The role of founder effects on the evolution of reproductive isolation

Reproductive isolation arises during laboratory adaptation to a novel hot environment

BACKGROUND

Reproductive isolation can result from adaptive processes (e.g., ecological speciation and mutation-order speciation) or stochastic processes such as "system drift" model. Ecological speciation predicts barriers to gene flow between populations from different environments, but not among replicate populations from the same environment. In contrast, reproductive isolation among populations independently adapted to the same/similar environment can arise from both mutation-order speciation or system drift.

RESULTS

In experimentally evolved populations adapting to a hot environment for over 100 generations, we find evidence for pre- and postmating reproductive isolation. On one hand, an altered lipid metabolism and cuticular hydrocarbon composition pointed to possible premating barriers between the ancestral and replicate evolved populations. On the other hand, the pronounced gene expression differences in male reproductive genes may underlie the postmating isolation among replicate evolved populations adapting to the same environment with the same standing genetic variation.

CONCLUSION

Our study confirms that replicated evolution experiments provide valuable insights into the mechanisms of speciation. The rapid emergence of the premating reproductive isolation during temperature adaptation showcases incipient ecological speciation. The potential evidence of postmating reproductive isolation among replicates gave rise to two hypotheses: (1) mutation-order speciation through a common selection on early fecundity leading to an inherent inter-locus sexual conflict; (2) system drift with genetic drift along the neutral ridges.

Landscape genetics across the Andes mountains: Environmental variation drives genetic divergence in the leaf-cutting ant Atta cephalotes

Distinguishing among the mechanisms underlying the spatial distribution of genetic variation resulting from the environmental or physical barriers from those arising due to simple geographic distance is challenging in complex landscapes. The Andean uplift represents one of the most heterogeneous habitats where multiple mechanisms may interact, confounding their relative roles. We explore this broad question in the leaf-cutting ant Atta cephalotes, a species that is distributed across the Andes mountains, using nuclear microsatellite markers and mtCOI gene sequences. We investigate spatial genetic divergence across the western range of the northern Andes in Colombia by testing the relative role of alternative scenarios of population divergence, including isolation by geographic distance (IBD), climatic conditions (IBE), and the physical barriers presented by the Andes mountains (IBB). Our results reveal substantial genetic differentiation among A. cephalotes populations for both types of markers, but only nuclear divergence followed a hierarchical pattern with multiple models of genetic divergence imposed by the western range. Model selection showed that the IBD, IBE (temperature and precipitation), and IBB (Andes mountains) models, often proposed as individual drivers of genetic divergence, interact, and explain up to 33% of the genetic divergence in A. cephalotes. The IBE model remained significant after accounting for IBD, suggesting that environmental factors play a more prominent role than IBB. These factors, in combination with the idiosyncratic dispersal patterns of ants, appear to determine the hierarchical patterns of gene flow. This study enriches our understanding of the forces shaping population divergence in complex habitat landscapes.

Population structure of lake whitefish (Coregonus clupeaformis) from the Mississippian lineage in North America

The lake whitefish ( Coregonus clupeaformis) is a commercially valuable freshwater species with a broad distribution in North America. Some phylogeographic work has been done on this species, but little is known about genetic population subdivision among populations of the widely dispersed Mississippian lineage. We used 3,173 single nucleotide polymorphisms in 508 lake whitefish from 22 different lakes to examine population structure across central Canada and the United States. Bayesian clustering, ordination, and fixation indices identified population subdivision that largely reflected geographic distance and hydrological connectivity, with greater differentiation between lakes that are farther apart. Population subdivision was hierarchical, with greater differentiation between Canadian provinces and less differentiation based on river basins within provincial boundaries. Interestingly, isolation by distance alone was not sufficient to account for all of the observed genetic differentiation among populations. We conclude that important components of lake whitefish genetic diversity are present at different spatial scales, and that populations within the Mississippian lineage have differentiated widely across their range.

An island-hopping bird reveals how founder events shape genome-wide divergence

When populations colonize new areas, both strong selection and strong drift can be experienced due to novel environments and small founding populations, respectively. Empirical studies have predominantly focused on the phenotype when assessing the role of selection, and limited neutral-loci when assessing founder-induced loss of diversity. Consequently, the extent to which processes interact to influence evolutionary trajectories is difficult to assess. Genomic-level approaches provide the opportunity to simultaneously consider these processes. Here, we examine the roles of selection and drift in shaping genomic diversity and divergence in historically documented sequential island colonizations by the silvereye (Zosterops lateralis). We provide the first empirical demonstration of the rapid appearance of highly diverged genomic regions following population founding, the position of which are highly idiosyncratic. As these regions rarely contained loci putatively under selection, it is most likely that these differences arise via the stochastic nature of the founding process. However, selection is required to explain rapid evolution of larger body size in insular silvereyes. Reconciling our genomic data with these phenotypic patterns suggests there may be many genomic routes to the island phenotype, which vary across populations. Finally, we show that accelerated divergence associated with multiple founding steps is the product of genome-wide rather than localized differences, and that diversity erodes due to loss of rare alleles. However, even multiple founder events do not result in divergence and diversity levels seen in evolutionary older subspecies, and therefore do not provide a shortcut to speciation as proposed by founder-effect speciation models.

Implications of viral transmitted/founder (T/F) dynamics on vaccine development

Viral infection typically originates from a limited number of virions known as transmitted/founder (T/F) viruses. Studies of cross-species transmission, and intra-species transmission of antigenically variable viruses, indicates T/F variants may express distinct, transmissibility enhancing phenotypes. However, with evidence that transmissibility is associated with not only intrinsic virological features, such as virion composition, but also extrinsic factors, such as viral population structure, the challenge of resolving T/F signatures that can be targeted by rational vaccine or antiviral design is substantial. Nonetheless, failure to develop vaccines for antigenically variable viruses, such as HIV/HCV, and the ongoing risk of cross-species transmission with pandemic potential, recommends development of T/F targeting vaccines. In this commentary, the T/F phenomena is introduced, explored in both the classical (HIV) and non-canonical (coronaviruses) instances, and discussed in relation to rational and preemptive vaccine design.

Population Genetics of Odontarrhena (Brassicaceae) from Albania: The Effects of Anthropic Habitat Disturbance, Soil, and Altitude on a Ni-Hyperaccumulator Plant Group from a Major Serpentine Hotspot

Albanian taxa and populations of the genus Odontarrhena are most promising candidates for research on metal tolerance and Ni-agromining, but their genetic structure remains unknown. We investigated phylogenetic relationships and genetic differentiation in relation to distribution and ploidy of the taxa, anthropic site disturbance, elevation, soil type, and trace metals at each population site. After performing DNA sequencing of selected accessions, we applied DNA-fingerprinting to analyze the genetic structure of 32 populations from ultramafic and non-ultramafic outcrops across Albania. Low sequence divergence resulted in poorly resolved phylograms, but supported affinity between the two diploid serpentine endemics O. moravensis and O. rigida. Analysis of molecular variance (AMOVA) revealed significant population differentiation, but no isolation by distance. Among-population variation was higher in polyploids than in diploids, in which genetic distances were lower. Genetic admixing at population and individual level occurred especially in the polyploids O. chalcidica, O. decipiens, and O. smolikana. Admixing increased with site disturbance. Outlier loci were higher in serpentine populations but decreased along altitude with lower drought and heat stress. Genetic variability gained by gene flow and hybridization at contact zones with "resident" species of primary ultramafic habitats promoted expansion of the tetraploid O. chalcidica across anthropogenic sites.

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.

Founder effects on trans-generational dynamics of closed inbreeding lineages of the predatory mite Phytoseiulus persimilis

Both close inbreeding and distant outbreeding may reduce fitness below the level of individuals with intermediate parental relatedness. In the haplodiploid plant-inhabiting predatory mite Phytoseiulus persimilis, which is patchily distributed within and among host plants, fitness is indeed reduced in the short term, i.e. by a single generation of inbreeding. However, in the medium to long term (multiple generations), distant out-breeding should provide for favorable demographic founder effects in isolated populations. We tested this prediction in isolated experimental lineages founded by females mated to a sibling (close inbreeding), a male from the same population (intermediate relatedness) or a male from another population (distant outbreeding) and monitored lineage growth and persistence over four generations. Cross-generationally, lineages founded by distantly outbred females performed the best, i.e. produced the most descendants. However, this was solely due to superior performance from the F₂ generation onwards, whereas in the F₁ generation, lineages founded by females mated to males from their own population (intermediate relatedness) performed the best, as predicted from short-term in- and out-breeding depression effects. At the genetic level, this result was most likely due to distantly outbred founders introducing higher allelic variability and lower homozygosity levels, counterbalancing inbreeding depression, which inevitably occurs in isolated lineages, from the F₂ generation onwards.

Genetic divergence and the number of hybridizing species affect the path to homoploid hybrid speciation

Hybridization can promote speciation, and examples of putative hybrid species have now been identified across the tree of life. However, we still know little about the conditions that are most conducive to hybrid speciation. We have used experimental evolution in fruit flies (Drosophila) to show that both the genetic difference between hybridizing species and the number of hybridizing species affect the probability that hybrids evolve reproductive isolation from their parental species. Our results provide a systematic test of factors that affect homoploid hybrid speciation. Biologists will now be able to test the predictions that our experiments outline in naturally hybridizing species. These types of data hold the potential to greatly increase our understanding of hybridization’s role in generating biodiversity.

Hybridization is often maladaptive and in some instances has led to the loss of biodiversity. However, hybridization can also promote speciation, such as during homoploid hybrid speciation, thereby generating biodiversity. Despite examples of homoploid hybrid species, the importance of hybridization as a speciation mechanism is still widely debated, and we lack a general understanding of the conditions most likely to generate homoploid hybrid species. Here we show that the level of genetic divergence between hybridizing species has a large effect on the probability that their hybrids evolve reproductive isolation. We find that populations of hybrids formed by parental species with intermediate levels of divergence were more likely to mate assortatively, and discriminate against their parental species, than those generated from weakly or strongly diverged parental species. Reproductive isolation was also found between hybrid populations, suggesting differential sorting of parental traits across populations. Finally, hybrid populations derived from three species were more likely to evolve reproductive isolation than those derived from two species, supporting arguments that hybridization-supplied genetic diversity can lead to the evolution of novel “adaptive systems” and promote speciation. Our results illustrate when we expect hybridization and admixture to promote hybrid speciation. Whether homoploid hybrid speciation is a common speciation mechanism in general remains an outstanding empirical question.

Genetic Variability of Melipona subnitida (Hymenoptera: Apidae) in Introduced and Native Populations

Melipona subnitida (Hymenoptera: Apidae) is a stingless bee native to Caatinga biome in Brazil, well adapted to hot and dry climate of that region and has been traditionally explored for honey production. Here, we evaluate the genetic structure of 173 colonies of M. subnitida in northeast Brazil by partially sequenced mitochondrial genes cytochrome oxidase I (COI) to compare an introduced population isolated for 30 yr into the Island of Fernando de Noronha (IFN) with the continental populations. We identified high haplotype diversity (0.8220) with 14 haplotypes on the continental populations, being three new ones, compared with the database GenBank. The haplotype H4 was present at the center of network, occurring in four localities on mainland and fixed as a single haplotype on IFN. We propose that the island populations originally introduced carried one haplotype (H4), even though IFN population is suffering pressure by island effect through changes on morphology. Studies on island populations could be a model to understand the dynamics of isolated populations and sustainable management of this biome to preserve M. subnitida.

Establishment of F1 hybrid mortality in real time

Background

Measuring the evolutionary rate of reproductive isolation is essential to understanding how new species form. Tempo calculations typically rely on fossil records, geological events, and molecular evolution analyses. The speed at which genetically-based hybrid mortality arises, or the “incompatibility clock”, is estimated to be millions of years in various diploid organisms and is poorly understood in general. Owing to these extended timeframes, seldom do biologists observe the evolution of hybrid mortality in real time.

Results

Here we report the very recent spread and fixation of complete asymmetric F₁ hybrid mortality within eight years of laboratory maintenance in the insect model Nasonia. The asymmetric interspecific hybrid mortality evolved in an isogenic stock line of N. longicornis and occurs in crosses to N. vitripennis males. The resulting diploid hybrids exhibit complete failure in dorsal closure during embryogenesis.

Conclusion

These results comprise a unique case whereby a strong asymmetrical isolation barrier evolved in real time. The spread of this reproductive isolation barrier notably occurred in a small laboratory stock subject to recurrent bottlenecks.

Two in one: cryptic species discovered in biological control agent populations using molecular data and crossbreeding experiments

There are many examples of cryptic species that have been identified through DNA‐barcoding or other genetic techniques. There are, however, very few confirmations of cryptic species being reproductively isolated. This study presents one of the few cases of cryptic species that has been confirmed to be reproductively isolated and therefore true species according to the biological species concept. The cryptic species are of special interest because they were discovered within biological control agent populations. Two geographically isolated populations of Eccritotarsus catarinensis (Carvalho) [Hemiptera: Miridae], a biological control agent for the invasive aquatic macrophyte, water hyacinth, Eichhornia crassipes (Mart.) Solms [Pontederiaceae], in South Africa, were sampled from the native range of the species in South America. Morphological characteristics indicated that both populations were the same species according to the current taxonomy, but subsequent DNA analysis and breeding experiments revealed that the two populations are reproductively isolated. Crossbreeding experiments resulted in very few hybrid offspring when individuals were forced to interbreed with individuals of the other population, and no hybrid offspring were recorded when a choice of mate from either population was offered. The data indicate that the two populations are cryptic species that are reproductively incompatible. Subtle but reliable diagnostic characteristics were then identified to distinguish between the two species which would have been considered intraspecific variation without the data from the genetics and interbreeding experiments. These findings suggest that all consignments of biological control agents from allopatric populations should be screened for cryptic species using genetic techniques and that the importation of multiple consignments of the same species for biological control should be conducted with caution.

From local adaptation to ecological speciation in copepod populations from neighboring lakes

Continental copepods have been derived from several independent invasive events from the sea, but the subsequent evolutionary processes that account for the current diversity in lacustrine environments are virtually unknown. Salinity is highly variable among lakes and constitutes a source of divergent selection driving potential reproductive isolation. We studied four populations of the calanoid copepod Leptodiaptomus cf. sicilis inhabiting four neighboring lakes with a common history (since the Late Pleistocene) located in the Oriental Basin, Mexico; one lake is shallow and varies in salinity periodically (1.4-10 g L(-1)), while three are deep and permanent, with constant salinity (0.5, 1.1 and 6.5 g L(-1), respectively). We hypothesized that (1) these populations belong to a different species than L. sicilis sensu stricto and (2) are experiencing ecologically based divergence due to salinity differences. We assessed morphological and molecular (mtDNA) COI variation, as well as fitness differences and tests of reproductive isolation. Although relationships of the Mexican populations with L. sicilis s.s. could not be elucidated, we identified a clear pattern of divergent selection driven by salinity conditions. The four populations can still be considered a single biological species (sexual recognition and hybridization are still possible in laboratory conditions), but they have diverged into at least three different phenotypes: two locally adapted, specialized in the lakes of constant salinity (saline vs. freshwater), and an intermediate generalist phenotype inhabiting the temporary lake with fluctuating salinity. The specialized phenotypes are poorly suited as migrants, so prezygotic isolation due to immigrant inviability is highly probable. This implication was supported by molecular evidence that showed restricted gene flow, persistence of founder events, and a pattern of allopatric fragmentation. This study showed how ecologically based divergent selection may explain diversification patterns in lacustrine copepods.

The roles of geography and founder effects in promoting host-associated differentiation in the generalist bogus yucca moth Prodoxus decipiens

There is ample evidence that host shifts in plant-feeding insects have been instrumental in generating the enormous diversity of insects. Changes in host use can cause host-associated differentiation (HAD) among populations that may lead to reproductive isolation and eventual speciation. The importance of geography in facilitating this process remains controversial. We examined the geographic context of HAD in the wide-ranging generalist yucca moth Prodoxus decipiens. Previous work demonstrated HAD among sympatric moth populations feeding on two different Yucca species occurring on the barrier islands of North Carolina, USA. We assessed the genetic structure of P. decipiens across its entire geographic and host range to determine whether HAD is widespread in this generalist herbivore. Population genetic analyses of microsatellite and mtDNA sequence data across the entire range showed genetic structuring with respect to host use and geography. In particular, genetic differentiation was relatively strong between mainland populations and those on the barrier islands of North Carolina. Finer scale analyses, however, among sympatric populations using different host plant species only showed significant clustering based on host use for populations on the barrier islands. Mainland populations did not form population clusters based on host plant use. Reduced genetic diversity in the barrier island populations, especially on the derived host, suggests that founder effects may have been instrumental in facilitating HAD. In general, results suggest that the interplay of local adaptation, geography and demography can determine the tempo of HAD. We argue that future studies should include comprehensive surveys across a wide range of environmental and geographic conditions to elucidate the contribution of various processes to HAD.

Revisiting the vanishing refuge model of diversification

Much of the debate around speciation and historical biogeography has focused on the role of stabilizing selection on the physiological (abiotic) niche, emphasizing how isolation and vicariance, when associated with niche conservatism, may drive tropical speciation. Yet, recent re-emphasis on the ecological dimensions of speciation points to a more prominent role of divergent selection in driving genetic, phenotypic, and niche divergence. The vanishing refuge model (VRM), first described by Vanzolini and Williams (1981), describes a process of diversification through climate-driven habitat fragmentation and exposure to new environments, integrating both vicariance and divergent selection. This model suggests that dynamic climates and peripheral isolates can lead to genetic and functional (i.e., ecological and phenotypic) diversity, resulting in sister taxa that occupy contrasting habitats with abutting distributions. Here, we provide predictions for populations undergoing divergence according to the VRM that encompass habitat dynamics, phylogeography, and phenotypic differentiation across populations. Such integrative analyses can, in principle, differentiate the operation of the VRM from other speciation models. We applied these principles to a lizard species, Coleodactylus meridionalis, which was used to illustrate the model in the original paper. We incorporate data on inferred historic habitat dynamics, phylogeography and thermal physiology to test for divergence between coastal and inland populations in the Atlantic Forest of Brazil. Environmental and genetic analyses are concordant with divergence through the VRM, yet physiological data are not. We emphasize the importance of multidisciplinary approaches to test this and alternative speciation models while seeking to explain the extraordinarily high genetic and phenotypic diversity of tropical biomes.

The magnitude of behavioral isolation is affected by characteristics of the mating community

Gene exchange between species occurs in areas of secondary contact, where two species have the opportunity to hybridize. If heterospecific males are more common than conspecific males, females will experience more encounters with males of other species. These encounters might increase the likelihood of heterospecific matings, and lead to the production of hybrid progeny. I studied the mating behavior of two pairs of sibling species endemic to Africa: Drosophila yakuba/Drosophila santomea and Drosophila simulans/Drosophila sechellia. Drosophila yakuba and D. simulans are cosmopolitan species widely distributed in the African continent, while D. santomea and D. sechellia are island endemics. These pairs of species hybridize in nature and have the potential to exchange genes in natural conditions. I used these two pairs of Drosophila species, and constructed mating communities of different size and different heterospecific:conspecific composition. I found that both the total number of potential mates and the relative frequency of conspecific versus heterospecific males affect female mating decisions in the cosmopolitan species but not in the island endemics. These results suggest that the population characteristics, in which mating occurs, may affect the magnitude of premating isolation. Community composition might thus facilitate, or impair, gene flow between species.