Search tips
Search criteria

Results 1-25 (787552)

Clipboard (0)

Related Articles

1.  Evolution of Mutational Robustness in the Yeast Genome: A Link to Essential Genes and Meiotic Recombination Hotspots 
PLoS Genetics  2009;5(6):e1000533.
Deleterious mutations inevitably emerge in any evolutionary process and are speculated to decisively influence the structure of the genome. Meiosis, which is thought to play a major role in handling mutations on the population level, recombines chromosomes via non-randomly distributed hot spots for meiotic recombination. In many genomes, various types of genetic elements are distributed in patterns that are currently not well understood. In particular, important (essential) genes are arranged in clusters, which often cannot be explained by a functional relationship of the involved genes. Here we show by computer simulation that essential gene (EG) clustering provides a fitness benefit in handling deleterious mutations in sexual populations with variable levels of inbreeding and outbreeding. We find that recessive lethal mutations enforce a selective pressure towards clustered genome architectures. Our simulations correctly predict (i) the evolution of non-random distributions of meiotic crossovers, (ii) the genome-wide anti-correlation of meiotic crossovers and EG clustering, (iii) the evolution of EG enrichment in pericentromeric regions and (iv) the associated absence of meiotic crossovers (cold centromeres). Our results furthermore predict optimal crossover rates for yeast chromosomes, which match the experimentally determined rates. Using a Saccharomyces cerevisiae conditional mutator strain, we show that haploid lethal phenotypes result predominantly from mutation of single loci and generally do not impair mating, which leads to an accumulation of mutational load following meiosis and mating. We hypothesize that purging of deleterious mutations in essential genes constitutes an important factor driving meiotic crossover. Therefore, the increased robustness of populations to deleterious mutations, which arises from clustered genome architectures, may provide a significant selective force shaping crossover distribution. Our analysis reveals a new aspect of the evolution of genome architectures that complements insights about molecular constraints, such as the interference of pericentromeric crossovers with chromosome segregation.
Author Summary
Sexual life cycles constitute a costly alternative to vegetative modes of reproduction. Two categories of hypotheses seek to explain why sexual life cycles exist: those investigating the selective advantages that have driven the evolution of individual parts of this life cycle and those rationalizing the advantages sexual life cycles may offer as a whole, e.g., in extant species. Sex and recombination can be understood as efficient ways to interact with mutations and their consequences. Mutations occur at random and are mostly either deleterious or neutral. A prominent hypothesis suggests that sex and recombination are advantageous since they enhance the purging of such deleterious mutations and create individuals with a lower than average deleterious load. Deleterious mutations should co-determine the parameters that govern recombination of genomes in meiosis. Using an evolutionary computer simulation of diploid, unicellular sexual populations, we show that recessive lethal mutations can drive the evolution of chromosome architectures, in which essential genes become genetically linked into clusters. Evolved architectures exhibit structural properties and fitness similar to digitized yeast chromosomes and provide mutational purging capabilities superior to those of randomly generated or unclustered architectures. Our study demonstrates the importance of sexual cycles in the context of lethal mutations.
PMCID: PMC2694357  PMID: 19557188
2.  Demographic costs of inbreeding revealed by sex-specific genetic rescue effects 
Inbreeding can slow population growth and elevate extinction risk. A small number of unrelated immigrants to an inbred population can substantially reduce inbreeding and improve fitness, but little attention has been paid to the sex-specific effects of immigrants on such "genetic rescue". We conducted two subsequent experiments to investigate demographic consequences of inbreeding and genetic rescue in guppies.
Populations established from pairs of full siblings that were descended either from two generations of full-sibling inbreeding or unrelated outbred guppies did not grow at different rates initially, but when the first generation offspring started breeding, outbred-founded populations grew more slowly than inbred-founded populations. In a second experiment, adding two outbred males to the inbred populations resulted in significantly faster population growth than in control populations where no immigrants were added. Adding females resulted in growth at a rate intermediate to the control and male-immigrant treatments.
The slower growth of the outbred-founded than inbred-founded populations is the opposite of what would be expected under inbreeding depression unless many deleterious recessive alleles had already been selectively purged in the inbreeding that preceded the start of the experiment, and that significant inbreeding depression occurred when the first generation offspring in outbred-founded populations started to inbreed. The second experiment revealed strong inbreeding depression in the inbred founded populations, despite the apparent lack thereof in these populations earlier on. Moreover, the fact that the addition of male immigrants resulted in the highest levels of population growth suggests that sex-specific genetic rescue may occur in promiscuous species, with male rescue resulting in higher levels of outbreeding than female rescue.
PMCID: PMC2797806  PMID: 20003302
3.  Frequency-Dependent Selection Predicts Patterns of Radiations and Biodiversity 
PLoS Computational Biology  2010;6(8):e1000892.
Most empirical studies support a decline in speciation rates through time, although evidence for constant speciation rates also exists. Declining rates have been explained by invoking pre-existing niches, whereas constant rates have been attributed to non-adaptive processes such as sexual selection and mutation. Trends in speciation rate and the processes underlying it remain unclear, representing a critical information gap in understanding patterns of global diversity. Here we show that the temporal trend in the speciation rate can also be explained by frequency-dependent selection. We construct a frequency-dependent and DNA sequence-based model of speciation. We compare our model to empirical diversity patterns observed for cichlid fish and Darwin's finches, two classic systems for which speciation rates and richness data exist. Negative frequency-dependent selection predicts well both the declining speciation rate found in cichlid fish and explains their species richness. For groups like the Darwin's finches, in which speciation rates are constant and diversity is lower, speciation rate is better explained by a model without frequency-dependent selection. Our analysis shows that differences in diversity may be driven by incipient species abundance with frequency-dependent selection. Our results demonstrate that genetic-distance-based speciation and frequency-dependent selection are sufficient to explain the high diversity observed in natural systems and, importantly, predict decay through time in speciation rate in the absence of pre-existing niches.
Author Summary
Ecological opportunity, or filling a pre-existing unoccupied adaptive zone, is considered the dominant mechanism explaining the initial explosion of diversity. Although this type of niche filling can explain rates of diversification in some lineages, it is not sufficient for a radiation to occur. Instead of attributing the propensity to have an explosion of new species to external influences like niche availability, an alternative hypothesis can be based in frequency-dependent selection driven by the ecology in which organisms are embedded or endogenous sources mediated by gametes during fertilization. We show that genome diversification driven by higher reproductive probability of rare genotypes generates rapid initial speciation followed by a plateau with very low speciation rates, as shown by most empirical data. The absence of advantage of rare genotypes generates speciation events at constant rates. We predict decline over time and constant speciation rate in the cichlids and Darwin's finches, respectively, thus providing an alternative hypothesis for the origin of radiations and biodiversity in the absence of pre-existing niche filling. In addition to predicting observed temporal trends in diversification, our analysis also highlights new mechanistic models of evolutionary biodiversity dynamics that may become suitable to generate neutral models for testing observed patterns in speciation rates and species diversity.
PMCID: PMC2928887  PMID: 20865126
4.  Demographic Divergence History of Pied Flycatcher and Collared Flycatcher Inferred from Whole-Genome Re-sequencing Data 
PLoS Genetics  2013;9(11):e1003942.
Profound knowledge of demographic history is a prerequisite for the understanding and inference of processes involved in the evolution of population differentiation and speciation. Together with new coalescent-based methods, the recent availability of genome-wide data enables investigation of differentiation and divergence processes at unprecedented depth. We combined two powerful approaches, full Approximate Bayesian Computation analysis (ABC) and pairwise sequentially Markovian coalescent modeling (PSMC), to reconstruct the demographic history of the split between two avian speciation model species, the pied flycatcher and collared flycatcher. Using whole-genome re-sequencing data from 20 individuals, we investigated 15 demographic models including different levels and patterns of gene flow, and changes in effective population size over time. ABC provided high support for recent (mode 0.3 my, range <0.7 my) species divergence, declines in effective population size of both species since their initial divergence, and unidirectional recent gene flow from pied flycatcher into collared flycatcher. The estimated divergence time and population size changes, supported by PSMC results, suggest that the ancestral species persisted through one of the glacial periods of middle Pleistocene and then split into two large populations that first increased in size before going through severe bottlenecks and expanding into their current ranges. Secondary contact appears to have been established after the last glacial maximum. The severity of the bottlenecks at the last glacial maximum is indicated by the discrepancy between current effective population sizes (20,000–80,000) and census sizes (5–50 million birds) of the two species. The recent divergence time challenges the supposition that avian speciation is a relatively slow process with extended times for intrinsic postzygotic reproductive barriers to evolve. Our study emphasizes the importance of using genome-wide data to unravel tangled demographic histories. Moreover, it constitutes one of the first examples of the inference of divergence history from genome-wide data in non-model species.
Author Summary
Demographic processes leave specific and detectable signatures within species genomes. Analysis of patterns of variation within and between closely related species can be used to unravel their divergence history and is crucial for understanding evolutionary processes such as speciation. We applied a set of novel population-genomic tools to investigate patterns of natural variation and infer demographic history of two avian speciation model species: pied flycatcher and collared flycatcher. The analysis supported a scenario consistent with allopatric speciation with recent, postglacial secondary contact. Most likely the ancestral species persisted through one of the glacial periods of the middle Pleistocene and then split into two large descendent populations that appear to have increased in size before experiencing severe bottlenecks during expansion into their current ranges. The two species established secondary contact after the last glacial maximum. This resulted in unidirectional gene flow from pied flycatcher to collared flycatcher. The results are consistent with a scenario where pied flycatcher recolonized northern Europe more rapidly than collared flycatcher. Our study increases the knowledge about the dynamics of the speciation process and constitutes one of the first examples of the inference of complex demographic history using information from genome-wide data in non-model species.
PMCID: PMC3820794  PMID: 24244198
5.  A new theory for the evolution of polyandry as a means of inbreeding avoidance 
We propose a novel theory for the evolution of polyandry driven by genetic benefits to females whose offspring interbreed. In species with an ecology characterized by frequent colonization of new habitat patches, consanguineous matings may be common during the early stages of colonization, but genetic diversity may grow as new colonizers arrive. We show that with levels of inbreeding depression similar to those found in predominantly inbreeding populations, a polyandrous female can benefit her descendants since matings among her brood are mainly between half siblings rather than full siblings. We examine the invasion by a polyandrous phenotype using explicit genetic models in which costs of inbreeding are themselves subject to selection. In common with other models of inbreeding, we find that underlying high levels of inbreeding tend to purge deleterious recessive alleles, and hence these are unlikely to maintain sufficient inbreeding depression to favour polyandry. However, if costs of inbreeding are due to overdominance, biologically realistic levels of inbreeding depression result in genetic benefits large enough to favour polyandry provided it is not too costly. The potential significance of polyandry as a mechanism to reduce inbreeding in grandchildren will depend upon the genetic basis of inbreeding depression in natural, inbreeding populations.
PMCID: PMC2288693  PMID: 17785268
deleterious recessive; inbreeding; overdominance; polyandry; modelling; multiple mating
6.  Roles of Mutation and Selection in Speciation: From Hugo de Vries to the Modern Genomic Era 
One of the most important problems in evolutionary biology is to understand how new species are generated in nature. In the past, it was difficult to study this problem because our lifetime is too short to observe the entire process of speciation. In recent years, however, molecular and genomic techniques have been developed for identifying and studying the genes involved in speciation. Using these techniques, many investigators have already obtained new findings. At present, however, the results obtained are complex and quite confusing. We have therefore attempted to understand these findings coherently with a historical perspective and clarify the roles of mutation and natural selection in speciation. We have first indicated that the root of the currently burgeoning field of plant genomics goes back to Hugo de Vries, who proposed the mutation theory of evolution more than a century ago and that he unknowingly found the importance of polyploidy and chromosomal rearrangements in plant speciation. We have then shown that the currently popular Dobzhansky–Muller model of evolution of reproductive isolation is only one of many possible mechanisms. Some of them are Oka’s model of duplicate gene mutations, multiallelic speciation, mutation-rescue model, segregation-distorter gene model, heterochromatin-associated speciation, single-locus model, etc. The occurrence of speciation also depends on the reproductive system, population size, bottleneck effects, and environmental factors, such as temperature and day length. Some authors emphasized the importance of natural selection to speed up speciation, but mutation is crucial in speciation because reproductive barriers cannot be generated without mutations.
PMCID: PMC3227404  PMID: 21903731
chromosomal mutation; Dobzhansky–Muller model; hybrid sterility; hybrid inviability; Oka model; polyploidy
7.  Outbreeding effects in an inbreeding insect, Cimex lectularius 
Ecology and Evolution  2014;5(2):409-418.
In some species, populations with few founding individuals can be resilient to extreme inbreeding. Inbreeding seems to be the norm in the common bed bug, Cimex lectularius, a flightless insect that, nevertheless, can reach large deme sizes and persist successfully. However, bed bugs can also be dispersed passively by humans, exposing inbred populations to gene flow from genetically distant populations. The introduction of genetic variation through this outbreeding could lead to increased fitness (heterosis) or be costly by causing a loss of local adaptation or exposing genetic incompatibility between populations (outbreeding depression). Here, we addressed how inbreeding within demes and outbreeding between distant populations impact fitness over two generations in this re-emerging public health pest. We compared fitness traits of families that were inbred (mimicking reproduction following a founder event) or outbred (mimicking reproduction following a gene flow event). We found that outbreeding led to increased starvation resistance compared to inbred families, but this benefit was lost after two generations of outbreeding. No other fitness benefits of outbreeding were observed in either generation, including no differences in fecundity between the two treatments. Resilience to inbreeding is likely to result from the history of small founder events in the bed bug. Outbreeding benefits may only be detectable under stress and when heterozygosity is maximized without disruption of coadaptation. We discuss the consequences of these results both in terms of inbreeding and outbreeding in populations with genetic and spatial structuring, as well as for the recent resurgence of bed bug populations.
PMCID: PMC4314272
Cimex lectularius; colonization; inbreeding; metapopulation dynamics; outbreeding depression
8.  Isolation-by-Distance and Outbreeding Depression Are Sufficient to Drive Parapatric Speciation in the Absence of Environmental Influences 
PLoS Computational Biology  2008;4(7):e1000126.
A commonly held view in evolutionary biology is that speciation (the emergence of genetically distinct and reproductively incompatible subpopulations) is driven by external environmental constraints, such as localized barriers to dispersal or habitat-based variation in selection pressures. We have developed a spatially explicit model of a biological population to study the emergence of spatial and temporal patterns of genetic diversity in the absence of predetermined subpopulation boundaries. We propose a 2-D cellular automata model showing that an initially homogeneous population might spontaneously subdivide into reproductively incompatible species through sheer isolation-by-distance when the viability of offspring decreases as the genomes of parental gametes become increasingly different. This simple implementation of the Dobzhansky-Muller model provides the basis for assessing the process and completion of speciation, which is deemed to occur when there is complete postzygotic isolation between two subpopulations. The model shows an inherent tendency toward spatial self-organization, as has been the case with other spatially explicit models of evolution. A well-mixed version of the model exhibits a relatively stable and unimodal distribution of genetic differences as has been shown with previous models. A much more interesting pattern of temporal waves, however, emerges when the dispersal of individuals is limited to short distances. Each wave represents a subset of comparisons between members of emergent subpopulations diverging from one another, and a subset of these divergences proceeds to the point of speciation. The long-term persistence of diverging subpopulations is the essence of speciation in biological populations, so the rhythmic diversity waves that we have observed suggest an inherent disposition for a population experiencing isolation-by-distance to generate new species.
Author Summary
A commonly held view in evolutionary biology is that new species form in response to environmental factors, such as habitat differences or barriers to individual movements that sever a population. We have developed a computer model, called EvoSpace, that illustrates how new species can emerge when a species range becomes very large compared with the dispersal distances of its individuals. This situation has been called isolation-by-distance because remote parts of the range can take different evolutionary paths even though there is no particular place where we would expect different populations to separate. When the extent of genetic difference between individuals is coupled with decreasing offspring viability (e.g., resulting from developmental problems), EvoSpace predicts that sharp spatial boundaries can emerge in arbitrary locations, separating subpopulations that occasionally persist long enough to become reproductively incompatible species. The model shows an inherent tendency toward spatial self-organization, in contrast with the traditional view of environmentally forced origins of new species. We think that isolation-by-distance is a common aspect of the evolutionary process and that spatial self-organization of gene pools may often facilitate the evolution of new species.
PMCID: PMC2440541  PMID: 18654617
9.  Does Haplodiploidy Purge Inbreeding Depression in Rotifer Populations? 
PLoS ONE  2009;4(12):e8195.
Inbreeding depression is an important evolutionary factor, particularly when new habitats are colonized by few individuals. Then, inbreeding depression by drift could favour the establishment of later immigrants because their hybrid offspring would enjoy higher fitness. Rotifers are the only major zooplanktonic group where information on inbreeding depression is still critically scarce, despite the fact that in cyclical parthenogenetic rotifers males are haploid and could purge deleterious recessive alleles, thereby decreasing inbreeding depression.
Methodology/Principal Findings
We studied the effects of inbreeding in two populations of the cyclical parthenogenetic rotifer Brachionus plicatilis. For each population, we compared both the parental fertilization proportion and F1 fitness components from intraclonal (selfed) and interclonal (outcrossed) crosses. The parental fertilization proportion was similar for both types of crosses, suggesting that there is no mechanism to avoid selfing. In the F1 generation of both populations, we found evidence of inbreeding depression for the fitness components associated with asexual reproduction; whereas inbreeding depression was only found for one of the two sexual reproduction fitness components measured.
Our results show that rotifers, like other major zooplanktonic groups, can be affected by inbreeding depression in different stages of their life cycle. These results suggest that haplodiploidy does not purge efficiently deleterious recessive alleles. The inbreeding depression detected here has important implications when a rotifer population is founded and intraclonal crossing is likely to occur. Thus, during the foundation of new populations inbreeding depression may provide opportunities for new immigrants, increasing gene flow between populations, and affecting genetic differentiation.
PMCID: PMC2785431  PMID: 19997616
10.  Invasive Species and Biodiversity Crises: Testing the Link in the Late Devonian 
PLoS ONE  2010;5(12):e15584.
During the Late Devonian Biodiversity Crisis, the primary driver of biodiversity decline was the dramatic reduction in speciation rates, not elevated extinction rates; however, the causes of speciation decline have been previously unstudied. Speciation, the formation of new species from ancestral populations, occurs by two primary allopatric mechanisms: vicariance, where the ancestral population is passively divided into two large subpopulations that later diverge and form two daughter species, and dispersal, in which a small subset of the ancestral population actively migrates then diverges to form a new species. Studies of modern and fossil clades typically document speciation by vicariance in much higher frequencies than speciation by dispersal. To assess the mechanism behind Late Devonian speciation reduction, speciation rates were calculated within stratigraphically constrained species-level phylogenetic hypotheses for three representative clades and mode of speciation at cladogenetic events was assessed across four clades in three phyla: Arthropoda, Brachiopoda, and Mollusca. In all cases, Devonian taxa exhibited a congruent reduction in speciation rate between the Middle Devonian pre-crisis interval and the Late Devonian crisis interval. Furthermore, speciation via vicariance is almost entirely absent during the crisis interval; most episodes of speciation during this time were due to dispersal. The shutdown of speciation by vicariance during this interval was related to widespread interbasinal species invasions. The lack of Late Devonian vicariance is diametrically opposed to the pattern observed in other geologic intervals, which suggests the loss of vicariant speciation attributable to species invasions during the Late Devonian was a causal factor in the biodiversity crisis. Similarly, modern ecosystems, in which invasive species are rampant, may be expected to exhibit similar shutdown of speciation by vicariance as an outcome of the modern biodiversity crisis.
PMCID: PMC3012059  PMID: 21206907
11.  Relative risks of inbreeding and outbreeding depression in the wild in endangered salmon 
Evolutionary Applications  2011;4(5):634-647.
Conservation biologists routinely face the dilemma of keeping small, fragmented populations isolated, wherein inbreeding depression may ensue, or mixing such populations, which may exacerbate population declines via outbreeding depression. The joint evaluation of inbreeding and outbreeding risks in the wild cannot be readily conducted in endangered species, so a suggested ‘safe’ strategy is to mix ecologically and genetically similar populations. To evaluate this strategy, we carried out a reciprocal transplant experiment involving three neighboring populations of endangered Atlantic salmon (Salmo salar) now bred in captivity and maintained in captive and wild environments. Pure, inbred, and outbred (first and second generation) cross types were released and recaptured in the wild to simultaneously test for local adaptation, inbreeding depression, and outbreeding depression. We found little evidence of inbreeding depression after one generation of inbreeding and little evidence of either heterosis or outbreeding depression via genetic incompatibilities after one or two generations of outbreeding. A trend for outbreeding depression via the loss of local adaptation was documented in one of three populations. The effects of inbreeding were not significantly different from the effects of outbreeding. Hence, at the geographic scale evaluated (34–50 km), inbreeding for one generation and outbreeding over two generations may have similar effects on the persistence of small populations. The results further suggested that outbreeding outcomes may be highly variable or unpredictable at small genetic distances. Our work highlights the necessity of evaluating the relative costs of inbreeding and outbreeding in the conservation and management of endangered species on a case-by-case basis.
PMCID: PMC3352539
Atlantic salmon; Canada; conservation; heterosis; local adaptation; risk assessment
Journal of mammalogy  2006;87(4):643-662.
We define a genetic species as a group of genetically compatible interbreeding natural populations that is genetically isolated from other such groups. This focus on genetic isolation rather than reproductive isolation distinguishes the Genetic Species Concept from the Biological Species Concept. Recognition of species that are genetically isolated (but not reproductively isolated) results in an enhanced understanding of biodiversity and the nature of speciation as well as speciation-based issues and evolution of mammals. We review criteria and methods for recognizing species of mammals and explore a theoretical scenario, the Bateson–Dobzhansky–Muller (BDM) model, for understanding and predicting genetic diversity and speciation in mammals. If the BDM model is operating in mammals, then genetically defined phylogroups would be predicted to occur within species defined by morphology, and phylogroups experiencing stabilizing selection will evolve genetic isolation without concomitant morphological diversification. Such species will be undetectable using classical skin and skull morphology (Morphological Species Concept). Using cytochrome-b data from sister species of mammals recognized by classical morphological studies, we estimated the number of phylogroups that exist within mammalian species and hypothesize that there will be >2,000 currently unrecognized species of mammals. Such an underestimation significantly affects conclusions on the nature of speciation in mammals, barriers associated with evolution of genetic isolation, estimates of biodiversity, design of conservation initiatives, zoonoses, and so on. A paradigm shift relative to this and other speciation-based issues will be needed. Data that will be effective in detecting these “morphologically cryptic genetic species” are genetic, especially DNA-sequence data. Application of the Genetic Species Concept uses genetic data from mitochondrial and nuclear genomes to identify species and species boundaries, the extent to which the integrity of the gene pool is protected, nature of hybridization (if present), and introgression. Genetic data are unique in understanding species because the use of genetic data 1) can quantify genetic divergence from different aspects of the genome (mitochondrial and nuclear genes, protein coding genes, regulatory genes, mobile DNA, microsatellites, chromosomal rearrangements, heterochromatin, etc.); 2) can provide divergence values that increase with time, providing an estimate of time since divergence; 3) can provide a population genetics perspective; 4) is less subject to convergence and parallelism relative to other sets of characters; 5) can identify monophyly, sister taxa, and presence or absence of introgression; and 6) can accurately identify hybrid individuals (kinship and source of hybrid individuals, F1s, backcrosses, direction of hybridization, and in concert with other data identify which hybrids are sterile or fertile). The proposed definition of the Genetic Species Concept is more compatible with a description of biodiversity of mammals than is “reproductively isolated species.” Genetic profiles of mammalian species will result in a genetic description of species and mammalian diversity, and such studies are being accelerated by technological advances that reduce cost and increase speed and efficiency of generating genetic data. We propose that this genetic revolution remain museum- and voucher specimen–based and that new names are based on a holotype (including associated tissues) deposited in an accredited museum.
PMCID: PMC2771874  PMID: 19890476
Bateson–Dobzhansky–Muller model; cryptic species; cytochrome b; genetic isolation; Genetic Species Concept; hybrid zones; phylogroups; reproductive isolation; speciation in mammals
13.  Reproductive Isolation among Sympatric Molecular Forms of An. gambiae from Inland Areas of South-Eastern Senegal 
PLoS ONE  2014;9(8):e104622.
The Anopheles gambiae species complex includes at least seven morphologically indistinguishable species, one of which, Anopheles gambiae sensu stricto, is the primary mosquito vector responsible for the transmission of malaria across sub-Saharan Africa. Sympatric ecological diversification of An. gambiae s.s. is in progress within this complex, leading to the emergence of at least two incipient species (the M and S molecular forms now recognized as good species and named An. coluzzii and An. gambiae respectively) that show heterogeneous levels of divergence in most parts of Africa. However, this process seems to have broken down in coastal areas of West Africa at the extreme edge of the distribution. We undertook a longitudinal study to describe An. gambiae s.s. populations collected from two inland transects with different ecological characteristics in south-eastern Senegal. Analysis of samples collected from 20 sites across these two transects showed the M and S molecular forms coexisted at almost all sampled sites. Overall, similar hybridization rates (2.16% and 1.86%) were recorded in the two transects; sites with relatively high frequencies of M/S hybrids (up to 7%) were clustered toward the north-western part of both transects, often near urban settings. Estimated inbreeding indices for this putative speciation event varied spatially (range: 0.52–1), with hybridization rates being generally lower than expected under panmictic conditions. Such observations suggest substantial reproductive isolation between the M and S molecular forms, and further support the ongoing process of speciation in these inland areas. According to a recent reclassification of the An. gambiae complex, the M and S molecular forms from this zone correspond to An. coluzzii and An. gambiae, respectively. There is considerable evidence that these molecular forms differ in their behavioural and ecological characteristics. Detailed study of these characteristics will allow the development and implementation of better insect control strategies for combating malaria.
PMCID: PMC4123975  PMID: 25098711
14.  Speciation genes in plants 
Annals of Botany  2010;106(3):439-455.
Analyses of speciation genes – genes that contribute to the cessation of gene flow between populations – can offer clues regarding the ecological settings, evolutionary forces and molecular mechanisms that drive the divergence of populations and species. This review discusses the identities and attributes of genes that contribute to reproductive isolation (RI) in plants, compares them with animal speciation genes and investigates what these genes can tell us about speciation.
Forty-one candidate speciation genes were identified in the plant literature. Of these, seven contributed to pre-pollination RI, one to post-pollination, prezygotic RI, eight to hybrid inviability, and 25 to hybrid sterility. Genes, gene families and genetic pathways that were frequently found to underlie the evolution of RI in different plant groups include the anthocyanin pathway and its regulators (pollinator isolation), S RNase-SI genes (unilateral incompatibility), disease resistance genes (hybrid necrosis), chimeric mitochondrial genes (cytoplasmic male sterility), and pentatricopeptide repeat family genes (cytoplasmic male sterility).
The most surprising conclusion from this review is that identities of genes underlying both prezygotic and postzygotic RI are often predictable in a broad sense from the phenotype of the reproductive barrier. Regulatory changes (both cis and trans) dominate the evolution of pre-pollination RI in plants, whereas a mix of regulatory mutations and changes in protein-coding genes underlie intrinsic postzygotic barriers. Also, loss-of-function mutations and copy number variation frequently contribute to RI. Although direct evidence of positive selection on speciation genes is surprisingly scarce in plants, analyses of gene family evolution, along with theoretical considerations, imply an important role for diversifying selection and genetic conflict in the evolution of RI. Unlike in animals, however, most candidate speciation genes in plants exhibit intraspecific polymorphism, consistent with an important role for stochastic forces and/or balancing selection in development of RI in plants.
PMCID: PMC2924826  PMID: 20576737
Speciation; reproductive isolation; mating system isolation; pollinator isolation; ecological isolation; unilateral incompatibility; hybrid necrosis; hybrid sterility; hybrid inviability; hybrid breakdown; cytoplasmic male sterility; restoration
15.  A genetically explicit model of speciation by sensory drive within a continuous population in aquatic environments 
The sensory drive hypothesis predicts that divergent sensory adaptation in different habitats may lead to premating isolation upon secondary contact of populations. Speciation by sensory drive has traditionally been treated as a special case of speciation as a byproduct of adaptation to divergent environments in geographically isolated populations. However, if habitats are heterogeneous, local adaptation in the sensory systems may cause the emergence of reproductively isolated species from a single unstructured population. In polychromatic fishes, visual sensitivity might become adapted to local ambient light regimes and the sensitivity might influence female preferences for male nuptial color. In this paper, we investigate the possibility of speciation by sensory drive as a byproduct of divergent visual adaptation within a single initially unstructured population. We use models based on explicit genetic mechanisms for color vision and nuptial coloration.
We show that in simulations in which the adaptive evolution of visual pigments and color perception are explicitly modeled, sensory drive can promote speciation along a short selection gradient within a continuous habitat and population. We assumed that color perception evolves to adapt to the modal light environment that individuals experience and that females prefer to mate with males whose nuptial color they are most sensitive to. In our simulations color perception depends on the absorption spectra of an individual's visual pigments. Speciation occurred most frequently when the steepness of the environmental light gradient was intermediate and dispersal distance of offspring was relatively small. In addition, our results predict that mutations that cause large shifts in the wavelength of peak absorption promote speciation, whereas we did not observe speciation when peak absorption evolved by stepwise mutations with small effect.
The results suggest that speciation can occur where environmental gradients create divergent selection on sensory modalities that are used in mate choice. Evidence for such gradients exists from several animal groups, and from freshwater and marine fishes in particular. The probability of speciation in a continuous population under such conditions may then critically depend on the genetic architecture of perceptual adaptation and female mate choice.
PMCID: PMC1941727  PMID: 17598893
16.  Divergent Selection Drives Genetic Differentiation in an R2R3-MYB Transcription Factor That Contributes to Incipient Speciation in Mimulus aurantiacus 
PLoS Genetics  2013;9(3):e1003385.
Identifying the molecular genetic basis of traits contributing to speciation is of crucial importance for understanding the ecological and evolutionary mechanisms that generate biodiversity. Despite several examples describing putative “speciation genes,” it is often uncertain to what extent these genetic changes have contributed to gene flow reductions in nature. Therefore, considerable interest lies in characterizing the molecular basis of traits that actively confer reproductive isolation during the early stages of speciation, as these loci can be attributed directly to the process of divergence. In Southern California, two ecotypes of Mimulus aurantiacus are parapatric and differ primarily in flower color, with an anthocyanic, red-flowered morph in the west and an anthocyanin-lacking, yellow-flowered morph in the east. Evidence suggests that the genetic changes responsible for this shift in flower color have been essential for divergence and have become fixed in natural populations of each ecotype due to almost complete differences in pollinator preference. In this study, we demonstrate that a cis-regulatory mutation in an R2R3-MYB transcription factor results in differential regulation of enzymes in the anthocyanin biosynthetic pathway and is the major contributor to differences in floral pigmentation. In addition, molecular population genetic data show that, despite gene flow at neutral loci, divergent selection has driven the fixation of alternate alleles at this gene between ecotypes. Therefore, by identifying the genetic basis underlying ecologically based divergent selection in flower color between these ecotypes, we have revealed the ecological and functional mechanisms involved in the evolution of pre-mating isolation at the early stages of incipient speciation.
Author Summary
A fundamental goal of evolutionary biology is to identify the genetic changes and evolutionary mechanisms involved in speciation. Knowledge of the genes allows us to address important unresolved questions about the genetics of speciation, such as what role does ecologically based natural selection play during the process of divergence? We characterize the evolutionary processes and genetic changes that influence the early stages of speciation between divergent populations of the wildflower Mimulus aurantiacus. Populations with different flower colors attract different animal pollinators, resulting in a prominent reproductive barrier that reduces gene exchange between populations. We provide multiple lines of corroborating evidence to verify the functional role of the major gene responsible for this flower color shift, including genetic mapping, gene expression analyses, and gene knockdown approaches. We then use molecular population genetic techniques to show a remarkably tight association between genetic variants in this gene and the geographic shift in flower color, which reflects a history of divergent natural selection on flower color between these populations. These results provide a striking demonstration of how adaptation to different environments can result in the early stages of divergence and the evolution of reproductive isolation between populations.
PMCID: PMC3605050  PMID: 23555295
17.  Consequences of life history for inbreeding depression and mating system evolution in plants. 
Many plants are perennial, but most studies of inbreeding depression and mating system evolution focus on annuals. This paper extends a population genetic model of inbreeding depression due to recessive deleterious mutations to perennials. The model incorporates life history and mating system variation, and multiplicative selection across many genetic loci. In the absence of substantial mitotic mutation, perennials have higher mean fitness and lower, or even negative, inbreeding depression than annuals with the same mating system. As in annuals, self fertilization exposes deleterious recessive mutations to selection, increasing mean fitness and decreasing inbreeding depression. Including mitotic mutation decreases mean fitness while increasing inbreeding depression. Perenniality introduces a kind of selective sieve, such that strongly recessive mutations contribute disproportionately to mean fitness and inbreeding depression. In the presence of high mitotic mutation, this selective sieve may provide a mechanistic basis for high inbreeding depression observed in some long lived perennials. Without substantial mitotic mutation, it is difficult to reconcile genetically based models of inbreeding depression with the empirical generalization that perennials outcross while related annuals self fertilize.
PMCID: PMC1088814  PMID: 11522201
18.  Conditions for mutation-order speciation 
Two models for speciation via selection have been proposed. In the well-known model of ‘ecological speciation’, divergent natural selection between environments drives the evolution of reproductive isolation. In a second ‘mutation-order’ model, different, incompatible mutations (alleles) fix in different populations adapting to the same selective pressure. How to demonstrate mutation-order speciation has been unclear, although it has been argued that it can be ruled out when gene flow occurs because the same, most advantageous allele will fix in all populations. However, quantitative examination of the interaction of factors influencing the likelihood of mutation-order speciation is lacking. We used simulation models to study how gene flow, hybrid incompatibility, selective advantage, timing of origination of new mutations and an initial period of allopatric differentiation affect population divergence via the mutation-order process. We find that at least some population divergence can occur under a reasonably wide range of conditions, even with moderate gene flow. However, strong divergence (e.g. fixation of different alleles in different populations) requires very low gene flow, and is promoted when (i) incompatible mutations have similar fitness advantages, (ii) less fit mutations arise slightly earlier in evolutionary time than more fit alternatives, and (iii) allopatric divergence occurs prior to secondary contact.
PMCID: PMC3013408  PMID: 20702458
Dobzhansky–Muller incompatibilities; ecological speciation; gene flow; migration; reproductive isolation; uniform selection
19.  Within-Host Speciation of Malaria Parasites 
PLoS ONE  2007;2(2):e235.
Sympatric speciation—the divergence of populations into new species in absence of geographic barriers to hybridization—is the most debated mode of diversification of life forms. Parasitic organisms are prominent models for sympatric speciation, because they may colonise new hosts within the same geographic area and diverge through host specialization. However, it has been argued that this mode of parasite divergence is not strict sympatric speciation, because host shifts likely cause the sudden effective isolation of parasites, particularly if these are transmitted by vectors and therefore cannot select their hosts. Strict sympatric speciation would involve parasite lineages diverging within a single host species, without any population subdivision.
Methodology/Principal Findings
Here we report a case of extraordinary divergence of sympatric, ecologically distinct, and reproductively isolated malaria parasites within a single avian host species, which apparently occurred without historical or extant subdivision of parasite or host populations.
This discovery of within-host speciation changes our current view on the diversification potential of malaria parasites, because neither geographic isolation of host populations nor colonization of new host species are any longer necessary conditions to the formation of new parasite species.
PMCID: PMC1794596  PMID: 17311104
20.  Nested biological variation and speciation 
The modes of speciation that are thought to have contributed most to the generation of biodiversity require population differentiation as the initial stage in the speciation process. Consequently, a complete understanding of the mechanisms of speciation requires that the process be examined not just after speciation is complete, or nearly so, but also much earlier. Because reproductive isolation defines biological species, and it evolves slowly, study of the process may require a prohibitive span of time. Even if speciation could be observed directly, selection of populations in the process of speciation is typically difficult or impossible, because those that will ultimately undergo speciation cannot be distinguished from those that will differentiate but never assume the status of new biological species. One means of circumventing this problem is to study speciation in taxa comprising several sibling species, at least one of which exhibits extensive population differentiation. We illustrate this approach by exploring patterns of population variation in the post-glacial radiation of the threespine stickleback, Gasterosteus aculeatus. We focus on lacustrine populations and species within this complex, demonstrating parallel axes of divergence within populations, among populations and among species. The pattern that emerges is one of parallel relationships between phenotype and fitness at all three hierarchical levels, a pattern that facilitates exploration of the causes and consequences of speciation and secondary contact. A second outcome of this exploration is the observation that speciation can be the consequence of a cascade of effects, beginning with selection on trophic or other characteristics that in turn force the evolution of other population characteristics that precipitate speciation. Neither of these conclusions could have been reached without comparative studies of wild populations at several hierarchical levels, a conclusion reinforced by a brief survey of similar efforts to elucidate the process of speciation. We address the issues most likely to be resolved using this approach, and suggest that comparisons of natural variation within taxa at several hierarchical levels may substantially increase our understanding of the speciation process.
PMCID: PMC1692212
21.  Interspecific Tests of Allelism Reveal the Evolutionary Timing and Pattern of Accumulation of Reproductive Isolation Mutations 
PLoS Genetics  2014;10(9):e1004623.
Despite extensive theory, little is known about the empirical accumulation and evolutionary timing of mutations that contribute to speciation. Here we combined QTL (Quantitative Trait Loci) analyses of reproductive isolation, with information on species evolutionary relationships, to reconstruct the order and timing of mutations contributing to reproductive isolation between three plant (Solanum) species. To evaluate whether reproductive isolation QTL that appear to coincide in more than one species pair are homologous, we used cross-specific tests of allelism and found evidence for both homologous and lineage-specific (non-homologous) alleles at these co-localized loci. These data, along with isolation QTL unique to single species pairs, indicate that >85% of isolation-causing mutations arose later in the history of divergence between species. Phylogenetically explicit analyses of these data support non-linear models of accumulation of hybrid incompatibility, although the specific best-fit model differs between seed (pairwise interactions) and pollen (multi-locus interactions) sterility traits. Our findings corroborate theory that predicts an acceleration (‘snowballing’) in the accumulation of isolation loci as lineages progressively diverge, and suggest different underlying genetic bases for pollen versus seed sterility. Pollen sterility in particular appears to be due to complex genetic interactions, and we show this is consistent with a snowball model where later arising mutations are more likely to be involved in pairwise or multi-locus interactions that specifically involve ancestral alleles, compared to earlier arising mutations.
Author Summary
The evolution of reproductive barriers between species, like inviability and sterility in hybrids, continues to fascinate and puzzle evolutionary biologists. However, very few studies have successfully identified the genes responsible for these barriers, or when the underlying mutations appeared during species' evolutionary history of divergence. Differentiating whether specific isolation-causing mutations evolved early versus late in the divergence history of lineages can reveal important insights into the mechanisms of speciation—how new species are formed. Here we infer the evolutionary timing of these loci using data on the chromosomal location of genes that cause reduced hybrid pollen and seed fertility among three species in the wild tomato group, and information on their evolutionary relationships. With genetic crosses that combine these sterility loci from different lineages, we evaluate whether sterility effects are due to the same mutational change(s)—earlier in the history of evolutionary divergence among these species—or to independent mutational changes—later in their evolutionary divergence. We show that most sterility loci separating species are unique to a single species pair, and most isolation-causing mutations arose on recent evolutionary branches. Our data are consistent with mathematical models that predict that these loci should ‘snowball’ between species as they diverge.
PMCID: PMC4161300  PMID: 25211473
22.  Independent S-Locus Mutations Caused Self-Fertility in Arabidopsis thaliana 
PLoS Genetics  2009;5(3):e1000426.
A common yet poorly understood evolutionary transition among flowering plants is a switch from outbreeding to an inbreeding mode of mating. The model plant Arabidopsis thaliana evolved to an inbreeding state through the loss of self-incompatibility, a pollen-rejection system in which pollen recognition by the stigma is determined by tightly linked and co-evolving alleles of the S-locus receptor kinase (SRK) and its S-locus cysteine-rich ligand (SCR). Transformation of A. thaliana, with a functional AlSRKb-SCRb gene pair from its outcrossing relative A. lyrata, demonstrated that A. thaliana accessions harbor different sets of cryptic self-fertility–promoting mutations, not only in S-locus genes, but also in other loci required for self-incompatibility. However, it is still not known how many times and in what manner the switch to self-fertility occurred in the A. thaliana lineage. Here, we report on our identification of four accessions that are reverted to full self-incompatibility by transformation with AlSRKb-SCRb, bringing to five the number of accessions in which self-fertility is due to, and was likely caused by, S-locus inactivation. Analysis of S-haplotype organization reveals that inter-haplotypic recombination events, rearrangements, and deletions have restructured the S locus and its genes in these accessions. We also perform a Quantitative Trait Loci (QTL) analysis to identify modifier loci associated with self-fertility in the Col-0 reference accession, which cannot be reverted to full self-incompatibility. Our results indicate that the transition to inbreeding occurred by at least two, and possibly more, independent S-locus mutations, and identify a novel unstable modifier locus that contributes to self-fertility in Col-0.
Author Summary
The mating system adopted by a species has a profound influence on extent of polymorphism, population structure, and evolutionary potential. In flowering plants, the switch from outbreeding to inbreeding has occurred repeatedly, yet little is known about the underlying genetic events. This is true even for the model species A. thaliana, a highly self-fertile member of the crucifer family. In this family, outbreeding is enforced by a self-incompatibility system controlled by the S locus, which involves the recognition of pollen by the stigma to prevent self-fertilization and familial inbreeding. We recently demonstrated that A. thaliana accessions may be reverted to full or partial self-incompatibility by transformation with S-locus genes isolated from its close self-incompatible relative A. lyrata. Despite much recent debate, however, we still do not know how A. thaliana became self-fertile. Here, we use our recently established A. thaliana transgenic self-incompatible experimental model to address these issues. Analysis of the S locus in accessions that can be reverted to full self-incompatibility demonstrates that self-fertility in A. thaliana arose by at least two independent S-locus mutations. Furthermore, analysis of an accession that expresses only partial self-incompatibility shows that self-fertility is associated with an unstable allele at a locus unlinked to the S locus.
PMCID: PMC2650789  PMID: 19300485
23.  Genetic Tests for Ecological and Allopatric Speciation in Anoles on an Island Archipelago 
PLoS Genetics  2010;6(4):e1000929.
From Darwin's study of the Galapagos and Wallace's study of Indonesia, islands have played an important role in evolutionary investigations, and radiations within archipelagos are readily interpreted as supporting the conventional view of allopatric speciation. Even during the ongoing paradigm shift towards other modes of speciation, island radiations, such as the Lesser Antillean anoles, are thought to exemplify this process. Geological and molecular phylogenetic evidence show that, in this archipelago, Martinique anoles provide several examples of secondary contact of island species. Four precursor island species, with up to 8 mybp divergence, met when their islands coalesced to form the current island of Martinique. Moreover, adjacent anole populations also show marked adaptation to distinct habitat zonation, allowing both allopatric and ecological speciation to be tested in this system. We take advantage of this opportunity of replicated island coalescence and independent ecological adaptation to carry out an extensive population genetic study of hypervariable neutral nuclear markers to show that even after these very substantial periods of spatial isolation these putative allospecies show less reproductive isolation than conspecific populations in adjacent habitats in all three cases of subsequent island coalescence. The degree of genetic interchange shows that while there is always a significant genetic signature of past allopatry, and this may be quite strong if the selection regime allows, there is no case of complete allopatric speciation, in spite of the strong primae facie case for it. Importantly there is greater genetic isolation across the xeric/rainforest ecotone than is associated with any secondary contact. This rejects the development of reproductive isolation in allopatric divergence, but supports the potential for ecological speciation, even though full speciation has not been achieved in this case. It also explains the paucity of anole species in the Lesser Antilles compared to the Greater Antilles.
Author Summary
Over the last 150 years, since Darwin's study of islands and his “Origin of Species,” island archipelagos have played a central role in the understanding of evolution and how species multiply (speciation). Islands epitomise the conventional view of geographic (allopatric) speciation, where genomes diverge in isolation until accumulated differences result in reproductive isolation and the capacity to coexist without interbreeding. Current-day Martinique in the Lesser Antilles is composed of several ancient islands that have only recently coalesced into a single entity. The molecular phylogeny and geology show that these ancient islands have had their own tree lizard (anole) species for a very long time, about six to eight million years. Now they have met, we can genetically test for reproductive isolation. However, when we use selectively neutral markers from the nuclear genome, on this naturally replicated system, we can see that these anoles are freely exchanging genes and not behaving as species. Indeed, there is more genetic isolation between adjacent populations of the same species from different habitats than between separate putative allospecies from the ancient islands. This rejects allopatric speciation in a case study from a system thought to exemplify it, and suggests the potential importance of ecological speciation.
PMCID: PMC2861690  PMID: 20442860
24.  Genetic Variability and Founder Effect in the Pitcher Plant Sarracenia purpurea (Sarraceniaceae) in Populations Introduced into Switzerland: from Inbreeding to Invasion 
Annals of Botany  2004;95(2):277-286.
• Background and Aims The long-lived and mainly outcrossing species Sarracenia purpurea has been introduced into Switzerland and become invasive. This creates the opportunity to study reactions to founder effect and how a species can circumvent deleterious effects of bottlenecks such as reduced genetic diversity, inbreeding and extinction through mutational meltdown, to emerge as a highly invasive plant.
• Methods A population genetic survey by random amplified polymorphism DNA markers (RAPD) together with historical insights and a field pollination experiment were carried out.
• Key Results At the regional scale, S. purpurea shows low structure (θst = 0·072) due to a recent founder event and important subsequent growth. Nevertheless, multivariate statistical analyses reveal that, because of a bottleneck that shifted allele frequencies, most of the variability is independent among populations. In one population (Tenasses) the species has become invasive and genetic analysis reveals restricted gene flow and family structure (θst = 0·287). Although inbreeding appears to be high (Fis > 0·410 from a Bayesian estimation), a field pollination experiment failed to detect significant inbreeding depression upon F1 seed number and seed weight fitness-traits. Furthermore, crosses between unrelated individuals produced F1 seeds with significantly reduced fitness, thus showing local outbreeding depression.
• Conclusions The results suggest that, under restricted gene flow among families, the species may not only have rapidly purged deleterious alleles, but also have undergone some form of selection for inbreeding due to co-adaptation between loci.
PMCID: PMC4246826  PMID: 15546932
Bottleneck; founder effect; introduced populations; Sarracenia purpurea; invasion; RAPD; multivariate analysis; field pollination; family structure; bi-parental purge; outbreeding depression
25.  Embryonic inbreeding depression varies among populations and by mating system in Witheringia solanacea (Solanaceae)1 
American journal of botany  2010;97(8):1328-1333.
Premise of the study
Embryonic inbreeding depression is a key influence on mating system evolution and can be difficult to estimate in self-incompatible species. A pollen chase experiment was used to estimate the magnitude of embryonic inbreeding depression in Costa Rican Witheringia solanacea, a species polymorphic for self-incompatibility (SI). In a pollen chase experiment, bud self-pollinations are followed after anthesis by outcross pollinations, with a comparable pair of outcross pollinations used as a control. Lowered seed set for the self-precedence treatment indicates embryonic inbreeding depression.
Embryonic inbreeding depression was assayed for self-compatible (SC) individuals and for SI plants from two populations that differ quantitatively in the onset and enzymatic activity of their SI response. Microsatellite markers were used to assay the selfing rate of a sample of surviving progeny from the prior self-pollination treatment.
Key results
SC individuals showed no evidence of embryonic inbreeding depression. In SI plants, prior self-pollination reduced seed number by 28–70%, depending on population. Microsatellite genotyping revealed that embryonic inbreeding depression was even more severe than estimated by the phenotypic data: for mature fruits resulting from self-pollination precedence, the majority of the progeny were the result of outcross fertilization.
Lineage-specific purging of recessive lethals has accompanied the evolution of SC in this species. SI populations show contrasting levels of embryonic inbreeding depression, with nearly complete embryonic lethality upon selfing in the Monteverde population. In the face of high embryonic inbreeding depression, an increase in selfing rate can evidently occur only under severe pollen limitation.
PMCID: PMC3673560  PMID: 21616885
Costa Rica; embryonic inbreeding depression; evolution; mating system; self-compatibility; self-incompatibility; Solanaceae; Witheringia solanacea

Results 1-25 (787552)