Extending multivariate distance matrix regression with an effect size measure and the asymptotic null distribution of the test statistic

McArtor, Daniel B.; Lubke, Gitta H.; Bergeman, C. S.

doi:10.1007/s11336-016-9527-8

Cited by 60 publications

(63 citation statements)

References 44 publications

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“…All libraries were included in this analysis, without any filter, since even libraries that do not share any locus provide relevant information. We modeled the relationship between this dissimilarity matrix as a response and several predictors that we believe could also be associated with the recovery of a more similar set of final loci (MDA, population (i.e., locality), size selection pool and log-transformed number of loci in the final dataset for each sample) using a multivariate distance matrix regression (MDMR) ( Anderson, 2001 ; Mcardle & Anderson, 2001 ) implemented in the R package MDMR v. 0.5.0 ( McArtor, Lubke & Bergeman, 2016 ; McArtor, 2017 , 2018 ). This kind of regression tests the relationship between several variables and a distance matrix, drawing significance from randomization.…”

Section: Methodsmentioning

confidence: 99%

Whole-genome amplification in double-digest RADseq results in adequate libraries but fewer sequenced loci

Medeiros¹,

Farrell²

2018

PeerJ

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Whole-genome amplification by multiple displacement amplification (MDA) is a promising technique to enable the use of samples with only limited amount of DNA for the construction of RAD-seq libraries. Previous work has shown that, when the amount of DNA used in the MDA reaction is large, double-digest RAD-seq (ddRAD) libraries prepared with amplified genomic DNA result in data that are indistinguishable from libraries prepared directly from genomic DNA. Based on this observation, here we evaluate the quality of ddRAD libraries prepared from MDA-amplified genomic DNA when the amount of input genomic DNA and the coverage obtained for samples is variable. By simultaneously preparing libraries for five species of weevils (Coleoptera, Curculionidae), we also evaluate the likelihood that potential contaminants will be encountered in the assembled dataset. Overall, our results indicate that MDA may not be able to rescue all samples with small amounts of DNA, but it does produce ddRAD libraries adequate for studies of phylogeography and population genetics even when conditions are not optimal. We find that MDA makes it harder to predict the number of loci that will be obtained for a given sequencing effort, with some samples behaving like traditional libraries and others yielding fewer loci than expected. This seems to be caused both by stochastic and deterministic effects during amplification. Further, the reduction in loci is stronger in libraries with lower amounts of template DNA for the MDA reaction. Even though a few samples exhibit substantial levels of contamination in raw reads, the effect is very small in the final dataset, suggesting that filters imposed during dataset assembly are important in removing contamination. Importantly, samples with strong signs of contamination and biases in heterozygosity were also those with fewer loci shared in the final dataset, suggesting that stringent filtering of samples with significant amounts of missing data is important when assembling data derived from MDA-amplified genomic DNA. Overall, we find that the combination of MDA and ddRAD results in high-quality datasets for population genetics as long as the sequence data is properly filtered during assembly.

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Section: Methodsmentioning

confidence: 99%

Whole-genome amplification in double-digest RADseq results in adequate libraries but fewer sequenced loci

Medeiros¹,

Farrell²

2018

PeerJ

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“…We used multivariate distance matrix regression (MDMR; Anderson, 2001 ; McArdle and Anderson, 2001 ; McArtor et al, 2017 ) to test for the effect of each environmental variable on both observed dissimilarity and dissimilarity deviation. MDMR is very similar to the widely used ordination method Redundancy Analysis.…”

Section: Methodsmentioning

confidence: 99%

Environmental Characteristics and Anthropogenic Impact Jointly Modify Aquatic Macrophyte Species Diversity

et al. 2018

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Species richness and spatial variation in community composition (i.e., beta diversity) are key measures of biodiversity. They are largely determined by natural factors, but also increasingly affected by anthropogenic factors. Thus, there is a need for a clear understanding of the human impact on species richness and beta diversity, the underlying mechanisms, and whether human-induced changes can override natural patterns. Here, we dissect the patterns of species richness, community composition and beta diversity in relation to different environmental factors as well as human impact in one framework: aquatic macrophytes in 66 boreal lakes in Eastern Finland. The lakes had been classified as having high, good or moderate status (according to ecological classification of surface waters in Finland) reflecting multifaceted human impact. We used generalized least square models to study the association between different environmental variables (Secchi depth, irregularity of the shoreline, total phosphorus, pH, alkalinity, conductivity) and species richness. We tested the null hypothesis that the observed community composition can be explained by random distribution of species. We used multivariate distance matrix regression to test the effect of each environmental variable on community composition, and distance-based test for homogeneity of multivariate dispersion to test whether lakes classified as high, good or moderate status have different beta diversity. We showed that environmental drivers of species richness and community composition were largely similar, although dependent on the particular life-form group studied. The most important ones were characteristics of water quality (pH, alkalinity, conductivity) and irregularity of the shoreline. Differences in community composition were related to environmental variables independently of species richness. Species richness was higher in lakes with higher levels of human impact. Lakes with different levels of human impact had different community composition. Between-lake beta diversity did not differ in high, good or moderate status groups. However, the variation in environmental variables shaping community composition was larger in lakes with moderate status compared to other lakes. Hence, beta diversity in lakes with moderate status was smaller than what could be expected on the basis of these environmental characteristics. This could be interpreted as homogenization.

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“…By design, this novelty index is not effective for other patterns such as gradual or seasonal changes. One promising approach to analyse multiple patterns and covariates simultaneously are multivariate distance matrix regressions (McArtor, Lubke, & Bergeman, ). This approach can test continuous as well as factorial predictors for distance matrices.…”

Section: Discussionmentioning

confidence: 99%

Long‐term movements and home‐range changes: Rapid territory shifts in meerkats

Kranstauber

Gall

Vink

et al. 2019

Journal of Animal Ecology

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Territoriality and stable home ranges are a common space‐use pattern among animals. These ranges provide its inhabitants with important resources and thus favourable territories are associated with an increased fitness. While the role of territory quality and changes of territory ownership have often been investigated, the changes of territorial boundaries have been less studied. Here, we investigated space‐use changes in a social mammal species, applying a novel analytical approach, calculating long‐term dissimilarity in space use using distancematrices based on periodic utilization distributions. This approach makes it possible to identify different space‐use patterns, which cannot be distinguished by only considering changes between consecutive time periods. We analysed meerkat (Suricata suricatta) movements of a total of 24 different groups over a 16‐year period, resulting in 134 group years. We then correlated the identified home‐range changes to life‐history events and possible environmental drivers. Groups had stable territories for several years before they abandoned their home range mostly to move quickly to new areas where they again remained for several years. Of 26 identified sudden shifts, 22 occurred in the summer months and often involved distances larger than the original home‐range size. Home‐range movements that were close together in time were often also spatially clustered and moved in a similar direction. These shifts were often preceded by more frequent interactions between groups, but did not seem to be a product of direct displacements by other groups. The normalized difference vegetation index as a measure of food production and social factors such as dominance changes did not correlate to changes. Against our expectation space‐use changes were not accumulations of small changes, but more often involved long‐distance moves into unknown ranges. This means that the groups enter areas where they cannot profit from local knowledge. The methods used identify episodes of long stability alternated by sudden changes in meerkats and in general provides insight into long‐term space use. Our methods can be used to analyse long‐term space use, either within or across species.

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Extending multivariate distance matrix regression with an effect size measure and the asymptotic null distribution of the test statistic

Cited by 60 publications

References 44 publications

Whole-genome amplification in double-digest RADseq results in adequate libraries but fewer sequenced loci

Whole-genome amplification in double-digest RADseq results in adequate libraries but fewer sequenced loci

Environmental Characteristics and Anthropogenic Impact Jointly Modify Aquatic Macrophyte Species Diversity

Long‐term movements and home‐range changes: Rapid territory shifts in meerkats

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