partial canonical correspondence analysis
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2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Arina L. Maltseva ◽  
Marina A. Varfolomeeva ◽  
Arseniy A. Lobov ◽  
Polina O. Tikanova ◽  
Egor A. Repkin ◽  
...  

AbstractSympatric coexistence of recently diverged species raises the question of barriers restricting the gene flow between them. Reproductive isolation may be implemented at several levels, and the weakening of some, e.g. premating, barriers may require the strengthening of the others, e.g. postcopulatory ones. We analysed mating patterns and shell size of mates in recently diverged closely related species of the subgenus Littorina Neritrema (Littorinidae, Caenogastropoda) in order to assess the role of premating reproductive barriers between them. We compared mating frequencies observed in the wild with those expected based on relative densities using partial canonical correspondence analysis. We introduced the fidelity index (FI) to estimate the relative accuracy of mating with conspecific females and precopulatory isolation index (IPC) to characterize the strength of premating barriers. The species under study, with the exception of L. arcana, clearly demonstrated preferential mating with conspecifics. According to FI and IPC, L. fabalis and L. compressa appeared reliably isolated from their closest relatives within Neritrema. Individuals of these two species tend to be smaller than those of the others, highlighting the importance of shell size changes in gastropod species divergence. L. arcana males were often found in pairs with L. saxatilis females, and no interspecific size differences were revealed in this sibling species pair. We discuss the lack of discriminative mate choice in the sympatric populations of L. arcana and L. saxatilis, and possible additional mechanisms restricting gene flow between them.


2016 ◽  
Vol 46 (7) ◽  
pp. 933-942 ◽  
Author(s):  
Marie-Audrey Nadeau Fortin ◽  
Luc Sirois ◽  
Martin-Hugues St-Laurent

Extensive forest management aims at minimizing differences between managed and natural forests and at contributing to the conservation of endangered species such as the Atlantic-Gaspésie caribou. The decline of this isolated population was exacerbated by intensive forest practices, as the over-representation of regenerating forests supports high densities of bears and coyotes. These predators select such stands for the high availability of berries and browse suitable to alternative prey, especially moose. Our objective was to verify whether extensive treatments can provide suitable habitat characteristics for caribou. We compared the impacts of different intensive and extensive treatments on habitat attributes known to be selected by caribou, moose, and their predators. We sampled 291 sites in seven treatments and in mature coniferous forests (as the control). A partial canonical correspondence analysis highlighted which treatments maintain habitat attributes that are comparable with those found in mature forests, including some characteristics suitable for caribou such as a substantial biomass of arboreal lichen and a lower availability of resources for predators. Although being more suitable than the three intensive treatments tested, none of the four extensive treatments we studied provided similar habitat conditions to mature forest. Favouring extensive treatments could nevertheless be a relevant conservation compromise at the forest stand level, but their utility remains uncertain under the maximum sustainable yield paradigm as they impact a larger area.


Botany ◽  
2011 ◽  
Vol 89 (10) ◽  
pp. 689-713 ◽  
Author(s):  
Joanna M. Lemly ◽  
David J. Cooper

We studied the vegetation of 166 fens in Yellowstone National Park, USA, to determine the relationship between species distribution in mountain peatlands and regional-, landscape-, and local-scale environmental variables. Plant communities were identified through hierarchical agglomerative cluster analysis, patterns in species distribution were explored using nonmetric multidimensional scaling, and the relative importance of variables was assessed though partial canonical correspondence analysis. Five major bedrock types influenced groundwater feeding fens: three volcanic types, a glacial till complex, and rock altered by acidic geothermal activity. Ionic concentrations generally increased with pH, but acidic geothermal fens had very low pH and high electrical conductivity. Bryophyte distribution was controlled by groundwater chemistry, while vascular plants responded to a broader range of variables. When partitioned by spatial scale, landscape variables accounted for >60% of the variation explained. When partitioned categorically, geochemical and topographic variables were more important than geographic factors. For fens in mountainous regions, the primary gradient is site-level water chemistry, which is strongly linked to regional bedrock geology. Site- and stand-level topography represent a secondary gradient. Most mountain fens fit within the established poor–rich gradient; however, geochemical acid production creates a distinct category outside the conventional paradigm.


2009 ◽  
Vol 66 (4) ◽  
pp. 589-601 ◽  
Author(s):  
Jussi Jyväsjärvi ◽  
Kimmo T. Tolonen ◽  
Heikki Hämäläinen

Modern biological assessment of aquatic systems is often based on the reference condition approach, which requires characterization of biota in undisturbed conditions. For this approach, it is essential to recognize the origins and degree of natural variation in communities. We used data from 55 minimally disturbed Finnish lake basins to investigate the natural variation of profundal macroinvertebrate community composition in relation to environmental factors. Partial canonical correspondence analysis showed that most (68% combined, 39% uniquely) of the total explained compositional variation (29%) was correlated with environmental variables insensitive to human activities, especially lake morphometry. In contrast, the unique contributions of geographical location and variables influenced by human activities (dissolved oxygen and total phosphorus) were substantially smaller (5.5% and 22%, respectively). All of the explained variation (38%–64%) of three widely used community metrics was also correlated with human-insensitive environmental factors. The results suggest that variation in undisturbed profundal invertebrate communities of reference sites is strongly dependent on variables insensitive to human activities and especially on those related to lake morphometry, suggesting that reference communities for bioassessment of impacted lakes should be rather predictable from these variables.


<em>Abstract.</em>—Habitat data collected at three spatial scales (catchments, reaches, and sites) were used to predict individual fish species occurrences and assemblage structure at 150 sites in the Kansas River basin. Habitat measurements for the catchments and reaches of each sample site were derived from available geographic information system (GIS) data layers. Habitat measurements at the sample sites were collected at the time of fish sampling. Because habitat measurements are typically more difficult to collect as the spatial scale of sampling decreases (i.e., field measurement versus a GIS analysis), our objective was to quantify the relative increase in predictive ability as we added habitat measurements from increasingly finer spatial scales. Although the addition of site-scale habitat variables increased the predictive performance of models, the relative magnitude of these increases was small. This was largely due to the general association of species occurrences with measurements of catchment area and soil factors, both of which could be quantified with a GIS. Habitat measurements taken at different spatial scales were often correlated; however, a partial canonical correspondence analysis showed that catchment- scale habitat measurements accounted for a slightly higher percent of the variation in fish-assemblage structure across the 150 sample sites than reach- or site-scale habitat measurements. We concluded that field habitat measurements were less informative for predicting species occurrences within the Kansas River basin than catchment data. However, because of the hierarchical nature of the geomorphological processes that form stream habitats, a refined understanding of the relationship between catchment-, reach- and site-scale habitats provides a mechanistic understanding of fish–habitat relations across spatial scales.


2005 ◽  
Vol 56 (6) ◽  
pp. 825 ◽  
Author(s):  
Nelli Horrigan ◽  
Satish Choy ◽  
Jonathan Marshall ◽  
Friedrich Recknagel

Many streams and wetlands have been affected by increasing salinity, leading to significant changes in flora and fauna. The study investigates relationships between macroinvertebrate taxa and conductivity levels (µS cm−1) in Queensland stream systems. The analysed dataset contained occurrence patterns of frequently found macroinvertebrate taxa from edge (2580 samples) and riffle (1367 samples) habitats collected in spring and autumn over 8 years. Sensitivity analysis with predictive artificial neural network models and the taxon-specific mean conductivity values were used to assign a salinity sensitivity score (SSS) to each taxon (1—very tolerant, 5—tolerant, 10—sensitive). Salinity index (SI) based on the cumulative SSS was proposed as a measurement of change in macroinvertebrate communities caused by salinity increase. Changes in macroinvertebrate communities were observed at relatively low salinities, with SI rapidly decreasing to ~800–1000 µS cm−1 and decreasing further at a slower rate. Natural variability and water quality factors were ruled out as potential primary causes of the observed changes by using partial canonical correspondence analysis and subsets of the data with only good water quality.


2003 ◽  
Vol 7 (2) ◽  
pp. 221-233 ◽  
Author(s):  
G. Beasley ◽  
P. E. Kneale

Abstract. This paper defines the spectrum of impairment to stream macroinvertebrates arising from urban runoff. Field sampling of stream sediments at 62 sites across Yorkshire, UK was used to investigate the influence of heavy metals and habitat on macroinvertebrate family distribution using partial Canonical Correspondence Analysis (pCCA). Increasing urbanization and trafficking was associated with increasing levels of metal pollution but, even when traffic is light, family numbers can be reduced by 50%. Industrial areas and motorway runoff depress macroinvertebrate numbers but drainage from streets with no off-road parking in residential areas can have similar impacts. The heavy metals in the sediment accounted for approximately 24% of the variation in macroinvertebrate community composition while the physical habitat variables used in RIVPACS (River InVertebrate Prediction And Classification System) (Wright, 2000) accounted for an additional 30%. Zinc and nickel were the main metal influences regardless of the time of sampling; at these sites copper is less than critical. Results agree with those reported in other studies in which families mainly from the orders Ephemeroptera (mayfly), Plecoptera (stonefly) and Tricoptera (caddisfly) displayed metal sensitivity in that they were absent from metal polluted streams. However, within each of these orders, a continuum of sensitivity is evident: this highlights the risks of generalising on orders rather than using family or indeed species data. Keywords: macroinvertebrates, heavy metals, urban streams, tolerance, sensitivity


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