| 268. | Hajdu, László; Bóta, András; Krész, Miklós; Khani, Alireza; Gardner, Lauren M Discovering the Hidden Community Structure of Public Transportation Networks Journal Article Networks and Spatial Economics, 2019, ISSN: 1572-9427. Abstract | Links | BibTeX @article{Hajdu2019,
title = {Discovering the Hidden Community Structure of Public Transportation Networks},
author = {László Hajdu and András Bóta and Miklós Krész and Alireza Khani and Lauren M Gardner},
url = {https://doi.org/10.1007/s11067-019-09476-3},
doi = {10.1007/s11067-019-09476-3},
issn = {1572-9427},
year = {2019},
date = {2019-08-20},
journal = {Networks and Spatial Economics},
abstract = {Advances in public transit modeling and smart card technologies can reveal detailed contact patterns of passengers. A natural way to represent such contact patterns is in the form of networks. In this paper we utilize known contact patterns from a public transit assignment model in a major metropolitan city, and propose the development of two novel network structures, each of which elucidate certain aspects of passenger travel behavior. We first propose the development of a transfer network, which can reveal passenger groups that travel together on a given day. Second, we propose the development of a community network, which is derived from the transfer network, and captures the similarity of travel patterns among passengers. We then explore the application of each of these network structures to identify the most frequently used travel paths, i.e., routes and transfers, in the public transit system, and model epidemic spreading risk among passengers of a public transit network, respectively. In the latter our conclusions reinforce previous observations, that routes crossing or connecting to the city center in the morning and afternoon peak hours are the most ``dangerous'' during an outbreak.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Advances in public transit modeling and smart card technologies can reveal detailed contact patterns of passengers. A natural way to represent such contact patterns is in the form of networks. In this paper we utilize known contact patterns from a public transit assignment model in a major metropolitan city, and propose the development of two novel network structures, each of which elucidate certain aspects of passenger travel behavior. We first propose the development of a transfer network, which can reveal passenger groups that travel together on a given day. Second, we propose the development of a community network, which is derived from the transfer network, and captures the similarity of travel patterns among passengers. We then explore the application of each of these network structures to identify the most frequently used travel paths, i.e., routes and transfers, in the public transit system, and model epidemic spreading risk among passengers of a public transit network, respectively. In the latter our conclusions reinforce previous observations, that routes crossing or connecting to the city center in the morning and afternoon peak hours are the most ``dangerous'' during an outbreak. |
| 267. | Wickman, Jonas; Diehl, Sebastian; Brännström, Åke Evolution of resource specialisation in competitive metacommunities Journal Article Ecology Letters, 0 (0), 2019. Abstract | Links | BibTeX @article{doi:10.1111/ele.13338,
title = {Evolution of resource specialisation in competitive metacommunities},
author = {Jonas Wickman and Sebastian Diehl and Åke Brännström},
url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/ele.13338},
doi = {10.1111/ele.13338},
year = {2019},
date = {2019-08-07},
journal = {Ecology Letters},
volume = {0},
number = {0},
abstract = {Abstract Spatial environmental heterogeneity coupled with dispersal can promote ecological persistence of diverse metacommunities. Does this premise hold when metacommunities evolve? Using a two-resource competition model, we studied the evolution of resource-uptake specialisation as a function of resource type (substitutable to essential) and shape of the trade-off between resource uptake affinities (generalist- to specialist-favouring). In spatially homogeneous environments, evolutionarily stable coexistence of consumers is only possible for sufficiently substitutable resources and specialist-favouring trade-offs. Remarkably, these same conditions yield comparatively low diversity in heterogeneous environments, because they promote sympatric evolution of two opposite resource specialists that, together, monopolise the two resources everywhere. Consumer diversity is instead maximised for intermediate trade-offs and clearly substitutable or clearly essential resources, where evolved metacommunities are characterised by contrasting selection regimes. Taken together, our results present new insights into resource-competition-mediated evolutionarily stable diversity in homogeneous and heterogeneous environments, which should be applicable to a wide range of systems.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Abstract Spatial environmental heterogeneity coupled with dispersal can promote ecological persistence of diverse metacommunities. Does this premise hold when metacommunities evolve? Using a two-resource competition model, we studied the evolution of resource-uptake specialisation as a function of resource type (substitutable to essential) and shape of the trade-off between resource uptake affinities (generalist- to specialist-favouring). In spatially homogeneous environments, evolutionarily stable coexistence of consumers is only possible for sufficiently substitutable resources and specialist-favouring trade-offs. Remarkably, these same conditions yield comparatively low diversity in heterogeneous environments, because they promote sympatric evolution of two opposite resource specialists that, together, monopolise the two resources everywhere. Consumer diversity is instead maximised for intermediate trade-offs and clearly substitutable or clearly essential resources, where evolved metacommunities are characterised by contrasting selection regimes. Taken together, our results present new insights into resource-competition-mediated evolutionarily stable diversity in homogeneous and heterogeneous environments, which should be applicable to a wide range of systems. |
| 266. | Sang Hoon Lee Yeonghoon Kim, Sungmin Lee Xavier Durang Per Stenberg Jae-Hyung Jeon Ludvig Lizana Mapping the spectrum of 3D communities in human chromosome conformation capture data Journal Article Scientific Reports, 9 , 2019. Abstract | Links | BibTeX @article{Lee2018,
title = {Mapping the spectrum of 3D communities in human chromosome conformation capture data},
author = {Sang Hoon Lee, Yeonghoon Kim, Sungmin Lee, Xavier Durang, Per Stenberg, Jae-Hyung Jeon, Ludvig Lizana},
doi = {https://doi.org/10.1038/s41598-019-42212-y},
year = {2019},
date = {2019-05-02},
journal = {Scientific Reports},
volume = {9},
abstract = {Several experiments show that the three dimensional (3D) organization of chromosomes affects genetic processes such as transcription and gene regulation. To better understand this connection, researchers developed the Hi-C method that is able to detect the pairwise physical contacts of all chromosomal loci. The Hi-C data shows that chromosomes are composed of 3D compartments that range over a variety of scales. However, it is challenging to systematically detect these cross-scale structures. Most studies have therefore designed methods for specific scales to study foremost topologically associated domains (TADs) and A/B compartments. To go beyond this limitation, we tailor a network community detection method that finds communities in compact fractal globule polymer systems. Our method allows us to continuously scan through all scales with a single resolution parameter. We found: (i) polymer segments belonging to the same 3D community do not have to be in consecutive order along the polymer chain. In other words, several TADs may belong to the same 3D community. (ii) CTCF proteins---a loop-stabilizing protein that is ascribed a big role in TAD formation---are correlated well with community borders only at one level of organization. (iii) TADs and A/B compartments are traditionally treated as two weakly related 3D structures and detected with different algorithms. With our method, we detect both by simply adjusting the resolution parameter. We therefore argue that they represent two specific levels of a continuous spectrum 3D communities, rather than seeing them as different structural entities.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Several experiments show that the three dimensional (3D) organization of chromosomes affects genetic processes such as transcription and gene regulation. To better understand this connection, researchers developed the Hi-C method that is able to detect the pairwise physical contacts of all chromosomal loci. The Hi-C data shows that chromosomes are composed of 3D compartments that range over a variety of scales. However, it is challenging to systematically detect these cross-scale structures. Most studies have therefore designed methods for specific scales to study foremost topologically associated domains (TADs) and A/B compartments. To go beyond this limitation, we tailor a network community detection method that finds communities in compact fractal globule polymer systems. Our method allows us to continuously scan through all scales with a single resolution parameter. We found: (i) polymer segments belonging to the same 3D community do not have to be in consecutive order along the polymer chain. In other words, several TADs may belong to the same 3D community. (ii) CTCF proteins---a loop-stabilizing protein that is ascribed a big role in TAD formation---are correlated well with community borders only at one level of organization. (iii) TADs and A/B compartments are traditionally treated as two weakly related 3D structures and detected with different algorithms. With our method, we detect both by simply adjusting the resolution parameter. We therefore argue that they represent two specific levels of a continuous spectrum 3D communities, rather than seeing them as different structural entities. |
| 265. | Sobhy, Haitham; Kumar, Rajendra; Lewerentz, Jacob; Lizana, Ludvig; Stenberg, Per Highly interacting regions of the human genome are enriched with enhancers and bound by DNA repair proteins Journal Article Scientific Reports, 9 , 2019. Abstract | Links | BibTeX @article{Sobhy2019,
title = {Highly interacting regions of the human genome are enriched with enhancers and bound by DNA repair proteins},
author = {Haitham Sobhy and Rajendra Kumar and Jacob Lewerentz and Ludvig Lizana and Per Stenberg},
url = {https://www.nature.com/articles/s41598-019-40770-9},
doi = {https://doi.org/10.1038/s41598-019-40770-9},
year = {2019},
date = {2019-03-14},
journal = {Scientific Reports},
volume = {9},
abstract = {In specific cases, chromatin clearly forms long-range loops that place distant regulatory elements in close proximity to transcription start sites, but we have limited understanding of many loops identified by Chromosome Conformation Capture (such as Hi-C) analyses. In efforts to elucidate their characteristics and functions, we have identified highly interacting regions (HIRs) using intra-chromosomal Hi-C datasets with a new computational method based on looking at the eigenvector that corresponds to the smallest eigenvalue (here unity). Analysis of these regions using ENCODE data shows that they are in general enriched in bound factors involved in DNA damage repair and have actively transcribed genes. However, both highly transcribed regions as well as transcriptionally inactive regions can form HIRs. The results also indicate that enhancers and super-enhancers in particular form long-range interactions within the same chromosome. The accumulation of DNA repair factors in most identified HIRs suggests that protection from DNA damage in these regions is essential for avoidance of detrimental rearrangements.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
In specific cases, chromatin clearly forms long-range loops that place distant regulatory elements in close proximity to transcription start sites, but we have limited understanding of many loops identified by Chromosome Conformation Capture (such as Hi-C) analyses. In efforts to elucidate their characteristics and functions, we have identified highly interacting regions (HIRs) using intra-chromosomal Hi-C datasets with a new computational method based on looking at the eigenvector that corresponds to the smallest eigenvalue (here unity). Analysis of these regions using ENCODE data shows that they are in general enriched in bound factors involved in DNA damage repair and have actively transcribed genes. However, both highly transcribed regions as well as transcriptionally inactive regions can form HIRs. The results also indicate that enhancers and super-enhancers in particular form long-range interactions within the same chromosome. The accumulation of DNA repair factors in most identified HIRs suggests that protection from DNA damage in these regions is essential for avoidance of detrimental rearrangements. |
| 264. | Kumar, Rajendra; Lizana, Ludvig; Stenberg, Per Genomic 3D compartments emerge from unfolding mitotic chromosomes Journal Article Chromosoma, 128 , pp. 15-20, 2019, ISSN: 1432-0886. Abstract | Links | BibTeX @article{Kumar2018,
title = {Genomic 3D compartments emerge from unfolding mitotic chromosomes},
author = {Rajendra Kumar and Ludvig Lizana and Per Stenberg},
url = {https://doi.org/10.1007/s00412-018-0684-7},
doi = {10.1007/s00412-018-0684-7},
issn = {1432-0886},
year = {2019},
date = {2019-03-01},
journal = {Chromosoma},
volume = {128},
pages = {15-20},
abstract = {The 3D organisation of the genome in interphase cells is not a randomly folded polymer. Rather, experiments show that chromosomes arrange into a network of 3D compartments that correlate with biological processes, such as transcription, chromatin modifications and protein binding. However, these compartments do not exist during cell division when the DNA is condensed, and it is unclear how and when they emerge. In this paper, we focus on the early stages after cell division as the chromosomes start to decondense. We use a simple polymer model to understand the types of 3D structures that emerge from local unfolding of a compact initial state. From simulations, we recover 3D compartments, such as TADs and A/B compartments that are consistently detected in chromosome capture experiments across cell types and organisms. This suggests that the large-scale 3D organisation is a result of an inflation process.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
The 3D organisation of the genome in interphase cells is not a randomly folded polymer. Rather, experiments show that chromosomes arrange into a network of 3D compartments that correlate with biological processes, such as transcription, chromatin modifications and protein binding. However, these compartments do not exist during cell division when the DNA is condensed, and it is unclear how and when they emerge. In this paper, we focus on the early stages after cell division as the chromosomes start to decondense. We use a simple polymer model to understand the types of 3D structures that emerge from local unfolding of a compact initial state. From simulations, we recover 3D compartments, such as TADs and A/B compartments that are consistently detected in chromosome capture experiments across cell types and organisms. This suggests that the large-scale 3D organisation is a result of an inflation process. |
| 263. | Rainey, Peter Lind; Eric Libby; Jenny Herzog; Paul A B Predicting mutational routes to new adaptive phenotypes Journal Article eLife, (38822), 2019. Abstract | Links | BibTeX @article{Lind2019,
title = {Predicting mutational routes to new adaptive phenotypes},
author = {Peter A. Lind; Eric Libby; Jenny Herzog; Paul B. Rainey},
url = {https://elifesciences.org/articles/38822},
doi = {10.7554/eLife.38822},
year = {2019},
date = {2019-01-08},
journal = {eLife},
number = {38822},
abstract = {Predicting evolutionary change poses numerous challenges. Here we take advantage of the model bacterium Pseudomonas fluorescens in which the genotype-to-phenotype map determining evolution of the adaptive ‘wrinkly spreader’ (WS) type is known. We present mathematical descriptions of three necessary regulatory pathways and use these to predict both the rate at which each mutational route is used and the expected mutational targets. To test predictions, mutation rates and targets were determined for each pathway. Unanticipated mutational hotspots caused experimental observations to depart from predictions but additional data led to refined models. A mismatch was observed between the spectra of WS-causing mutations obtained with and without selection due to low fitness of previously undetected WS-causing mutations. Our findings contribute toward the development of mechanistic models for forecasting evolution, highlight current limitations, and draw attention to challenges in predicting locus-specific mutational biases and fitness effects.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Predicting evolutionary change poses numerous challenges. Here we take advantage of the model bacterium Pseudomonas fluorescens in which the genotype-to-phenotype map determining evolution of the adaptive ‘wrinkly spreader’ (WS) type is known. We present mathematical descriptions of three necessary regulatory pathways and use these to predict both the rate at which each mutational route is used and the expected mutational targets. To test predictions, mutation rates and targets were determined for each pathway. Unanticipated mutational hotspots caused experimental observations to depart from predictions but additional data led to refined models. A mismatch was observed between the spectra of WS-causing mutations obtained with and without selection due to low fitness of previously undetected WS-causing mutations. Our findings contribute toward the development of mechanistic models for forecasting evolution, highlight current limitations, and draw attention to challenges in predicting locus-specific mutational biases and fitness effects. |
| 262. | Libby, Eric; Hébert-Dufresne, Laurent; Hosseini, Sayed-Rzgar; Wagner, Andreas Syntrophy emerges spontaneously in complex metabolic systems Journal Article PLOS Computational Biology, 15 (7), pp. 1-17, 2019. Abstract | Links | BibTeX @article{10.1371/journal.pcbi.1007169,
title = {Syntrophy emerges spontaneously in complex metabolic systems},
author = {Eric Libby and Laurent Hébert-Dufresne and Sayed-Rzgar Hosseini and Andreas Wagner},
url = {https://doi.org/10.1371/journal.pcbi.1007169},
doi = {10.1371/journal.pcbi.1007169},
year = {2019},
date = {2019-01-01},
journal = {PLOS Computational Biology},
volume = {15},
number = {7},
pages = {1-17},
publisher = {Public Library of Science},
abstract = {Author summary By exchanging resources, the members of a microbial community can survive in environments where individual species cannot. Despite the abundance of such syntrophy, little is known about its evolutionary origin. The predominant hypothesis is that syntrophy arises when originally independent organisms in the same community become interdependent by accumulating mutations. In this view, syntrophy arises when organisms co-evolve. In sharp contrast we find that different metabolism can interact syntrophically without a shared evolutionary history. We show that syntrophy is an inherent and emergent property of the complex chemical reaction networks that constitute metabolism.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Author summary By exchanging resources, the members of a microbial community can survive in environments where individual species cannot. Despite the abundance of such syntrophy, little is known about its evolutionary origin. The predominant hypothesis is that syntrophy arises when originally independent organisms in the same community become interdependent by accumulating mutations. In this view, syntrophy arises when organisms co-evolve. In sharp contrast we find that different metabolism can interact syntrophically without a shared evolutionary history. We show that syntrophy is an inherent and emergent property of the complex chemical reaction networks that constitute metabolism. |
| 261. | Rojas A., Sandy Michael R Early Cretaceous (Valanginian) brachiopods from the Rosablanca Formation, Colombia, South America: Biostratigraphic significance and paleogeographic implications Journal Article Forthcoming Cretaceous Research, Forthcoming. Abstract | Links | BibTeX @article{Rojas2018,
title = {Early Cretaceous (Valanginian) brachiopods from the Rosablanca Formation, Colombia, South America: Biostratigraphic significance and paleogeographic implications},
author = {Rojas, A., Sandy, Michael R.},
url = {https://www.sciencedirect.com/science/article/pii/S0195667118303665},
doi = {10.1016/j.cretres.2018.12.011},
year = {2018},
date = {2018-12-18},
journal = {Cretaceous Research},
abstract = {The Mesozoic fossil record of brachiopods in northern South America is relatively scarce and their biogeographical history is not well understood. Cretaceous brachiopods in this region are restricted to carbonate platforms of Colombia. Here we examine the brachiopod fauna from the middle part of the Rosablanca Formation near the town of Zapatoca, Eastern Cordillera of Colombia. We describe Sellithyris elizabetha nov. sp. combining traditional morphometrics and serial sectioning. This new terebratulide species shows morphological similarities with other species of the genus Sellithyris, including a Valanginian species from the ancient Gulf of Mexico. Using a semi-quantitative taphonomic analysis, we identified reworked specimens restricted to a single stratigraphic horizon, and consistent with a large-scale erosional hiatus that may affect the biochronology of the Rosablanca Formation. In addition, phosphatic shells of the lingulide Lingularia sp. were recovered from two stratigraphic horizons and are valuable for local correlations. Although much of the material is fragmentary, it represents the oldest occurrences of Cretaceous lingulides in the region so far. Lingulide brachiopods have traditionally been considered as rare elements in Cretaceous near-shore marine communities, however, the material reported here suggests that they may have been common locally.},
keywords = {},
pubstate = {forthcoming},
tppubtype = {article}
}
The Mesozoic fossil record of brachiopods in northern South America is relatively scarce and their biogeographical history is not well understood. Cretaceous brachiopods in this region are restricted to carbonate platforms of Colombia. Here we examine the brachiopod fauna from the middle part of the Rosablanca Formation near the town of Zapatoca, Eastern Cordillera of Colombia. We describe Sellithyris elizabetha nov. sp. combining traditional morphometrics and serial sectioning. This new terebratulide species shows morphological similarities with other species of the genus Sellithyris, including a Valanginian species from the ancient Gulf of Mexico. Using a semi-quantitative taphonomic analysis, we identified reworked specimens restricted to a single stratigraphic horizon, and consistent with a large-scale erosional hiatus that may affect the biochronology of the Rosablanca Formation. In addition, phosphatic shells of the lingulide Lingularia sp. were recovered from two stratigraphic horizons and are valuable for local correlations. Although much of the material is fragmentary, it represents the oldest occurrences of Cretaceous lingulides in the region so far. Lingulide brachiopods have traditionally been considered as rare elements in Cretaceous near-shore marine communities, however, the material reported here suggests that they may have been common locally. |
| 260. | Landi, Pietro; Minoarivelo, Henintsoa O; Brännström, Åke; Hui, Cang; Dieckmann, Ulf Complexity and stability of ecological networks: a review of the theory Journal Article Population Ecology, 60 (4), pp. 319–345, 2018, ISSN: 1438-390X. Abstract | Links | BibTeX @article{Landi2018b,
title = {Complexity and stability of ecological networks: a review of the theory},
author = {Pietro Landi and Henintsoa O Minoarivelo and Åke Brännström and Cang Hui and Ulf Dieckmann},
url = {https://doi.org/10.1007/s10144-018-0628-3},
doi = {10.1007/s10144-018-0628-3},
issn = {1438-390X},
year = {2018},
date = {2018-10-01},
journal = {Population Ecology},
volume = {60},
number = {4},
pages = {319--345},
abstract = {Our planet is changing at paces never observed before. Species extinction is happening at faster rates than ever, greatly exceeding the five mass extinctions in the fossil record. Nevertheless, our lives are strongly based on services provided by ecosystems, thus the responses to global change of our natural heritage are of immediate concern. Understanding the relationship between complexity and stability of ecosystems is of key importance for the maintenance of the balance of human growth and the conservation of all the natural services that ecosystems provide. Mathematical network models can be used to simplify the vast complexity of the real world, to formally describe and investigate ecological phenomena, and to understand ecosystems propensity of returning to its functioning regime after a stress or a perturbation. The use of ecological-network models to study the relationship between complexity and stability of natural ecosystems is the focus of this review. The concept of ecological networks and their characteristics are first introduced, followed by central and occasionally contrasting definitions of complexity and stability. The literature on the relationship between complexity and stability in different types of models and in real ecosystems is then reviewed, highlighting the theoretical debate and the lack of consensual agreement. The summary of the importance of this line of research for the successful management and conservation of biodiversity and ecosystem services concludes the review.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Our planet is changing at paces never observed before. Species extinction is happening at faster rates than ever, greatly exceeding the five mass extinctions in the fossil record. Nevertheless, our lives are strongly based on services provided by ecosystems, thus the responses to global change of our natural heritage are of immediate concern. Understanding the relationship between complexity and stability of ecosystems is of key importance for the maintenance of the balance of human growth and the conservation of all the natural services that ecosystems provide. Mathematical network models can be used to simplify the vast complexity of the real world, to formally describe and investigate ecological phenomena, and to understand ecosystems propensity of returning to its functioning regime after a stress or a perturbation. The use of ecological-network models to study the relationship between complexity and stability of natural ecosystems is the focus of this review. The concept of ecological networks and their characteristics are first introduced, followed by central and occasionally contrasting definitions of complexity and stability. The literature on the relationship between complexity and stability in different types of models and in real ecosystems is then reviewed, highlighting the theoretical debate and the lack of consensual agreement. The summary of the importance of this line of research for the successful management and conservation of biodiversity and ecosystem services concludes the review. |
| 259. | Diehl, Sebastian; Thomsson, Gustaf; Kahlert, Maria; Guo, Junwen; Karlsson, Jan; Liess, Antonia Inverse relationship of epilithic algae and pelagic phosphorus in unproductive lakes: Roles of N2 fixers and light Journal Article Freshwater Biology, 2018. Links | BibTeX @article{diehlinverse,
title = {Inverse relationship of epilithic algae and pelagic phosphorus in unproductive lakes: Roles of N2 fixers and light},
author = {Sebastian Diehl and Gustaf Thomsson and Maria Kahlert and Junwen Guo and Jan Karlsson and Antonia Liess},
doi = {https://doi.org/10.1111/fwb.13103},
year = {2018},
date = {2018-03-30},
journal = {Freshwater Biology},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
|
| 258. | Francisco Rivera Vasconcelos Sebastian Diehl, Patricia Rodríguez Jan Karlsson ; Byström, Pär Effects of Terrestrial Organic Matter on Aquatic Primary Production as Mediated by Pelagic--Benthic Resource Fluxes Journal Article Ecosystems, pp. 1–14, 2018. Links | BibTeX @article{vasconceloseffects,
title = {Effects of Terrestrial Organic Matter on Aquatic Primary Production as Mediated by Pelagic--Benthic Resource Fluxes},
author = {Francisco Rivera Vasconcelos, Sebastian Diehl, Patricia Rodríguez, Jan Karlsson and Pär Byström},
doi = {https://doi.org/10.1007/s10021-017-0217-x},
year = {2018},
date = {2018-01-17},
journal = {Ecosystems},
pages = {1--14},
publisher = {Springer US},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
|
| 257. | Bernardo-Madrid, Rubén; Calatayud, Joaquín; González-Suarez, Manuela; Rosvall, Martin; Lucas, Pablo M; Rueda, Marta; Antonelli, Alexandre; Revilla, Eloy Human activity is altering the world's zoogeographical regions Journal Article bioRxiv, pp. 287300, 2018. Abstract | Links | BibTeX @article{bernardo2018human,
title = {Human activity is altering the world's zoogeographical regions},
author = {Rubén Bernardo-Madrid and Joaquín Calatayud and Manuela González-Suarez and Martin Rosvall and Pablo M Lucas and Marta Rueda and Alexandre Antonelli and Eloy Revilla},
doi = {10.1101/287300},
year = {2018},
date = {2018-01-01},
journal = {bioRxiv},
pages = {287300},
abstract = {Human activity leading to both species introductions and extinctions is widely known to influence diversity patterns on local and regional scales. Yet, it is largely unknown whether the intensity of this activity is enough to affect the configuration of biodiversity at broader levels of spatial organization. Zoogeographical regions, or zooregions, are surfaces of the Earth defined by characteristic pools of species, which reflect ecological, historical, and evolutionary processes acting over millions of years. Consequently, it is widely assumed that zooregions are robust and unlikely to change on a human timescale. Here, however, we show that human-mediated introductions and extinctions can indeed reconfigure the currently recognized zooregions of amphibians, mammals, and birds. In particular, introductions homogenize the African and Eurasian zooregions in mammals; reshape boundaries with the reallocation of Oceania to the New World zooregion in amphibians; and divide bird zooregions by increasing biotic heterogeneity. Furthermore, the combined effect of amphibian introductions and extinctions has the potential to divide two zooregions largely representing the Old and the New World. Interestingly, the robustness of zooregions against changes in species composition may largely explain such zoogeographical changes. Altogether, our results demonstrate that human activities can erode the higher-level organization of biodiversity formed over millions of years. Comparable reconfigurations have previously been detectable in Earth's history only after glaciations and mass extinction events, highlighting the profound and far-reaching impact of ongoing human activity and the need to protect the uniqueness of biotic assemblages from the effects of future species introductions and extinctions.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Human activity leading to both species introductions and extinctions is widely known to influence diversity patterns on local and regional scales. Yet, it is largely unknown whether the intensity of this activity is enough to affect the configuration of biodiversity at broader levels of spatial organization. Zoogeographical regions, or zooregions, are surfaces of the Earth defined by characteristic pools of species, which reflect ecological, historical, and evolutionary processes acting over millions of years. Consequently, it is widely assumed that zooregions are robust and unlikely to change on a human timescale. Here, however, we show that human-mediated introductions and extinctions can indeed reconfigure the currently recognized zooregions of amphibians, mammals, and birds. In particular, introductions homogenize the African and Eurasian zooregions in mammals; reshape boundaries with the reallocation of Oceania to the New World zooregion in amphibians; and divide bird zooregions by increasing biotic heterogeneity. Furthermore, the combined effect of amphibian introductions and extinctions has the potential to divide two zooregions largely representing the Old and the New World. Interestingly, the robustness of zooregions against changes in species composition may largely explain such zoogeographical changes. Altogether, our results demonstrate that human activities can erode the higher-level organization of biodiversity formed over millions of years. Comparable reconfigurations have previously been detectable in Earth's history only after glaciations and mass extinction events, highlighting the profound and far-reaching impact of ongoing human activity and the need to protect the uniqueness of biotic assemblages from the effects of future species introductions and extinctions. |
| 256. | Blöcker, Christopher; Hoffmann, Ulrich Pardis: A Process Calculus for Parallel and Distributed Programming in Haskell Journal Article The Journal of Supercomputing, 74 (4), pp. 1473–1484, 2018. Links | BibTeX @article{pardis2018,
title = {Pardis: A Process Calculus for Parallel and Distributed Programming in Haskell},
author = {Christopher Blöcker and Ulrich Hoffmann},
doi = {10.1007/s11227-018-2289-6},
year = {2018},
date = {2018-01-01},
journal = {The Journal of Supercomputing},
volume = {74},
number = {4},
pages = {1473--1484},
publisher = {Springer},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
|
| 255. | Lim, Weng Khong; Davila, Sonia; Teo, Jing Xian; Yang, Chengxi; Pua, Chee Jian; Blöcker, Christopher; Lim, Jing Quan; Ching, Jianhong; Yap, Jonathan Jiunn Liang; Tan, Swee Yaw; Sahlén, Anders; Chin, Calvin Woon-Loong; Teh, Bin Tean; Rozen, Steven G; Cook, Stuart Alexander; Yeo, Khung Keong; Tan, Patrick Beyond fitness tracking: The use of consumer-grade wearable data from normal volunteers in cardiovascular and lipidomics research Journal Article PLoS Biology, 16 , 2018. Links | BibTeX @article{fitness2018,
title = {Beyond fitness tracking: The use of consumer-grade wearable data from normal volunteers in cardiovascular and lipidomics research},
author = {Weng Khong Lim and Sonia Davila and Jing Xian Teo and Chengxi Yang and Chee Jian Pua and Christopher Blöcker and Jing Quan Lim and Jianhong Ching and Jonathan Jiunn Liang Yap and Swee Yaw Tan and Anders Sahlén and Calvin Woon-Loong Chin and Bin Tean Teh and Steven G Rozen and Stuart Alexander Cook and Khung Keong Yeo and Patrick Tan},
doi = {10.1371/journal.pbio.2004285},
year = {2018},
date = {2018-01-01},
journal = {PLoS Biology},
volume = {16},
publisher = {PLoS},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
|
| 254. | Brush, Eleanor; Brännström, Åke; Dieckmann, Ulf Indirect Reciprocity With Negative Assortment and Limited Information Can Promote Cooperation Journal Article Journal of theoretical biology, 2018. Links | BibTeX @article{brush2018indirect,
title = {Indirect Reciprocity With Negative Assortment and Limited Information Can Promote Cooperation},
author = {Eleanor Brush and Åke Brännström and Ulf Dieckmann},
doi = {10.1016/j.jtbi.2018.01.005},
year = {2018},
date = {2018-01-01},
journal = {Journal of theoretical biology},
publisher = {Academic Press},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
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| 253. | Hellström, Lars; Carlsson, Linus; Falster, Daniel S; Westoby, Mark; Brännström, Åke Branch Thinning and the Large-Scale, Self-Similar Structure of Trees Journal Article The American Naturalist, 192 (1), pp. E000–E000, 2018. Links | BibTeX @article{hellstrom2018branch,
title = {Branch Thinning and the Large-Scale, Self-Similar Structure of Trees},
author = {Lars Hellström and Linus Carlsson and Daniel S Falster and Mark Westoby and Åke Brännström},
doi = {10.1086/697429},
year = {2018},
date = {2018-01-01},
journal = {The American Naturalist},
volume = {192},
number = {1},
pages = {E000--E000},
publisher = {University of Chicago Press Chicago, IL},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
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| 252. | Landi, Pietro; Minoarivelo, Henintsoa O; Brännström, Åke; Hui, Cang; Dieckmann, Ulf Complexity and Stability of Adaptive Ecological Networks: A Survey of the Theory in Community Ecology Incollection Systems Analysis Approach for Complex Global Challenges, pp. 209–248, Springer, Cham, 2018. Links | BibTeX @incollection{landi2018complexity,
title = {Complexity and Stability of Adaptive Ecological Networks: A Survey of the Theory in Community Ecology},
author = {Pietro Landi and Henintsoa O Minoarivelo and Åke Brännström and Cang Hui and Ulf Dieckmann},
doi = {10.1007/978-3-319-71486-8_12},
year = {2018},
date = {2018-01-01},
booktitle = {Systems Analysis Approach for Complex Global Challenges},
pages = {209--248},
publisher = {Springer, Cham},
keywords = {},
pubstate = {published},
tppubtype = {incollection}
}
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| 251. | Libby, Eric; Driscoll, William W; Ratcliff, William C Programmed cell death can increase the efficacy of microbial bet-hedging Journal Article Scientific reports, 8 (1), pp. 1120, 2018. Links | BibTeX @article{libby2018programmed,
title = {Programmed cell death can increase the efficacy of microbial bet-hedging},
author = {Eric Libby and William W Driscoll and William C Ratcliff},
doi = {10.1038/s41598-017-18687-y
publisher=Nature Publishing Group},
year = {2018},
date = {2018-01-01},
journal = {Scientific reports},
volume = {8},
number = {1},
pages = {1120},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
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| 250. | Lind, Peter A; Libby, Eric; Herzog, Jenny; Rainey, Paul B Disentangling the effects of genetic architecture, mutational bias and selection on evolutionary forecasting Journal Article bioRxiv, pp. 335711, 2018. Links | BibTeX @article{lind2018disentangling,
title = {Disentangling the effects of genetic architecture, mutational bias and selection on evolutionary forecasting},
author = {Peter A Lind and Eric Libby and Jenny Herzog and Paul B Rainey},
doi = {10.1101/335711
publisher=Cold Spring Harbor Laboratory},
year = {2018},
date = {2018-01-01},
journal = {bioRxiv},
pages = {335711},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
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| 249. | Nahali, N; Rosa, A Nanoprobe diffusion in entangled polymer solutions: Linear vs. unconcatenated ring chains Journal Article The Journal of Chemical Physics, 148 (19), pp. 194902, 2018. Links | BibTeX @article{Negar2018,
title = {Nanoprobe diffusion in entangled polymer solutions: Linear vs. unconcatenated ring chains},
author = {N Nahali and A Rosa},
url = {https://doi.org/10.1063/1.5022446},
doi = {10.1063/1.5022446},
year = {2018},
date = {2018-01-01},
journal = {The Journal of Chemical Physics},
volume = {148},
number = {19},
pages = {194902},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
|
