Evidence for low‐level hybridization between two allochronic populations of the pine processionary moth,Thaumetopoea pityocampa (Lepidoptera: Notodontidae)

Divergence between populations sharing the same habitat can be initiated by different reproductive times, leading to allochronic differentiation. A spatially localized allochronic summer population (SP) of the pine processionary moth Thaumetopoea pityocampa, recently discovered in Portugal, occurs in sympatry with the local winter population (WP). We examined the level of genetic differentiation between the two populations and estimated the current gene flow within the spatial framework of their co‐occurrence. Mitochondrial data indicated that the two sympatric populations were genetically closer than other WP populations. Conversely, microsatellite genotyping uncovered greater differentiation between the two sympatric populations than between allopatric ones. While male trapping confirmed that reproduction of SP and WP occurred at distinct times, clustering approaches demonstrated the presence of a few LateSP individuals emerging within the WP flight period, although genetically identified as SP. We also identified rare recent hybridization events apparently occurring mainly in the margins of the current SP range. The ongoing gene flow detected between the ancestral and the emerging allochronic populations revealed an incomplete reproductive isolation, which must therefore be taken into account and integrated with studies focussed on ecological drivers, so that a complete understanding of the ongoing speciation process might be achieved.     

Deciphering the demographic history of allochronic differentiation in the pine processionary moth Thaumetopoea pityocampa

Understanding the processes of adaptive divergence, which may ultimately lead to speciation, is a major question in evolutionary biology. Allochronic differentiation refers to a particular situation where gene flow is primarily impeded by temporal isolation between early and late reproducers. This process has been suggested to occur in a large array of organisms, even though it is still overlooked in the literature. We here focused on a well‐documented case of incipient allochronic speciation in the winter pine processionary moth Thaumetopoea pityocampa. This species typically reproduces in summer and larval development occurs throughout autumn and winter. A unique, phenologically shifted population (SP) was discovered in 1997 in Portugal. It was proved to be strongly differentiated from the sympatric “winter population” (WP), but its evolutionary history could only now be explored. We took advantage of the recent assembly of a draft genome and of the development of pan‐genomic RAD‐seq markers to decipher the demographic history of the differentiating populations and develop genome scans of adaptive differentiation. We showed that the SP diverged relatively recently, that is, few hundred years ago, and went through two successive bottlenecks followed by population size expansions, while the sympatric WP is currently experiencing a population decline. We identified outlier SNPs that were mapped onto the genome, but none were associated with the phenological shift or with subsequent adaptations. The strong genetic drift that occurred along the SP lineage certainly challenged our capacity to reveal functionally important loci.     

Genetic isolation through time: allochronic differentiation of a phenologically atypical population of the pine processionary moth

Allochronic speciation refers to a mode of sympatric speciation in which the differentiation of populations is primarily due to a phenological shift without habitat or host change. However, it has been so far rarely documented. The present paper reports on a plausible case of allochronic differentiation between sympatric populations of the pine processionary moth (PPM), Thaumetopoea pityocampa. The PPM is a Mediterranean insect with winter larval development. A phenologically atypical population with early adult activity and summer larval development was detected 10 years ago in Portugal. Mitochondrial and nuclear sequences strongly suggest that the 'summer' individuals are closely related to the sympatric winter population, while microsatellite data show a reduction in allelic richness, a distortion of allelic frequencies and significant genetic differentiation. Moreover, monitoring of adult flights suggests that reproductive activity does not overlap between the summer and winter populations. We postulate that the summer population appeared after a sudden phenological shift of some individuals of the sympatric winter population, leading to a founder effect and complete reproductive isolation. Given that the individuals showing this new phenology are subject to different selection pressures, the observed allochronic differentiation may rapidly lead to deeper divergence.     

Temperature niche shift observed in a Lepidoptera population under allochronic divergence

A process of adaptive divergence for tolerance to high temperatures was identified using a rare model system, consisting of two sympatric populations of a Lepidoptera (Thaumetopoea pityocampa) with different life cycle timings, a 'mutant' population with summer larval development, Leiria SP, and the founder natural population, having winter larval development, Leiria WP. A third, allopatric population (Bordeaux WP) was also studied. First and second instar larvae were experimentally exposed to daily-cycles of heat treatment reaching maximum values of 36, 38, 40 and 42 °C; control groups placed at 25 °C. A lethal temperature effect was only significant at 42 °C, for Leiria SP, whereas all temperatures tested had a significant negative effect upon Leiria WP, thus indicating an upper threshold of survival c.a. 6 °C above that of the WP. Cox regression model, for pooled heat treatments, predicted mortality hazard to increase for Leiria WP (+108%) and Bordeaux WP (+78%) in contrast to Leiria SP; to increase by 24% for each additional °C; and to decrease by 53% from first to second instar larvae. High variability among individuals was observed, a population characteristic that may favour selection and consequent adaptation. Present findings provide an example of ecological differentiation, following a process of allochronic divergence. Results further contribute to a better understanding of the implications of climate change for ecological genetics.     

Phylogenetic and molecular evidence for allochronic speciation in gall-forming aphids (Pemphigus)

Sympatric populations can diverge when variation in phenology or life cycle causes them to mate at distinctly different times. We report patterns consistent with this process (allochronic speciation) in North American gall-forming aphids, in the absence of a host or habitat shift. Pemphigus populi-transversus Riley and P. obesinymphae Aoki form a monophyletic clade within the North American Pemphigus group. They are sympatric on the eastern cottonwood, Populus deltoides (Salicaceae), but have distinctly different life cycles, with sexual stages offset by approximately six months. Field evidence indicates that intermediate phenotypes do not commonly occur, and mitochondrial and bacterial endosymbiont DNA sequences show no maternal gene flow between the two species. Because a genetically distinct population of P. obesinymphae occurs in the southwestern United States on Populus fremontii, we consider the possibility of an initial allopatric phase in the divergence. We discuss the likely origins of the host use patterns in P. obesinymphae, and the larger sequence of evolutionary changes that likely led to the sympatric divergence of P. populi-transversus and P. obesinymphae. A plausible interpretation at this stage of investigation is that a shift in timing of the life cycle in an ancestral population, correlated with an underlying phenological complexity in its host plant, spurred divergence between the incipient species.     

Rapid evolution and specialization following host colonization in a yucca moth

Host shifts followed by specialization can result in sympatric genetic differentiation, and may have fuelled the diversification of phytophagous insects. This study examines a recent colonization of a non‐native host by Prodoxus quinquepunctellus (Lepidoptera: Prodoxidae). Allozyme differentiation was detected among different host feeding populations, yet was nearly absent among similar host feeding populations in sympatry. Geographical patterns of allozyme variation showed a much higher level of population structure among populations feeding on the derived host. Conversely, mtDNA haplotype frequencies were nearly homogeneous in the derived populations compared to the ancestral populations, suggesting a bottleneck and/or rapid fixation of haplotypes following host colonization. Moth emergence coincided with host plant flowering, and phenological differences between host species translated into allochronic isolation between populations feeding on different hosts. Derived moth populations also differed significantly in three ovipositor characters from ancestral populations. These findings suggest rapid host‐specific genetic differentiation, and specialization of moth emergence time and ovipositor morphology following host colonization.     

Do different rates of gene flow underlie variation in phenotypic and phenological clines in a montane grasshopper community?

Species responses to environmental change are likely to depend on existing genetic and phenotypic variation, as well as evolutionary potential. A key challenge is to determine whether gene flow might facilitate or impede genomic divergence among populations responding to environmental change, and if emergent phenotypic variation is dependent on gene flow rates. A general expectation is that patterns of genetic differentiation in a set of codistributed species reflect differences in dispersal ability. In less dispersive species, we predict greater genetic divergence and reduced gene flow. This could lead to covariation in life‐history traits due to local adaptation, although plasticity or drift could mirror these patterns. We compare genome‐wide patterns of genetic structure in four phenotypically variable grasshopper species along a steep elevation gradient near Boulder, Colorado, and test the hypothesis that genomic differentiation is greater in short‐winged grasshopper species, and statistically associated with variation in growth, reproductive, and physiological traits along this gradient. In addition, we estimate rates of gene flow under competing demographic models, as well as potential gene flow through surveys of phenological overlap among populations within a species. All species exhibit genetic structure along the elevation gradient and limited gene flow. The most pronounced genetic divergence appears in short‐winged (less dispersive) species, which also exhibit less phenological overlap among populations. A high‐elevation population of the most widespread species, Melanoplus sanguinipes, appears to be a sink population derived from low elevation populations. While dispersal ability has a clear connection to the genetic structure in different species, genetic distance does not predict growth, reproductive, or physiological trait variation in any species, requiring further investigation to clearly link phenotypic divergence to local adaptation.     

POPULATION STRUCTURE ALONG A STEEP ENVIRONMENTAL GRADIENT: CONSEQUENCES OF FLOWERING TIME AND HABITAT VARIATION IN THE SNOW BUTTERCUP,RANUNCULUS ADONEUS

Few studies have determined how gene flow and selection interact to generate population genetic structure in heterogeneous environments. One way to identify the potential role played by natural selection is to compare patterns of spatial genetic structure between different life cycle stages and among microenvironments. We examined patterns of spatial structure in a population of the snow buttercup (Ranunculus adoneus), using both adult plants and newly emerged seedlings. The study population spans a steep environmental gradient caused by gradual melting of snow within a permanent snowbed. Early-melting sites are characterized by denser vegetation, more fertile soils, and a longer growing season than late-melting sites tens of meters away. The flowering time of R. adoneus is controlled entirely by time of snowmelt, so the contiguous population is phenologically substructured into a series of successively flowering cohorts, reducing the opportunity for direct pollen transfer between early- and late-melting sites. For four highly polymorphic enzyme loci in this tetraploid species, there was subtle, but statistically significant, genetic differentiation between early, middle, and late-melting cohorts; adults usually showed greater differentiation among snowmelt zones than did seedlings. At two loci in adults and one locus in seedlings, homozygotes were more common than predicted at Hardy-Weinberg equilibrium, even when assuming maximum levels of double reduction during meiosis. This pattern suggests the occurrence of self-fertilization and/or population substructure. To determine how spatial isolation and phenological separation each contribute to genetic substructure, we used bivariate regression models to predict the numbers of allele differences between randomly paired individuals as a function of meters separation in space and days separation in flowering time. For newly emerged seedlings, we found that spatial separation was positively associated with genetic difference, but that the additional contribution of phenological separation to genetic difference was not significant. This implies that seeds and/or pollen move effectively across the snowmelt gradient, despite differences in flowering time. As was true for seedlings, spatial separation between paired adults contributed to greater genetic difference, but for a given spatial separation, the genetic difference between adult plants was reduced by phenological separation. This result implies that postemergence selection is favoring at least some seeds that migrate across the snowmelt gradient. Directional gene flow across the snowmelt gradient probably results from a genetic source-sink interaction, that is, the colonization of ecologically marginal late-melting sites by high quality seeds produced by the larger subpopulation in early-melting sites. Effective gene flow from high to low quality microenvironments is likely to impede adaptation to late-melting locations.     

Assortative mating and gene flow generate clinal phenological variation in trees

ABSTRACT: BACKGROUND: On-going climate change is shifting the timing of bud burst (TBB) of broad leaf and conifer trees in temperate areas, raising concerns about the abilities of natural populations to respond to these shifts. The level of expected evolutionary change depends on the level and distribution of genetic variation of TBB. While numerous experimental studies have highlighted the role of divergent selection in promoting clinal TBB differentiation, we explored whether the observed patterns of variation could be generated by the joint effects of assortative mating for TBB and gene flow among natural populations. We tested this hypothesis using an in silico approach based on quantitative genetic models. RESULTS: Our simulations showed that genetic clines can develop even without divergent selection. Assortative mating in association with environmental gradients substantially shifted the mean genetic values of populations. Owing to assortative mating, immigrant alleles were screened for proximal or distant populations depending on the strength of the environmental cline. Furthermore, we confirmed that assortative mating increases the additive genetic variance within populations. However, we observed also a rapid decline of the additive genetic variance caused by restricted gene flow between neighboring populations resulting from preferential matings between phenologically-matching phenotypes. CONCLUSIONS: We provided evidence that the patterns of genetic variation of phenological traits observed in forest trees can be generated solely by the effects of assortative mating and gene flow. We anticipate that predicted temperature increases due to climate change will further enhance genetic differentiation across the landscape. These trends are likely to be reinforced or counteracted by natural selection if phenological traits are correlated to fitness.     

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

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

Identifying potential evolutionary consequences of climate-driven phenological shifts

Climate change is shifting the phenology of many species throughout the world. While the interspecific consequences of these phenological shifts have been well documented, the intraspecific shifts and their resultant evolutionary consequences remain relatively unexplored. Here, we present a conceptual framework and overview of how phenological shifts within species can drive evolutionary change. We suggest that because the impacts of climate change are likely to vary across the range of a species and differentially impact individuals, phenological shifts may often be highly variable both within and among populations. Together these changes have the potential to alter existing patterns of gene flow and influence evolutionary trajectories by increasing phenological isolation and connectivity. Recent research examining the response of species to contemporary climate change suggests that both phenological isolation and connectivity may be likely responses to future climate change. However, recent studies also show mixed results on whether adaptive responses to climate change are likely to occur, as some populations have already shown adaptive responses to changing climate, while others have not despite fitness costs. While predicting the exact consequences of intraspecific phenological shifts may be difficult, identifying the evolutionary implications of these shifts will allow a better understanding of the effects of future climate change on species persistence and adaptation.     

The phenology ofProcladius crassinervis (Zett),Procladius signatus (Zett) andProcladius choreus (Mg) (Diptera,Chironomidae) at Lake Hald,Denmark

In an investigation of the phenology of the chironomid species of Lake Hald, Denmark, a very late flight activity (September–November) of the univoltine speciesProcladius choreus (Mg.) was observed. Among observations of the phenological patterns of univoltine chironomids inhabiting lakes of the Baltic type in Denmark, the phenological pattern ofProcladius choreus stands alone (JÓNSSON, 1987; LARSEN, 1991). Further two species of the genusProcladius Skuse,viz. Procladius crassinervis (Zett) andProcladius signatus (Zett), were found in the investigation and the phenological pattern of the three congeneric species was clearly allochronic, withProcladius crassinervis flying in spring,Procladius signatus flying in summer andProcladius choreus flying in autumn.     

Experimental evidence for heritable reproductive time in 2 allochronic populations of pine processionary moth

Phenology allows organisms to overcome seasonally variable conditions through life‐cycle adjustment. Changes in phenology can drastically modify the evolutionary trajectory of a population, while a shift in the reproductive time may cause allochronic differentiation. The hypothesis of heritable reproductive time was experimentally tested, by studying a unique population of the pine processionary moth Thaumetopoea pityocampa (Den. & Schiff.) which has a shifted phenology, and however co‐occurs with the typical population following the classical life cycle. When populations of both types were reared under controlled conditions, the reproductive time was maintained asynchronous, as observed in the field. The shifted population was manipulated in the laboratory to reproduce later than usual, yet the offspring emerged in the next year at the expected dates thus “coming back” to the usual cycle. Hybrids from crosses performed between the 2 populations showed an intermediate phenology. From the emergence times of parents and offspring, a high heritability of the reproductive time (h = 0.76) was observed. The offspring obtained from each type of cross was genetically characterized using microsatellite markers. Bayesian clustering analysis confirmed that hybrids can be successfully identified and separated from the parental genetic classes by genotyping. Findings support the hypothesis that, for this particular population, incipient allochronic speciation is due to a heritable shift in the reproductive time that further causes assortative mating and might eventually cause ecological adaptation/maladaptation in response to environmental changes.     

Divergence with gene flow and fine-scale phylogeographical structure in the wedge-billed woodcreeper, Glyphorynchus spirurus, a Neotropical rainforest bird

Determining the relative roles of vicariance and selection in restricting gene flow between populations is of central importance to the evolutionary process of population divergence and speciation. Here we use molecular and morphological data to contrast the effect of isolation (by mountains and geographical distance) with that of ecological factors (altitudinal gradients) in promoting differentiation in the wedge-billed woodcreeper, Glyphorynchus spirurus , a tropical forest bird, in Ecuador. Tarsus length and beak size increased relative to body size with altitude on both sides of the Andes, and were correlated with the amount of moss on tree trunks, suggesting the role of selection in driving adaptive divergence. In contrast, molecular data revealed a considerable degree of admixture along these altitudinal gradients, suggesting that adaptive divergence in morphological traits has occurred in the presence of gene flow. As suggested by mitochondrial DNA sequence data, the Andes act as a barrier to gene flow between ancient subspecific lineages. Genome-wide amplified fragment length polymorphism markers reflected more recent patterns of gene flow and revealed fine-scale patterns of population differentiation that were not detectable with mitochondrial DNA, including the differentiation of isolated coastal populations west of the Andes. Our results support the predominant role of geographical isolation in driving genetic differentiation in G. spirurus , yet suggest the role of selection in driving parallel morphological divergence along ecological gradients.     

Demographic fluctuations lead to rapid and cyclic shifts in genetic structure among populations of an alpine butterfly,Parnassius smintheus

Many populations, especially in insects, fluctuate in size, and periods of particularly low population size can have strong effects on genetic variation. Effects of demographic bottlenecks on genetic diversity of single populations are widely documented. Effects of bottlenecks on genetic structure among multiple interconnected populations are less studied, as are genetic changes across multiple cycles of demographic collapse and recovery. We take advantage of a long‐term data set comprising demographic, genetic and movement data from a network of populations of the butterfly, Parnassius smintheus, to examine the effects of fluctuating population size on spatial genetic structure. We build on a previous study that documented increased genetic differentiation and loss of spatial genetic patterns (isolation by distance and by intervening forest cover) after a network‐wide bottleneck event. Here, we show that genetic differentiation was reduced again and spatial patterns returned to the system extremely rapidly, within three years (i.e. generations). We also show that a second bottleneck had similar effects to the first, increasing differentiation and erasing spatial patterns. Thus, bottlenecks consistently drive random divergence of allele frequencies among populations in this system, but these effects are rapidly countered by gene flow during demographic recovery. Our results reveal a system in which the relative influence of genetic drift and gene flow continually shift as populations fluctuate in size, leading to cyclic changes in genetic structure. Our results also suggest caution in the interpretation of patterns of spatial genetic structure, and its association with landscape variables, when measured at only a single point in time.     

Evolutionary and demographic processes shaping geographic patterns of genetic diversity in a keystone species,the African forest elephant (Loxodonta cyclotis)

The past processes that have shaped geographic patterns of genetic diversity may be difficult to infer from current patterns. However, in species with sex differences in dispersal, differing phylogeographic patterns between mitochondrial (mt) and nuclear (nu) DNA may provide contrasting insights into past events. Forest elephants (Loxodonta cyclotis) were impacted by climate and habitat change during the Pleistocene, which likely shaped phylogeographic patterns in mitochondrial (mt) DNA that have persisted due to limited female dispersal. By contrast, the nuclear (nu) DNA phylogeography of forest elephants in Central Africa has not been determined. We therefore examined the population structure of Central African forest elephants by genotyping 94 individuals from six localities at 21 microsatellite loci. Between forest elephants in western and eastern Congolian forests, there was only modest genetic differentiation, a pattern highly discordant with that of mtDNA. Nuclear genetic patterns are consistent with isolation by distance. Alternatively, male‐mediated gene flow may have reduced the previous regional differentiation in Central Africa suggested by mtDNA patterns, which likely reflect forest fragmentation during the Pleistocene. In species like elephants, male‐mediated gene flow erases the nuclear genetic signatures of past climate and habitat changes, but these continue to persist as patterns in mtDNA because females do not disperse. Conservation implications of these results are discussed.     

Analyzing expression of perforin, Runx3, and Thpok genes during positive selection reveals activation of CD8-differentiation programs by MHC II-signaled thymocytes

Intrathymic positive selection matches CD4-CD8 lineage differentiation to MHC specificity. However, it is unclear whether MHC signals induce lineage choice or simply select thymocytes of the appropriate lineage. To investigate this issue, we assessed thymocytes undergoing positive selection for expression of the CD8 lineage markers perforin and Runx3. Using both population-based and single-cell RT-PCR analyses, we found large subsets of MHC class II (MHC-II)-signaled thymocytes expressing these genes within the CD4+ 8+ and CD4+ 8(int), but not the CD4+ 8- populations of signaling competent mice. This indicates that MHC-II signals normally fail to impose CD4 differentiation and further implies that the number of mature CD8 single-positive (SP) thymocytes greatly underestimates CD8 lineage choice. We next examined whether MHC-II-restricted CD4+ 8- thymocytes remain competent to initiate CD8 lineage gene expression. In mice in which expression of the tyrosine kinase Zap70 and thereby TCR signaling were impaired selectively in SP thymocytes, MHC-II-signaled CD4+ 8- thymocytes expressed perforin and Runx3 and failed to up-regulate the CD4 marker Thpok. This indicated that impairing TCR signals at the CD4 SP stage switched gene expression patterns from CD4- to CD8-lineage specific. We conclude from these findings that MHC-II-signaled thymocytes remain competent to initiate CD8-specific gene expression even after CD8 down-regulation and that CD4 lineage differentiation is not fixed before the CD4 SP stage.     

The roles of shifting and filtering in generating community‐level flowering phenology

Plant phenologies are key components of community assembly and ecosystem function, yet we know little about how phenological patterns differ among ecosystems. Community‐level phenological patterns may be driven by the filtering of species into communities based on their phenology or by intraspecific responses to local conditions that shift when species flower. To understand the relative roles of filtering and shifting on community‐level phenological patterns we compared patterns of first flowering dates (FFD) for herbaceous species at Konza Prairie, KS, USA with those from the colder Fargo, ND, USA area and from Chinnor, England, which has a less continental climate. Comparing patterns of FFD supports that Konza's flowering patterns are potentially influenced both by filtering species that flower early in the growing season and by phenological shifting. Konza species flowering dates were earlier in the spring and later in the fall compared to Fargo, but were not shifted compared to Chinnor, which had a unique suite of early‐flowering species. In all, comparing flowering phenology among three sites reveals that intraspecific responses to climate can generate phenological shifts that compress or stretch community‐level phenological patterns, while novel niches in phenological space can also alter community‐level patterns. Community flowering patterns related to climate suggest that climatic warming has the potential to further distribute flowering of the Konza flora over a longer period, but also could further open it to introductions of non‐native species that have evolved to flower early in the season.     

Temporal mating isolation driven by a behavioral gene in Drosophila

Speciation is the evolutionary process in which new barriers to gene exchange are created. These barriers may be physical, leading to spatial separation of subpopulations and resulting in allopatric speciation, or they may be temporal, giving rise to allochronic speciation, and may include the time of day or the time of year when mating takes place. Drosophila melanogaster and D. pseudoobscura show different temporal patterns of circadian locomotor activity that are determined by the circadian clock gene period (per). Genes that control aspects of behavior that might be relevant to courtship and mating, such as locomotor patterns, become obvious candidates for involvement in the speciation process. However, evidence for the role of individual genes in the mechanism of mate choice has proved elusive. We have used transgenic flies carrying the natural per genes from these two Drosophila species to reveal that per has the potential to provide the permissive conditions for speciation, by affecting mate choice through a mechanism involving the species-specific timing of mating behavior.