TY - JOUR A1 - Potente, Giacomo A1 - Léveillé-Bourret, Étienne A1 - Yousefi, Narjes A1 - Choudhury, Rimjhim Roy A1 - Keller, Barbara A1 - Diop, Seydina Issa A1 - Duijsings, Daniël A1 - Pirovano, Walter A1 - Lenhard, Michael A1 - Szövényi, Péter A1 - Conti, Elena T1 - Comparative genomics elucidates the origin of a supergene controlling floral heteromorphism JF - Molecular biology and evolution : MBE N2 - Supergenes are nonrecombining genomic regions ensuring the coinheritance of multiple, coadapted genes. Despite the importance of supergenes in adaptation, little is known on how they originate. A classic example of supergene is the S locus controlling heterostyly, a floral heteromorphism occurring in 28 angiosperm families. In Primula, heterostyly is characterized by the cooccurrence of two complementary, self-incompatible floral morphs and is controlled by five genes clustered in the hemizygous, ca. 300-kb S locus. Here, we present the first chromosome-scale genome assembly of any heterostylous species, that of Primula veris (cowslip). By leveraging the high contiguity of the P. veris assembly and comparative genomic analyses, we demonstrated that the S-locus evolved via multiple, asynchronous gene duplications and independent gene translocations. Furthermore, we discovered a new whole-genome duplication in Ericales that is specific to the Primula lineage. We also propose a mechanism for the origin of S-locus hemizygosity via nonhomologous recombination involving the newly discovered two pairs of CFB genes flanking the S locus. Finally, we detected only weak signatures of degeneration in the S locus, as predicted for hemizygous supergenes. The present study provides a useful resource for future research addressing key questions on the evolution of supergenes in general and the S locus in particular: How do supergenes arise? What is the role of genome architecture in the evolution of complex adaptations? Is the molecular architecture of heterostyly supergenes across angiosperms similar to that of Primula? KW - genome architecture KW - supergene KW - heterostyly KW - evolutionary genomics KW - chromosome-scale genome assembly KW - primula Y1 - 2022 U6 - https://doi.org/10.1093/molbev/msac035 SN - 0737-4038 SN - 1537-1719 VL - 39 IS - 2 PB - Oxford Univ. Press CY - Oxford ER - TY - JOUR A1 - Lucena-Perez, María A1 - Bazzicalupo, Enrico A1 - Paijmans, Johanna A1 - Kleinman-Ruiz, Daniel A1 - Dalén, Love A1 - Hofreiter, Michael A1 - Delibes, Miguel A1 - Clavero, Miguel A1 - Godoy, José A. T1 - Ancient genome provides insights into the history of Eurasian lynx in Iberia and Western Europe JF - Quaternary science reviews : the international multidisciplinary research and review journal N2 - The Eurasian lynx (Lynx lynx) is one of the most widely distributed felids in the world. However, most of its populations started to decline a few millennia ago. Historical declines have been especially severe in Europe, and particularly in Western Europe, from where the species disappeared in the last few centuries. Here, we analyze the genome of an Eurasian lynx inhabiting the Iberian Peninsula 2500 ya, to gain insights into the phylogeographic position and genetic status of this extinct population. Also, we contextualize previous ancient data in the light of new phylogeographic studies of the species. Our results suggest that the Iberian population is part of an extinct European lineage closely related to the current Carpathian-Baltic lineages. Also, this sample holds the lowest diversity reported for the species so far, and similar to that of the highly endangered Iberian lynx. A combination of historical factors, such as a founder effect while colonizing the peninsula, together with intensified human impacts during the Holocene in the Cantabrian strip, could have led to a genetic impoverishment of the population and precipitated its extinction. Mitogenomic lineages distribution in space and time support the long-term coexistence of several lineages of Eurasian lynx in Western Europe with fluctuating ranges. While mitochondrial sequences related to the lineages currently found in Balkans and Caucasus were predominant during the Pleistocene, those more closely related to the lineage currently distributed in Central Europe prevailed during the Holocene. The use of ancient genomics has proven to be a useful tool to understand the biogeographic pattern of the Eurasian lynx in the past. Y1 - 2022 U6 - https://doi.org/10.1016/j.quascirev.2022.107518 SN - 0277-3791 SN - 1873-457X VL - 285 PB - Elsevier CY - Oxford ER - TY - JOUR A1 - Nwosu, Ebuka Canisius A1 - Roeser, Patricia Angelika A1 - Yang, Sizhong A1 - Pinkerneil, Sylvia A1 - Ganzert, Lars A1 - Dittmann, Elke A1 - Brauer, Achim A1 - Wagner, Dirk A1 - Liebner, Susanne T1 - Species-level spatio-temporal dynamics of cyanobacteria in a hard-water temperate lake in the Southern Baltics JF - Frontiers in microbiology N2 - Cyanobacteria are important primary producers in temperate freshwater ecosystems. However, studies on the seasonal and spatial distribution of cyanobacteria in deep lakes based on high-throughput DNA sequencing are still rare. In this study, we combined monthly water sampling and monitoring in 2019, amplicon sequence variants analysis (ASVs; a proxy for different species) and quantitative PCR targeting overall cyanobacteria abundance to describe the seasonal and spatial dynamics of cyanobacteria in the deep hard-water oligo-mesotrophic Lake Tiefer See, NE Germany. We observed significant seasonal variation in the cyanobacterial community composition (p < 0.05) in the epi- and metalimnion layers, but not in the hypolimnion. In winter-when the water column is mixed-picocyanobacteria (Synechococcus and Cyanobium) were dominant. With the onset of stratification in late spring, we observed potential niche specialization and coexistence among the cyanobacteria taxa driven mainly by light and nutrient dynamics. Specifically, ASVs assigned to picocyanobacteria and the genus Planktothrix were the main contributors to the formation of deep chlorophyll maxima along a light gradient. While Synechococcus and different Cyanobium ASVs were abundant in the epilimnion up to the base of the euphotic zone from spring to fall, Planktothrix mainly occurred in the metalimnetic layer below the euphotic zone where also overall cyanobacteria abundance was highest in summer. Our data revealed two potentially psychrotolerant (cold-adapted) Cyanobium species that appear to cope well under conditions of lower hypolimnetic water temperature and light as well as increasing sediment-released phosphate in the deeper waters in summer. The potential cold-adapted Cyanobium species were also dominant throughout the water column in fall and winter. Furthermore, Snowella and Microcystis-related ASVs were abundant in the water column during the onset of fall turnover. Altogether, these findings suggest previously unascertained and considerable spatiotemporal changes in the community of cyanobacteria on the species level especially within the genus Cyanobium in deep hard-water temperate lakes. KW - Cyanobium KW - picocyanobacteria diversity KW - amplicon sequencing KW - lake monitoring KW - ecological succession KW - lake stratification KW - psychrotolerant Y1 - 2021 U6 - https://doi.org/10.3389/fmicb.2021.761259 SN - 1664-302X VL - 12 PB - Frontiers Media CY - Lausanne ER - TY - JOUR A1 - Escalante, Ignacio A1 - Dominguez, Marisol A1 - Gomez-Ruiz, Daisy Alejandra A1 - Machado, Glauco T1 - Benefits and costs of mixed-species aggregations in Harvestmen (Arachnida: Opiliones) JF - Frontiers in ecology and evolution N2 - Many animals form aggregations with individuals of the same species (single-species aggregations, SSA). Less frequently, individuals may also aggregate with individuals of other species (mixed-species aggregations, MSA). Although the benefits and costs of SSA have been intensively studied, the same is not true for MSA. Here, we first review the cases of MSA in harvestmen, an arachnid order in which the records of MSA are more frequent than other arthropod orders. We then propose several benefits and costs of MSA in harvestmen, and contrast them with those of SSA. Second, using field-gathered data we describe gregariousness in seven species of Prionostemma harvestmen from Costa Rica. These species form MSA, but individuals are also found solitarily or in SSA. We tested one possible benefit and one possible cost of gregariousness in Prionostemma harvestmen. Regarding the benefit, we hypothesized that individuals missing legs would be more exposed to predation than eight-legged individuals and thus they should be found preferentially in aggregations, where they would be more protected from predators. Our data, however, do not support this hypothesis. Regarding the cost, we hypothesized that gregariousness increases the chances of parasitism. We found no support for this hypothesis either because both mite prevalence and infestation intensity did not differ between solitary or aggregated individuals. Additionally, the type of aggregation (SSA or MSA) was not associated with the benefit or the cost we explored. This lack of effect may be explained by the fluid membership of the aggregations, as we found high turnover over time in the number of individuals and species composition of the aggregations. In conclusion, we hope our review and empirical data stimulate further studies on MSA, which remains one of the most elusive forms of group living in animals. KW - alarm signals KW - aggregation size KW - autotomy KW - chemical defenses KW - dilution KW - effect KW - ectoparasitism KW - group living KW - roosting site Y1 - 2022 U6 - https://doi.org/10.3389/fevo.2021.766323 SN - 2296-701X VL - 9 PB - Frontiers Media CY - Lausanne ER - TY - JOUR A1 - Lozada-Gobilard, Sissi Donna A1 - Jeltsch, Florian A1 - Zhu, Jinlei T1 - High matrix vegetation decreases mean seed dispersal distance but increases long wind dispersal probability connecting local plant populations in agricultural landscapes JF - Agriculture, ecosystems & environment : an international journal for scientific research on the relationship of agriculture and food production to the biosphere N2 - Seed dispersal plays an important role in population dynamics in agricultural ecosystems, but the effects of surrounding vegetation height on seed dispersal and population connectivity on the landscape scale have rarely been studied. Understanding the effects of surrounding vegetation height on seed dispersal will provide important information for land-use management in agricultural landscapes to prevent the spread of undesired weeds or enhance functional connectivity. We used two model species, Phragmites australis and Typha latifolia, growing in small natural ponds known as kettle holes, in an agricultural landscape to evaluate the effects of surrounding vegetation height on wind dispersal and population connectivity between kettle holes. Seed dispersal distance and the probability of long-distance dispersal (LDD) were simulated with the mechanistic WALD model under three scenarios of "low", "dynamic" and "high" surrounding vegetation height. Connectivity between the origin and target kettle holes was quantified with a connectivity index adapted from Hanski and Thomas (1994). Our results show that mean seed dispersal distance decreases with the height of surrounding matrix vegetation, but the probability of long-distance dispersal (LDD) increases with vegetation height. This indicates an important vegetation-based trade-off between mean dispersal distance and LDD, which has an impact on connectivity. Matrix vegetation height has a negative effect on mean seed dispersal distance but a positive effect on the probability of LDD. This positive effect and its impact on connectivity provide novel insights into landscape level (meta-)population and community dynamics - a change in matrix vegetation height by land-use or climatic changes could strongly affect the spread and connectivity of wind-dispersed plants. The opposite effect of vegetation height on mean seed dispersal distance and the probability of LDD should therefore be considered in management and analyses of future land-use and climate change effects. KW - Seed dispersal by wind KW - Long-distance seed dispersal KW - Matrix vegetation KW - Kettle holes KW - Agricultural landscapes KW - Metapopulation dynamics Y1 - 2021 U6 - https://doi.org/10.1016/j.agee.2021.107678 SN - 0167-8809 SN - 1873-2305 VL - 322 PB - Elsevier CY - Amsterdam ER - TY - JOUR A1 - Krumbholz, Julia A1 - Ishida, Keishi A1 - Baunach, Martin A1 - Teikari, Jonna A1 - Rose, Magdalena M. A1 - Sasso, Severin A1 - Hertweck, Christian A1 - Dittmann, Elke T1 - Deciphering chemical mediators regulating specialized metabolism in a symbiotic cyanobacterium JF - Angewandte Chemie : a journal of the Gesellschaft Deutscher Chemiker. International edition N2 - Genomes of cyanobacteria feature a variety of cryptic biosynthetic pathways for complex natural products, but the peculiarities limiting the discovery and exploitation of the metabolic dark matter are not well understood. Here we describe the discovery of two cell density-dependent chemical mediators, nostoclide and nostovalerolactone, in the symbiotic model strain Nostoc punctiforme, and demonstrate their pronounced impact on the regulation of specialized metabolism. Through transcriptional, bioinformatic and labeling studies we assigned two adjacent biosynthetic gene clusters to the biosynthesis of the two polyketide mediators. Our findings provide insight into the orchestration of specialized metabolite production and give lessons for the genomic mining and high-titer production of cyanobacterial bioactive compounds. KW - Biosynthesis KW - Cyanobacteria KW - Genomic Mining KW - Quorum Sensing KW - Specialized KW - Metabolism Y1 - 2022 U6 - https://doi.org/10.1002/anie.202204545 SN - 1433-7851 SN - 1521-3773 PB - Wiley-VCH CY - Weinheim ER - TY - JOUR A1 - Scheffler, Christiane A1 - Bogin, Barry A1 - Hermanussen, Michael T1 - Catch-up growth is a better indicator of undernutrition than thresholds for stunting JF - Public health nutrition : PHN / The Nutrition Society N2 - Objective: Stunting (height-for-age < −2 SD) is one of the forms of undernutrition and is frequent among children of low- and middle-income countries. But stunting perSe is not a synonym of undernutrition. We investigated association between body height and indicators of energetic undernutrition at three critical thresholds for thinness used in public health: (1) BMI SDS < −2; (2) mid-upper arm circumference divided by height (MUAC (mm) × 10/height (cm) < 1·36) and (3) mean skinfold thickness (SF) < 7 mm and to question the reliability of thresholds as indicators of undernutrition. Design: Cross-sectional study; breakpoint analysis. Setting: Rural and urban regions of Indonesia and Guatemala – different socio-economic status (SES). Participants: 1716 Indonesian children (6·0–13·2 years) and 3838 Guatemalan children (4·0–18·9 years) with up to 50 % stunted children. Results: When separating the regression of BMI, MUAC or SF, on height into distinguishable segments (breakpoint analysis), we failed to detect relevant associations between height, and BMI, MUAC or SF, even in the thinnest and shortest children. For BMI and SF, the breakpoint analysis either failed to reach statistical significance or distinguished at breakpoints above critical thresholds. For MUAC, the breakpoint analysis yielded negative associations between MUAC/h and height in thin individuals. Only in high SES Guatemalan children, SF and height appeared mildly associated with R2 = 0·017. Conclusions: Currently used lower thresholds of height-for-age (stunting) do not show relevant associations with anthropometric indicators of energetic undernutrition. We recommend using the catch-up growth spurt during early re-feeding instead as immediate and sensitive indicator of past undernourishment. We discuss the primacy of education and social-economic-political-emotional circumstances as responsible factors for stunting. KW - no threshold for stunting KW - catch-up growth KW - social-economic-political-emotional KW - (SEPE) factors Y1 - 2020 U6 - https://doi.org/10.1017/S1368980020003067 SN - 1475-2727 SN - 1368-9800 VL - 24 IS - 1 SP - 52 EP - 61 PB - Cambridge University Press CY - Cambridge ; New York, NY ER - TY - JOUR A1 - Horn, Juliane A1 - Becher, Matthias A. A1 - Johst, Karin A1 - Kennedy, Peter J. A1 - Osborne, Juliet L. A1 - Radchuk, Viktoriia A1 - Grimm, Volker T1 - Honey bee colony performance affected by crop diversity and farmland structure BT - a modeling framework JF - Ecological applications N2 - Forage availability has been suggested as one driver of the observed decline in honey bees. However, little is known about the effects of its spatiotemporal variation on colony success. We present a modeling framework for assessing honey bee colony viability in cropping systems. Based on two real farmland structures, we developed a landscape generator to design cropping systems varying in crop species identity, diversity, and relative abundance. The landscape scenarios generated were evaluated using the existing honey bee colony model BEEHAVE, which links foraging to in-hive dynamics. We thereby explored how different cropping systems determine spatiotemporal forage availability and, in turn, honey bee colony viability (e.g., time to extinction, TTE) and resilience (indicated by, e.g., brood mortality). To assess overall colony viability, we developed metrics,P(H)andP(P,)which quantified how much nectar and pollen provided by a cropping system per year was converted into a colony's adult worker population. Both crop species identity and diversity determined the temporal continuity in nectar and pollen supply and thus colony viability. Overall farmland structure and relative crop abundance were less important, but details mattered. For monocultures and for four-crop species systems composed of cereals, oilseed rape, maize, and sunflower,P(H)andP(P)were below the viability threshold. Such cropping systems showed frequent, badly timed, and prolonged forage gaps leading to detrimental cascading effects on life stages and in-hive work force, which critically reduced colony resilience. Four-crop systems composed of rye-grass-dandelion pasture, trefoil-grass pasture, sunflower, and phacelia ensured continuous nectar and pollen supply resulting in TTE > 5 yr, andP(H)(269.5 kg) andP(P)(108 kg) being above viability thresholds for 5 yr. Overall, trefoil-grass pasture, oilseed rape, buckwheat, and phacelia improved the temporal continuity in forage supply and colony's viability. Our results are hypothetical as they are obtained from simplified landscape settings, but they nevertheless match empirical observations, in particular the viability threshold. Our framework can be used to assess the effects of cropping systems on honey bee viability and to develop land-use strategies that help maintain pollination services by avoiding prolonged and badly timed forage gaps. KW - apis mellifera KW - BEEHAVE KW - colony viability KW - crop diversity KW - cropping system KW - decline KW - forage availability KW - forage gaps KW - honey bees KW - landscape generator KW - modeling Y1 - 2020 U6 - https://doi.org/10.1002/eap.2216 SN - 1939-5582 SN - 1051-0761 VL - 31 IS - 1 SP - 1 EP - 22 PB - Wiley Periodicals LLC CY - Washington DC ER - TY - JOUR A1 - Li, Chenzhi A1 - Postl, Alexander K. A1 - Böhmer, Thomas A1 - Cao, Xianyong A1 - Dolman, Andrew M. A1 - Herzschuh, Ulrike T1 - Harmonized chronologies of a global late Quaternary pollen dataset (LegacyAge 1.0) JF - Earth system science data : ESSD N2 - We present a chronology framework named LegacyAge 1.0 containing harmonized chronologies for 2831 pollen records (downloaded from the Neotoma Paleoecology Database and the supplementary Asian datasets) together with their age control points and metadata in machine-readable data formats. All chronologies use the Bayesian framework implemented in Bacon version 2.5.3. Optimal parameter settings of priors (accumulation.shape, memory.strength, memory.mean, accumulation.rate, and thickness) were identified based on information in the original publication or iteratively after preliminary model inspection. The most common control points for the chronologies are radiocarbon dates (86.1 %), calibrated by the latest calibration curves (IntCal20 and SHCal20 for the terrestrial radiocarbon dates in the Northern Hemisphere and Southern Hemisphere and Marine20 for marine materials). The original publications were consulted when dealing with outliers and inconsistencies. Several major challenges when setting up the chronologies included the waterline issue (18.8% of records), reservoir effect (4.9 %), and sediment deposition discontinuity (4.4 %). Finally, we numerically compare the LegacyAge 1.0 chronologies to those published in the original publications and show that the reliability of the chronologies of 95.4% of records could be improved according to our assessment. Our chronology framework and revised chronologies provide the opportunity to make use of the ages and age uncertainties in synthesis studies of, for example, pollen-based vegetation and climate change. The LegacyAge 1.0 dataset, including metadata, datings, harmonized chronologies, and R code used, is openaccess and available at PANGAEA (https://doi.org/10.1594/PANGAEA.933132; Li et al., 2021) and Zenodo (https://doi.org/10.5281/zenodo.5815192; Li et al., 2022), respectively. Y1 - 2022 U6 - https://doi.org/10.5194/essd-14-1331-2022 SN - 1866-3508 SN - 1866-3516 VL - 14 IS - 3 SP - 1331 EP - 1343 PB - Copernics Publications CY - Katlenburg-Lindau ER - TY - JOUR A1 - Omranian, Sara A1 - Angeleska, Angela A1 - Nikoloski, Zoran T1 - Efficient and accurate identification of protein complexes from protein-protein interaction networks based on the clustering coefficient JF - Computational and structural biotechnology journal N2 - Identification of protein complexes from protein-protein interaction (PPI) networks is a key problem in PPI mining, solved by parameter-dependent approaches that suffer from small recall rates. Here we introduce GCC-v, a family of efficient, parameter-free algorithms to accurately predict protein complexes using the (weighted) clustering coefficient of proteins in PPI networks. Through comparative analyses with gold standards and PPI networks from Escherichia coli, Saccharomyces cerevisiae, and Homo sapiens, we demonstrate that GCC-v outperforms twelve state-of-the-art approaches for identification of protein complexes with respect to twelve performance measures in at least 85.71% of scenarios. We also show that GCC-v results in the exact recovery of similar to 35% of protein complexes in a pan-plant PPI network and discover 144 new protein complexes in Arabidopsis thaliana, with high support from GO semantic similarity. Our results indicate that findings from GCC-v are robust to network perturbations, which has direct implications to assess the impact of the PPI network quality on the predicted protein complexes. (C) 2021 The Author(s). Published by Elsevier B.V. on behalf of Research Network of Computational and Structural Biotechnology. KW - Protein complexes KW - Protein-protein interaction KW - Network clustering KW - Species comparison Y1 - 2021 U6 - https://doi.org/10.1016/j.csbj.2021.09.014 SN - 2001-0370 VL - 19 SP - 5255 EP - 5263 PB - Elsevier CY - Amsterdam ER -