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Balao F, Trucchi E, Wolfe T, Hao B, Lorenzo M, Baar J et al. (2017)
Adaptive sequence evolution is driven by biotic stress in a pair of orchid species ( Dactylorhiza ) with distinct ecological optima
The orchid family is the largest in the angiosperms, but little is known about the molecular basis of the significant variation they exhibit. We investigate here the transcriptomic divergence between two European terrestrial orchids, Dactylorhiza incarnata and D. fuchsii, and integrate these results in the context of their distinct ecologies that we also document. Clear signals of lineage-specific adaptive evolution of protein-coding sequences are identified, notably targeting elements of biotic defence, including both physical and chemical adaptations in the context of divergent pools of pathogens and herbivores. In turn, a substantial regulatory divergence between the two species appears linked to adaptation/acclimation to abiotic conditions. Several of the pathways affected by differential expression are also targeted by deviating post-transcriptional regulation via sRNAs. Finally, Dactylorhiza incarnata appears to suffer from insufficient sRNA control over the activity of RNA-dependent DNA polymerase, resulting in increased activity of class I transposable elements and, over time, in larger genome size than that of D. fuchsii. The extensive molecular divergence between the two species suggests significant genomic and transcriptomic shock in their hybrids and offers insights into the difficulty of coexistence at the homoploid level. Altogether, biological response to selection, accumulated during the history of these orchids, appears governed by their microenvironmental context, in which biotic and abiotic pressures act synergistically to shape transcriptome structure, expression and regulation.
Keywords: Abiotic stress, Defence, Ecological divergence, Positive selection, Small RNAs, Transcriptomics
Bellot S, Cusimano N, Luo S, Sun G, Zarre S, Gröger A et al. (2016)
Assembled Plastid and Mitochondrial Genomes, as well as Nuclear Genes, Place the Parasite Family Cynomoriaceae in the Saxifragales
Genome Biology and Evolution 8(7) 2214-2230.
Cynomoriaceae, one of the last unplaced families of flowering plants, comprises one or two species or subspecies of root parasites that occur from the Mediterranean to the Gobi Desert. Using Illumina sequencing, we assembled the mitochondrial and plastid genomes as well as some nuclear genes of a Cynomorium specimen from Italy. Selected genes were also obtained by Sanger sequencing from individuals collected in China and Iran, resulting in matrices of 33 mitochondrial, 6 nuclear, and 14 plastid genes and rDNAs enlarged to include a representative angiosperm taxon sampling based on data available in GenBank. We also compiled a new geographic map to discern possible discontinuities in the parasites’ occurrence. Cynomorium has large genomes of 13.70-13.61 (Italy) to 13.95-13.76 pg (China). Its mitochondrial genome consists of up to 49 circular subgenomes and has an overall gene content similar to that of photosynthetic angiosperms, while its plastome retains only 27 of the normally 116 genes. Nuclear plastid and mitochondrial phylogenies place Cynomoriaceae in Saxifragales, and we found evidence for several horizontal gene transfers from different hosts, as well as intracellular gene transfers.
Keywords: Chondriome, Cynomorium, Mediterranean-Irano-Turanian, horizontal gene transfer, parasitic plants, plastome
Chandler M, See L, Copas K, Bonde A, López B, Danielsen F et al. (2016)
To meet collective obligations towards biodiversity conservation and monitoring, it is essential that the world's governments and non-governmental organisations as well as the research community tap all possible sources of data and information, including new, fast-growing sources such as citizen science (CS), in which volunteers participate in some or all aspects of environmental assessments. Through compilation of a database on CS and community-based monitoring (CBM, a subset of CS) programs, we assess where contributions from CS and CBM are significant and where opportunities for growth exist. We use the Essential Biodiversity Variable framework to describe the range of biodiversity data needed to track progress towards global biodiversity targets, and we assess strengths and gaps in geographical and taxonomic coverage. Our results show that existing CS and CBM data particularly provide large-scale data on species distribution and population abundance, species traits such as phenology, and ecosystem function variables such as primary and secondary productivity. Only birds, Lepidoptera and plants are monitored at scale. Most CS schemes are found in Europe, North America, South Africa, India, and Australia. We then explore what can be learned from successful CS/CBM programs that would facilitate the scaling up of current efforts, how existing strengths in data coverage can be better exploited, and the strategies that could maximise the synergies between CS/CBM and other approaches for monitoring biodiversity, in particular from remote sensing. More and better targeted funding will be needed, if CS/CBM programs are to contribute further to international biodiversity monitoring.
Keywords: Citizen science, Community-based monitoring, Databases, Essential biodiversity variables (EBV), Global Biodiversity Information Facility (GBIF), Group on Earth Observations Biodiversity Observati
Dullinger I, Wessely J, Bossdorf O, Dawson W, Essl F, Gattringer A et al. (2016)
Global Ecology and Biogeography.
Aim Plant invasions often follow initial introduction with a considerable delay. The current non-native flora of a region may hence contain species that are not yet naturalized but may become so in the future, especially if climate change lifts limitations on species spread. In Europe, non-native garden plants represent a huge pool of potential future invaders. Here, we evaluate the naturalization risk from this species pool and how it may change under a warmer climate. Location Europe. Methods We selected all species naturalized anywhere in the world but not yet in Europe from the set of non-native European garden plants. For this subset of 783 species, we used species distribution models to assess their potential European ranges under different scenarios of climate change. Moreover, we defined geographical hotspots of naturalization risk from those species by combining projections of climatic suitability with maps of the area available for ornamental plant cultivation. Results Under current climate, 165 species would already find suitable conditions in > 5% of Europe. Although climate change substantially increases the potential range of many species, there are also some that are predicted to lose climatically suitable area under a changing climate, particularly species native to boreal and Mediterranean biomes. Overall, hotspots of naturalization risk defined by climatic suitability alone, or by a combination of climatic suitability and appropriate land cover, are projected to increase by up to 102% or 64%, respectively. Main conclusions Our results suggest that the risk of naturalization of European garden plants will increase with warming climate, and thus it is very likely that the risk of negative impacts from invasion by these plants will also grow. It is therefore crucial to increase awareness of the possibility of biological invasions among horticulturalists, particularly in the face of a warming climate.
Keywords: Alien species, horticulture, hotspot analysis, invasion debt, ornamental plants, species distribution model
Hantemirova E, Heinze B, Knyazeva S, Musaev A, Lascoux M, Semerikov V (2016)
A new Eurasian phylogeographical paradigm? Limited contribution of southern populations to the recolonization of high latitude populations in Juniperus communis L. (Cupressaceae)
Journal of Biogeography.
Aim The aims of this population genetics study of the common juniper across Eurasia were to (1) assess the contribution of southern mountain ranges to the post-glacial recolonization of high latitudes and (2) test whether recent expansion or high gene flow could explain the low genetic differentiation in Northern Eurasia. Location Northern Eurasia and mountain regions of Central Europe and Asia. Methods Six hundred and twenty-two individuals were sampled in 42 populations. Two chloroplast DNA (cpDNA) fragments were investigated (trnT-trnL and 16S-trnA). Analyses of the distribution of haplotypes across the continent included a suite of phylogeographical and phylogenetic tests. Putative geographical distribution in the past was reconstructed using environmental niche modelling. Results Eighty-four haplotypes clustered into four main clades (GL1-GL4). The largest clade, GL3, corresponds to populations from the Alps, northern Europe, Western Caucasus and Siberia. These populations were moderately differentiated (28%) compared to the total range (76%) and Fu's Fs statistic was negative, indicating a population expansion. Some haplotypes within GL3 form subclades with a restricted geographical distribution, suggesting a local origin of the mutation and limited dispersal. In line with these findings, modelling of ecological niches found no significant reduction in the expected range during the LGM. Remarkably, populations from the eastern part of North Caucasus, the Himalayas, Tien Shan and south Siberia were distinctly different from populations in the rest of the range. Main conclusions As in Siberian larch species, the pattern of genetic diversity at cpDNA across the natural range of J. communis suggests that colonization of northern Europe and Siberia started from a limited area and predated the last glaciation. It is likely that juniper survived the subsequent glacial epoch at high latitudes in cryptic refugia serving as secondary centres of recolonization. Southern mountain refugia contribution to the recolonization of high latitudes was, at best, limited.
Keywords: Cupressaceae, Eurasia, chloroplast DNA, common juniper, glacial cycles, phylogeography
Hutter S, Brugger K, Sancho Vargas V, González R, Aguilar O, León B et al. (2016)
Rabies in Costa Rica: Documentation of the Surveillance Program and the Endemic Situation from 1985 to 2014.
Vector borne and zoonotic diseases (Larchmont, N.Y.).
This is the first comprehensive epidemiological analysis of rabies in Costa Rica. We characterized the occurrence of the disease and demonstrated its endemic nature in this country. In Costa Rica, as in other countries in Latin America, hematophagous vampire bats are the primary wildlife vectors transmitting the rabies virus to cattle herds. Between 1985 and 2014, a total of 78 outbreaks of bovine rabies was reported in Costa Rica, with documented cases of 723 dead cattle. Of cattle outbreaks, 82% occurred between 0 and 500 meters above sea level, and seasonality could be demonstrated on the Pacific side of the country, with significantly more outbreaks occurring during the wet season. A total of 1588 animal samples, or an average of 55 samples per year, was received by the veterinary authority (SENASA) for rabies diagnostic testing at this time. Of all samples tested, 9% (143/1588) were positive. Of these, 85.6% (125/1588) were from cattle; four dogs (0.3% [4/1588]) were diagnosed with rabies in this 30-year period. Simultaneously, an extremely low number (n = 3) of autochthonous rabies cases were reported among human patients, all of which were fatal. However, given the virus' zoonotic characteristics and predominantly fatal outcome among both cattle and humans, it is extremely important for healthcare practitioners and veterinarians to be aware of the importance of adequate wound hygiene and postexpositional rabies prophylaxis when dealing with both wild and domestic animal bites.
Keywords: Bats, Cattle, Rabies, Vector, Zoonosis
Razanajatovo M, Maurel N, Dawson W, Essl F, Kreft H, Pergl J et al. (2016)
Nature Communications 7 13313.
Many plant species have established self-sustaining populations outside their natural range because of human activities. Plants with selfing ability should be more likely to establish outside their historical range because they can reproduce from a single individual when mates or pollinators are not available. Here, we compile a global breeding-system database of 1,752 angiosperm species and use phylogenetic generalized linear models and path analyses to test relationships between selfing ability, life history, native range size and global naturalization status. Selfing ability is associated with annual or biennial life history and a large native range, which both positively correlate with the probability of naturalization. Path analysis suggests that a high selfing ability directly increases the number of regions where a species is naturalized. Our results provide robust evidence across flowering plants at the global scale that high selfing ability fosters alien plant naturalization both directly and indirectly.
Keywords: Bats, Cattle, Rabies, Vector, Zoonosis
Sungani H, Ngatunga B, Koblmüller S, Mäkinen T, Skelton P, Genner M (2016)
Molecular Phylogenetics and Evolution.
It has been proposed that the fish faunas of African rivers assemble through multiple colonisation events, while lake faunas form additionally through intralacustine speciation. While this pattern has been established for many lineages, most notably cichlids, there are opportunities to further investigate the concept using phylogenies of congeneric endemic species within ancient lake catchments. The Lake Malawi catchment contains three river-spawning cyprinids of the genus Opsaridium, two of which are endemic. These species differ in body size, migratory behaviour and habitat use, but it has never previously been tested if these represent a monophyletic radiation, or have instead colonised the lake independently. We placed these species in a broader phylogeny of Opsaridium and the related genus Raiamas, including all known species from the river systems surrounding Lake Malawi. Our results suggest that each of the species has independently colonised the lake catchment, with all three taxa having well-defined sister taxa outside of the lake, and all sharing a common ancestor ∼14.9 million years ago, before the Lake Malawi basin started to form ∼8.6 million years ago. Additionally, the results strongly support previous observations that Opsaridium is not a monophyletic group, but instead contains Raiamas from the Congo drainage. Together these results are supportive of the concept that river fish faunas within African catchments are primarily assembled through a process of accumulation from independent origins, rather than within-catchment speciation and adaptive radiation. In light of these results we also suggest there is scope for a re-evaluation of systematics of both Opsaridium and Raiamas.
Keywords: Chedrina, East Africa, Molecular phylogeny, phylogeography, river fishes
Dellinger A, Essl F, Hojsgaard D, Kirchheimer B, Klatt S, Dawson W et al. (2015)
The New phytologist.
Biological invasions can be associated with shifts of the species' climatic niches but the incidence of such shifts is under debate. The reproductive system might be a key factor controlling such shifts because it influences a species' evolutionary flexibility. However, the link between reproductive systems and niche dynamics in plant invasions has been little studied so far. We compiled global occurrence data sets of 13 congeneric sexual and apomictic species pairs, and used principal components analysis (PCA) and kernel smoothers to compare changes in climatic niche optima, breadths and unfilling/expansion between native and alien ranges. Niche change metrics were compared between sexual and apomictic species. All 26 species showed changes in niche optima and/or breadth and 14 species significantly expanded their climatic niches. However, we found no effect of the reproductive system on niche dynamics. Instead, species with narrower native niches showed higher rates of niche expansion in the alien ranges. Our results suggest that niche shifts are frequent in plant invasions but evolutionary potential may not be of major importance for such shifts. Niche dynamics rather appear to be driven by changes of the realized niche without adaptive change of the fundamental climatic niche.
Keywords: adaptation, asexual reproduction, niche shifts, plant invasion, reproductive system, species distribution modelling
Neubauer T, Harzhauser M, Mandic O, Georgopoulou E, Kroh A (2015)
Palaeogeography, Palaeoclimatology, Palaeoecology.
We investigate the distributions of representatives of the family Melanopsidae (Gastropoda: Caenogastropoda: Cerithioidea) from the late Cretaceous to present-day. The present contribution discusses and partly revises former schemes of melanopsid dispersal during the Cenozoic, all of which were based on outdated stratigraphic and tectonic concepts as well as an incompletely considered fossil record. Conflating a comprehensive and stratigraphically well-constrained fossil record, modern paleogeographical reconstructions and contemporary climate data, our goal is to present a thorough model of melanopsid distribution and its changes over the Cenozoic as well as its paleogeographical and climatic constraints. The family Melanopsidae evolved about 90Ma ago in the late Turonian from brackish cerithioidean ancestors. Cretaceous and Paleogene species occur in marginal marine to brackish environments along the shores of the Tethys and Paratethys seas. The extant clades of Melanopsis likely derive from the evolution of freshwater Melanopsis on the Balkan Peninsula back in the late early Miocene. Up to the Pliocene, freshwater species spread toward southwestern and southeastern Europe and successively replaced brackish-water representatives, paralleling a general decline of latter systems during the late Cenozoic. The southwards expansion of Melanopsis and its simultaneous retreat from northern latitudes resulted in the disjunct distribution pattern observed today. The genus Holandriana first appeared in northern Italy in the late early Miocene. The genera Microcolpia and Esperiana both first occurred in the late Miocene and likely derive from brackish-water Melanopsis species native to peri-Paratethyan lakes. The present-day biogeographic isolation of the three latter genera and Melanopsis roots in the climatic deterioration and the disappearance of major lake systems in southeastern Europe. While thermophilous Melanopsis retreated to the warm, dry climates of the Mediterranean and Middle East, Holandriana, Microcolpia and Esperiana adapted to the seasonal, cold-temperate climate of southeastern and eastern Europe and some species became restricted to thermal springs.
Keywords: Biodiversity, Biogeography, Brackish-water, Climate, Freshwater, Gastropoda