scholarly journals Fine-grained habitat-associated genetic connectivity in an admixed population of mussels in the small isolated Kerguelen Islands

2017 ◽  
Author(s):  
Christelle Fraïsse ◽  
Anne Haguenauer ◽  
Karin Gérard ◽  
Alexandra Anh-Thu Weber ◽  
Nicolas Bierne ◽  
...  
Keyword(s):  
Spatial Distance ◽  
Genetic Connectivity ◽  
Sequencing Data ◽  
Kerguelen Islands ◽  
Fine Grained ◽  
Ideal System ◽  
Connectivity Patterns ◽  
Environmental Variations ◽  
Admixed Population ◽  
Northern Species

AbstractReticulated evolution -i.e. secondary introgression / admixture between sister taxa-is increasingly recognized as playing a key role in structuring infra-specific genetic variation and revealing cryptic genetic connectivity patterns. When admixture zones coincide with ecological transitions, the connectivity patterns often follow environmental variations better than distance and introgression clines may easily be confounded with local adaptation signatures. The Kerguelen mussels is an ideal system to investigate the potential role of admixture in enhancing micro-geographic structure, as they inhabit a small isolated island in the Southern Ocean characterized by a highly heterogeneous environment. Furthermore, genomic reticulation between Northern species (M. edulis, M. galloprovincialis and M. trossulus) and Southern species (M. platensis: South America and the Kerguelen Islands; and M. planulatus: Australasia) has been suspected. Here, we extended a previous analysis by using targeted-sequencing data (51,878 SNPs) across the three Northern species and the Kerguelen population. Spatial structure in the Kerguelen was then analyzed with a panel of 33 SNPs, including SNPs that were more differentiated than the genomic average between Northern species (i.e., ancestry-informative SNPs). We first showed that the Kerguelen lineage splitted very shortly after M. edulis and M. galloprovincialis initiated speciation, and it subsequently experienced admixture with the three Northern taxa. We then demonstrated that the Kerguelen mussels were significantly differentiated over small spatial distance, and that this local genetic structure was associated with environmental variations and mostly revealed by ancestry-informative markers. Simulations of admixture in the island highlight that genetic-environment associations can be better explained by introgression clines between heterogeneously differentiated genomes than by adaptation.

scholarly journals Fine-grained habitat-associated genetic connectivity in an admixed population of mussels in the small isolated Kerguelen Islands

2021 ◽  
Vol 1 ◽  
pp. 1-None
Author(s):  
Christelle Fraïsse ◽  
Anne Haguenauer ◽  
Karin Gérard ◽  
Alexandra Anh-Thu Weber ◽  
Nicolas Bierne ◽  
...  
Keyword(s):  
Genetic Connectivity ◽  
Kerguelen Islands ◽  
Fine Grained ◽  
Admixed Population

scholarly journals All Populations Matter: Conservation Genomics of Australia’s Iconic Purple Wattle, Acacia purpureopetala

Diversity ◽  
2021 ◽  
Vol 13 (4) ◽  
pp. 139
Author(s):  
Marlien M. van der Merwe ◽  
Jia-Yee S. Yap ◽  
Peter D. Wilson ◽  
Helen T. Murphy ◽  
Andrew Ford
Keyword(s):  
Genetic Diversity ◽  
Allelic Variation ◽  
Germplasm Conservation ◽  
Snp Markers ◽  
Genomic Diversity ◽  
Ex Situ ◽  
Spatial Distance ◽  
Genetic Connectivity ◽  
Conservation Genomics ◽  
Modelling Framework

Maximising genetic diversity in conservation efforts can help to increase the chances of survival of a species amidst the turbulence of the anthropogenic age. Here, we define the distribution and extent of genomic diversity across the range of the iconic but threatened Acacia purpureopetala, a beautiful sprawling shrub with mauve flowers, restricted to a few disjunct populations in far north Queensland, Australia. Seed production is poor and germination sporadic, but the species occurs in abundance at some field sites. While several thousands of SNP markers were recovered, comparable to other Acacia species, very low levels of heterozygosity and allelic variation suggested inbreeding. Limited dispersal most likely contributed towards the high levels of divergence amongst field sites and, using a generalised dissimilarity modelling framework amongst environmental, spatial and floristic data, spatial distance was found to be the strongest factor explaining the current distribution of genetic diversity. We illustrate how population genomic data can be utilised to design a collecting strategy for a germplasm conservation collection that optimises genetic diversity. For this species, inclusion of all field sites will capture maximum genetic diversity for both in situ and ex situ conservation. Assisted cross pollination, within and between field sites and genetically structured groups, is recommended to enhance heterozygosity particularly at the most disjunct sites and further fragmentation should be discouraged to avoid loss of genetic connectivity.

DAFI

2021 ◽  
Vol 5 (4) ◽  
pp. 1-21
Author(s):  
Hang Li ◽  
Xi Chen ◽  
Ju Wang ◽  
Di Wu ◽  
Xue Liu
Keyword(s):  
Indoor Localization ◽  
Domain Adaptation ◽  
Target Domain ◽  
Localization Accuracy ◽  
Source Domain ◽  
Fine Grained ◽  
Time Signals ◽  
Environmental Variations ◽  
Device Free ◽  
Localization Approach

WiFi-based Device-free Passive (DfP) indoor localization systems liberate their users from carrying dedicated sensors or smartphones, and thus provide a non-intrusive and pleasant experience. Although existing fingerprint-based systems achieve sub-meter-level localization accuracy by training location classifiers/regressors on WiFi signal fingerprints, they are usually vulnerable to small variations in an environment. A daily change, e.g., displacement of a chair, may cause a big inconsistency between the recorded fingerprints and the real-time signals, leading to significant localization errors. In this paper, we introduce a Domain Adaptation WiFi (DAFI) localization approach to address the problem. DAFI formulates this fingerprint inconsistency issue as a domain adaptation problem, where the original environment is the source domain and the changed environment is the target domain. Directly applying existing domain adaptation methods to our specific problem is challenging, since it is generally hard to distinguish the variations in the different WiFi domains (i.e., signal changes caused by different environmental variations). DAFI embraces the following techniques to tackle this challenge. 1) DAFI aligns both marginal and conditional distributions of features in different domains. 2) Inside the target domain, DAFI squeezes the marginal distribution of every class to be more concentrated at its center. 3) Between two domains, DAFI conducts fine-grained alignment by forcing every target-domain class to better align with its source-domain counterpart. By doing these, DAFI outperforms the state of the art by up to 14.2% in real-world experiments.

scholarly journals The role of cryptic dispersal in shaping connectivity patterns of marine populations in a changing world

2017 ◽  
Vol 98 (4) ◽  
pp. 647-655 ◽  
Author(s):  
Andrew A. David ◽  
Benjamin R. Loveday
Keyword(s):  
Marine Species ◽  
Short Review ◽  
Marine Ecology ◽  
Larval Transport ◽  
Genetic Connectivity ◽  
World Population ◽  
Dispersal Patterns ◽  
Connectivity Patterns ◽  
Integrated Methods ◽  
Evolutionary Consequences

Genetic connectivity directly shapes the demographic profile of marine species, and has become one of the most intensely researched areas in marine ecology. More importantly, it has changed the way we design and describe Marine Protected Areas across the world. Population genetics is the preferred tool when measuring connectivity patterns, however, these methods often assume that dispersal patterns are (1) natural and (2) follow traditional metapopulation models. In this short review, we formally introduce the phenomenon of cryptic dispersal, where multiple introductory events can undermine these assumptions, resulting in grossly inaccurate connectivity estimates. We also discuss the evolutionary consequences of cryptic dispersal and advocate for a cross-disciplinary approach that incorporates larval transport models into population genetic studies to provide a level of oceanographic realism that will result in more accurate estimates of dispersal. As globalized trade continues to expand, the rate of anthropogenic movement of marine organisms is also expected to increase and as such, integrated methods will be required to meet the inevitable conservation challenges that will arise from it.

Within-river genetic connectivity patterns reflect contrasting geomorphology

2015 ◽  
Vol 42 (12) ◽  
pp. 2452-2460 ◽  
Author(s):  
Jonathan M. Waters ◽  
Dave Craw ◽  
Christopher P. Burridge ◽  
Martyn Kennedy ◽  
Tania M. King ◽  
...  
Keyword(s):  
Genetic Connectivity ◽  
Connectivity Patterns

scholarly journals The neural basis of intelligence in fine-grained cortical topographies

2020 ◽  
Author(s):  
Ma Feilong ◽  
J. Swaroop Guntupalli ◽  
James V. Haxby
Keyword(s):  
Coarse Grained ◽  
Brain Anatomy ◽  
Neural Basis ◽  
Vertex Connectivity ◽  
Population Responses ◽  
Fine Grained ◽  
Connectivity Patterns ◽  
Neural Information ◽  
Neural Information Processing ◽  
And Function

AbstractIntelligent thought is the product of efficient neural information processing, which is embedded in fine-grained, topographically-organized population responses and supported by fine-grained patterns of connectivity among cortical fields. Previous work on the neural basis of intelligence, however, has focused on coarse-grained features of brain anatomy and function, because cortical topographies are highly idiosyncratic at a finer scale, obscuring individual differences in fine-grained connectivity patterns. We used a computational algorithm, hyperalignment, to resolve these topographic idiosyncrasies, and found that predictions of general intelligence based on fine-grained (vertex-by-vertex) connectivity patterns were markedly stronger than predictions based on coarse-grained (region-by-region) patterns. Intelligence was best predicted by fine-grained connectivity in the default and frontoparietal cortical systems, both of which are associated with self-generated thought. Previous work overlooked fine-grained architecture because existing methods couldn’t resolve idiosyncratic topographies, preventing investigation where the keys to the neural basis of intelligence are more likely to be found.

scholarly journals Genetic connectivity patterns of Pocillopora verrucosa in southern African Marine Protected Areas

2008 ◽  
Vol 354 ◽  
pp. 161-168 ◽  
Author(s):  
T Ridgway ◽  
C Riginos ◽  
J Davis ◽  
O Hoegh-Guldberg
Keyword(s):  
Protected Areas ◽  
Marine Protected Areas ◽  
Genetic Connectivity ◽  
Connectivity Patterns ◽  
Pocillopora Verrucosa

scholarly journals Microbial function is related to behavior of an invasive anuran

2020 ◽  
Author(s):  
Jia Zhou ◽  
Tiffanie Maree Nelson ◽  
Carlos Rodriguez Lopez ◽  
Shao Jia Zhou ◽  
Georgia Ward-Fear ◽  
...  
Keyword(s):  
P Value ◽  
Compositional Variation ◽  
Sequencing Data ◽  
Cane Toad ◽  
Functional Variation ◽  
Wild Female ◽  
Microbial Composition ◽  
Behavioral Traits ◽  
Microbial Functional Groups ◽  
Ideal System

AbstractInvasive species cause negative environmental and economic impacts worldwide. Their management may be improved by clarifying the role of behavior in advancing invasions. Gut microbial communities are known to affect behavior of wild populations, but their impact on behavior underlying invasiveness remains unexplored. Invasive populations of the cane toad (Rhinella marina) in Australia have expanded across the continent and exhibit variation in behavioral traits along their expansion trajectory, making this an ideal system to investigate the relationship between gut microbes and behaviors. We collected wild female toads from six locations in Queensland (n = 30) and Western Australia (n = 30), and conducted simple tests on behavioral traits previously associated with invasion ability. We investigated the relationships between toad gut microbiota, behavioral traits and the presence and intensity of co-introduced lungworms (Rhabdias pseudosphaerocephala) in toad samples from both ends of their Australian range. Based on 16S rRNA sequencing data, we found that microbiota in cane toad colons were dominated by the phyla Bacteroidetes, Proteobacteria, Firmicutes, Verrucomicrobia, and Fusobacteria. We found significant differences in microbiota composition (p-value < 0.001) between regions and in predicted microbial functional groups (p-value = 0.002). The occurrence of lungworms was strongly associated with variation in both microbial composition and microbial functions. However, the behavioral traits were associated with microbial functional variation, but not microbial compositional variation. These results support the “holobiont concept” (investigating the assemblage associated with a host) to fully understand drivers of invasion and highlight the need for experimental manipulations to detect causal relationships between microbiota, parasites and host behavior.

A Model of Potential Encounters in the Workplace: The Relationships of Homophily, Spatial Distance, Organizational Structure, and Perceived Networks

2016 ◽  
Vol 49 (6) ◽  
pp. 638-662 ◽  
Author(s):  
Felichism W. Kabo
Keyword(s):  
Organizational Structure ◽  
Spatial Distance ◽  
Network Ties ◽  
Manufacturing Firm ◽  
Face To Face ◽  
Fine Grained ◽  
Location Data ◽  
Dyadic Network ◽  
Knowledge Intensive ◽  
The Relationship

Potential face-to-face encounters are foundational to most workplace social interactions. There is little resolution on the question of what factors are antecedent to these encounters. This study examines the association of potential encounters with homophily, spatial distance, organizational structure, and perceived networks. Real-time, fine-grained data were collected using ultrawide-band location-tracking technology deployed at a knowledge-intensive subunit of a global manufacturing firm. The organization comprised scientists and engineers responsible for environmental policy, and emissions reporting and trading at the parent company. Potential encounters were constructed from the location data and modeled on the factors above using dyadic network regression models. The results show that spatial distance, organizational structure, and perceived network ties are all significantly related to potential encounters. Surprisingly, the homophily variables were nonsignificant. The contributions of this research regarding the relationship between potential face-to-face encounters and homophily, spatial distance, organizational structure, and perceived networks are discussed.

scholarly journals Connectome: computation and visualization of cell-cell signaling topologies in single-cell systems data

2021 ◽  
Author(s):  
Micha Sam Brickman Raredon ◽  
Junchen Yang ◽  
James Garritano ◽  
Meng Wang ◽  
Dan Kushnir ◽  
...  
Keyword(s):  
Cell Signaling ◽  
Single Cell ◽  
Rna Sequencing ◽  
Software Package ◽  
Sequencing Data ◽  
Single Cell Rna Sequencing ◽  
Rapid Calculation ◽  
Connectivity Patterns ◽  
Network Topologies ◽  
Cell Cell

AbstractSingle-cell RNA-sequencing data can revolutionize our understanding of the patterns of cell-cell and ligand-receptor connectivity that influence the function of tissues and organs. However, the quantification and visualization of these patterns are major computational and epistemological challenges. Here, we present Connectome, a software package for R which facilitates rapid calculation, and interactive exploration, of cell-cell signaling network topologies contained in single-cell RNA-sequencing data. Connectome can be used with any reference set of known ligand-receptor mechanisms. It has built-in functionality to facilitate differential and comparative connectomics, in which complete mechanistic networks are quantitatively compared between systems. Connectome includes computational and graphical tools designed to analyze and explore cell-cell connectivity patterns across disparate single-cell datasets. We present approaches to quantify these topologies and discuss some of the biologic theory leading to their design.

Sign in / Sign up

Export Citation Format

Share Document