Articles

Recent Submissions

  • Leppanen, Jaakko; Siitonen, Susanna; Weckstrom, Jan (2017)
    It is difficult to plan restoration projects or study the amount of disturbance in aquatic ecosystems if background conditions are not known. Zooplankton, especially cladocerans (water fleas), has proven highly useful as a reliable indicator of environmental change. Cladocerans preserve well in sediments and thus allow for the analysis of historical communities. To assess the stability of cladoceran communities in lakes with low human impact, we compared pre-industrial and modern cladoceran assemblages (top-bottom analysis) in 32 sub-Arctic lakes in NW Finnish Lapland. We used a dataset of measured environmental variables to determine their explanatory power on cladoceran assemblages. While cladoceran assemblages at the community level have remained relatively stable between the pre-industrial and modern samples, a clear change at the genus level was observed with a significant proportional increase in Bosmina (Eubosmina) spp. (Wilcoxon signed-rank test z = 2.75 p = 0.006). The amount of organic matter in the sediment [measured as loss on ignition (LOI)] explained the largest proportion of the variation in the cladoceran community. Since LOI is strongly correlated to climatic factors, the increased abundance of B. (Eubosmina) spp. may ultimately be related to climate warming. As the top-bottom approach is comprised of two temporal snapshots, it cannot provide the exact time of community change. This shortcoming is of special importance for restoration and management planning.
  • Dhaygude, Kishor Uttam; Trontti, Niilo Kalevi; Paviala, Jenni Katariina; Morandin, Claire Marthe; Wheat, Christopher West; Sundström, Liselotte Björnsdotter; Helanterä, Heikki Oskari (2017)
    Transcriptome resources for social insects have the potential to provide new insight into polyphenism, i.e., how divergent phenotypes arise from the same genome. Here we present a transcriptome based on paired-end RNA sequencing data for the ant Formica exsecta (Formicidae, Hymenoptera). The RNA sequencing libraries were constructed from samples of several life stages of both sexes and female castes of queens and workers, in order to maximize representation of expressed genes. We first compare the performance of common assembly and scaffolding software (Trinity, Velvet-Oases, and SOAPdenovo-trans), in producing de novo assemblies. Second, we annotate the resulting expressed contigs to the currently published genomes of ants, and other insects, including the honeybee, to filter genes that have annotation evidence of being true genes. Our pipeline resulted in a final assembly of altogether 39,262 mRNA transcripts, with an average coverage of >300X, belonging to 17,496 unique genes with annotation in the related ant species. From these genes, 536 genes were unique to one caste or sex only, highlighting the importance of comprehensive sampling. Our final assembly also showed expression of several splice variants in 6,975 genes, and we show that accounting for splice variants affects the outcome of downstream analyses such as gene ontologies. Our transcriptome provides an outstanding resource for future genetic studies on F. exsecta and other ant species, and the presented transcriptome assembly can be adapted to any non-model species that has genomic resources available from a related taxon.
  • Veach, Victoria; Moilanen, Atte; Di Minin, Enrico (2017)
    Including threats in spatial conservation prioritization helps identify areas for conservation actions where biodiversity is at imminent risk of extinction. At the global level, an important limitation when identifying spatial priorities for conservation actions is the lack of information on the spatial distribution of threats. Here, we identify spatial conservation priorities under three prominent threats to biodiversity (residential and commercial development, agricultural expansion, and forest loss), which are primary drivers of habitat loss and threaten the persistence of the highest number of species in the International Union for the Conservation of Nature (IUCN) Red List, and for which spatial data is available. We first explore how global priority areas for the conservation of vertebrate (mammals, birds, and amphibians) species coded in the Red List as vulnerable to each threat differ spatially. We then identify spatial conservation priorities for all species vulnerable to all threats. Finally, we identify the potentially most threatened areas by overlapping the identified priority areas for conservation with maps for each threat. We repeat the same with four other well-known global conservation priority area schemes, namely Key Biodiversity Areas, Biodiversity Hotspots, the global Protected Area Network, and Wilderness Areas. We find that residential and commercial development directly threatens only about 4% of the global top 17% priority areas for species vulnerable under this threat. However, 50% of the high priority areas for species vulnerable to forest loss overlap with areas that have already experienced some forest loss. Agricultural expansion overlapped with similar to 20% of high priority areas. Biodiversity Hotspots had the greatest proportion of their total area under direct threat from all threats, while expansion of low intensity agriculture was found to pose an imminent threat to Wilderness Areas under future agricultural expansion. Our results identify areas where limited resources should be allocated to mitigate risks to vertebrate species from habitat loss.
  • Rannikko, Janina; Zliobaite, Indre; Fortelius, Mikael (2017)
    Most suids (Mammalia: Suidae, pigs) worldwide are omnivores living in closed environments, but the African warthog (Phacochoerus) has special adaptations for grazing in open environments. Similar specializations have been recorded from Plio-Pleistocene African suids. Four genera, Nyanzachoerus, Notochoerus, Kolpochoerus, and Metridiochoerus, have been discovered in late Miocene to middle Pleistocene locations around the Turkana Basin. We analyse the relative abundances of these four suid genera compared to other mammals, from approximately 8-0.7 Ma. The dataset includes most of the mammal specimens collected from locations around the Kenyan side of the Turkana Basin. Species of genus Nyanzachoerus were dominant before 4 Ma, but their relative abundance decreases through time thereafter. At the same time, Notochoerus increases in relative abundance, followed by Kolpochoerus, and finally Metridiochoerus. Their peak relative abundances do not overlap: Notochoerus peaks at 3.44-2.53 Ma, Kolpochoerus at 2.53-1.87 Ma, and Metridiochoerus at 1.38-0.7 Ma. We interpret the palaeoecology of these suids based on their relative abundances over time and on published isotope and pollen data. We find that Nyanzachoerus was replaced by its abrasive-diet-specialized successor Notochoerus, possibly in response to a rapid decrease in forest cover. Notochoerus adapted at first to the expanding wood- and grasslands, and then to more arid shrublands. After a period of severe aridity around 2.7-2.5 Ma, more variable environments allowed Kolpochoerus and Metridiochoerus to disperse, while Notochoerus disappeared, perhaps having lost its competitive edge. Further changes in the environment encouraged the expansion of grasslands over shrublands, favouring Metridiochoerus. Kolpochoerus persisted in the more closed environments near water sources.
  • Vaahtera, Touko (2016)
    This article introduces the concept of able-bodied belonging,' and pays particular attention to the cultural mechanisms in which ableism intertwines with the forms of belonging. Taking a cultural studies viewpoint, the article focuses on present evolutionary biological accounts, and explores the ableist and speciesist assumptions that frame evolutionary biology. The article investigates how these accounts invoke a feeling of belonging to the animal world in ways which reinforce the idea that only a particular kind of body is species-typical of humans. First, the article explores how the cultural stories that emphasize the connection between human beings and non-human species eventually distance particular bodies from humanity. Second, the article shows how humans' connection to the animal world could emerge in a way that contests the exceptionality of able-bodied humanity.
  • Zhang, Kangle (Torkel Opsahl Academic Epublisher, 2016)
    The FICHL Policy Brief Series
  • Zhang, Kangle (2017)
    The ecological vulnerability of the regions within the Silk Road Economic Belt requires environmental protection. The infrastructure-pillared structure of the Belt and the legal procedures for the environmental impact assessment (EIA) of various infrastructures inform this article’s approach to environmental protection along the Belt through the right to information about, and involvement in, environmental decision making (the right to in- formation and involvement). How to protect this right along the Belt? The rights approach to the environment, as this article first examines, leads to an exploration of the social and historical background of the adoption of the Convention on Access to Information, Public Participation in Decision-making and Access to Justice in Environmental Matters (Aarhus Convention).1 Parties to the Aarhus Convention largely overlap with the countries within the Belt. Critical analysis of the EIA legislation and its practice, and the contradiction within the principle of ‘public participation’ reveal the inadequacy of formal legislation in protecting the right to information and involvement. A case study on informal participa- tion in environmental decision making in China illustrates the value of informal participa- tion in protecting this right. Informal participation is forming a communicative form of environmental governance in Singapore, in which the right to information and involvement is protected. This article argues that informal participation can facilitate the protection of the right to information and involvement along the Belt.
  • Al-Chalabi, Ammar; Andersen, Peter M.; Chandran, Siddharthan; Chio, Adriano; Corcia, Philippe; Couratier, Philippe; Danielsson, Olof; de Carvalho, Mamede; Desnuelle, Claude; Grehl, Torsten; Grosskreutz, Julian; Holmoy, Trygve; Ingre, Caroline; Karlsborg, Merete; Kleveland, Grethe; Christoph Koch, Jan; Koritnik, Blaz; KuzmaKozakiewicz, Magdalena; Laaksovirta, Hannu; Ludolph, Albert; McDermott, Christopher; Meyer, Thomas; Ropero, Bernardo Mitre; Pardina, Jesus Mora; Nygren, Ingela; Petri, Susanne; Povedano Panades, Monica; Salachas, Francois; Shaw, Pamela; Silani, Vincenzo; Staaf, Gert; Svenstrup, Kirsten; Talbot, Kevin; Tysnes, Ole-Bjorn; Van Damme, Philip; van der Kooi, Anneke; Weber, Markus; Weydt, Patrick; Wolf, Joachim; Hardiman, Orla; van den Berg, Leonard H. (2017)
  • Schmierer, Bernhard; Botla, Sandeep K.; Zhang, Jilin; Turunen, Mikko; Kivioja, Teemu; Taipale, Jussi (2017)
    Loss-of-function screening by CRISPR/Cas9 gene knockout with pooled, lentiviral guide libraries is a widely applicable method for systematic identification of genes contributing to diverse cellular phenotypes. Here, Random Sequence Labels (RSLs) are incorporated into the guide library, which act as unique molecular identifiers (UMIs) to allow massively parallel lineage tracing and lineage dropout screening. RSLs greatly improve the reproducibility of results by increasing both the precision and the accuracy of screens. They reduce the number of cells needed to reach a set statistical power, or allow a more robust screen using the same number of cells.
  • Pihlström, Sami Johannes; Kivistö, Sari Anneli (2017)
  • Eskelinen, Teppo; Ylonen, Matti (2017)
    Tax havens and tax flight have lately received increasing attention, while interest toward multilateral trade policies has somewhat diminished. We argue that more attention needs to be paid exactly to the interrelations between trade and tax policies. Drawing from two case studies on Panama's trade disputes, we show how World Trade Organization (WTO) rules can be used both to resist attempts to sanction secrecy structures and to promote measures against tax flight. The theory of new constitutionalism can help to explain how trade treaties can 'lock in' tax policies. However, our case studies show that trade policy not only 'locks in' democratic policy-making, but also enables tax havens to use their commercialized sovereignty to resists anti-secrecy measures. What is being 'locked in' are the policy tools, not necessarily the policies. The changing relationship between trade and tax policies can also create new and unexpected tools for tackling tax evasion, underlining the importance of epistemic arbitrage in the context of new constitutionalism. In principle, political actors with sufficient technical and juridical knowledge can shape global tax governance to various directions regardless of their formal position in the world political hierarchies. This should be taken into account when trade treaties are being negotiated or revised.
  • Dudel, Christian; Myrskylae, Mikko (2017)
    A key concern about population aging is the decline in the size of the economically active population. Working longer is a potential remedy. However, little is known about the length of working life and how it relates to macroeconomic conditions. We use the U.S. Health and Retirement Study for 1992-2011 and multistate life tables to analyze working life expectancy at age 50 and study the impact of the Great Recession in 2007-2009. Despite declines of one to two years following the recession, in 2008-2011, American men aged 50 still spent 13 years, or two-fifths of their remaining life, working; American women of the same age spent 11 years, or one-third of their remaining life, in employment. Although educational differences in working life expectancy have been stable since the mid-1990s, racial differences started changing after the onset of the Great Recession. Our results show that although Americans generally work longer than people in other countries, considerable subpopulation heterogeneity exists. We also find that the time trends are fluctuating, which may prove troublesome as the population ages. Policies targeting the weakest performing groups may be needed to increase the total population trends.
  • Pulkka, Olli-Pekka; Nilsson, Bengt; Sarlomo-Rikala, Maarit; Reichardt, Peter; Eriksson, Mikael; Hall, Kirsten Sundby; Wardelmann, Eva; Vehtari, Aki; Joensuu, Heikki; Sihto, Harri (2017)
    Background: The SLUG transcription factor has been linked with the KIT signalling pathway that is important for gastrointestinal stromal tumour (GIST) tumourigenesis. Its clinical significance in GIST is unknown. Methods: Influence of SLUG expression on cell proliferation and viability were investigated in GIST48 and GIST882 cell lines. The association between tumour SLUG expression in immunohistochemistry and recurrence-free survival (RFS) was studied in two clinical GIST series, one with 187 patients treated with surgery alone, and another one with 313 patients treated with surgery and adjuvant imatinib. Results: SLUG downregulation inhibited cell proliferation, induced cell death in both cell lines, and sensitised GIST882 cells to lower imatinib concentrations. SLUG was expressed in 125 (25.0%) of the 500 clinical GISTs evaluated, and expression was associated with several factors linked with unfavourable prognosis. SLUG expression was associated with unfavourable RFS both when patients were treated with surgery alone (HR = 3.40, 95% CI = 1.67-6.89, P = 0.001) and when treated with surgery plus adjuvant imatinib (HR = 1.83, 95% CI = 1.29-2.60, P = 0.001). Conclusions: GIST patients with high tumour SLUG expression have unfavourable RFS. SLUG may mediate pro-survival signalling in GISTs.