Detection and visualization of spatial genetic structure in continuous Eucalyptus globulus forest

Visualizing the pattern of variation using microsatellites within a Eucalyptus globulus forest on the island of Tasmania provided surprising insights into the complex nature of the fine-scale spatial genetic structure that resides in these forests. We used spatial autocorrelation and principal coordinate analysis to compare fine-scale genetic structure between juvenile and mature cohorts in a study area, 140 m in diameter, located within a typical, continuous E. globulus forest. In total, 115 juvenile and 168 mature individuals were genotyped with eight highly polymorphic microsatellite loci. There was no significant difference in the level of genetic diversity between cohorts. However, there were differences in the spatial distribution of the genetic variation. Autocorrelation analysis provided clear evidence for significant spatial genetic structure in the mature cohort and significant, but weaker, structure in the juvenile cohort. The spatial interpolation of principal coordinate axes, derived from ordination of the genetic distance matrix between individuals, revealed a spatially coherent family group which was evident in both cohorts. Direct comparison of the genetic structure within each cohort allowed visualization of a shift in the spatial distribution of genetic variation within the population of approximately 10 m. As the shift coincided with the direction of prevailing winds, it is hypothesized that this phenomenon is due to downwind dispersal of seeds and is indicative of the important role of prevailing winds in forcing eastward gene flow in these high-latitude forests.     

Parallel evolution of lake whitefish dwarf ecotypes in association with limnological features of their adaptive landscape

Sympatric fish populations observed in many north temperate lakes are among the best models to study the processes of population divergence and adaptive radiation. Despite considerable research on such systems, little is known about the associations between ecological conditions and the extent of ecotypic divergence. In this study, we examined the biotic and abiotic properties of postglacial lakes in which lake whitefish, Coregonus clupeaformis, occur as a derived dwarf ecotype in sympatry with an ancestral normal ecotype. We compared 19 limnological variables between two groups of lakes known from previous studies to harbour sympatric dwarf and normal ecotypes with high and low levels of phenotypic and genetic differentiation respectively. We found clear environmental differences between the two lake groups. Namely, oxygen was the most discriminant variable, where lakes harbouring the most divergent populations were characterized by the greatest hypolimnetic oxygen depletion. These lakes also had lower zooplankton densities and a narrower distribution of zooplantonic prey length. These results suggest that the highest differentiation between sympatric ecotypes occurs in lakes with reduced habitat and prey availability that could increase competition for resources. This in turns supports the hypothesis that parallelism in the extent of phenotypic divergence among sympatric whitefish ecotypes is associated with parallelism in adaptive landscape in terms of differences in limnological characteristics, as well as availability and structure of the zooplanktonic community.     

The rare silver gum, Eucalyptus cordata, is leaving its trace in the organellar gene pool of Eucalyptus globulus

The process of genetic assimilation of rare species by hybridizing congeners has been documented in a number of plant genera. This raises the possibility that some of the genetic diversity found in phylogeographical studies of widespread species has been acquired through hybridization with species that are now rare or extinct. In this fine-scale phylogeographical analysis, we show that a rare eucalypt species is leaving its trace in the chloroplast genome of a more abundant congener. The heart-leafed silver gum, Eucalyptus cordata, is a rare endemic of south-eastern Tasmania. Its populations are scattered amidst populations of more abundant related species, including the Tasmanian blue gum, Eucalyptus globulus. Using 339 samples from across the full range of both species, we compared chloroplast (cp) DNA haplotype phylogeography in E. globulus and E. cordata. The genealogy and distribution of chloroplast haplotypes suggest that E. globulus has acquired cpDNA from E. cordata in at least four different mixed populations. Shared haplotypes are highest in E. globulus sampled within 2 km of known E. cordata populations and drop to zero at a distance of 25 km from the nearest known E. cordata population. Localized haplotype sharing occurs in the absence of obvious hybrid zones or locally shared nuclear ribosomal DNA sequences. Given that the future loss of E. cordata from some mixed populations is likely, these findings indicate that phylogeographical analyses of organellar DNA should consider the possibility of introgression, even from species that have been eliminated from the sites of interest.     

Phenology of Eucalyptus weevil, Gonipterus scutellatus Gyllenhal (Coleoptera: Curculionidae), and chrysomelid beetles in Eucalyptus globulus plantations in south-western Australia

1 In south‐western Australia, Eucalyptus globulus plantations are defoliated by a complex of beetle species, yet only scant information exists on these species under such climatic conditions. To improve management of these defoliating beetles in the region, canopy fogging and shoot clipping were conducted in plantations between 1999 and 2002 to identify and document the phenology of the beetle species present. 2 Eucalyptus weevil, Gonipterus scutellatus, was the most common and destructive defoliating beetle. Gonipterus scutellatus undergoes one principal generation each year with a lesser second generation or cohort in some seasons, which contrasts greatly with reports of two to four annual generations for the species in other regions. This limited reproduction by G. scutellatus may be due to the limited availability from summer onwards of new flushing foliage, which is essential for feeding and oviposition. 3 Several species of chrysomelid beetles were collected in plantations, but these were present in much lower numbers than G. scutellatus and were only a minor concern. However, some species, such as Chrysophtharta variicollis, appear to be capable of developing short‐lived outbreaks. 4 A diverse suite of natural enemies was fogged from plantations but they were significantly less abundant than defoliating beetles and are not likely to provide significant control of beetles. 5 In terms of managing these defoliating beetles, monitoring and control should focus on G. scutellatus, and be conducted during spring when most damage occurs.     

High frequency plant regeneration from Eucalyptus globulus Labill. hypocotyls: Ontogenesis and ploidy level of the regenerants

Up to 70% regenerating hypocotyls provided with 5 to 20 buds were obtained on MS medium containing 0.01 or 1 mg l^-1 NAA and 0.2 mg l^-1 BA or 0.2 mg l^-1 BA and 0.2 mg l^-1 TDZ. The ability to regenerate buds was correlated with the presence of oil glands at a stage in germination when oil secretion was not yet occurring. The regeneration of shoot meristems took place from the cells involved in the differentiation of these glands. Such glands could also appear during callus redifferentiation, giving rise to indirect regeneration. Rooting of the regenerants was efficient using a two-step procedure of induction under darkness in the presence of 3 mg l^-1 IBA, followed by root development on medium devoid of growth regulators under a 16-h photoperiod, the medium being solidified with Gelrite. Regenerated plants showed no phenotypic alterations. Nuclear DNA contents in mother-plant material and regenerants were analysed using flow cytometry. There was no evidence of polyploidy in any of the samples, indicating the absence of polyploidisation during cell differentiation and under in vitro conditions. No regeneration was obtained from leaf or stem explants from micropropagated plantlets. This revised version was published online in June 2006 with corrections to the Cover Date.     

Multiple evolutionary processes drive the patterns of genetic differentiation in a forest tree species complex

Forest trees frequently form species complexes, complicating taxonomic classification and gene pool management. This is certainly the case in Eucalyptus, and well exemplified by the Eucalyptus globulus complex. This ecologically and economically significant complex comprises four taxa (sspp. bicostata, globulus, maidenii, pseudoglobulus) that are geographically and morphologically distinct, but linked by extensive “intergrade” populations. To resolve their genetic affinities, nine microsatellites were used to genotype 1200 trees from throughout the natural range of the complex in Australia, representing 33 morphological core and intergrade populations. There was significant spatial genetic structure (F_ST = 0.10), but variation was continuous. High genetic diversity in southern ssp. maidenii indicates that this region is the center of origin. Genetic diversity decreases and population differentiation increases with distance from this area, suggesting that drift is a major evolutionary process. Many of the intergrade populations, along with other populations morphologically classified as ssp. pseudoglobulus or ssp. globulus, belong to a “cryptic genetic entity” that is genetically and geographically intermediate between core ssp. bicostata, ssp. maidenii, and ssp. globulus. Geography, rather than morphology, therefore, is the best predictor of overall genetic affinities within the complex and should be used to classify germplasm into management units for conservation and breeding purposes.     

A parapatric propensity for breeding precludes the completion of speciation in common teal (Anas crecca, sensu lato)

Speciation is a process in which genetic drift and selection cause divergence over time. However, there is no rule dictating the time required for speciation, and even low levels of gene flow hinder divergence, so that taxa may be poised at the threshold of speciation for long periods of evolutionary time. We sequenced mitochondrial DNA (mtDNA) and eight nuclear introns (nuDNA) to estimate genomic levels of differentiation and gene flow between the Eurasian common teal (Anas crecca crecca) and the North American green‐winged teal (Anas crecca carolinensis). These ducks come into contact in Beringia (north‐eastern Asia and north‐western North America) and have probably done so, perhaps cyclically, since the Pliocene–Pleistocene transition, ～2.6 Ma, when they apparently began diverging. They have diagnosable differences in male plumage and are 6.9% divergent in the mtDNA control region, with only 1 of 58 crecca and 2 of 86 carolinensis having haplotypes grouping with the other. Two nuclear loci were likewise strongly structured between these teal (Φ_st ≥ 0.35), but six loci were undifferentiated or only weakly structured (Φ_st = 0.0–0.06). Gene flow between crecca and carolinensis was ～1 individual per generation in both directions in mtDNA, but was asymmetrical in nuDNA, with ～1 and ～20 individuals per generation immigrating into crecca and carolinensis, respectively. This study illustrates that species delimitation using a single marker oversimplifies the complexity of the speciation process, and it suggests that even with divergent selection, moderate levels of gene flow may stall the speciation process short of completion.     

Genetic and morphological divergence between Littorina fabalis ecotypes in Northern Europe

Low dispersal marine intertidal species facing strong divergent selective pressures associated with steep environmental gradients have a great potential to inform us about local adaptation and reproductive isolation. Among these, gastropods of the genus Littorina offer a unique system to study parallel phenotypic divergence resulting from adaptation to different habitats related with wave exposure. In this study, we focused on two Littorina fabalis ecotypes from Northern European shores and compared patterns of habitat‐related phenotypic and genetic divergence across three different geographic levels (local, regional and global). Geometric morphometric analyses revealed that individuals from habitats moderately exposed to waves usually present a larger shell size with a wider aperture than those from sheltered habitats. The phenotypic clustering of L. fabalis by habitat across most locations (mainly in terms of shell size) support an important role of ecology in morphological divergence. A genome scan based on amplified fragment length polymorphisms (AFLPs) revealed a heterogeneous pattern of differentiation across the genome between populations from the two different habitats, suggesting ecotype divergence in the presence of gene flow. The contrasting patterns of genetic structure between nonoutlier and outlier loci, and the decreased sharing of outlier loci with geographic distance among locations are compatible with parallel evolution of phenotypic divergence, with an important contribution of gene flow and/or ancestral variation. In the future, model‐based inference studies based on sequence data across the entire genome will help unravelling these evolutionary hypotheses, improving our knowledge about adaptation and its influence on diversification within the marine realm.     

Gene flow of the canker pathogen Botryosphaeria australis between Eucalyptus globulus plantations and native eucalypt forests in Western Australia

Abstract The eucalypt plantation industry in Western Australia provides a unique opportunity to study the movement of pathogens between closely related host taxa. Eucalyptus globulus, a native to Tasmania and south‐eastern Australia, is the predominant species in Western Australian plantations, often being planted adjacent to native forest containing Eucalyptus marginata and Eucalyptus diversicolor. Since the commencement of the plantation industry 20 years ago, several fungal species, previously known only to eastern Australia or overseas, have been reported on E. globulus in Western Australia. Botryosphaeria australis is a newly described species, recently found causing cankers on Acacia spp. in eastern Australia. However, during a routine survey, B. australis was found to be the predominant species associated with E. globulus plantations and native Eucalyptus spp. in Western Australia. In this study, six short simple repeat markers were used to evaluate genetic diversity and gene flow between collections of B. australis from native eucalypt forest and E. globulus plantations at two locations in south‐western Australia. In both cases, there was no restriction to gene flow between the plantations and the adjacent native forest. Botryosphaeria australis has now been isolated from a wide range of hosts across south‐western Australia and was not isolated from E. globulus in Tasmania or South Australia. This extensive distribution and host range suggests B. australis is native to Western Australia. This study demonstrates the ability of a pathogen to move between plantation and forests.     

Role of epibenthic resource opportunities in the parallel evolution of lake whitefish species pairs (Coregonus sp.)

Parallel evolution of a dwarf and normal whitefish has been documented in six post-glacial lakes. Here, we relate the structure and seasonal variations of the epibenthic invertebrate communities to the extent of phenotypic differentiation in these species pairs. The highest phenotypic differentiation occurs in lakes characterized by less overlap in size distribution between limnetic and epibenthic prey which could represent enhanced ecological opportunities for trophic specialization and adaptive divergence. Differences in community assemblages and seasonal variation of biotic and abiotic conditions may also play a role. Accumulating evidence indicates that strong directional selection acting on dwarf whitefish may be more important than divergent selection acting on both sympatric forms in driving whitefish phenotypic divergence and ultimately, ecological speciation. Along with Landry et al. (2007), this study supports the general hypothesis that parallelism in divergence among sympatric dwarf and normal whitefish is associated with parallelism in limnological adaptive landscape.     

Labile ecotypes accompany rapid cladogenesis in an adaptive radiation of Mandarina (Bradybaenidae) land snails

The endemic land snail genus Mandarina of the oceanic Bonin Islands shows exceptionally diverse morphological and ecological traits. Previous studies have already provided evidence that speciation on different islands of the three main archipelagos was such that similar ecotypes evolved independently in different lineages and islands. Here we present data to show that the same species can have different ecotypes. As most of the characters involved are inherited, then variation between ecotypes must represent genetic differences between populations. We then show that the radiation on the Bonin Islands is derived from a single colonization event, and use a mitochondrial phylogeny to provide evidence for a burst of cladogenesis soon after colonization. As divergent selection has previously been implicated in causing differences between Mandarina species, and theory predicts that most of the speciation should have taken place early in their history, then the study adds to the evidence for an adaptive radiation by ecological speciation in Mandarina . However, while the diversity of ecotypes present at each site is dependent on the regime of natural selection and competition, geography still must have an important role.  © 2006 The Linnean Society of London, Biological Journal of the Linnean Society , 2006, 88 , 269–282.     

生态物种形成及其研究进展

物种形成是基本的进化过程, 也是生物多样性形成的基础。自然选择可以导致新物种的产生。生态物种形成是指以生态为基础的歧化选择使不同群体分化产生生殖隔离的物种形成过程。本文首先回顾了生态物种形成的研究历史, 并详细介绍了生态物种形成的3个要素, 即歧化选择的来源、生殖隔离的形式以及关联歧化选择与生殖隔离的遗传机制。歧化选择的来源主要包括不同的环境或生态位、不同形式的性选择, 以及群体间的相互作用。生殖隔离的形式多种多样, 我们总结了合子前和合子后隔离的遗传学机制以及在生态物种形成中起到的作用。控制适应性性状的基因与导致生殖隔离的基因可以通过基因多效性或连锁不平衡相互关联起来。借助于第二代测序技术, 研究者可以对生态物种形成的遗传学与基因组学基础进行研究。此外, 本文还总结了生态物种形成领域最新的研究进展, 包括平行进化的全基因组基础, 以及基因流影响群体分化的理论基础。通过归纳比较由下至上和由上至下这两种不同的研究思路, 作者认为这两种思路的结合可以为生态物种形成基因的筛选提供更有力也更精确的方法。同时, 作者还提出生态物种形成的研究应该基于更好的表型描述以及更完整的基因组信息, 研究的物种也应该具有更广泛的代表性。     

Chloroplast DNA variation and population structure in the widespread forest tree, Eucalyptus grandis

Recognition of genetic structure of populations and the ability to identify vulnerable populations is useful for the formation of conservation management strategies for plants. Eucalyptus grandis is a tall forest tree that has a major area of occurrence in subtropical eastern Australia, with smaller populations located in the east coast tropics. Many widespread forest species exhibit population differentiation that corresponds to geographic regions. However, Eucalyptus grandis appears to be an exception based on isozyme and morphological data. This is intriguing given a large discontinuity between northern populations and those in the southern part of the species range. In this study, the distribution of a maternally inherited chloroplast locus was examined because it was more likely to reveal genetic structure due to the slower evolution of the chloroplast genome and limited dispersal of seed in eucalypts. As expected, the G _ST for chloroplast DNA was higher than that for nuclear DNA but indicated low population differentiation for a forest tree species. Phylogeographic analysis indicated that the 15 populations grouped into three broad geographical regions; however, overall population structure was weak suggesting that the large geographical disjunction in the distribution of E. grandis may be relatively recent. A paradigm for conservation management of E. grandis based on chloroplast DNA haplotype distribution would take into account the low differentiation among populations.     

Nutrient dynamics throughout the rotation of Eucalyptus clonal stands in Congo

The dynamics of the main nutrient fluxes of the biological cycle were quantified in a clonal Eucalyptus plantation throughout the whole planted crop rotation: current annual requirements of nutrients, uptake from the soil, internal translocations within trees, return to soil (litterfall and crown leaching) and decomposition in the forest floor. As reported for other species, two growth periods were identified in these short-rotation plantations: (1) a juvenile phase up to canopy closure, during which the uptake of nutrients from the soil reserves supplied most of the current requirements; and (2) a second phase up to harvest, characterized by intense nutrient recycling processes. Internal translocation within trees supplied about 30 % of the annual requirements of N and P from 2 years of age onwards, and about 50 % of the K requirement. The mineralization of large amounts of organic matter returned to the soil with litterfall during stand development represented a key process providing nutrients to the stand at the end of the rotation. The importance of the recycling processes was clearly shown by the small amounts of nutrients permanently immobilized in the ligneous components of trees, compared with the total requirements accumulated over the stand rotation which were two to four times higher. Small pools of nutrients circulating quickly in the ecosystem made it possible to produce high amounts of biomass in poor soils. The sustainability of these plantations will require fertilizer inputs that match the changes in soil fertility over successive rotations, mainly linked to the dynamics of organic matter in this tropical soil.     

Parallel evolution of an alpine type ecomorph in a scorpionfly: Independent adaptation to high‐altitude environments in multiple mountain locations

Elucidation of the diversification process of organisms is one of the important tasks of biology. From the viewpoint of species diversity, insects are the most successful group among the diverse organisms on earth and evolutionary adaptation is one of the important factors driving this pattern. Evolutionary adaptation is one of the important factors in the diversification of insects. One of the representative examples of environmental adaptation in insects is the shortening and loss of wings in subalpine and alpine zones. In this study, we focused on the Japanese scorpionfly, Panorpodes paradoxus. In this species, individuals that inhabit mountainous regions and subalpine zones have long wings (the “general type”), and individuals that inhabit higher altitudinal ranges have short wings (the “alpine type”). We collected samples of all Japanese Panorpodes species and one Korean Panorpodes species, and conducted molecular phylogenetic analyses of the mtDNA COI (610 bp), COII (688 bp), and 16S rRNA (888 bp) and nuDNA EF1‐α (658 bp) and 28S rRNA (524 bp) regions in order to reveal the evolutionary history of the alpine type of P. paradoxus. As a result of molecular phylogenetic analyses, it was revealed that the alpine type of P. paradoxus was polyphyletic, and had evolved to become the alpine type at least twice independently at separate mountain locations. In addition, the result of divergence time estimation suggested that the alpine type is an “ecomorph”, having recently adapted to low temperature habitats following mountain uplift within the Japanese Archipelago and subsequent glacial‐interglacial cycles.     

Parallel phenotypic evolution in a wolf spider radiation on Galápagos

Within island archipelagos, repeated ecological settings may lead to radiations wherein similar niches are recurrently occupied. Although it has been shown that species with common habitat requirements share particular traits, it remains relatively unexplored to what extent this may lead to the repeated evolution of almost identical phenotypes (phenocopies) and how this correlates with traits subjected to sexual selection. Exploring divergence patterns of ecological and sexual relevant traits within spiders seem promising to enhance our understanding of the relative role of natural and sexual selection. Here, we conduct a detailed morphological analysis on a large set of genital and non‐genital traits (morphometrics, colour pattern) within a radiation of the wolf spider genus Hogna Simon, 1885 on Galápagos and interpret these data, taking into account their known phylogenetic relationship. Our results show that recurrent environmental gradients have led to the parallel evolution of almost identical phenotypes, which not only proves that natural selection has driven morphological divergence, but also suggests that a similar genetic or developmental basis most likely underlies this divergence. Among‐species variation in genital traits in contrast rather reflects the phylogenetic relationships on Santa Cruz and San Cristóbal. The combination of these data indicate that speciation in this system is driven by the combined effect of ecological mechanisms and allopatric divergence in sexual traits. © 2012 The Linnean Society of London, Biological Journal of the Linnean Society, 2012, 106 , 123–136.     

Counteracting selective regimes and host preference evolution in ecotypes of two species of walking-sticks

The evolution of ecological specialization has been a central topic in ecology because specialized adaptations to divergent environments can result in reproductive isolation and facilitate speciation. However, the order in which different aspects of habitat adaptation and habitat preference evolve is unclear. Timema walking-stick insects feed and mate on the host plants on which they rest. Previous studies of T. cristinae ecotypes have documented divergent, host-specific selection from visual predators and the evolution of divergent host and mate preferences between populations using different host-plant species (Ceanothus or Adenostoma). Here we present new data that show that T. podura, a nonsister species of T. cristinae, has also formed ecotypes on these host genera and that in both species these ecotypes exhibit adaptive divergence in color-pattern and host preference. Color-pattern morphs exhibit survival trade-offs on different hosts due to differential predation. In contrast, fecundity trade-offs on different hosts do not occur in either species. Thus, host preference in both species has evolved before divergent physiological adaptation but in concert with morphological adaptations. Our results shed light onto which traits are involved in the initial stages of ecological specialization and ecologically based reproductive isolation.     

Divergence and evolution of assortative mating in a polygenic trait model of speciation with gene flow

Assortative mating is an important driver of speciation in populations with gene flow and is predicted to evolve under certain conditions in few‐locus models. However, the evolution of assortment is less understood for mating based on quantitative traits, which are often characterized by high genetic variability and extensive linkage disequilibrium between trait loci. We explore this scenario for a two‐deme model with migration, by considering a single polygenic trait subject to divergent viability selection across demes, as well as assortative mating and sexual selection within demes, and investigate how trait divergence is shaped by various evolutionary forces. Our analysis reveals the existence of sharp thresholds of assortment strength, at which divergence increases dramatically. We also study the evolution of assortment via invasion of modifiers of mate discrimination and show that the ES assortment strength has an intermediate value under a range of migration‐selection parameters, even in diverged populations, due to subtle effects which depend sensitively on the extent of phenotypic variation within these populations. The evolutionary dynamics of the polygenic trait is studied using the hypergeometric and infinitesimal models. We further investigate the sensitivity of our results to the assumptions of the hypergeometric model, using individual‐based simulations.     

Parallel evolution and vicariance in the guppy (Poecilia reticulata) over multiple spatial and temporal scales

Well-studied model systems present ideal opportunities to understand the relative roles of contemporary selection versus historical processes in determining population differentiation and speciation. Although guppy populations in Trinidad have been a model for studies of evolutionary ecology and sexual selection for more than 50 years, this work has been conducted with little understanding of the phylogenetic history of this species. We used variation in nuclear (X-src) and mitochondrial DNA (mtDNA) sequences to examine the phylogeographic history of Poecilia reticulata Peters (the guppy) across its entire natural range, and to test whether patterns of morphological divergence are a consequence of parallel evolution. Phylogenetic, nested clade, population genetic, and demographic analyses were conducted to investigate patterns of genetic structure at several temporal scales and are discussed in relation to vicariant events, such as tectonic activity and glacial cycles, shaping northeast South American river drainages. The mtDNA phylogeny defined five major lineages, each associated with one or more river drainages, and analysis of molecular variance also detected geographic structuring among these river drainages in an evolutionarily conserved nuclear (X-src) locus. Nested clade and other demographic analyses suggest that the eastern Venezuela/ western Trinidad region is likely the center of origin of P. reticulata. Mantel tests show that the divergence of morphological characters, known to differentiate on a local scale in response to natural and sexual selection pressures, is not associated with mtDNA genetic distance; however, TreeScan analysis identified several significant associations of these characters with the haplotype tree. Parallel upstream/downstream patterns of morphological adaptation in response to selection pressures reported in P. reticulata within Trinidad rivers appears to persist across the natural range. Our results together with previous studies suggest that, although morphological variation in P. reticulata is primarily attributed to selection, phylogeographic history may also play a role.