Genetic and phenotypic divergence in an island bird: isolation by distance,by colonization or by adaptation?

Discerning the relative roles of adaptive and nonadaptive processes in generating differences among populations and species, as well as how these processes interact, is a fundamental aim in biology. Both genetic and phenotypic divergence across populations can be the product of limited dispersal and gradual genetic drift across populations (isolation by distance), of colonization history and founder effects (isolation by colonization) or of adaptation to different environments preventing migration between populations (isolation by adaptation). Here, we attempt to differentiate between these processes using island populations of Berthelot's pipit (Anthus berthelotii), a passerine bird endemic to three Atlantic archipelagos. Using microsatellite markers and approximate Bayesian computation, we reveal that the northward colonization of this species ca. 8500 years ago resulted in genetic bottlenecks in the colonized archipelagos. We then show that high levels of genetic structure exist across archipelagos and that these are consistent with a pattern of isolation by colonization, but not with isolation by distance or adaptation. Finally, we show that substantial morphological divergence also exists and that this is strongly concordant with patterns of genetic structure and bottleneck history, but not with environmental differences or geographic distance. Overall, our data suggest that founder effects are responsible for both genetic and phenotypic changes across archipelagos. Our findings provide a rare example of how founder effects can persist over evolutionary timescales and suggest that they may play an important role in the early stages of speciation.     

Do annual and perennial populations of an insect-pollinated plant species differ in mating system?

Background and AimsTheory predicts that outcrossing should be more prevalent among perennials than annuals, a pattern confirmed by comparative evidence from diverse angiosperm families. However, intraspecific comparisons between annual and perennial populations are few because such variation is uncommon among flowering plants. Here, we test the hypothesis that perennial populations outcross more than annual populations by investigating Incarvillea sinensis, a wide-ranging insect-pollinated herb native to China. The occurrence of both allopatric and sympatric populations allows us to examine the stability of mating system differences between life histories under varying ecological conditions.MethodsWe estimated outcrossing rates and biparental inbreeding in 16 allopatric and five sympatric populations in which both life histories coexisted using 20 microsatellite loci. In each population we measured height, branch number, corolla size, tube length and herkogamy for ~30 individuals. In a sympatric population, we recorded daily flower number, pollinator visitation and the fruit and seed set of annual and perennial plants.Key ResultsAs predicted, outcrossing rates (t) were considerably higher in perennial (mean = 0.76) than annual (mean = 0.09) populations. This difference in mating system was also maintained at sympatric sites where plants grew intermixed. In both allopatric and sympatric populations the degree of herkogamy was consistently larger in outcrossing than selfing plants. Perennials were more branched, with more and larger flowers than in annuals. In a sympatric population, annuals had a significantly higher fruit and seed set than perennials.ConclusionsGenetically based differences in herkogamy between annuals and perennials appear to play a key role in governing outcrossing rates in populations, regardless of variation in local ecological conditions. The maintenance of mating system and life history trait differentiation between perennial and annual populations of I. sinensis probably results from correlated evolution in response to local environmental conditions.     

The relative of species pools in determining plant species richness: an alternative explanation of species coexistence?

Explanations of the pattern of species have traditionally relied on small-scale, local processes occurring in ecological time. Differences in species richness have associated with different mechanisms avoiding competition, such as spatiotemporal heterogeneity (weaker competitors may find a more favourable place or time) or environmental stress (competition is assumed to be less intensive under difficult conditions). More recently, large-scale process have been taken into account, raising such questions as: which plant species may potentially grow in a certain community? Are evolutionary processes and species dispersal responsible for the differences between communities? The species-pool theory attempts to answer these general questions, and information about species pools is needed for the design of experiments where the number of species in a community is manipulated.     

Do plant populations on distinct inselbergs talk to each other? A case study of genetic connectivity of a bromeliad species in an Ocbil landscape

Here, we explore the historical and contemporaneous patterns of connectivity among Encholirium horridum populations located on granitic inselbergs in an Ocbil landscape within the Brazilian Atlantic Forest, using both nuclear and chloroplast microsatellite markers. Beyond to assess the E. horridum population genetic structure, we built species distribution models across four periods (current conditions, mid‐Holocene, Last Glacial Maximum [LGM], and Last Interglacial) and inferred putative dispersal corridors using a least‐cost path analysis to elucidate biogeographic patterns. Overall, high and significant genetic divergence was estimated among populations for both nuclear and plastid DNA (Φ_ST(n) = 0.463 and Φ_ST(plastid) = 0.961, respectively, p < .001). For nuclear genome, almost total absence of genetic admixture among populations and very low migration rates were evident, corroborating with the very low estimates of immigration and emigration rates observed among E. horridum populations. Based on the cpDNA results, putative dispersal routes in Sugar Loaf Land across cycles of climatic fluctuations in the Quaternary period revealed that the populations’ connectivity changed little during those events. Genetic analyses highlighted the low genetic connectivity and long‐term persistence of populations, and the founder effect and genetic drift seemed to have been very important processes that shaped the current diversity and genetic structure observed in both genomes. The genetic singularity of each population clearly shows the need for in situ conservation of all of them.     

What best explains vigilance in elk: characteristics of prey, predators, or the environment?

We quantified the vigilance levels of elk (Cervus elaphus) preyedon by wolves (Canis lupus) in Yellowstone National Park, betweenJanuary and May in 2005 and 2006, and used Akaike's informationcriterion to compare a set of 38 regression models for vigilancelevels. These models combined up to 9 predictor variables of3 types: characteristics of the prey group (herd size and composition),characteristics of the predator (wolf pack size, distance away,and the presence/absence of a kill), and characteristics ofthe local environment (distance to woodland edges, snow depth,and snow cover). The set of models spanned a range of complexityfrom simple univariate models to complex combinations with upto 3 variables of each type. Complex models incorporating thecharacteristics of the wolf pack, the structure of the elk herd,and the environmental conditions had higher information contentthan simple models. Although univariate models of vigilancedetect significant relationships, they have low informationcontent relative to multivariate models. These results showthat elk assesses factors of several types when assessing riskand deciding how much time to allocate to vigilance. In particular,we found that all well-supported models of vigilance includedseveral "prey" variables and several "predator" variables. Thisresult highlights the need to consider information about predatorswhen trying to explain variation in vigilance levels in prey.     

Genetics of recent habitat contraction and reduction in population size: does isolation by distance matter?

Fragmentation and loss of natural habitats are recognized as major threats to contemporary flora and fauna. Detecting past or current reductions in population size is therefore a major aim in conservation genetics. Statistical methods developed to this purpose have tended to ignore the effects of spatial population structure. However in many species, individual dispersal is restricted in space and fine-scale spatial structure such as isolation by distance (IBD) is commonly observed in continuous populations. Using a simulation-based approach, we investigated how comparative and single-point methods, traditionally used in a Wright-Fisher (WF) population context for detecting population size reduction, behave for IBD populations. We found that a complex 'quartet' of factors was acting that includes restricted dispersal, population size (i.e. habitat size), demographic history, and sampling scale. After habitat reduction, IBD populations were characterized by a stronger inertia in the loss of genetic diversity than WF populations. This inertia increases with the strength of IBD, and decreases when the sampling scale increases. Depending on the method used to detect a population size reduction, a local sampling can be more informative than a sample scaled to habitat size or vice versa. However, IBD structure led in numerous cases to incorrect inferences on population demographic history. The reanalysis of a real microsatellite data set of skink populations from fragmented and intact rainforest habitats confirmed most of our simulation results.     

Do closely related species share of feeding niche along growth? Diets of three sympatric species of the mojarras (Actinopterygii: Gerreidae) in a tropical bay in southeastern Brazil

Understanding the trophic relationships among closely related species is a way to obtain subsidies for their management and conservation of their habitats. The diets of three co-occurring abundant fish species of the Gerreidae family (Diapterus rhombeus, Eucinostomus argenteus and Eucinostomus gula) in a tropical bay were described. The tested hypothesis was that the three sympatric species present shifts in their use of resource during the ontogenetic development to facilitate their coexistence. Size groups for each species were categorized according to breakpoints in the morphological structures determined by piecewise regression models. Significant overlapping in diets was found for all size classes of D. rhombeus but not for size classes of the Eucinostomus genus. Furthermore, different size classes of D. rhombeus did not overlap diet with size classes of the Eucinostomus genus. The specialization in feeding niches corresponding to growth seems to bring benefits for this group of fish rather than a generalist feeding strategy. The hypothesis of the available resources partitioning was accepted only between the two genera (Diapterus and Eucinostomus), and among size classes of the Eucinostomus genus that seemed to follow the principle of limiting similarity. However, different size classes of D. rhombeus exhibited strong evidence of an intraspecific overlapping of the trophic niche. It seems that different processes related to use of the trophic niche dimension are structuring these closely related fish species.     

Variation in the geometry of foreleg claws in sympatric giant water bug species: an adaptive trait for catching prey?

When giant water bugs (Heteroptera: Belostomatidae) encounter prey animals that are larger than they are themselves, they first hook the claw of their raptorial legs onto the animal, and then use all their legs to pin it. The claws of the raptorial legs in giant water bugs play an important role in catching larger prey, but the relationship between the claws, body lengths of predators, and prey size has not been fully investigated. To elucidate the functioning of claws in catching prey, we investigated prey body size relative to predator size in nymphs of two sympatric belostomatid giant water bug species, the vertebrate eater Kirkaldyia (=Lethocerus) deyrolli Vuillefroy and the invertebrate eater Appasus japonicus Vuillefroy, captured in rice fields. The younger nymphs of K. deyrolli caught preys that were larger than themselves, whereas those of A. japonicus caught preys that were smaller. Younger nymphs of K. deyrolli had claws that were curved more sharply than those of A. japonicus. The more curved claws of younger nymphs of K. deyrolli probably hook more easily onto larger vertebrates and thus this shape represents an adaptation for acquiring such prey.     

Stimulation of soil nitrification and denitrification by grazing in grasslands: do changes in plant species composition matter?

Stimulation of nitrification and denitrification by long term (from years to decades) grazing has commonly been reported in different grassland ecosystems. However, grazing generally induces important changes in plant species composition, and whether changes in nitrification and denitrification are primarily due to changes in vegetation composition has never been tested. We compared soil nitrification- and denitrification-enzyme activities (NEA and DEA, respectively) between semi-natural grassland sites experiencing intensive (IG) and light (LG) grazing/mowing regimes for 13 years. Mean NEA and DEA (i.e. observed from random soil sampling) were higher in IG than LG sites. The NEA/DEA ratio was higher in IG than LG sites, indicating a higher stimulation of nitrification. Marked changes in plant species composition were observed in response to the grazing/mowing regime. In particular, the specific phytomass volume of Elymus repens was lower in IG than LG sites, whereas the specific volume of Lolium perenne was higher in IG than LG sites. In contrast, the specific volume of Holcus lanatus, Poa trivialis and Arrhenatherum elatius were not significantly different between treatments. Soils sampled beneath grass tussocks of the last three species exhibited higher DEA, NEA and NEA/DEA ratio in IG than LG sites. For a given grazing regime, plant species did not affect significantly soil DEA, NEA and NEA/DEA ratio. The modification of plant species composition is thus not the primary factor driving changes in nitrification and denitrification in semi-natural grassland ecosystems experiencing long term intensive grazing. Factors such as trampling, N returned in animal excreta, and/or modification of N uptake and C exudation by frequently defoliated plants could be responsible for the enhanced microbial activities.     

Lack of genetic differentiation among four sympatric southeast African intertidal limpets (Siphonariidae): phenotypic plasticity in a single species?

Specimens of four sympatric intertidal limpet species (Siphonariadayi, S. tenuicostulata, S. anneae and S. nigerrima) were collectedfrom four localities on the east coast of South Africa and southernMozambique. Their phylogenetic relationships were investigatedusing sequences of the mitochondrial COI gene and the intron-containingnuclear ATPSß gene. Two closely related lineages wererecovered, which grouped specimens on the basis of geographyrather than morphology. One lineage was associated with thesubtropical coastline of South Africa's east coast and the otherwith the tropical coastline of northeastern South Africa andsouthern Mozambique. This genetic discontinuity coincides witha biogeographic boundary located in the vicinity of Cape StLucia. Combined genetic diversity of the four species was lowerthan that of three other southern African congeners, and fellwithin the range determined for single southern African marinemollusc species. We suggest that the four limpet species arein fact different morphotypes of a single species. (Received 6 October 2006; accepted 29 March 2007)     

Mutual replacement of species in space in a grassland community: is there an evidence for functional complementarity of replacement groups?

Many plant communities show strong fine‐scale spatiotemporal dynamics due to frequent natality and mortality events. This process is often non‐random, implying that the community can be broken into groups within which species mutually replace each other in time and are distinct from the other such groups. We examined whether such groups fill separate niches and are functionally complementary in a species‐rich mountain grassland. We used cluster analysis of fine‐scale spatial data time series to discern which species were more likely to replace each other in space. Next, a four‐year removal experiment (removing one group in each experimental treatment, or similar amount of biomass across all groups) was used to determine whether simultaneous occurrence of all these groups would maintain a greater total biomass than if an entire group were eliminated. The results do not support the hypothesis that the simultaneous presence of groups of species that replace each other in space is necessary for the community to attain its maximum biomass. However, the experiment showed strong differences among the replacement groups in their capacity for opportunistic behaviour: some groups responded quickly to space made available by removal while others did not. Furthermore, there were strong differences between groups composed primarily of grasses and groups composed primarily of dicots. In spite of the large differences among these groups, they are not functionally complementary. We therefore conclude that replacement processes in this grassland community more closely resemble a neutral process with sets of species differing in the speed at which they fill empty spaces.     

Evolution of antipredator behavior in an island lizard species,Podarcis erhardii (Reptilia: Lacertidae): The sum of all fears?

Organisms generally have many defenses against predation, yet may lack effective defenses if from populations without predators. Evolutionary theory predicts that “costly” antipredator behaviors will be selected against when predation risk diminishes. We examined antipredator behaviors in Aegean wall lizards, Podarcis erhardii, across an archipelago of land-bridge islands that vary in predator diversity and period of isolation. We examined two defenses, flight initiation distance and tail autotomy. Flight initiation distance generally decreased with declining predator diversity. All predator types had distinctive effects on flight initiation distance with mammals and birds having the largest estimated effects. Rates of autotomy observed in the field were highest on predator-free islands, yet laboratory-induced autotomy increased linearly with overall predator diversity. Against expectation from previous work, tail autotomy was not explained solely by the presence of vipers. Analyses of populations directly isolated from rich predator communities revealed that flight initiation distance decreased with increased duration of isolation in addition to the effects of current predator diversity, whereas tail autotomy could be explained simply by current predator diversity. Although selection against costly defenses should depend on time with reduced threats, different defenses may diminish along different trajectories even within the same predator–prey system.     

Contrasting levels of extra-pair paternity in mainland and island populations of the house sparrow (Passer domesticus): is there an 'island effect'?

Despite the many studies that have investigated the genetic mating system of socially monogamous birds, very little is known about the underlying causes of extra-pair paternity and few studies have attempted to test those hypotheses which have been suggested. This study describes die analysis of die genetic mating system of two populations of the house sparrow [Passer domesticus) , and uses the results from four other populations to test existing hypodieses using an intra-specific comparative approach. The parentage analysis was conducted using a combination of published and newly presented microsatellite loci isolated from the house sparrow. One population in Kentucky, U.S.A. was found to contain what may be considered to be a typical level of extra-pair paternity for mis species (10.5%, 19/185 offspring). The second, a population on the island of Lundy, UK, exhibited a very low level (1.3%, 4/305 offspring), significandy lower dian that in all the other populations studied so far. The finding of such diverse rates of extra-pair paternity, along with the existing estimates from ofher populations, has allowed us to test the effects of breeding density and genetic variation on die level of extra-pair paternity. We found no effect of either factor on the frequency of extra-pair paternity in the house sparrow, leaving the cause of this variation open to fresh ideas.     

Pollination of Ravenala madagascariensis (Strelitziaceae) by lemurs in Madagascar: evidence for an archaic coevolutionary system?

Investigations of the floral biology of the traveler's tree (Ravenala madagascariensis) and the ecology of the ruffed lemur (Varecia variegata), both endemic to the island of Madagascar, suggest a plant-pollinator relationship. Ravenala exhibits many specializations for visitation by large nonflying animals: inflorescences placed below the crown of the plant and easily accessible to arboreal animals; large flowers enclosed in tough, protective bracts that require a strong pollinator to open; stiff, rodlike styles that withstand the rough handling of the visitors; and copious, sucrose-dominant nectar that provides a renewable reward for a sizable animal for a long time period. Our observations in the field also show that Varecia variegata: consistently and almost exclusively visit the flowers of Ravenala; carry pollen on their fur between flowers on the same plant and between conspecific plants; do not destroy the flowers while obtaining the nectar; and appear to be highly dependent on nectar as a food source during specific times of the year. The basal phylogenetic position of Ravenala in the family Strelitziaceae, as indicated by molecular sequence data, and the distribution of reproductive traits in the three extant genera are consistent with the hypothesis that pollination by nonflying mammals is an archaic system, whereas bird and bat pollination are derived.     

What causes changes in plant litter quality and quantity as consequence of grazing in the Patagonian Monte: Plant cover reduction or changes in species composition?

In Patagonian Monte, as in other arid ecosystems, grazing has triggered changes in vegetation and soil such as plant cover reduction, changes in species composition and soil nutrient losses. Several mechanisms were proposed interconnecting these changes, but evidence supporting them is very scarce. On the basis of published data concerning plant cover by species along grazing gradients and leaf litter production of dominant species, we estimated the effects of grazing on a – quality (N, soluble phenolics and lignin concentrations) and b – quantity (leaf litterfall (LLF) and inputs of nitrogen, soluble phenolics and lignin to the soil) of leaf litter in the Patagonian Monte, discriminating the effect of plant cover reduction from that of species composition. We also evaluated the relationship between senesced leaves traits and the response of species to grazing (i.e. their relative change in plant cover). Grazing causes a reduction in LLF and in the inputs of nitrogen, soluble phenolics and lignin to the soil. In the case of LLF, this reduction was not only a result of the decrease in plant cover but also due to changes in species composition. In contrast, our results showed that the reduction in nitrogen, soluble phenolics and lignin inputs to the soil by LLF is only a consequence of plant cover reduction. Additionally, litter quality was affected through increasing concentration of N and secondary compounds (soluble phenolics and lignin). N and soluble phenolics concentration on senesced leaves were positively related to the response of species to grazing, suggesting that other factors instead of N are relevant to sheep foraging decisions.     

Differences in levels of heterozygosity in populations of the common gudgeon (Gobio gobio,Cyprinidae) among adjacent drainages in Central Europe: an effect of postglacial range dynamics?

Twenty-nine allozyme loci analyzed in 295 common gudgeons (Gobio gobio) from the Rhine, the upper Danube and the Elbe river systems revealed variability measures of P = 0.590, H(e) = 0.066, and G(ST) = 0.1415. Gene flow was estimated at N(e)m = 1.88 over 223 river km in the Danube basin, and at N(e)m = 1.96 over 300 river km in the Rhine system. Isolation-by-distance was not observed. Danubian gudgeons proved significantly more heterozygous (H(e) = 0.106) than those from the Rhine (H(e) = 0.057) or the Elbe drainages (H(e) = 0.029). Nine polymorphic enzymes contributed to this difference, which probably indicates dispersal bottlenecking of the postglacial immigrants into the Atlantic drainages of the study area. Refugial bottlenecking of gudgeons from Atlantic drainages in a Pleistocene refuge located in oceanic northwest Europe also seems possible. Slightly deeper genetic lineages in the Danube (G(ST) = 0.0859) than in the Rhine (G(ST) = 0.0793) agree with this explanation, as does the greater mean genetic distance among pairs of population samples from the Danube (D = 0.0138) than from the Rhine (D = 0.0054). A genetic distance of D = 0.0085 separated Rhenish and Danubian gudgeons.     

Bones and genes: resolution problems in three Vietnamese species of Crocidura (Mammalia,Soricomorpha, Soricidae) and the description of?an?additional new species

Recent investigations of Southeast Asian white toothed shrews belonging to the genus Crocidura have revealed discrepancies between the results of morphological and molecular studies. The following study concerns three species of Crocidura occurring in Vietnam, namely Crocidura attenuata, Crocidura tanakae and Crocidura wuchihensis, and an undescribed fourth species revealed by molecular analysis. For many years Crocidura attenuata has been known to occur in Vietnam but, until very recently, the morphologically similar and comparably sized Crocidura tanakae was believed to be restricted to Taiwan. Following several molecular studies over the last few years, this species is now believed to be considerably more widespread and recognised as occuring also in Vietnam. The results of one of these recent molecular studies also revealed the presence of an undescribed species of Crocidura, similar in size and morphology to Crocidura wuchihensis, which is herein described. Data are provided on geographical variation in Vietnam and the problems of defining morphologically similar yet molecularly disparate species are discussed.     

Leaf photosynthesis and respiration of three bioenergy crops in relation to temperature and leaf nitrogen: how conserved are biochemical model parameters among crop species?

Given the need for parallel increases in food and energy production from crops in the context of global change, crop simulation models and data sets to feed these models with photosynthesis and respiration parameters are increasingly important. This study provides information on photosynthesis and respiration for three energy crops (sunflower, kenaf, and cynara), reviews relevant information for five other crops (wheat, barley, cotton, tobacco, and grape), and assesses how conserved photosynthesis parameters are among crops. Using large data sets and optimization techniques, the C(3) leaf photosynthesis model of Farquhar, von Caemmerer, and Berry (FvCB) and an empirical night respiration model for tested energy crops accounting for effects of temperature and leaf nitrogen were parameterized. Instead of the common approach of using information on net photosynthesis response to CO(2) at the stomatal cavity (A(n)-C(i)), the model was parameterized by analysing the photosynthesis response to incident light intensity (A(n)-I(inc)). Convincing evidence is provided that the maximum Rubisco carboxylation rate or the maximum electron transport rate was very similar whether derived from A(n)-C(i) or from A(n)-I(inc) data sets. Parameters characterizing Rubisco limitation, electron transport limitation, the degree to which light inhibits leaf respiration, night respiration, and the minimum leaf nitrogen required for photosynthesis were then determined. Model predictions were validated against independent sets. Only a few FvCB parameters were conserved among crop species, thus species-specific FvCB model parameters are needed for crop modelling. Therefore, information from readily available but underexplored A(n)-I(inc) data should be re-analysed, thereby expanding the potential of combining classical photosynthetic data and the biochemical model.