Long‐term monitoring of shrub species translocation in degraded Neotropical mountain grassland

The introduction of plant species is a central topic in restoration ecology research. It is an effective technique to restore degraded ecosystems that present low resilience, such as the rupestrian grasslands. Once implemented, the transplantation of native species is monitored only in the short term, whereas long‐term monitoring should be preferred to identify potential changes in the restoration results. Our study is the first assessment of the transplantation success of 10 native shrub species in a degraded area of rupestrian grasslands, 8.5 years after transplantation. Survival, growth, and recruitment were assessed in 2004, 2008, and 2012. For all species, survival, growth, and recruitment varied over time. Although some species exhibited great mortality during the last 4 years, they also showed a great resprouting ability. Our results highlighted a trade‐off between survival and recruitment capacity. Most of the studied species showed remarkable ability to adapt to the extreme environment of the degraded area, persisting either through surviving or recruiting new individuals. We list nine native species, which are well appropriated for rupestrian grasslands restoration. In constrained environments, survival and resistance should represent criteria to select species for restoration project rather than fast growth and ground cover.     

Maintenance of species boundaries in a Neotropical radiation of Begonia

A major goal of evolutionary biology is to determine the mechanisms generating biodiversity. In Begonia, one of the largest plant genera (1900+ species), it has been postulated that the high number of endemic species is a by‐product of low gene flow among populations, which predisposes the group to speciation. However, this model of divergence requires that reproductive barriers accumulate rapidly among diverging species that overlap in their geographic ranges, otherwise speciation will be opposed by homogenizing gene flow in zones of secondary contact. Here, we test the outcomes of secondary contact in Begonia by genotyping multiple sympatric sites with 12 nuclear and seven plastid loci. We show that three sites of secondary contact between B. heracleifolia and B. nelumbiifolia are highly structured, mostly containing parental genotypes, with few F1 hybrids. A sympatric site between B. heracleifolia and B. sericoneura contains a higher proportion of F1s, but little evidence of introgression. The lack of later‐generation hybrids contrasts with that documented in many other plant taxa, where introgression is extensive. Our results, in conjunction with previous genetic work, show that Begonia demonstrate properties making them exceptionally prone to speciation, at multiple stages along the divergence continuum. Not only are populations weakly connected by gene flow, promoting allopatric speciation, but species often show strong reproductive barriers in secondary contact. Whether similar mechanisms contribute to diversification in other large genera remains to be tested.     

Intraspecific trait variation increases species diversity in a trait‐based grassland model

Intraspecific trait variation (ITV) is thought to play a significant role in community assembly, but the magnitude and direction of its influence are not well understood. Although it may be critical to better explain population persistence, species interactions, and therefore biodiversity patterns, manipulating ITV in experiments is challenging. We therefore incorporated ITV into a trait‐ and individual‐based model of grassland community assembly by adding variation to the plants’ functional traits, which then drive life‐history tradeoffs. Varying the amount of ITV in the simulation, we examine its influence on pairwise‐coexistence and then on the species diversity in communities of different initial sizes. We find that ITV increases the ability of the weakest species to invade most, but that this effect does not scale to the community level, where the primary effect of ITV is to increase the persistence and abundance of the competitively‐average species. Diversity of the initial community is also of critical importance in determining ITV's efficacy; above a threshold of interspecific diversity, ITV does not increase diversity further. For communities below this threshold, ITV mainly helps to increase diversity in those communities that would otherwise be low‐diversity. These findings suggest that ITV actively maintains diversity by helping the species on the margins of persistence, but mostly in habitats of relatively low alpha and beta diversity.     

Scale‐dependent biases in species counts in a grassland

Abstract. Numbers of plant species were recorded in species‐rich meadows in the Bílé Karpaty Mts., SE Czech Republic, with the aim to evaluate the sampling error made by well‐trained observers. Five observers recorded vascular plants in seven plots ranging from 9.8 cm² to 4 m² independently and were not time‐limited. In larger plots a discrepancy of 10–20% was found between individual estimates, in smaller plots discrepancy increased to 33%, on average. The gain in observed species richness by combining records of individual observers (in comparison with the mean numbers estimated by single observers) decreased from the smallest plot (27–82% for two to five observers) to the largest one (13–25%). However, after misidentified and suspicious records were eliminated, the gain was much lower and became scale‐independent; two observers added 12% species, on average, and the increase by combining species lists made by three or more observers was negligible (3% more on average). It is concluded that most discrepancies between individual observers were caused by misidentification of rare seedlings and young plants. We suggest that in species‐rich meadows plants should be recorded by at least three observers together and that they should consult all problematic plant specimens together in the field, to minimize errors.     

Temporary grazing exclusion promotes rapid recovery of species richness and productivity in a long‐term overgrazed Campos grassland

Moderate grazing intensity is considered the basic requirement to enhance ecosystem function in grasslands. Yet, deterioration by overgrazing is common in many biomes, including Campos grasslands in South America. Understanding how grazing management can lead to recovery of ecosystem function is essential to design and implement effective strategies for sustainable use of this resource. In a long‐term field experiment carried out in Southern Brazil, we studied the effects of temporal grazing exclusions (spring or fall) at moderate and severe livestock grazing intensities (maintained by adjusting contrasting forage allowances) on the species richness, botanical composition, forage mass, sward height, and photosynthetic active radiation intercepted. The experiment was arranged in a completely randomized design with three replications of grazing exclusions, applied simultaneously at moderate and severe grazing intensities. Moderate grazing intensity showed a bimodal structure of shorter and taller canopies, and high species richness. Severe grazing created a shorter and homogeneous sward structure characterized by less standing biomass and species loss. In response to grazing exclusions, sward height, standing biomass, and light interception recovered almost to the levels of moderate grazing. Further, within 2 years grass species richness increased and botanical composition changed toward grasses with erect habit prevailing in moderate grazing intensity. Our study confirms that (1) moderate grazing intensities allow the coexistence of high number of species and (2) spring grazing exclusions of long‐term overgrazed grasslands can lead to a quick start to recover the grass species richness, primary productivity, and species composition like that prevailing in well‐managed grasslands.     

Correlates of species richness in the largest Neotropical amphibian radiation

Although tropical environments are often considered biodiversity hotspots, it is precisely in such environments where least is known about the factors that drive species richness. Here, we use phylogenetic comparative analyses to study correlates of species richness for the largest Neotropical amphibian radiation: New World direct-developing frogs. Clade-age and species richness were nonsignificantly, negatively correlated, suggesting that clade age alone does not explain among-clade variation in species richness. A combination of ecological and morphological traits explained 65% of the variance in species richness. A more vascularized ventral skin, the ability to colonize high-altitude ranges, encompassing a large variety of vegetation types, correlated significantly with species richness, whereas larger body size was marginally correlated with species richness. Hence, whereas high-altitude ranges play a role in shaping clade diversity in the Neotropics, intrinsic factors, such as skin structures and possibly body size, might ultimately determine which clades are more speciose than others.     

Fine‐scale belowground species associations in temperate grassland

Evaluating how belowground processes contribute to plant community dynamics is hampered by limited information on the spatial structure of root communities at the scale that plants interact belowground. In this study, roots were mapped to the nearest one mm and molecularly identified by species on vertical (0–15 cm deep) surfaces of soil blocks excavated from dry and mesic grasslands in Yellowstone National Park (YNP) to examine the spatial relationships among species at the scale that roots interact. Our results indicated that average interspecific root – root distances for the majority of species were within a distance (3 mm) that roots have been shown to compete for resources. Most species placed their roots at random, although low root numbers for many species probably led to overestimating the occurrence of random patterns. According to theory, we expected that most of the remaining species would segregate their root systems to avoid competition. Instead we found that more species aggregated than segregated from others. Based on previous investigations, we hypothesize that species aggregate to increase uptake of water, nitrogen and/or phosphorus made available by neighbouring roots, or as a consequence of a reduction in the pathogenicity of soil biota growing in multispecies mixtures. Our results indicate that YNP grassland root communities are organized as closely interdigitating networks of species that potentially can support strong interactions among many species combinations. Future root research should address the prevalence and functional consequences of species aggregation across plant communities.     

Song‐type sharing in a population of Song Sparrows in the eastern United States

Male Song Sparrows (Melospiza melodia) sometimes interact with neighboring territory owners by song‐type matching or repertoire matching. In some Song Sparrow populations, levels of song sharing are high and most neighbors can interact by matching, but levels of song sharing are much lower in other populations, limiting the degree to which males can match their neighbors. One explanation for variation in sharing levels is that the importance of song‐type and repertoire matching, and therefore the extent of song sharing, varies geographically in North America, being greater in western populations than eastern populations. However, to date, two studies of eastern populations have provided conflicting evidence concerning levels of song sharing by Song Sparrows. Thus, we measured sharing of whole songs and introductory phrases of songs between males with adjacent territories in another population of Song Sparrows in the eastern United States (North Carolina), near the eastern and southern limits of the species’ breeding range. Males (N = 17) in our study shared an average of only 8.7% of their song types with neighbors, and more than half of neighbor pairs shared no whole songs. Sharing of introductory phrases was more common (mean = 22.8%). The level of whole song sharing in our study is the second lowest yet reported for any Song Sparrow population, supporting the hypothesis that sharing is generally lower in eastern than in western populations.     

Life‐history constraints in grassland plant species: a growth‐defence trade‐off is the norm

Plant growth can be limited by resource acquisition and defence against consumers, leading to contrasting trade‐off possibilities. The competition‐defence hypothesis posits a trade‐off between competitive ability and defence against enemies (e.g. herbivores and pathogens). The growth‐defence hypothesis suggests that strong competitors for nutrients are also defended against enemies, at a cost to growth rate. We tested these hypotheses using observations of 706 plant populations of over 500 species before and following identical fertilisation and fencing treatments at 39 grassland sites worldwide. Strong positive covariance in species responses to both treatments provided support for a growth‐defence trade‐off: populations that increased with the removal of nutrient limitation (poor competitors) also increased following removal of consumers. This result held globally across 4 years within plant life‐history groups and within the majority of individual sites. Thus, a growth‐defence trade‐off appears to be the norm, and mechanisms maintaining grassland biodiversity may operate within this constraint.     

VIP Barcoding: composition vector‐based software for rapid species identification based on DNA barcoding

Species identification based on short sequences of DNA markers, that is, DNA barcoding, has emerged as an integral part of modern taxonomy. However, software for the analysis of large and multilocus barcoding data sets is scarce. The Basic Local Alignment Search Tool (BLAST) is currently the fastest tool capable of handling large databases (e.g. >5000 sequences), but its accuracy is a concern and has been criticized for its local optimization. However, current more accurate software requires sequence alignment or complex calculations, which are time‐consuming when dealing with large data sets during data preprocessing or during the search stage. Therefore, it is imperative to develop a practical program for both accurate and scalable species identification for DNA barcoding. In this context, we present VIP Barcoding: a user‐friendly software in graphical user interface for rapid DNA barcoding. It adopts a hybrid, two‐stage algorithm. First, an alignment‐free composition vector (CV) method is utilized to reduce searching space by screening a reference database. The alignment‐based K2P distance nearest‐neighbour method is then employed to analyse the smaller data set generated in the first stage. In comparison with other software, we demonstrate that VIP Barcoding has (i) higher accuracy than Blastn and several alignment‐free methods and (ii) higher scalability than alignment‐based distance methods and character‐based methods. These results suggest that this platform is able to deal with both large‐scale and multilocus barcoding data with accuracy and can contribute to DNA barcoding for modern taxonomy. VIP Barcoding is free and available at http://msl.sls.cuhk.edu.hk/vipbarcoding/ .     

Morphofunctional patterns in Neotropical felids: species co‐existence and historical assembly

Extant felids are morphologically homogeneous, probably as a result of recent radiation and constraints from their predatory specializations. The Neotropical assemblage comprises 12 of the 41 extant felid species, which occupy all habitats available, with many species coexisting locally. We studied this assemblage on the basis of 31 craniodental variables reflecting morphofunctional variation, measured from 229 specimens representing all 12 species. Multivariate patterns were summarized allowing for phylogenetic covariation. Additional factors (geographical distribution, use of habitat and stratum, and activity pattern) were coded for each species. As expected, body size accounted for most variation, covarying with membership to three deep clades and, to a lesser extent, with large‐scale geographic variation. The species tend to segregate in morphospace plus one or more factors (e.g. habits) that make interspecific overlap in niche space minimal. Using dated phylogenies, biogeographic history, and the fossil record, we reconstructed the historical assembly of the Neotropical felid guild. We found a pattern of successive invasions and speciation in which new lineages occupied previously vacant areas of morphospace, or new species occupied overlapping areas but with contrasting habits. This may be general among antagonistic species of historically structured guilds, and we predict similar patterns in other continents. © 2010 The Linnean Society of London, Biological Journal of the Linnean Society, 2010, 100 , 711–724.     

Identifying drivers of species compositional change in a semi‐natural upland grassland over a 40‐year period

Question: Few long‐term studies exist with integrated vegetation and soil composition data, coupled with detailed environmental driver records. Can changes in community composition in an upland grassland be identified by revisitation after a 40‐year period and allow the main environmental drivers of change to be identified? Location: Snowdon, Wales, UK. Methods: Changes in plant community and soil composition were assessed by resurveying an upland Agrostis–Festuca grassland in 2008, 40 years after the original survey. PCA and ecological indicators were used to determine changes in plant community composition. Redundancy analysis (RDA) allowed the impact of soil chemical composition on the vegetation community to be assessed. Results: A significant shift in community composition was found between years. A 35% reduction in species richness and an increase in the grass:forb ratio, suggest significant ecosystem degradation. Indicator values suggest acidification of the community with an increased acidity preference of species recorded in 2008. However, soil pH measurements showed that soil pH had increased. RDA suggested that the main shifts in species composition were correlated with an increase in pH and a reduction in soil exchangeable base cation concentration. Clear ecosystem responses to climate, land‐use change or nitrogen enrichment were not observed. Conclusions: Shifts in vegetation and soil composition are clearly identifiable after 40 years. The shifts in community composition are consistent with ecosystem degradation due to acidification during the period between surveys. Ecological indicator values and soil chemical composition displayed differing degrees of change. Whilst soils appear to be recovering from historic effects of sulphur deposition, vegetation community composition changes appear to lag behind those in soil chemistry.     

Seasonal carbon isotope discrimination in a grassland community

Summary Grassland communities of arid western North America are often characterized by a seasonal increase in ambient temperature and evaporative demand and a corresponding decline in soil moisture availability. As the environment changes, particular species could respond differently, which should be reflected in a number of physiological processes. Carbon isotope discrimination varies during photosynthetic activity as a function of both stomatal aperture and the biochemistry of the fixation process, and provides an integrated measure of plant response to seasonal changes in the environment. We measured the seasonal course of carbon isotope discrimination in 42 grassland species to evaluate changes in gas exchange processes in response to these varying environmental factors. The seasonal courses were then used to identify community-wide patterns associated with life form, with phenology and with differences between grasses and forbs. Significant differences were detected in the following comparisons: (1) Carbon isotope discrimination decreased throughout the growing season; (2) perennial species discriminated less than annual species; (3) grasses discriminated less than forbs; and (4) early flowering species discriminated more than the later flowering ones. These comparisons suggested that (1) species active only during the initial, less stressful months of the growing season used water less efficiently, and (2) that physiological responses increasing the ratio of carbon fixed to water lost were common in these grassland species, and were correlated with the increase in evaporative demand and the decrease in soil moisture.     

Top‐down control of rare species abundances by native ungulates in a grassland restoration

Ecological restorations are predicted to increase in species diversity over time until they reach reference levels. However, chronosequence studies in grasslands often show that diversity peaks after the first few years and then declines over time as grasses become more dominant. We addressed whether bison grazing and seed additions could prevent this decline in diversity. Exclosures that prevented bison grazing were compared with grazed plots over 4 years, and seed additions were conducted inside and outside exclosures to test for seed and microsite limitations. A previous study conducted 4‐months post seeding found that local species richness was primarily seed limited, but that grazing could sometimes increase seedling emergence. Here, we tested whether increased seedling emergence led to longer‐term increases in the species diversity of the plant community. We found that the seed addition effect grew smaller and the grazing effect grew stronger over time, and that seed additions affected the abundance of added species only when plots were grazed. Grazed plots had higher species diversity and lower biomass and litter buildup compared to non‐grazed plots. Our results suggest that moderate grazing by bison or management that mimics grazing can maintain diversity in grass‐dominated situations. Our results also emphasize the need to follow seed additions over several years to assess correctly whether seed limitation exists.     

Genome and cuticular hydrocarbon‐based species delimitation shed light on potential drivers of speciation in a Neotropical ant species complex

Geographic separation that leads to the evolution of reproductive isolation between populations generally is considered the most common form of speciation. However, speciation may also occur in the absence of geographic barriers due to phenotypic and genotypic factors such as chemical cue divergence, mating signal divergence, and mitonuclear conflict. Here, we performed an integrative study based on two genome‐wide techniques (3RAD and ultraconserved elements) coupled with cuticular hydrocarbon (CHC) and mitochondrial (mt) DNA sequence data, to assess the species limits within the Ectatomma ruidum species complex, a widespread and conspicuous group of Neotropical ants for which heteroplasmy (i.e., presence of multiple mtDNA variants in an individual) has been recently discovered in some populations from southeast Mexico. Our analyses indicate the existence of at least five distinct species in this complex: two widely distributed across the Neotropics, and three that are restricted to southeast Mexico and that apparently have high levels of heteroplasmy. We found that species boundaries in the complex did not coincide with geographic barriers. We therefore consider possible roles of alternative drivers that may have promoted the observed patterns of speciation, including mitonuclear incompatibility, CHC differentiation, and colony structure. Our study highlights the importance of simultaneously assessing different sources of evidence to disentangle the species limits of taxa with complicated evolutionary histories.     

DNA‐based discrimination between the sibling species Aphis gossypii Glover and Aphis frangulae Kaltenbach

Abstract Morphologically similar species occur in various groups of insects, including aphid pests. In Europe, Aphis frangulae Kaltenbach and Aphis gossypii Glover (sometimes considered as subspecies) are differentiated usually on the basis of life cycle and host plant. We used a sexual population of A. frangulae collected on the primary host and samples of A. gossypii collected on cucurbits or cotton for the development of molecular markers. DNA sequence data for the gene encoding cytochrome b and for the barcode region of cytochrome oxidase I, as well as a length polymorphism for an intron in the sodium channel para‐type gene discriminated unambiguously between the two taxa. These markers were also used as identification keys for aphids collected on crops belonging to the Solanaceae. The cytochrome b marker differentiates host‐related Aphis gossypii haplotypes, and the para‐type gene intron might be suitable for the resolution of taxonomic problems in other aphid species complexes.     

A DNA assay for rapid discrimination between beaver species as a tool for alien species management

The confirmed presence of alien North American beavers in some regions of Eurasia may compete with and hinder the successful recolonisation of the native Eurasian species back to its former range. Distinguishing the two species in the field can be problematic, time consuming and expensive, thereby potentially limiting appropriate conservation actions. Here, a rapid and inexpensive genetic SNP assay is described that can separate the two species from either non-invasively collected samples or samples taken directly from restrained individuals. We applied these new genetic assays to free-living beavers of unknown origin sampled in Scotland.