Comparison of distance matrices in studies of population structure and genetic microdifferentiation: Quadratic assignment

Dow, Malcolm M.; Cheverud, James M.

doi:10.1002/ajpa.1330680307

Cited by 127 publications

(88 citation statements)

References 33 publications

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“…Applications in other fields are also possible. In anthropology, for example, the migration patterns of human populations (Keegan and Diamond, 1987;Irwin, 1992) could be reconstructed from site similarities in archeological artifacts, linguistics, genetics (Dow and Cheverud, 1985) or genetic surrogates (e.g. surnames) (Lasker, 1985;Piazza et al, 1987).…”

Section: Discussionmentioning

confidence: 99%

“…Furthermore, the matrix comparison method can be used in an exploratory context to reveal underlying geographic structure, or it can be applied in a confirmatory inference mode to test geographic hypotheses (Hubert, 1980). Applications of the Mantel test in evolutionary biology (Douglas and Endler, 1982;Dietz, 1983;Dow and Cheverud, 1985;Schnell et al, 1985;Manly, 1985Manly, , 1986 and ecology (Schnell et ai, 1986;Burgman, 1987;Harvey etal., 1988;Legendre and Fortin, 1989) have demonstrated its inferential advantages. Manly (1991) and Upton and Fingleton (1985) provide numerous examples of biogeographical interest.…”

Section: Hypothesis Testingmentioning

confidence: 99%

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Spatial patterns of inter‐island plant and bird species movements in the Galápagos Islands

Harvey

1994

Journal of the Royal Society of New Zealand

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An asymmetric similarity index, defined as the proportion of species that one island has in common with a second, was introduced to infer inter-island colonization patterns from species lists. The matrix comparison or Mantel test was used to analyze the index for spatial patterns of species composition. Directional inter-island colonization was inferred from the skew-symmetric component of the index. Four biogeographical hypotheses were tested for the inter-island colonization of plants among 17 Galapagos islands and among 15 islands for birds. Plant and bird species composition and their inter-island colonization patterns are distance-dependent. More specifically, species density gradients are a function of the configuration of islands in the archipelago. The net direction of bird and plant density gradients for the archipelago increases from the south. Plant density gradients are significantly correlated with the prevailing northwest flow of the Humboldt Current, but bird density gradients are uncorrelated with the Humboldt Current or with the gradients of plant species. These results corroborate the most popular model of colonization for the Galapagos Archipelago: an initial colonization of islands in the southeast, and subsequent colonization of islands to the north and northwest.

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Section: Discussionmentioning

confidence: 99%

Section: Hypothesis Testingmentioning

confidence: 99%

Spatial patterns of inter‐island plant and bird species movements in the Galápagos Islands

Harvey

1994

Journal of the Royal Society of New Zealand

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“…Finally, the similarity between a D 2 distance matrix and the corresponding size or shape distance matrix was assessed by Mantel's matrix permutation procedure (Mantel, 1967;Dietz, 1983;Dow and Cheverud, 1985;Mizoguchi, 1993b). This indicates the degree of contribution of size or shape differences across common factors, which may be genes, common environmental factors, or composites of both, to the D 2 distances.…”

Section: Statistical Methods Usedmentioning

confidence: 99%

Typicality probabilities of Late Pleistocene human fossils from East Asia, Southeast Asia, and Australia: implications for the Jomon population in Japan

Mizoguchi

2011

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The question of the origins of the Jomon population is examined by Campbell's predictive approach, a method using 'typicality probability' which is currently the best way of comparing a single specimen with a reference population. Among the five Pleistocene fossils compared with a Late/Final Jomon sample from the Tohoku district, the analysis based on 13 cranial measurements revealed that Keilor from Australia was more likely a member of the Jomon population than Minatogawa I from Okinawa and Liujiang from southern China. Although, from a chronological viewpoint, it is not possible for Keilor to be an ancestor of the Jomon, these results suggest that the Australian Late Pleistocene population, or their ancestors, should also be considered when seeking the origins of the Jomon.

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“…Matrix permutations (10,000 iterations) were then used to assess significance, with the alpha level set at α = 0.05. Subsequently, Dow-Cheverud tests (Dow and Cheverud, 1985) were conducted to determine whether any of the morphological distance matrices were more strongly correlated with the genetic distance matrix than were others. Dow-Cheverud tests were executed in R using a script written by the lab of Charles Roseman.…”

Section: Comparing Morphometric and Genetic Distance Matricesmentioning

confidence: 99%

The relative correspondence of cranial and genetic distances in papionin taxa and the impact of allometric adjustments

Smith

Cramon‐Taubadel

2015

Journal of Human Evolution

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The reconstruction of phylogenetic relationships in the primate fossil record is dependent upon a thorough understanding of the phylogenetic utility of craniodental characters. Here, we test three previously proposed hypotheses for the propensity of primate craniomandibular data to exhibit homoplasy using a study design based on the relative congruence between cranial distance matrices and a consensus genetic distance matrix ("genetic congruence") for papionin taxa: 1.Matrices based on cranial regions subjected to less masticatory strain are more genetically congruent than high-strain cranial matrices; 2. Matrices based on cranial regions developing earlier in ontogeny are more genetically congruent than matrices based on regions that develop later; 3.Matrices based on cranial regions with greater anatomical/functional complexity are more genetically congruent than matrices based on anatomically simpler regions.Morphological distance matrices based on the shape of 15 different cranial regions, delineated on the basis of previous catarrhine studies, were statistically compared to matrices of known genetic distances in papionins. Since sexual dimorphism and allometry are known to characterize this clade, several analytical iterations were conducted: 1) mixed-sex, male-only, and female-only analyses; 2) with and without an allometric scaling adjustment. Across all data sets, the chondrocranium matrix was the most consistently correlated with genetic distances, which is also consistent with previous studies of cercopithecoid taxa, however there was no consistent support for the internal predictions of the three hypotheses tested. Allometric scaling corrections had the largest impact on the genetic congruence of facial shape matrices, a result which is consistent with previous studies that have described facial homoplasy in papionin taxa. These findings differ from patterns described for hominoid taxa, suggesting that no single predictive criterion can explain phylogenetic utility of cranial datasets across catarrhine primate taxa. Many of the differences in morphological-genetic matrix correlations could result from different levels of phenotypic integration and evolvability in cercopithecoids and hominoids, suggesting that further study of these phenomena in extant primates is warranted.2

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Comparison of distance matrices in studies of population structure and genetic microdifferentiation: Quadratic assignment

Cited by 127 publications

References 33 publications

Spatial patterns of inter‐island plant and bird species movements in the Galápagos Islands

Spatial patterns of inter‐island plant and bird species movements in the Galápagos Islands

Typicality probabilities of Late Pleistocene human fossils from East Asia, Southeast Asia, and Australia: implications for the Jomon population in Japan

The relative correspondence of cranial and genetic distances in papionin taxa and the impact of allometric adjustments

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