ruppel, Timothy H. Bonner, Chris C. Nice, Noland H. Martin, Asymmetric introgression between fishes in the Red River basin of Texas is associated with variation in water quality, Ecology and Evolution, 10.1002/ece3.4901, 9 , 4, (2083-2095), (2019). Wiley Online Library
• Matej Bocek, Dominik Kusy, Michal Motyka, Ladislav Bocak, Persistence of multiple patterns and intraspecific polymorphism in multi-species Müllerian communities of net-winged beetles, Frontiers in Zoology, 10.1186/s12983-019-0335-8, 16 , 1, (2019). Crossref
• Nicola J. Nadeau, Takeshi Kawakami, Population Genomics of Speciation and Admixture, , 10.1007/13836_2018_24, (2018). Crossref
• Amanda Roe, Julian Dupuis, Felix Sperling, Molecular Dimensions of Insect Taxonomy in the Genomics Era, Insect Biodiversity, 10.1002/9781118945568, (547-573), (2017). Wiley Online Library

Volume 23 , Issue 18 September 2014

Pages 4441-4443     

Ghost Introgression: Spooky Gene Flow in the Distant Past

Evolution is a continuous trial and error process in which most lineages go extinct without leaving fossil remains. Many of these lineages would be closely related and occasionally hybridized with lineages that gave rise to extant species. Hence, it is likely that one can find genetic signatures of these ancient introgression events in present-day genomes, so-called ghost introgression. The increasing availability of high-quality genome assemblies for non-model organisms and the development of more sophisticated methods for detecting introgression will undoubtedly reveal more cases of ghost introgression, indicating that the Tree of Life is even more reticulated than assumed. The presence of ghost introgression has important consequences for the study of numerous evolutionary processes, including adaptation, speciation, and macroevolutionary patterns. In addition, detailed studies of introgressed regions could provide insights into the morphology of the extinct lineage, providing an unexpected link between genomics and the fossil record. Hence, new methods that take into account ghost introgression will need to be developed.