To Fork or Not to Fork: Fork Motivations in SourceForge Projects

A project fork occurs when software developers take a copy of source code from one software package and use it to begin an independent development work that is maintained separately from its origin. Although forking in open source software does not require the permission of the original authors, the new version, nevertheless, competes for the attention of the same developers that have worked on the original version. The motivations developers have for performing forks are many, but in general they have received little attention. In this paper, we present the results of a study of forks performed in SourceForge (http://sourceforge.net/) and list the developers’ motivations for their actions. The main motivation, seen in close to half of the cases of forking, was content modification; either adding content to the original program or focusing the content to the needs of a specific segment of users. In a quarter of the cases the motivation was technical modification; either porting the program to new hardware or software, or improving the original

The first report of gall induction in the sawfly subfamily Allantinae (Hymenoptera: Tenthredinidae)

Great Burnet, Sanguisorba officinalis L. (Rosaceae), is the previously unknown larval host plant of the sawfly Empria testaceipes (Konow, 1896) (Tenthredinidae: Allantinae).We report here that young, endophagous larvae inhabit galls in the leaves, while later instars are external feeders on leaves. This is the first report of a gall-inducing habit in the subfamily Allantinae. The galls of E. testaceipes on S. officinalis and the larvae are described and illustrated, and the distribution of this rarely recorded sawfly is summarise

Forking: the Invisible Hand of Sustainability in Open Source Software

The ability to create and maintain high-quality software artifacts that preserve their usability over time is one of the most essential characteristics of the software business. In such a setting, open source software offers excellent examples of sustainability. In particular, safeguarding mechanisms against planned obsolescence by any single actor are built into the very definition of open source development. The most powerful of these safeguarding mechanisms is the ability to fork the project as a whole. In this position paper, we argue that the possibility to fork any open source program serves as the invisible hand of sustainability, ensuring that the code can always remain open and that the code that best fulfills the needs of the community will live on

Environmental responses of fruiting fungal communities are phylogenetically structured

Through their ephemeral reproductive structures (fruiting bodies), ectomycorrhizal forest soil fungi provide a resource for a plethora of organisms. Thus, resolving what biotic and abiotic factors determine the occurrence and abundance of fruiting bodies is fundamental for understanding the dynamics of forest trophic networks. While the influence of abiotic factors such as moisture and temperature on fungal fruiting are relatively well established, little is known about how these processes interact with the evolutionary history of fungal species to determine when, where, and in which abundance fungal fruiting bodies will emerge. A specific knowledge gap relates to whether species' responses to their environment are phylogenetically structured. Here, we ask whether related fungal taxa respond similarly to climatic factors and forest habitat characteristics, and whether such correlated responses will affect the assembly of fungal fruiting communities. To resolve these questions, we fitted joint species distribution models combining data on the species composition and abundance of fungal fruiting bodies, environmental variation, and phylogenetic relationships among fungal taxa. Our results show that both site-level forest characteristics (dominant tree species and forest age) and climatic factors related to phenology (effective heat sum) greatly influence the occurrence and abundance of fruiting bodies. More importantly, while different fungal species responded unequally to their shared environment, there was a strong phylogenetic signal in their responses, so that related fungal species tended to fruit under similar environmental conditions. Thus, not only are fruiting bodies short-lived and patchily distributed, but the availability of similar resources will be further aggregated in time and space. These strong constraints on resource availability for fungus-associated taxa highlight the potential of fungus-based networks as a model system for studies on the ecology and evolution of resource-consumer relations in ephemeral systems of high spatiotemporal patchiness

How common is ecological speciation in plant-feeding insects? A 'Higher' Nematinae perspective

<p>Abstract</p> <p>Background</p> <p>Ecological speciation is a process in which a transiently resource-polymorphic species divides into two specialized sister lineages as a result of divergent selection pressures caused by the use of multiple niches or environments. Ecology-based speciation has been studied intensively in plant-feeding insects, in which both sympatric and allopatric shifts onto novel host plants could speed up diversification. However, while numerous examples of species pairs likely to have originated by resource shifts have been found, the overall importance of ecological speciation in relation to other, non-ecological speciation modes remains unknown. Here, we apply phylogenetic information on sawflies belonging to the 'Higher' Nematinae (Hymenoptera: Tenthredinidae) to infer the frequency of niche shifts in relation to speciation events.</p> <p>Results</p> <p>Phylogenetic trees reconstructed on the basis of DNA sequence data show that the diversification of higher nematines has involved frequent shifts in larval feeding habits and in the use of plant taxa. However, the inferred number of resource shifts is considerably lower than the number of past speciation events, indicating that the majority of divergences have occurred by non-ecological allopatric speciation; based on a time-corrected analysis of sister species, we estimate that a maximum of <it>c</it>. 20% of lineage splits have been triggered by a change in resource use. In addition, we find that postspeciational changes in geographic distributions have led to broad sympatry in many species having identical host-plant ranges.</p> <p>Conclusion</p> <p>Our analysis indicates that the importance of niche shifts for the diversification of herbivorous insects is at present implicitly and explicitly overestimated. In the case of the Higher Nematinae, employing a time correction for sister-species comparisons lowered the proportion of apparent ecology-based speciation events from <it>c</it>. 50-60% to around 20%, but such corrections are still lacking in other herbivore groups. The observed convergent but asynchronous shifting among dominant northern plant taxa in many higher-nematine clades, in combination with the broad overlaps in the geographic distributions of numerous nematine species occupying near-identical niches, indicates that host-plant shifts and herbivore community assembly are largely unconstrained by direct or indirect competition among species. More phylogeny-based studies on connections between niche diversification and speciation are needed across many insect taxa, especially in groups that exhibit few host shifts in relation to speciation.</p

Spatial and temporal variation in community composition of herbivorous insects on Neoboutonia macrocalyx in a primary tropical rain forest

Spatial and temporal variation of tropical insect communities has rarely been studied, although such variation influences estimates of global species richness. Therefore, we compared spatial and temporal variation of herbivorous insect communities on Neoboutonia macrocalyx trees among seven sites over 1 y in a primary tropical rain forest in Kibale National Park, Uganda. The distance between the study sites varied from 4.8 to 31.2 km and altitudinal differences ranged from 20 to 242 m. Permutational multivariate analysis of variance (PERMANOVA) revealed significant spatial changes in community composition of the herbivorous insects and study sites differed also in insect abundance (6.9-26.2 individuals m−2 of leaf area). This is likely to be caused by differences in vegetation, altitude and microclimate among the study sites. The similarity of insect species composition was negatively correlated with geographic and altitudinal distances among sites and positively correlated with the similarity of tree community composition. Species richness varied significantly between sampling dates, ranging from 33 to 41 species. Also community compositions changed between sampling dates, which likely follows from marked seasonal changes in climate and the phenology of other host plants used by the generalist insect species also living on Neoboutonia macrocalyx. In general our study supports the idea of high variability of herbivorous insect communities in primary rain forests even at a small spatial scale. This should be considered when estimations of insect biodiversity are mad

Sealed in a lake : Biology and conservation of the endangered Saimaa ringed seal

Wildlife species living in proximity with humans often suffer from various anthropogenic factors. Here, we focus on the endangered Saimaa ringed seal (Pusa hispida saimensis), which lives in close connection with humans in Lake Saimaa, Finland. This unique endemic population has remained landlocked since the last glacial period, and it currently consists of only similar to 400 individuals. In this review, we summarize the current knowledge on the Saimaa ringed seal, identify the main risk factors and discuss the efficacy of conservation actions put in place to ensure its long-term survival. The main threats for this rare subspecies are bycatch mortality, habitat destruction and increasingly mild winters. Climate change, together with small population size and an extremely impoverished gene pool, forms a new severe threat. The main conservation actions and priorities for the Saimaa ringed seal are implementation of fishing closures, land-use planning, protected areas, and reduction of pup mortality. Novel innovations, such as provisioning of artificial nest structures, may become increasingly important in the future. Although the Saimaa ringed seal still faces the risk of extinction, the current positive trend in the number of seals shows that endangered wildlife populations can recover even in regions with considerable human inhabitation, when legislative protection is combined with intensive research, engagement of local inhabitants, and innovative conservation actions. Such multifaceted conservation approaches are needed in a world with a growing human population and a rapidly changing climate.Peer reviewe

Patterns of Microbiome Variation Among Infrapopulations of Permanent Bloodsucking Parasites

While interspecific variation in microbiome composition can often be readily explained by factors such as host species identity, there is still limited knowledge of how microbiomes vary at scales lower than the species level (e.g., between individuals or populations). Here, we evaluated variation in microbiome composition of individual parasites among infrapopulations (i.e., populations of parasites of the same species living on a single host individual). To address this question, we used genome-resolved and shotgun metagenomic data of 17 infrapopulations (balanced design) of the permanent, bloodsucking seal louse Echinophthirius horridus sampled from individual Saimaa ringed seals Pusa hispida saimensis. Both genome-resolved and read-based metagenomic classification approaches consistently show that parasite infrapopulation identity is a significant factor that explains both qualitative and quantitative patterns of microbiome variation at the intraspecific level. This study contributes to the general understanding of the factors driving patterns of intraspecific variation in microbiome composition, especially of bloodsucking parasites, and has implications for understanding how wellknown processes occurring at higher taxonomic levels, such as phylosymbiosis, might arise in these systems

A curated DNA barcode reference library for parasitoids of northern European cyclically outbreaking geometrid moths

Large areas of forests are annually damaged or destroyed by outbreaking insect pests. Understanding the factors that trigger and terminate such population eruptions has become crucially important, as plants, plant-feeding insects, and their natural enemies may respond differentially to the ongoing changes in the global climate. In northernmost Europe, climate-driven range expansions of the geometrid moths Epirrita autumnata and Operophtera brumata have resulted in overlapping and increasingly severe outbreaks. Delayed density-dependent responses of parasitoids are a plausible explanation for the 10-year population cycles of these moth species, but the impact of parasitoids on geometrid outbreak dynamics is unclear due to a lack of knowledge on the host ranges and prevalences of parasitoids attacking the moths in nature. To overcome these problems, we reviewed the literature on parasitism in the focal geometrid species in their outbreak range and then constructed a DNA barcode reference library for all relevant parasitoid species based on reared specimens and sequences obtained from public databases. The combined recorded parasitoid community of E. autumnata and O. brumata consists of 32 hymenopteran species, all of which can be reliably identified based on their barcode sequences. The curated barcode library presented here opens up new opportunities for estimating the abundance and community composition of parasitoids across populations and ecosystems based on mass barcoding and metabarcoding approaches. Such information can be used for elucidating the role of parasitoids in moth population control, possibly also for devising methods for reducing the extent, intensity, and duration of outbreaks.publishedVersio

Imprints of latitude, host taxon, and decay stage on fungus-associated arthropod communities

Interactions among fungi and insects involve hundreds of thousands of species. While insect communities on plants have formed some of the classic model systems in ecology, fungus-based communities and the forces structuring them remain poorly studied by comparison. We characterize the arthropod communities associated with fruiting bodies of eight mycorrhizal basidiomycete fungus species from three different orders along a 1200-km latitudinal gradient in northern Europe. We hypothesized that, matching the pattern seen for most insect taxa on plants, we would observe a general decrease in fungal-associated species with latitude. Against this backdrop, we expected local communities to be structured by host identity and phylogeny, with more closely related fungal species sharing more similar communities of associated organisms. As a more unique dimension added by the ephemeral nature of fungal fruiting bodies, we expected further imprints generated by successional change, with younger fruiting bodies harboring communities different from older ones. Using DNA metabarcoding to identify arthropod communities from fungal fruiting bodies, we found that latitude left a clear imprint on fungus-associated arthropod community composition, with host phylogeny and decay stage of fruiting bodies leaving lesser but still-detectable effects. The main latitudinal imprint was on a high arthropod species turnover, with no detectable pattern in overall species richness. Overall, these findings paint a new picture of the drivers of fungus-associated arthropod communities, suggesting that latitude will not affect how many arthropod species inhabit a fruiting body but, rather, what species will occur in it and at what relative abundances (as measured by sequence read counts). These patterns upset simplistic predictions regarding latitudinal gradients in species richness and in the strength of biotic interactions.Peer reviewe