Assessing spatial genetic structure from molecular marker data via principal component analyses: A case study in a &lt;i&gt;Prosopis&lt;/i&gt; sp. forest

Expressed sequence tag – polymerase chain reaction (EST-PCR) molecular markers were used to infer spatial genetic structure of four lowbush blueberry ( Vaccinium angustifolium Ait.) fields in Maine. Genetic structure was quantified at three spatial scales: (1) within apparent clones (intrapatch), (2) among clones within a field, and (3) among fields separated by as much as 65 km. Of five “clones” or putative individuals examined in the intrapatch study, two showed complete genetic homogeneity within the patch, while three showed some band differences at their edges compared with their interiors. These differences at the edges, however, matched adjacent clones (so-called “intruders”), from which it was concluded that lowbush blueberry exhibits a fairly tight, phalanx clonal architecture with no evidence of invasive seedling establishment within clones. No significant correlation between genetic and physical distance was found among clones within fields via several statistical approaches. Significant among-field genetic differentiation was found via AMOVA (ΦPT = 8.4%; p ≤ 0.01) based upon transect samples across four fields ranging from 12.5 to 65 km apart. Principal component analysis and spatial autocorrelation (SA) corroborated these findings. Significant positive SA was found at the within-field distance class of <350 m, but SA decreased to an insignificant value by the first interfield distance of 12.5 km. A special form of SA analysis was employed to detect “hotspots” of genetic similarity between pairs of adjacent clones in two fields. Results indicated that 5 of 23 pairs of clones (21.7%) were genetically similar to each other, while the majority of pairs (18 of 23; 78.3%) showed random, decreasing patterns of genetic similarity. Results are discussed in terms of clonal dynamics including architecture, seedling recruitment, and inferred pollen or seed dispersal distances.

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Comparison of fine-scale spatial genetic structure of two sympatric Rhododendron shrub species in forest habitat having different seed weights: A case study

Silvae Genetica ◽

10.1515/sg-2016-0015 ◽

2016 ◽

Vol 65 (2) ◽

pp. 39-45 ◽

Cited By ~ 1

Author(s):

Mineaki Aizawa ◽

Chisa Nakayama ◽

Tatsuhiro Ohkubo

Keyword(s):

Genetic Structure ◽

Seed Dispersal ◽

Spatial Genetic Structure ◽

Safe Sites ◽

Shortest Distance ◽

Nuclear Microsatellite ◽

Kanto District ◽

The Difference ◽

Selection Of

Abstract Restricted seed dispersal is one of the most prevalent determinants of spatial genetic structure (SGS) at a fine spatial scale within a plant population. Rhododendron kaempferi and R. semibarbatum are common and coexistent Ericaceous species in the shrub layer of secondary deciduous broad-leaved forests in the northern Kanto District, central Japan. The two species have entomophilous flowers and are thought to have similar pollination styles. However, R. kaempferi produces threefold heavier seeds than R. semibarbatum. Therefore, we tested the hypothesis that the intensity of SGS was stronger in R. kaempferi than in R. semibarbatum in a forest stand. We comparatively examined the SGS for 73 individuals of R. kaempferi and 36 individuals of R. semibarbatum by using highly variable nuclear microsatellite loci. The analysis revealed significant SGS in both species at the shortest distance (<3 m); a measure to quantify SGS showed a counterintuitive result: R. semibarbatum exhibited stronger SGS than R. kaempferi. This result might be explained by the ecological consequences of R. semibarbatum producing lighter seeds, which might have greater dispersal efficacy, but its safe sites could be more restricted than those of R. kaempferi; in contrast, R. kaempferi producing heavier seeds might have more limited seed dispersal, but its safe sites for seedling establishment could be more prevalent than those for R. semibarbatum. The different strategies for the trade-off between seed weight and site selection of the two Rhododendron species might be reflected in the difference in the intensity of SGS in this study plot.

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Analysis of function in the absence of extant functional homologues: a case study using mesotheriid notoungulates (Mammalia)

Paleobiology ◽

10.1666/05052.1 ◽

2007 ◽

Vol 33 (2) ◽

pp. 227-247 ◽

Cited By ~ 38

Author(s):

Bruce J. Shockey ◽

Darin A. Croft ◽

Federico Anaya

Keyword(s):

Morphological Traits ◽

Principal Component ◽

Axial Skeleton ◽

Estimating Function ◽

Analog Method ◽

Principal Component Analyses ◽

Analysis Of Function ◽

Functional Homologues ◽

Discriminant Function Analyses

We use two approaches to test hypotheses regarding function in a group of extinct mammals (Family Mesotheriidae, Order Notoungulata) that lack any close extant relatives: a principle-derived paradigm method and empirically derived analog method. Metric and discrete morphological traits of mesotheriid postcranial elements are found to be consistent with the morphology predicted by a modified version of Hildebrand's paradigm for scratch diggers. Ratios of in-force to out-force lever arms based on skeletal elements indicate that the mesotheriids examined had limbs modified for high out-forces (i.e., they were “low geared”), consistent with the digging hypothesis. Other mesotheriid characters, such as cleft ungual phalanges, a curved olecranon, and a highly modified pelvis (with extra vertebrae incorporated into the sacrum and fusion between the ischium and the axial skeleton) are regarded as being functionally significant for digging and also occur in a variety of extant diggers. Analog methods indicate that mesotheriids share numerous traits common to a variety of extant diggers. Principal component analyses of postcranial elements indicate that mesotheriids consistently share morphometric space with larger extant fossorial mammals: aardvark, anteaters, wombats, and badger. Likewise, discriminant function analyses categorized mesotheriids as fossorial, though imperfectly analogous to the extant diggers analyzed. Thus, both theory-driven and empirically derived methods of estimating function in these extinct taxa support a digging hypothesis for the mesotheriids examined. Adaptations for digging in both the forelimb and sacropelvic functional complexes of mesotheriids provide independent support for the fossorial hypothesis.

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