Phylogenetic relationships, evolutionary origin, taxonomic status, and genetic structure of the endangered local Lower Elbe river (Germany) endemic Oenanthe conioides (Nolte ex Rchb.f.) Lange (Apiaceae): ITS and AFLP evidence

Oenanthe conioides is an endangered local endemic of the Lower Elbe river region in Germany where it is found in areas with freshwater tides. Internal transcribed spacer (ITS) and amplified fragment length polymorphism (AFLP) markers were used to investigate its phylogenetic relationships, evolutionary origin, taxonomic status, and genetic structure.Oe. conioides is most closely related to Oe. aquatica and Oe. fluviatilis, and cannot be distinguished from Oe. aquatica by ITS sequence variation. Oe. aquatica is found mainly in standing or slow-flowing freshwater habitats. The AFLP analysis indicated that Oe. conioides may constitute a monophyletic lineage nested within Oe. aquatica. Considering this result on the background of the sympatric distribution of the two species and their ecological differentiation, it is hypothesized that Oe. conioides arose sympatrically from Oe. aquatica through ecological divergence. It is concluded that Oe. conioides is best considered a subspecies of Oe. aquatica.AFLP analysis of Oe. conioides revealed low levels of genetic differentiation among populations reflecting the small geographical distance, the recent decline in population number and size, the connection of populations through the river, and their presumably high population dynamics.Considering this pattern of genetic variation, it is concluded that no individual population can be singled out as being particularly important from a genetic point of view. Also, all populations could be used as source material should the establishment of new populations or the enlargement of small populations be considered as a measure to consolidate the persistence of the species.     

Genetic evidence for divergent selection on Oenanthe conioides and Oe. aquatica (Apiaceae), a candidate case for sympatric speciation

The opportunity for habitat shift in sympatry is thought to be an important factor in sympatric speciation by facilitating assortative mating and offering opportunities for divergent selection. Oenanthe conioides (Apiaceae) is a narrow endemic from the lower Elbe river area (Germany) where it is restricted to areas experiencing fresh water tides inundating the plants twice a day. The species was shown to have originated from Oe. aquatica which is widely distributed in Europe and grows in still or slowly flowing fresh water. Reciprocal transplant experiments have previously shown that in both habitats the non‐native species is less fit than the native, and several phenotypic traits have been linked to this difference in fitness. We performed an amplified fragment length polymorphism genome scan with 333 polymorphic markers searching for candidate markers for divergent selection. A relatively small fraction (2.1%) of the markers was identified as divergence outliers which fits theoretical expectations for speciation with gene flow. Some of the markers that were potentially under divergent selection showed evidence of being clustered in the genome. This suggests that there may have been a role for mechanisms that reduce breaking‐up of trait complexes in the speciation process. © 2014 The Linnean Society of London, Biological Journal of the Linnean Society, 2014, 113 , 50–56.     

Germination ecology of two closely related taxa in the genus Oenanthe: Fine tuning for the habitat?

For two closely related amphibious plant taxa of the genus Oenanthe (Apiaceae) germination traits were examined. Habitats of the two taxa differ in hydroregime. The endemic Oenanthe conioides of the river Elbe estuary experiences daily tidal fluctuations whereas the widespread Oenanthe aquatica grows at the edge of ponds and in freshwater wetlands with rare and unpredictable fluctuations of water table.Seeds of both taxa could be characterized as non-dormant and light dependent. Under temperature fluctuations, germination percentage was higher than under constant temperatures. Salinity was tolerated to up to 3.3‰. At 10‰ there was a strong decrease in germination percentage, which did not result from ionic toxicity, as experiments with a gradient in osmolarity showed.Differences between the taxa were found concerning hydrological and temperature fluctuations. While O. aquatica showed no reduction in germination percentage under permanent 1 cm flooding, O. conioides did. On the other hand, germination under an artificial tidal hydroregime was better in O. conioides than in O. aquatica. During fluctuating temperatures of 3/22 and 6/22 °C O. conioides germinated much quicker and had a higher final germination percentage.Differences between the taxa could be correlated with differences of the hydrological regime in the specific habitat. Taking into account that O. conioides is phylogenetically a relatively young taxon, it may be hypothesized that a quick adaptation to the tidal conditions might have taken place.     

Germination ecology of two closely related taxa in the genus Oenanthe: Fine tuning for the habitat?

For two closely related amphibious plant taxa of the genus Oenanthe (Apiaceae) germination traits were examined. Habitats of the two taxa differ in hydroregime. The endemic Oenanthe conioides of the river Elbe estuary experiences daily tidal fluctuations whereas the widespread Oenanthe aquatica grows at the edge of ponds and in freshwater wetlands with rare and unpredictable fluctuations of water table.     

WEAK CROSSABILITY BARRIER BUT STRONG JUVENILE SELECTION SUPPORTS ECOLOGICAL SPECIATION OF THE HYBRID PINE PINUS DENSATA ON THE TIBETAN PLATEAU

Determining how a new hybrid lineage can achieve reproductive isolation is a key to understanding the process and mechanisms of homoploid hybrid speciation. Here, we evaluated the degree and nature of reproductive isolation between the ecologically successful hybrid species Pinus densata and its parental species P. tabuliformis and P. yunnanensis. We performed interspecific crosses among the three species to assess their crossability. We then conducted reciprocal transplantation experiments to evaluate their fitness differentiation, and to examine how natural populations representing different directions of introgression differ in adaptation. The crossing experiments revealed weak genetic barriers among the species. The transplantation trials showed manifest evidence of local adaptation as the three species all performed best in their native habitats. Pinus densata populations from the western edge of its distribution have evolved a strong local adaptation to the specific habitat in that range; populations representing different directions of introgressants with the two parental species all showed fitness disadvantages in this P. densata habitat. These observations illustrate that premating isolation through selection against immigrants from other habitat types or postzygotic isolation through selection against backcrosses between the three species is strong. Thus, ecological selection in combination with endogenous components and geographic isolation has likely played a significant role in the speciation of P. densata.     

GENETIC DIFFERENTIATION AND SELECTION AGAINST MIGRANTS IN EVOLUTIONARILY REPLICATED EXTREME ENVIRONMENTS

We investigated mechanisms of reproductive isolation in livebearing fishes (genus Poecilia) inhabiting sulfidic and nonsulfidic habitats in three replicate river drainages. Although sulfide spring fish convergently evolved divergent phenotypes, it was unclear if mechanisms of reproductive isolation also evolved convergently. Using microsatellites, we found strongly reduced gene flow between adjacent populations from different habitat types, suggesting that local adaptation to sulfidic habitats repeatedly caused the emergence of reproductive isolation. Reciprocal translocation experiments indicate strong selection against immigrants into sulfidic waters, but also variation among drainages in the strength of selection against immigrants into nonsulfidic waters. Mate choice experiments revealed the evolution of assortative mating preferences in females from nonsulfidic but not from sulfidic habitats. The inferred strength of sexual selection against immigrants (RI_s) was negatively correlated with the strength of natural selection (RI_m), a pattern that could be attributed to reinforcement, whereby natural selection strengthens behavioral isolation due to reduced hybrid fitness. Overall, reproductive isolation and genetic differentiation appear to be replicated and direct consequences of local adaptation to sulfide spring environments, but the relative contributions of different mechanisms of reproductive isolation vary across these evolutionarily independent replicates, highlighting both convergent and nonconvergent evolutionary trajectories of populations in each drainage.     

Ecological reproductive isolation of coast and inland races of Mimulus guttatus

Adaptive divergence due to habitat differences is thought to play a major role in formation of new species. However it is rarely clear the extent to which individual reproductive isolating barriers related to habitat differentiation contribute to total isolation. Furthermore, it is often difficult to determine the specific environmental variables that drive the evolution of those ecological barriers, and the geographic scale at which habitat-mediated speciation occurs. Here, we address these questions through an analysis of the population structure and reproductive isolation between coastal perennial and inland annual forms of the yellow monkeyflower, Mimulus guttatus. We found substantial morphological and molecular genetic divergence among populations derived from coast and inland habitats. Reciprocal transplant experiments revealed nearly complete reproductive isolation between coast and inland populations mediated by selection against immigrants and flowering time differences, but not postzygotic isolation. Our results suggest that selection against immigrants is a function of adaptations to seasonal drought in inland habitat and to year round soil moisture and salt spray in coastal habitat. We conclude that the coast and inland populations collectively comprise distinct ecological races. Overall, this study suggests that adaptations to widespread habitats can lead to the formation of reproductively isolated species.     

Highly variable reproductive isolation among pairs of Catostomus species

Hybridization between diverged taxa tests the strength of reproductive isolation and can therefore reveal mechanisms of reproductive isolation. However, it remains unclear how consistent reproductive isolation is across species' ranges and to what extent reproductive isolation might remain polymorphic as species diverge. To address these questions, we compared outcomes of hybridization across species pairs of Catostomus fishes in three rivers in the Upper Colorado River basin, where an introduced species, C. commersoni, hybridizes with at least two native species, C. discobolus and C. latipinnis. We observed substantial heterogeneity in outcomes of hybridization, both between species pairs and across geographically separate rivers within each species pair. We also observed hybridization of additional related species with our focal species, suggesting that reproductive isolation in this group involves interactions of multiple evolutionary and ecological factors. These findings suggest that a better understanding of the determinants of variation in reproductive isolation is needed and that studies of reproductive isolation in hybrids should consider how the dynamics and mechanisms of reproductive isolation vary over ecological space and over evolutionary time. Our results also have implications for the conservation and management of native catostomids in the Colorado River basin. Heterogeneity in outcomes of hybridization suggests that the threat posed by hybridization and genetic introgression to the persistence of native species probably varies with extent of reproductive isolation, both across rivers and across species pairs.     

Perspective: Reproductive isolation caused by natural selection against immigrants from divergent habitats

The classification of reproductive isolating barriers laid out by Dobzhansky and Mayr has motivated and structured decades of research on speciation. We argue, however, that this classification is incomplete and that the unique contributions of a major source of reproductive isolation have often been overlooked. Here, we describe reproductive barriers that derive from the reduced survival of immigrants upon reaching foreign habitats that are ecologically divergent from their native habitat. This selection against immigrants reduces encounters and thus mating opportunities between individuals from divergently adapted populations. It also reduces the likelihood that successfully mated immigrant females will survive long enough to produce their hybrid offspring. Thus, natural selection against immigrants results in distinctive elements of premating and postmating reproductive isolation that we hereby dub "immigrant inviability." We quantify the contributions of immigrant inviability to total reproductive isolation by examining study systems where multiple components of reproductive isolation have been measured and demonstrate that these contributions are frequently greater than those of traditionally recognized reproductive barriers. The relevance of immigrant inviability is further illustrated by a consideration of population-genetic theory, a review of selection against immigrant alleles in hybrid zone studies, and an examination of its participation in feedback loops that influence the evolution of additional reproductive barriers. Because some degree of immigrant inviability will commonly exist between populations that exhibit adaptive ecological divergence, we emphasize that these barriers play critical roles in ecological modes of speciation. We hope that the formal recognition of immigrant inviability and our demonstration of its evolutionary importance will stimulate more explicit empirical studies of its contributions to speciation.     

Effects of a habitat-altering invader on nesting sparrows: An ecological trap?

Many invading species impact native species through predation, parasitism or competition, while others affect natives indirectly by restructuring their habitat. How invasive plants affect native animals, and to what extent native animals respond to changes in their habitat and the novel selection pressures that follow, is not well known. We investigated the impacts of a habitat-altering invader, the Atlantic cordgrass Spartina alterniflora, on the nesting success of Alameda song sparrows (Melospiza melodia pusillula), a California Species of Special Concern, in tidal marshes in three sites in San Francisco Bay. Date of laying was the most influential factor in determining daily survival rate of nests, but whether the nest was placed in exotic Spartina was the most important ecological variable. Nests placed in exotic Spartina had a success rate that was 30% lower than those placed in native vegetation. Nests in exotic Spartina were significantly more likely to fail due to tidal flooding than were nests placed in native vegetation, because the densest stands of exotic Spartina occurred at significantly lower elevations relative to the tides. Our results suggest that exotic Spartina may be an ecological trap for song sparrows in San Francisco Bay, attracting birds to nest sites that are often destroyed by tidal flooding.     

Divergent selection and drift shape the genomes of two avian sister species spanning a saline–freshwater ecotone

The role of species divergence due to ecologically based divergent selection—or ecological speciation—in generating and maintaining biodiversity is a central question in evolutionary biology. Comparison of the genomes of phylogenetically related taxa spanning a selective habitat gradient enables discovery of divergent signatures of selection and thereby provides valuable insight into the role of divergent ecological selection in speciation. Tidal marsh ecosystems provide tractable opportunities for studying organisms' adaptations to selective pressures that underlie ecological divergence. Sharp environmental gradients across the saline–freshwater ecotone within tidal marshes present extreme adaptive challenges to terrestrial vertebrates. Here, we sequence 20 whole genomes of two avian sister species endemic to tidal marshes—the saltmarsh sparrow (Ammospiza caudacutus) and Nelson's sparrow (A. nelsoni)—to evaluate the influence of selective and demographic processes in shaping genome‐wide patterns of divergence. Genome‐wide divergence between these two recently diverged sister species was notably high (genome‐wide F_ST = 0.32). Against a background of high genome‐wide divergence, regions of elevated divergence were widespread throughout the genome, as opposed to focused within islands of differentiation. These patterns may be the result of genetic drift resulting from past tidal march colonization events in conjunction with divergent selection to different environments. We identified several candidate genes that exhibited elevated divergence between saltmarsh and Nelson's sparrows, including genes linked to osmotic regulation, circadian rhythm, and plumage melanism—all putative candidates linked to adaptation to tidal marsh environments. These findings provide new insights into the roles of divergent selection and genetic drift in generating and maintaining biodiversity.     

Populations composed entirely of hybrid colonies: bidirectional hybridization and polyandry in harvester ants

In eusocial Hymenoptera, haplodiploid life cycles, obligate sterile castes, and polyandry may facilitate selection for hybridization. We analyzed a broad hybrid zone between the ecologically distinct seed‐harvester ants Pogonomyrmex occidentalis (Cresson) and Pogonomyrmex maricopa (Wheeler) using mitochondrial (mt)DNA sequence data, eight morphological markers, and 14 random amplified polymorphic DNA (RAPD) markers. Average mtDNA sequence divergence among parental species was 11.34%, indicating secondary contact. RAPD markers were significantly correlated with morphological variation, confirming the interspecific hybrid origin of all morphologically putative hybrid colonies. A morphological hybrid index indicates an abundance of both F₁ hybrids and parental morphotypes within colonies. Individual character frequencies plotted against distance show coincident and concordant clines, suggesting little to no introgression. The structure of the hybrid zone is two‐fold. Within the western region, stark reversals in character frequencies coincide with overt soil differences, indicating a mosaic hybrid zone structure. The eastern region is a riparian habitat where four adjacent populations were composed entirely of hybrid colonies. These habitat associations suggest that hybrid worker genomes permit dispersal into intermediate environments that select against one or both parental species. The present study suggests that, in addition to retaining reproductive compatibility, ecologically distinct species of ants may generate hybrid colonies maintained by environmental selection. © 2008 The Linnean Society of London, Biological Journal of the Linnean Society, 2008, 95 , 320–336.     

The mechanism of background extinction

Following publication of On the Origin of Species, biologists concentrated on and resolved the mechanisms of adaptation and speciation, but largely ignored extinction. Thus, extinction remained essentially a discipline of palaeontology. Adequate language is not available to describe extinction phenomena because they must be discussed in the passive voice, wherein populations simply ‘go extinct’ without reference to process, specifics, effects, or causality. Extinction is also described typically in terms of its dynamics (including rate or risk), and although correlative variables enhance our ability to predict extinction, they do not necessarily enable an understanding of process. Yet background extinction, like evolution, is a process requiring a functional explanation, without which it is impossible to formulate mechanisms. We define the mechanism of background extinction as a typically long‐term, multi‐generational loss of reproductive fitness. This simple concept has received little credence because of a perception that excess generation of progeny ensures population sustainability, and perhaps the misconception that the loss of reproductive fitness somehow constitutes selection against reproduction itself. During environmental shifts, reproductive fitness is compromised when biotic or abiotic extremes consistently exceed existing norms of reaction. Subsequent selection will now favour individual survival over reproductive fitness, initiating long‐term negative selection pressure and population decline. Background extinction consists typically of two intergrading phases: habitat attenuation and habitat dissolution. These processes generate the relict populations that characterize many species undergoing background extinction. © 2011 The Linnean Society of London, Biological Journal of the Linnean Society, 2012, 105 , 255–268.     

Selection on hybrids of ecologically divergent ecotypes of a marine snail: the relative importance of exogenous and endogenous barriers

Unravelling the form of selection acting on hybrids of ecotypes undergoing ecological speciation is essential to understand the mechanisms behind the evolution of reproductive isolation in the face of gene flow. Shell phenotype is known to be affected by natural selection and is involved in the fitness of the marine snail Littorina saxatilis. Here, we studied the association between shell traits and fitness in hybrids in order to determine the relative role of exogenous and endogenous selection in this hybrid zone of L. saxatilis. We show that directional selection is the predominant mode of selection among hybrids. We also show its heterogeneity, affecting different shell traits, within populations at the level of the microhabitat. Therefore, endogenous selection mechanisms are most probably lacking in this hybrid zone and exogenous barriers (pre‐ and post‐zygotic) are possibly one of the main forces behind the evolution of barriers to gene flow between these ecologically divergent ecotypes. This study shows how this barrier might represent an important type of reproductive isolation within ecological speciation, and this should be taken into account in future studies of speciation in hybrid zones. © 2013 The Linnean Society of London, Biological Journal of the Linnean Society, 2014, 111 , 391–400.     

The effectiveness of pre‐ and post‐zygotic barriers in avoiding hybridization between two snapdragons (Antirrhinum L.: Plantaginaceae)

Reproductive barriers play an important role in the maintenance of species boundaries. However, to date, few studies have provided a detailed analysis of reproductive isolation barriers between species or examined their importance in maintaining species identity. This is the first detailed study into pre‐ and post‐zygotic reproductive isolation barriers in Antirrhinum, based on a mixed population with two species that rarely co‐occur. The study revealed that pollinator constancy and preference and poor hybrid seed viability were the most important reproductive isolating mechanisms. Reproductive isolation was practically complete by both pre‐ and post‐zygotic barriers. Average pre‐zygotic isolation was greater than post‐zygotic isolation, in accordance with the trend observed in flowering plants in which reproductive isolation is principally caused by pre‐zygotic mechanisms. However, average post‐zygotic isolation was also high, in contrast to what was expected among Antirrhinum spp. This case highlights the importance of quantifying the reproductive isolation barriers thoroughly to understand how and why species boundaries are maintained. © 2014 The Linnean Society of London, Botanical Journal of the Linnean Society, 2014, 176 , 159–172.     

The evolution of sex pheromones in an ecologically diverse genus of flies

In theory, pheromones important in specific mate recognition should evolve via large shifts in composition (saltational changes) at speciation events. However, where other mechanisms exist to ensure reproductive isolation, no such selection for rapid divergence is expected. In Bactrocera fruit flies (Diptera: Tephritidae), males produce volatile chemicals to attract females for mating. Bactrocera species exhibit great ecological diversity, with a wide range of geographical locations and host plants used. They also have other mechanisms, including temporal and behavioural differences, which ensure reproductive isolation. Therefore, we predicted that their sex pheromones would not exhibit rapid divergence at speciation events. In the present study, we tested this idea by combining data on male sex pheromone composition for 19 species of Bactrocera with a phylogeny constructed from DNA sequence data. Analyses of the combined data revealed positive correlations between pheromone differences and nucleotide divergence between species, and between the number of pheromone changes along the phylogeny and the branch lengths associated with these changes. These results suggest a gradual rather than saltational mode of evolution. However, remarkable differences in sex pheromones composition exist, even between closely-related species. It appears therefore that the mode of evolution of sex pheromones in Bactrocera is best described by rapid saltational changes associated with speciation, followed by gradual divergence thereafter. Furthermore, species that do not overlap ecologically are just as different pheromonally as species that do. Thus, large changes in pheromone composition appear to be achieved, even in cases where other mechanisms to ensure reproductive isolation exist. We suggest that these differences are closely associated with rapid changes in host plant use, which is a characteristic feature of Bactrocera speciation. © 2009 The Linnean Society of London, Biological Journal of the Linnean Society, 2009, 97 , 594–603.     

Genetic differentiation without mimicry shift in a pair of hybridizing Heliconius species (Lepidoptera: Nymphalidae)

Butterflies in the genus Heliconius have undergone rapid adaptive radiation for warning patterns and mimicry, and are excellent models to study the mechanisms underlying diversification. In Heliconius, mimicry rings typically involve distantly related species, whereas closely related species often join different mimicry rings. Genetic and behavioural studies have n how reproductive isolation in many pairs of Heliconius taxa is largely mediated by natural and sexual selection on wing colour patterns. However, recent studies have uncovered new cases in which pairs of closely related species are near‐perfect mimics of each other. Here, we provide morphometric and genetic evidence for the coexistence of two closely related, hybridizing co‐mimetic species on the eastern slopes of the Andes, H. melpomene amaryllis and H. timareta ssp. nov. , which is described here as H. timareta thelxinoe . A joint analysis of multilocus genotyping and geometric morphometrics of wing shape shows a high level of differentiation between the two species, with only limited gene flow and mixing. Some degree of genetic mixing can be detected, but putative hybrids were rare, only one of 175 specimens being a clear hybrid. In contrast, we found phenotypic differentiation between populations of H. timareta thelxinoe , possibly indicative of strong selection for local mimicry in different communities. In this pair of species, the absence of breakdown of genetic isolation despite near‐identical wing patterns implies that factors other than wing patterns keep the two taxa apart, such as chemical or behavioural signals, or ecological adaptation along a strong altitudinal gradient. © 2013 The Linnean Society of London, Biological Journal of the Linnean Society, 2013, 109 , 830–847.     

Immigrant inviability promotes reproductive isolation among host‐associated populations of the gall wasp Belonocnema treatae

Ecological speciation describes the evolutionary process whereby divergent natural selection between environments generates reproductive isolation. Studying the magnitude of sequential reproductive barriers between ecologically divergent populations improves our understanding of the way these barriers evolve and how each contributes to the speciation process. Immigrant inviability describes the lower fitness of immigrants in non‐native environments and is an important, but long underexplored, reproductive barrier. In this study, we test the role of immigrant inviability among host‐associated populations of the gall wasp Belonocnema treataeMayr (Hymenoptera: Cynipini: Cynipidae) by measuring the ability of gall wasps to initiate and complete gall formation, while avoiding host immune responses, on closely related native and non‐native live oaks, Quercus virginianaMill., Quercus fusiformisSmall, and Quercus geminataSmall (Fagaceae). In general, we found evidence for immigrant inviability when B. treatae populations colonized non‐native host species. However, patterns were variable among years, suggesting that episodic events may play an important role in connecting ecologically divergent populations.     

Effects of conspecific and heterospecific residents on patterns of immigration in two species of voles

Studies with birds have shown that presence and density of resident conspecifics and heterospecifics can influence patterns of habitat selection. There have been few studies on the effects of social cues on rates of immigration in mammals. We report results from a long-term live trapping study of immigration in two species of voles, Microtus ochrogaster Wagner, 1842 and Microtus pennsylvanicus Ord, 1815, in bluegrass habitat in east-central Illinois, USA. We compare immigration into control sites from which no individuals of either species were removed with immigration into experimental sites from which either conspecifics or heterospecifics were removed. We focus on characteristics of immigrants and rates of immigration in relation to density in destination habitats. Within each species, immigrants into control and removal sites were similar with respect to body mass and reproductive condition, indicating no major differences in the physical condition of immigrants into sites with established populations and sites without established populations. For both species, density of conspecifics at a site positively influenced rate of immigration at that site. Density of heterospecifics at destination sites did not significantly influence rate of immigration for either species. These results suggest that site selection by dispersing M. ochrogaster and M. pennsylvanicus is characterized by conspecific attraction.