Examination of prezygotic and postzygotic isolating barriers in tropical Ulva (Ulvophyceae,Chlorophyta): evidence for ongoing speciation

Phylogenetic clades based on DNA sequences such as the chloroplast rbcL gene and the nuclear ITS region are frequently used to delimit algal species. However, these molecular markers cannot accurately delimit boundaries among some Ulva species. Although Ulva reticulata and Ulva ohnoi occasionally bloom in tropical to warm‐temperate regions and are clearly distinguishable by their reticulate or plain blade morphology, they have few or no sequence divergences in these molecular markers and form a monophyletic clade. In this study, to clarify the speciation and species delimitation in the U. reticulata‐ohnoi complex clade, reproductive relationships among several sexual strains from the Philippines and Japan including offspring that originated from the type specimen of U. ohnoi were examined by culturing and hybridization in addition to the ITS‐based analysis. As a result, both prezygotic and postzygotic reproductive isolation were revealed to occur between genetically perforated U. reticulata and imperforate U. ohnoi. They were also separated on the basis of sequence analysis of the ITS region. That strongly supports that the two taxa are independent biological species. Although no prezygotic barrier among the Philippine and Japanese strains of U. reticulata was observed, unexpectedly zoospores produced by hybrid sporophytes in some of their combinations mostly failed to develop, indicating partial formation of a postzygotic barrier despite a 0.2% divergence in the ITS sequence. These findings suggest speciation is still ongoing in U. reticulata.     

Habitat use,but not gene flow,is influenced by human activities in two ecotypes of Egyptian fruit bat (Rousettus aegyptiacus)

Understanding the ecological, behavioural and evolutionary response of organisms to changing environments is of primary importance in a human‐altered world. It is crucial to elucidate how human activities alter gene flow and what are the consequences for the genetic structure of a species. We studied two lineages of the Egyptian fruit bat (Rousettus aegyptiacus) throughout the contact zone between mesic and arid Ecozones in the Middle East to evaluate the species' response to the growing proportion of human‐altered habitats in the desert. We integrated population genetics, morphometrics and movement ecology to analyse population structure, morphological variation and habitat use from GPS‐ or radio‐tagged individuals from both desert and Mediterranean areas. We classified the spatial distribution and environmental stratification by describing physical–geographical conditions and land cover. We analysed this information to estimate patch occupancy and used an isolation‐by‐resistance approach to model gene flow patterns. Our results suggest that lineages from desert and Mediterranean habitats, despite their admixture, are isolated by environment and by adaptation supporting their classification as ecotypes. We found a positive effect of human‐altered habitats on patch occupancy and habitat use of fruit bats by increasing the availability of roosting and foraging areas. While this commensalism promotes the distribution of fruit bats throughout the Middle East, gene flow between colonies has not been altered by human activities. This discrepancy between habitat use and gene flow patterns may, therefore, be explained by the breeding system of the species and modifications of natal dispersal patterns.     

Hybridization occurs between Drosophila simulans and D. sechellia in the Seychelles archipelago

Drosophila simulans and D. sechellia are sister species that serve as a model to study the evolution of reproductive isolation. While D. simulans is a human commensal that has spread all over the world, D. sechellia is restricted to the Seychelles archipelago and is found to breed exclusively on the toxic fruit of Morinda citrifolia. We surveyed the relative frequency of males from these two species in a variety of substrates found on five islands of the Seychelles archipelago. We sampled different fruits and found that putative D. simulans can be found in a variety of substrates, including, surprisingly, M. citrifolia. Putative D. sechellia was found preferentially on M. citrifolia fruits, but a small proportion was found in other substrates. Our survey also shows the existence of putative hybrid males in areas where D. simulans is present in Seychelles. The results from this field survey support the hypothesis of current interbreeding between these species in the central islands of Seychelles and open the possibility for fine measurements of admixture between these two Drosophila species to be made.     

Persistent postmating,prezygotic reproductive isolation between populations

Studying reproductive barriers between populations of the same species is critical to understand how speciation may proceed. Growing evidence suggests postmating, prezygotic (PMPZ) reproductive barriers play an important role in the evolution of early taxonomic divergence. However, the contribution of PMPZ isolation to speciation is typically studied between species in which barriers that maintain isolation may not be those that contributed to reduced gene flow between populations. Moreover, in internally fertilizing animals, PMPZ isolation is related to male ejaculate—female reproductive tract incompatibilities but few studies have examined how mating history of the sexes can affect the strength of PMPZ isolation and the extent to which PMPZ isolation is repeatable or restricted to particular interacting genotypes. We addressed these outstanding questions using multiple populations of Drosophila montana. We show a recurrent pattern of PMPZ isolation, with flies from one population exhibiting reproductive incompatibility in crosses with all three other populations, while those three populations were fully fertile with each other. Reproductive incompatibility is due to lack of fertilization and is asymmetrical, affecting female fitness more than males. There was no effect of male or female mating history on reproductive incompatibility, indicating that PMPZ isolation persists between populations. We found no evidence of variability in fertilization outcomes attributable to different female × male genotype interactions, and in combination with our other results, suggests that PMPZ isolation is not driven by idiosyncratic genotype × genotype interactions. Our results show PMPZ isolation as a strong, consistent barrier to gene flow early during speciation and suggest several targets of selection known to affect ejaculate‐female reproductive tract interactions within species that may cause this PMPZ isolation.     

Allotetraploid Mimulus sookensis are highly interfertile despite independent origins

Polyploidy (whole‐genome duplication) has contributed significantly to angiosperm evolution and diversification. To date, it has been found that most polyploids are the result of multiple formation events, which may contribute to genetic diversity and affect interfertility among polyploid lineages of independent origin. A recently discovered allotetraploid derivative of Mimulus guttatus and M. nasutus, Mimulus sookensis, is found throughout the valleys of western Oregon and Vancouver Island. Here, we analyse the patterns of nucleotide diversity at three chloroplast and six nuclear loci in M. guttatus, M. nasutus and M. sookensis, to gain insight into the formation of M. sookensis. By analysing the patterns of genetic variation seen in the diploid progenitors in comparison with the variation seen in M. sookensis, we are able to show that M. sookensis has recurrently formed. We also observed that most M. sookensis individuals are fixed heterozygotes at all of the nuclear loci examined, suggesting that duplicate gene loss is not extensive in M. sookensis. To assess the possibility that hybridization among M. sookensis has contributed to genetic diversity, we conducted crossing experiments within M. sookensis. We found that M. sookensis of independent origin are highly interfertile, suggesting that crossing barriers do not exist within M. sookensis, and that hybridization among M. sookensis may result in new recombinant genotypes. Together, the data suggest that although recurrent origins may be common, they can contribute to genetic diversity without contributing to reproductive isolation among independently arisen polyploid lineages.     

Variable hybridization outcomes in trout are predicted by historical fish stocking and environmental context

Hybridization can profoundly affect the genomic composition and phenotypes of closely related species, and provides an opportunity to identify mechanisms that maintain reproductive isolation between species. Recent evidence suggests that hybridization outcomes within a species pair can vary across locations. However, we still do not know how variable outcomes of hybridization are across geographic replicates, and what mechanisms drive that variation. In this study, we described hybridization outcomes across 27 locations in the North Fork Shoshone River basin (Wyoming, USA) where native Yellowstone cutthroat trout and introduced rainbow trout co‐occur. We used genomic data and hierarchical Bayesian models to precisely identify ancestry of hybrid individuals. Hybridization outcomes varied across locations. In some locations, only rainbow trout and advanced backcrossed hybrids towards rainbow trout were present, while trout in other locations had a broader range of ancestry, including both parental species and first‐generation hybrids. Later‐generation intermediate hybrids were rare relative to backcrossed hybrids and rainbow trout individuals. Using an individual‐based simulation, we found that outcomes of hybridization in the North Fork Shoshone River basin deviate substantially from what we would expect under null expectations of random mating and no selection against hybrids. Since this deviation implies that some mechanisms of reproductive isolation function to maintain parental taxa and a diversity of hybrid types, we then modelled hybridization outcomes as a function of environmental variables and stocking history that are likely to affect prezygotic barriers to hybridization. Variables associated with history of fish stocking were the strongest predictors of hybridization outcomes, followed by environmental variables that might affect overlap in spawning time and location.     

The role of geography and ecology in shaping repeated patterns of morphological and genetic differentiation between European minnows (Phoxinus phoxinus) from the Pyrenees and the Alps

Neutral and selective processes can drive repeated patterns of evolution in different groups of populations experiencing similar ecological gradients. In this paper, we used a combination of nuclear and mitochondrial DNA markers, as well as geometric morphometrics, to investigate repeated patterns of morphological and genetic divergence of European minnows in two mountain ranges: the Pyrenees and the Alps. European minnows (Phoxinus phoxinus) are cyprinid fish inhabiting most freshwater bodies in Europe, including those in different mountain ranges that could act as major geographical barriers to gene flow. We explored patterns of P. phoxinus phenotypic and genetic diversification along a gradient of altitude common to the two mountain ranges, and tested for isolation by distance (IBD), isolation by environment (IBE) and isolation by adaptation (IBA). The results indicated that populations from the Pyrenees and the Alps belong to two well differentiated, reciprocally monophyletic mtDNA lineages. Substantial genetic differentiation due to geographical isolation within and between populations from the Pyrenees and the Alps was also found using rapidly evolving AFLPs markers (isolation by distance or IBD), as well as morphological differences between mountain ranges. Also, morphology varied strongly with elevation and so did genetic differentiation to a lower extent. Despite moderate evidence for IBE and IBA, and therefore of repeated evolution, substantial population heterogeneity was found at the genetic level, suggesting that selection and population specific genetic drift act in concert to affect genetic divergence.     

The influence of landscape configuration and environment on population genetic structure in a sedentary passerine: insights from loci located in different genomic regions

The study of the factors structuring genetic variation can help to infer the neutral and adaptive processes shaping the demographic and evolutionary trajectories of natural populations. Here, we analyse the role of isolation by distance (IBD), isolation by resistance (IBR, defined by landscape composition) and isolation by environment (IBE, estimated as habitat and elevation dissimilarity) in structuring genetic variation in 25 blue tit (Cyanistes caeruleus) populations. We typed 1385 individuals at 26 microsatellite loci classified into two groups by considering whether they are located into genomic regions that are actively (TL; 12 loci) or not (NTL; 14 loci) transcribed to RNA. Population genetic differentiation was mostly detected using the panel of NTL. Landscape genetic analyses showed a pattern of IBD for all loci and the panel of NTL, but genetic differentiation estimated at TL was only explained by IBR models considering high resistance for natural vegetation and low resistance for agricultural lands. Finally, the absence for IBE suggests a lack of divergent selection pressures associated with differences in habitat and elevation. Overall, our study shows that markers located in different genomic regions can yield contrasting inferences on landscape‐level patterns of realized gene flow in natural populations.     

Ecological connectivity assessment in a strongly structured fire salamander (Salamandra salamandra) population

Small populations are more prone to extinction if the dispersal among them is not adequately maintained by ecological connections. The degree of isolation between populations could be evaluated measuring their genetic distance, which depends on the respective geographic (isolation by distance, IBD) and/or ecological (isolation by resistance, IBR) distances. The aim of this study was to assess the ecological connectivity of fire salamander Salamandra salamandra populations by means of a landscape genetic approach. The species lives in broad‐leaved forest ecosystems and is particularly affected by fragmentation due to its habitat selectivity and low dispersal capability. We analyzed 477 biological samples collected in 47 sampling locations (SLs) in the mainly continuous populations of the Prealpine and Eastern foothill lowland (PEF) and 10 SLs in the fragmented populations of the Western foothill (WF) lowland of Lombardy (northern Italy). Pairwise genetic distances (Chord distance, D_C) were estimated from allele frequencies of 16 microsatellites loci. Ecological distances were calculated using one of the most promising methodology in landscape genetics studies, the circuit theory, applied to habitat suitability maps. We realized two habitat suitability models: one without barriers (EcoD) and a second one accounting for the possible barrier effect of main roads (EcoD_b). Mantel tests between distance matrices highlighted how the Log‐D_C in PEF populations was related to log‐transformed geographic distance (confirming a prevalence of IBD), while it was explained by the Log‐EcoD, and particularly by the Log‐EcoD_b, in WF populations, even when accounting for the confounding effect of geographic distance (highlighting a prevalence of IBR). Moreover, we also demonstrated how considering the overall population, the effect of Euclidean or ecological distances on genetic distances acting at the level of a single group (PEF or WF populations) could not be detected, when population are strongly structured.     

Species divergence in field crickets: genetics,song, ecomorphology,and pre‐ and postzygotic isolation

Studies that simultaneously estimate levels of species divergence in genetics, reproductive and ecological traits, and pre‐ and postzygotic isolation are relatively rare. Here we compare levels of divergence in three allopatric sister species of field crickets. We compare divergence in both nuclear and mitochondrial DNA, male song, female ovipositor length, levels of pre‐ and postzygotic isolation, and male versus female contributions to prezygotic isolation. Taken together, our data show the accumulation of a multitude of potential reproductive isolating barriers if secondary contact were to become established. Furthermore, ecological and behavioural prezygotic isolation appear significantly more advanced than postzygotic isolation, with prezygotic isolation due to female behaviour exceeding that due to male behaviour.     

Reproductive isolation and environmental adaptation shape the phylogeography of mountain pine beetle (Dendroctonus ponderosae)

Chromosomal rearrangement can be an important mechanism driving population differentiation and incipient speciation. In the mountain pine beetle (MPB, Dendroctonus ponderosae), deletions on the Y chromosome that are polymorphic among populations are associated with reproductive incompatibility. Here, we used RAD sequencing across the entire MPB range in western North America to reveal the extent of the phylogeographic differences between Y haplotypes compared to autosomal and X‐linked loci. Clustering and geneflow analyses revealed three distinct Y haplogroups geographically positioned within and on either side of the Great Basin Desert. Despite close geographic proximity between populations on the boundaries of each Y haplogroup, there was extremely low Y haplogroup mixing among populations, and gene flow on the autosomes was reduced across Y haplogroup boundaries. These results are consistent with a previous study suggesting that independent degradation of a recently evolved neo‐Y chromosome in previously isolated populations causes male sterility or inviability among Y haplotype lineages. Phylogeographic results supported historic contraction of MPB into three separate Pleistocene glacial refugia followed by postglacial range expansion and secondary contact. Distinct sets of SNPs were statistically associated with environmental data among the most genetically distinct sets of geographic populations. This finding suggests that the process of adaptation to local climatic conditions is influenced by population genetic structure, with evidence for largely independent evolution in the most genetically isolated Y haplogroup.     

Environmental selection is a main driver of divergence in house sparrows (Passer domesticus) in Romania and Bulgaria

Both neutral and adaptive evolutionary processes can cause population divergence, but their relative contributions remain unclear. We investigated the roles of these processes in population divergence in house sparrows (Passer domesticus) from Romania and Bulgaria, regions characterized by high landscape heterogeneity compared to Western Europe. We asked whether morphological divergence, complemented with genetic data in this human commensal species, was best explained by environmental variation, geographic distance, or landscape resistance—the effort it takes for an individual to disperse from one location to the other—caused by either natural or anthropogenic barriers. Using generalized dissimilarity modeling, a matrix regression technique that fits biotic beta diversity to both environmental predictors and geographic distance, we found that a small set of climate and vegetation variables explained up to ~30% of the observed divergence, whereas geographic and resistance distances played much lesser roles. Our results are consistent with signals of selection on morphological traits and of isolation by adaptation in genetic markers, suggesting that selection by natural environmental conditions shapes population divergence in house sparrows. Our study thus contributes to a growing body of evidence that adaptive evolution may be a major driver of diversification.     

Bioassay‐Guided Isolation of Antifungal Compounds from Disporopsis aspersa (Hua) Engl. ex Diels against Pseudoperonospora cubensis and Phytophthora infestans

Oomycetes are one type of the most highly destructive of the diseases that cause damage to some important crop plants, such as potato late blight, cucumber downy mildew, and grape downy mildew. As main approach of the ongoing search for new botanical fungicide from plant, the secondary metabolites of D. aspersa were investigated. Through efficient bioassay‐guided isolation, two new ( 1 and 2 ) and 12 known compounds ( 3  –  14 ) were isolated, and their structures were determined via extensive NMR, HR‐ESI‐MS, and IR. They were isolated from this genus for the first time except for compounds 11 and 12 . The biological properties of 1  –  14 were evaluated against Pseudoperonospora cubensis and Phytophthora infestans. Compounds 1  –  8 showed potent antifungal activity in vitro. Additionally, compound 3 has preferable control effect on cucumber downy mildew, showing dual effect of protection and treatment in vivo.     

Walk,swim or fly? Locomotor mode predicts genetic differentiation in vertebrates

Limited dispersal is commonly used to explain differences in diversification rates. An obvious but unexplored factor affecting dispersal is the mode of locomotion used by animals. Whether individuals walk, swim or fly can dictate the type and severity of geographical barriers to dispersal, and determine the general range over which genetic differentiation might occur. We collated information on locomotion mode and genetic differentiation (F_ST) among vertebrate populations from over 400 published articles. Our results showed that vertebrate species that walk tend to have higher genetic differentiation among populations than species that swim or fly. Within species that swim, vertebrates in freshwater systems have higher genetic differentiation than those in marine systems, which is consistent with the higher number of species in freshwater environments. These results show that locomotion mode can impact gene flow among populations, supporting at a broad‐scale what has previously been proposed at smaller taxonomical scales.     

Isolation and Identification of a Novel Antifungal Protein from a Rhizobacterium Bacillus subtilis Strain F3

Bacillus subtilis strain F3, isolated from peach rhizosphere soil, is an antifungal bacterium against many plant pathogens. In this study, the antifungal protein was isolated and purified by ammonium sulphate and chromatography, then identified by mass spectrum analysis. By sequential chromatography of Sephadex G‐50, DEAE‐Sephadex A‐25 anion exchange and Sephadex G‐100, a fraction designated as F3A was isolated to show a single protein band in SDS‐PAGE and be antagonistic towards Monilinia fructicola. The peptide mass fingerprinting of the protein band of F3A had high similarity with the amino acid sequences of several flagellin protein of B. subtilis. There were seven amino acid fragments matched with the protein having the highest score, and sequence coverage was 33%. F3A showed a strongly inhibitory effect to the growth and sporulation of M. fructicola. There were little aerial hyphae and conidia at the antifungal zone, and the hyphae were abnormal with some cell wall collapse and several vacuoles in cells.     

Living in two worlds: Evolutionary mechanisms act differently in the native and introduced ranges of an invasive plant

Identifying the factors that influence spatial genetic structure among populations can provide insights into the evolution of invasive plants. In this study, we used the common reed (Phragmites australis), a grass native in Europe and invading North America, to examine the relative importance of geographic, environmental (represented by climate here), and human effects on population genetic structure and its changes during invasion. We collected samples of P. australis from both the invaded North American and native European ranges and used molecular markers to investigate the population genetic structure within and between ranges. We used path analysis to identify the contributions of each of the three factors—geographic, environmental, and human‐related—to the formation of spatial genetic patterns. Genetic differentiation was observed between the introduced and native populations, and their genetic structure in the native and introduced ranges was different. There were strong effects of geography and environment on the genetic structure of populations in the native range, but the human‐related factors manifested through colonization of anthropogenic habitats in the introduced range counteracted the effects of environment. The between‐range genetic differences among populations were mainly explained by the heterogeneous environment between the ranges, with the coefficient 2.6 times higher for the environment than that explained by the geographic distance. Human activities were the primary contributor to the genetic structure of the introduced populations. The significant environmental divergence between ranges and the strong contribution of human activities to the genetic structure in the introduced range suggest that invasive populations of P. australis have evolved to adapt to a different climate and to human‐made habitats in North America.