A long‐term habitat fragmentation experiment leads to morphological change in a species of carabid beetle

1. Habitat fragmentation and transformation are key drivers of species declines in landscapes. Most of the current understanding of species' responses to environmental change originates from studies of populations and communities. However, phenotypic variation offers another key aspect of species responses and could provide additional insights into the functional drivers of population change. 2. The goal of this study was to address this gap by exploring the morphological changes of a species of carabid beetle (Notonomus resplendens) with a known population response to the Wog Wog Habitat Fragmentation Experiment in Australia. We measured morphological traits associated with body size, head width, and dispersal ability. We quantified patterns of morphological variation over time and between native Eucalyptus forest fragments and the surrounding pine plantation matrix and the continuous intact native Eucalyptus forest controls. 3. We found sexually dimorphic morphological changes in response to the experimental treatments. Males increased in size, had larger legs and had smaller interocular widths in the matrix in both the short and long terms. Conversely, females became comparatively smaller and had increased interocular widths in the same treatments. Effects in the fragments were similar to those in the matrix, but exhibited more uncertainty. 4. Our results demonstrate that species can show morphological change in response to environmental change over very short time periods. We demonstrate that using both population and morphological data allows stronger inferences about the mechanisms behind species responses to environmental change.     

Changes in plant species density in an experimentally fragmented forest landscape: Are the effects scale‐dependent?

The establishment of commercial tree plantations is a common cause of habitat fragmentation globally, yet the influence of this land use on plant species density in fragmented native forests requires further understanding. Theory predicts species density will be highest in large areas of habitat, and should decline as area is reduced, but whether these effects are scale‐dependent is largely unknown. We assessed plant species density (total, common and uncommon species) in experimentally fragmented eucalypt forest remnants (0.25, 0.88, 3.06 ha) surrounded by a pine plantation, at three spatial scales using nested quadrats. Specifically, we consider how plant species density varies across three different sized fragments, and whether the response of species density is magnified in common or uncommon species. Species density in small fragments was higher than continuous forest for all species groupings at the smallest spatial scale (1 m²), and for total and common species at the next smallest spatial scale (16 m²). No species groupings responded to reductions in habitat area at the largest spatial scale (144 m²). We suggest that pine plantations may cause higher species density in small fragments via two mechanisms, either by allowing species to infill unoccupied areas within small fragments, or by buffering small fragments from species losses during a severe and prolonged drought. In both cases we suspect reduced moisture stress (e.g. increased soil moisture, higher shading and reduced temperature) in small fragments has led to the observed changes in species density.     

A large-scale forest fragmentation experiment: the Stability of Altered Forest Ecosystems Project

Opportunities to conduct large-scale field experiments are rare, but provide a unique opportunity to reveal the complex processes that operate within natural ecosystems. Here, we review the design of existing, large-scale forest fragmentation experiments. Based on this review, we develop a design for the Stability of Altered Forest Ecosystems (SAFE) Project, a new forest fragmentation experiment to be located in the lowland tropical forests of Borneo (Sabah, Malaysia). The SAFE Project represents an advance on existing experiments in that it: (i) allows discrimination of the effects of landscape-level forest cover from patch-level processes; (ii) is designed to facilitate the unification of a wide range of data types on ecological patterns and processes that operate over a wide range of spatial scales; (iii) has greater replication than existing experiments; (iv) incorporates an experimental manipulation of riparian corridors; and (v) embeds the experimentally fragmented landscape within a wider gradient of land-use intensity than do existing projects. The SAFE Project represents an opportunity for ecologists across disciplines to participate in a large initiative designed to generate a broad understanding of the ecological impacts of tropical forest modification.     

Nematodes associated with Ips cembrae (Coleoptera: Curculionidae): comparison of generations,sexes and sampling methods

A study of nematodes associated with the large larch bark beetle Ips cembrae (Heer 1836) was carried out at three locations in the Czech Republic. The proportion of beetles infested by endoparasitic nematodes (representatives of genera Contortylenchus, Parasitylenchus, Cryptaphelenchus and Parasitorhabditis) ranged from 29.9 to 50.9%. Significant differences were determined in nematode infestation levels among locations, generations and sampling methods. No differences were found in infestation rates between males and females. The percentage of bark beetles with phoretic nematodes ranged from 18 to 42.9%. Phoretic nematodes directly found under elytra, on wings and between body segments of the bark beetles belong to the genus Micoletzkya. However, adults and juveniles of other two phoretic species Laimaphelenchus penardi and Bursaphelenchus sp. were found in the gallery frass of I. cembrae. Infestation by phoretic nematodes positively correlated with the presence of mites under elytra.     

Population viability analysis of Walia ibex (Capra walie) at Simien Mountains National Park (SMNP), Ethiopia

Population viability analysis (PVA) has been applied to the management of many threatened populations. The objective of this study was, therefore, to estimate the PVA of Walia ibex at the Simen Mountains National Park, in the north‐central highlands of Ethiopia, with respect to population growth parameters, the probability of the population reaching a lower extinction threshold and the mean time to extinction. Direct census of the population was carried out in 2009. Secondary census data were also collected from park authorities and the literature reviews. The result revealed that the estimates of the infinitesimal mean, μ (0.04117) was greater than the infinitesimal variance, σ² (0.0219). The probability that the population reaches the extinction threshold was very low (0.15%). The mean time required for the counts to decline from the existing population size to one individual animal was 160 years. But threatened species are adversely affected by changes in landscape. These changes can be brought by short‐ and long‐term human and climate change impacts, respectively. Therefore, with the absence of environmental and demographic stochasticity and, with the application of appropriate reproductions and habitat management, the population of Walia ibex will be viable and reaches its mean time of extinctions after 160 years.     

Pyrazine emission by a tropical firefly: An example of chemical aposematism?

Although famous for photic courtship displays, fireflies (Coleoptera: Lampyridae) are also notable for emitting strong odors when molested. The identity of volatile emissions and their possible role, along with photic signals, as aposematic warnings of unpalatability have been little explored, especially in tropical species. Pursuant to the observation that the widespread Neotropical fireflies, Photuris trivittata and Bicellonycha amoena, emit pungent odors, glows, and flashes when handled, we investigated their cuticular and headspace chemistry. Gas chromatography–mass spectrometry analyses revealed that both fireflies have species‐specific cuticular hydrocarbon profiles. Photuris trivittata headspace was dominated by 2‐methoxy‐3‐(1‐methylpropyl) pyrazine (hereafter, pyrazine), on the order of 1.59 ng/individual and a suite of sesquiterpenes, while B. amoena emitted 3‐methoxy‐2‐butenoic acid methyl ester and a few ketones. This is the first report of such compounds in fireflies. We investigated the role of pyrazine in P. trivittata's interactions with potential predators: sympatric ants, toads, and bats. Solvent‐washed P. trivittata painted with pyrazine incurred lower ant predation than did their solvent‐washed counterparts. Pyrazine significantly repelled ants at baits in concentrations as low as 9.8 × 10^?4 ng/μl. The toad, Rhinella marina, readily accepted intact fireflies, pyrazine‐coated and uncoated mealworms. Both Myotis nigricans and Molossus molossus bats rejected fireflies, but accepted both pyrazine‐coated and uncoated mealworms. While pyrazine repels ants, its role as an aposematic signal warning other potential predators of firefly distastefulness requires further investigation. Our results underscore the idea that multiple enemies exert conflicting selection on firefly defenses.     

Molecular mechanism underlying pseudopeloria in Habenaria radiata (Orchidaceae)

Habenaria radiata (Orchidaceae) has two whorls of perianth, comprising three greenish sepals, two white petals and one lip (labellum). By contrast, the pseudopeloric (with a decreased degree of zygomorphy) mutant cultivar of H. radiata , ‘Hishou’, has changes in the identities of the dorsal sepal to a petaloid organ and the two ventral sepals to lip‐like organs. Here, we isolated four DEFICIENS ‐ like and two AGL 6 ‐like genes from H. radiata , and characterized their expression. Most of these genes revealed similar expression patterns in the wild type and in the ‘Hishou’ cultivar, except Hr DEF ‐C3. The Hr DEF ‐C3 gene was expressed in petals and lip in the wild type but was ectopically expressed in sepal, petals, lip, leaf, root and bulb in ‘Hishou’. Sequence analysis of the Hr DEF ‐C3 loci revealed that the ‘Hishou’ genome harbored two types of Hr DEF ‐C3 genes: one identical to wild‐type Hr DEF ‐C3 and the other carrying a retrotransposon insertion in its promoter. Genetic linkage analysis of the progeny derived from an intraspecific cross between ‘Hishou’ and the wild type demonstrated that the mutant pseudopeloric trait was dominantly inherited and was linked to the Hr DEF ‐C3 gene carrying the retrotransposon. These results indicate that the pseudopeloric phenotype is caused by retrotransposon insertion in the Hr DEF ‐C3 promoter, resulting in the ectopic expression of Hr DEF ‐C3 . As the expression of Hr AGL 6‐C2 was limited to lateral sepals and lip, the overlapping expression of Hr DEF ‐C3 and Hr AGL 6‐C2 is likely to be responsible for the sepal to lip‐like identity in the lateral sepals of the ‘Hishou’ cultivar.     

Evolution of the Dynein Heavy Chain Family in Ciliates

Dynein heavy chains are motor proteins that comprise a large gene family found across eukaryotes. We have investigated this gene family in four ciliate species: Ichthyophthirius, Oxytricha, Paramecium, and Tetrahymena. Ciliates appear to encode more dynein heavy chain genes than most eukaryotes. Phylogenetic comparisons demonstrated that the last common ancestor of the ciliates that were examined expressed at least 14 types of dynein heavy chains with most of the expansion coming from the single‐headed inner arm dyneins. Each of the dyneins most likely performed different functions within the cell.     

Evaluating the capacity of plant DNA barcodes to discriminate species of cotton (Gossypium: Malvaceae)

Although two plastid regions have been adopted as the standard markers for plant DNA barcoding, their limited resolution has provoked the consideration of other gene regions, especially in taxonomically diverse genera. The genus Gossypium (cotton) includes eight diploid genome groups (A–G, and K) and five allotetraploid species which are difficult to discriminate morphologically. In this study, we tested the effectiveness of three widely used markers (matK, rbcL, and ITS2) in the discrimination of 20 diploid and five tetraploid species of cotton. Sequences were analysed locus‐wise and in combinations to determine the most effective strategy for species identification. Sequence recovery was high, ranging from 92% to 100% with mean pairwise interspecific distance highest for ITS2 (3.68%) and lowest for rbcL (0.43%). At a 0.5% threshold, the combination of matK+ITS2 produced the greatest number of species clusters. Based on ‘best match’ analysis, the combination of matK+ITS2 was best, while based on ‘all species barcodes’ analysis, ITS2 gave the highest percentage of correct species identifications (98.93%). The combination of sequences for all three markers produced the best resolved tree. The disparity index test based on matK+rbcL+ITS2 was significant (P < 0.05) for a higher number of species pairs than the individual gene sequences. Although all three barcodes separated the species with respect to their genome type, no single combination of barcodes could differentiate all the Gossypium species, and tetraploid species were particularly difficult.     

Effects of cyanobacteria,fish kairomones,and the presence of ostracods on the demography of Simocephalus vetulus (Cladocera)

Simocephalus vetulus is a large (2.0–4.0 mm at maturity) cladoceran often found in the littoral region of lakes and ponds, and capable of moderate growth rates even on poor‐quality cyanobacterial diets. It frequently co‐occurs with fishes and similar sized ostracods such as Heterocypris incongruens, but little is known of its response to fish kairomones or its interactions with potential competitors. We studied the demographic responses of S. vetulus fed the green alga Scenedesmus acutus, Microcystis cf. aeruginosa strain A, Microcystis cf. aeruginosa strain B, or Limnothrix sp. Experiments were conducted separately and together in the presence of Heterocypris incongruens and cichlid fish (Oreochromis) kairomones. A diet of Limnothrix sp. resulted in the lowest population growth rate (0.21±0.023 d^?1), while on diets of S. acutus or Microcystis, population growth was higher (0.30±0.009 d^?1). The presence of ostracods resulted in significantly higher growth rates of S. vetulus fed Limnothrix (0.33±0.01 d^?1), but not Microcystis or S. acutus. Regardless of the diet, the presence of fish kairomones resulted in significantly higher growth rates as compared with controls, particularly when ostracods were also present. Coexistence with ostracods may be beneficial to S. vetulus, particularly when food quality is poor.     

Train crash crinoids revisited

‘Train crash crinoids’ represent an unusual mode of preservation of crinoid columns, superficially resembling to the carriages of a crashed train. They were exhumed from the White Peak (Mississippian limestones) of the Peak District in the Treak Cliff area of Castleton, Derbyshire, north‐central England, and were presented by Broadhurst & Simpson as part of a varied suite of observations supporting the recognition of an ancient apron reef (= fore‐reef slope). A re‐examination of these specimens shows that they were not live crinoids at or near the reef crest, but were recently dead specimens, recumbent on the sediment surface. Something triggered their movement into deeper water, and some travelled downslope parallel to the direction of movement and broke into a ‘train crash pattern’ when the lower end impacted on an immovable object.     

The 12th International Workshops on Opportunistic Protists (IWOP‐12)

The 12th International Workshops on Opportunistic Protists (IWOP‐12) was held in August 2012 in Tarrytown, New York. The objectives of the IWOP meetings are to: (1) serve as a forum for exchange of new information among active researchers concerning the basic biology, molecular genetics, immunology, biochemistry, pathogenesis, drug development, therapy, and epidemiology of these immunodeficiency‐associated pathogenic eukaryotic microorganisms that are seen in patients with AIDS and (2) foster the entry of new and young investigators into these underserved research areas. The IWOP meeting focuses on opportunistic protists, e.g. the free‐living amoebae, Pneumocystis, Cryptosporidium, Toxoplasma, the Microsporidia, and kinetoplastid flagellates. This conference represents the major conference that brings together research groups working on these opportunistic pathogens. Slow but steady progress is being achieved on understanding the biology of these pathogenic organisms, their involvement in disease causation in both immune‐deficient and immune‐competent hosts, and is providing critical insights into these emerging and reemerging pathogens. This IWOP meeting demonstrated the importance of newly developed genomic level information for many of these pathogens and how analysis of such large data sets is providing key insights into the basic biology of these organisms. A great concern is the loss of scientific expertise and diversity in the research community due to the ongoing decline in research funding. This loss of researchers is due to the small size of many of these research communities and a lack of appreciation by the larger scientific community concerning the state of art and challenges faced by researchers working on these organisms.     

Efficient distinction of invasive aquatic plant species from non‐invasive related species using DNA barcoding

Biological invasions are regarded as threats to global biodiversity. Among invasive aliens, a number of plant species belonging to the genera Myriophyllum, Ludwigia and Cabomba, and to the Hydrocharitaceae family pose a particular ecological threat to water bodies. Therefore, one would try to prevent them from entering a country. However, many related species are commercially traded, and distinguishing invasive from non‐invasive species based on morphology alone is often difficult for plants in a vegetative stage. In this regard, DNA barcoding could become a good alternative. In this study, 242 samples belonging to 26 species from 10 genera of aquatic plants were assessed using the chloroplast loci trnH‐psbA, matK and rbcL. Despite testing a large number of primer sets and several PCR protocols, the matK locus could not be amplified or sequenced reliably and therefore was left out of the analysis. Using the other two loci, eight invasive species could be distinguished from their respective related species, a ninth one failed to produce sequences of sufficient quality. Based on the criteria of universal application, high sequence divergence and level of species discrimination, the trnH‐psbA noncoding spacer was the best performing barcode in the aquatic plant species studied. Thus, DNA barcoding may be helpful with enforcing a ban on trade of such invasive species, such as is already in place in the Netherlands. This will become even more so once DNA barcoding would be turned into machinery routinely operable by a nonspecialist in botany and molecular genetics.     

Host‐associated genomic differentiation in congeneric butterflies: now you see it,now you do not

Ecotypic variation among populations may become associated with widespread genomic differentiation, but theory predicts that this should happen only under particular conditions of gene flow, selection and population size. In closely related species, we might expect the strength of host‐associated genomic differentiation (HAD) to be correlated with the degree of phenotypic differentiation in host‐adaptive traits. Using microsatellite and Amplified Fragment Length Polymorphism (AFLP) markers, and controlling for isolation by distance between populations, we sought HAD in two congeneric species of butterflies with different degrees of host plant specialization. Prior work on Euphydryas editha had shown strong interpopulation differentiation in host‐adapted traits, resulting in incipient reproductive isolation among host‐associated ecotypes. We show here that Euphydryas aurinia had much weaker host‐associated phenotypic differentiation. Contrary to our expectations, we detected HAD in Euphydryas aurinia, but not in E. editha. Even within an E. aurinia population that fed on both hosts, we found weak but significant sympatric HAD that persisted in samples taken 9 years apart. The finding of significantly stronger HAD in the system with less phenotypic differentiation may seem paradoxical. Our findings can be explained by multiple factors, ranging from differences in dispersal or effective population size, to spatial variation in genomic or phenotypic traits and to structure induced by past histories of host‐adapted populations. Other infrequently measured factors, such as differences in recombination rates, may also play a role. Our result adds to recent work as a further caution against assumptions of simple relationships between genomic and adaptive phenotypic differentiation.     

Increases in crop pests caused by Wasmannia auropunctata in Solomon Islands subsistence gardens

The impacts of Wasmannia auropunctata (the little fire ant) on the native biota and subsistence agriculture in the Solomon Islands are poorly understood. This species was originally introduced as a biological control against nut‐fall bugs (Amblypelta sp.) around 30 years ago and in the intervening time has spread throughout the Solomon Islands, aided movement of produce and planting material. It is now itself a major pest of coconut, cocoa and subsistence agriculture. In this study, we show the negative effects of this invasive ant on subsistence agriculture in the Solomon Islands. We do this by (i) assessing the presence of insect pests that develop a mutual relationship with W. auropunctata on four common subsistence crops; and (ii) measuring the impact of a significant pest (Tarophagus sp.) and its natural predator the bug Cyrtohinus fulvus, in the presence and absence of W. auropunctata on taro crops. The existence of insect pests that form a mutual relationship with W. auropunctata was measured in a total of 36 gardens of the four subsistence crops. This was conducted through standardized visual searches, plus identification and collecting from randomly selected plants within the gardens. A number of additional insect pests causing major problems to subsistence crops have also developed mutual relationships with W. auropunctata. Infested taro gardens have more Tarophagus sp. compared with taro plants that are free of the little fire ant. The presence and abundance of Wasmannia therefore has the potential to inflict considerable crop loss in rural subsistence gardens in the Solomon Islands.     

Molecular diversity and landscape genomics of the crop wild relative Triticum urartu across the Fertile Crescent

Modern plant breeding can benefit from the allelic variation that exists in natural populations of crop wild relatives that evolved under natural selection in varying pedoclimatic conditions. In this study, next‐generation sequencing was used to generate 1.3 million genome‐wide single nucleotide polymorphisms (SNPs) on ex situ collections of Triticum urartu L., the wild donor of the A^u subgenome of modern wheat. A set of 75 511 high‐quality SNPs were retained to describe 298 T. urartu accessions collected throughout the Fertile Crescent. Triticum urartu showed a complex pattern of genetic diversity, with two main genetic groups distributed sequentially from west to east. The incorporation of geographical information on sampling points showed that genetic diversity was correlated to the geographical distance (R² = 0.19) separating samples from Jordan and Lebanon, from Syria and southern Turkey, and from eastern Turkey, Iran and Iraq. The wild emmer genome was used to derive the physical positions of SNPs on the seven chromosomes of the A^u subgenome, allowing us to describe a relatively slow decay of linkage disequilibrium in the collection. Outlier loci were described on the basis of the geographic distribution of the T. urartu accessions, identifying a hotspot of directional selection on chromosome 4A. Bioclimatic variation was derived from grid data and related to allelic variation using a genome‐wide association approach, identifying several marker–environment associations (MEAs). Fifty‐seven MEAs were associated with altitude and temperature measures while 358 were associated with rainfall measures. The most significant MEAs and outlier loci were used to identify genomic loci with adaptive potential (some already reported in wheat), including dormancy and frost resistance loci. We advocate the application of genomics and landscape genomics on ex situ collections of crop wild relatives to efficiently identify promising alleles and genetic materials for incorporation into modern crop breeding.