Statistical method for testing the neutral mutation hypothesis by DNA polymorphism.

Genotypes are frequently used to identify parentage. Such analysis is notoriously vulnerable to genotyping error, and there is ongoing debate regarding how to solve this problem. Many scientists have used the computer program CERVUS to estimate parentage, and have taken advantage of its option to allow for genotyping error. In this study, we show that the likelihood equations used by versions 1.0 and 2.0 of CERVUS to accommodate genotyping error miscalculate the probability of observing an erroneous genotype. Computer simulation and reanalysis of paternity in Rum red deer show that correcting this error increases success in paternity assignment, and that there is a clear benefit to accommodating genotyping errors when errors are present. A new version of CERVUS (3.0) implementing the corrected likelihood equations is available at http://www.fieldgenetics.com.

Revising how the computer program CERVUS accommodates genotyping error increases success in paternity assignment.

The genetic effects of pleistocene ice ages are approached by deduction from paleoenvironmental information, by induction from the genetic structure of populations and species, and by their combination to infer likely consequences. (1) Recent palaeoclimatic information indicate rapid global reversals and changes in ranges of species which would involve elimination with spreading from the edge. Leading edge colonization during a rapid expansion would be leptokurtic and lead to homozygosity and spatial assortment of genomes. In Europe and North America, ice age contractions were into southern refugia, which would promote genome reorganization. (2) The present day genetic structure of species shows frequent geographic subdivision, with parapatric genomes, hybrid zones and suture zones. A survey of recent DNA phylogeographic information supports and extends earlier work. (3) The grasshopperChorthippus parallelusis used to illustrate such data and processes. Its range in Europe is divided on DNA sequences into five parapatric races, with southern genomes showing greater haplotype diversity — probably due to southern mountain blocks acting as refugia and northern expansion reducing diversity. (4) Comparison with other recent studies shows a concordance of such phylogeographic data over pleistocene time scales. (5) The role that ice age range changes may have played in changing adaptations is explored, including the limits of range, rapid change in new invasions and refugial differentiation in a variety of organisms. (6) The effects of these events in causing divergence and speciation are explored usingChorthippusas a paradigm. Repeated contraction and expansion would accumulate genome differences and adaptations, protected from mixing by hybrid zones, and such a composite mode of speciation could apply to many organisms.

https://www.fc.up.pt/mestr_biodiv/aulas/hewitt_1996.pdf

Some genetic consequences of ice ages, and their role in divergence and speciation

I. the origin of species by means of natural selection

The principles of classification and a classification of mammals. Bulletin of the AMNH ; v. 85

Microsatellite analysis was used to examine parentage and spatial distributions of 62 adult bur oaks Quercus macrocarpa, and 100 saplings in a single stand. Using genotypes scored by PCR products at four microsatellite loci, we determined that 94 saplings matched at least one parent in the stand. Saplings often occur as dense clusters of half-sibs around the presumed maternal parent, and only four adults were seed parents to a large proportion of the saplings sampled. A stump apparently was the seed parent of the largest cluster of half-sibs, which occupied a sizeable light gap opened up by the death of their maternal tree. Approximately half of the saplings appeared to have grown from seeds that had not been removed after falling from the tree, and half from seeds that were dispersed beyond the crown of their maternal parent. Long-distance seed dispersal may be more common than has been previously reported. Extremely high levels of long-distance pollination were indicated, and pollen donors within the stand were generally distributed randomly around maternal trees. More than half of the saplings had paternal parents outside of the stand. This study demonstrates the utility of microsatellite analysis for studying mating systems, seed dispersal and seedling establishment in natural plant populations.

Microsatellite analysis of seed dispersal and parentage of saplings in bur oak, Quercus macrocarpa

The relative success of chimpanzee male mating strategies, the role of male dominance rank and the success of inbreeding avoidance behaviour can only be assessed when paternities are known. We report the probable paternities of 14 chimpanzees included in a long-term behavioural study of chimpanzees ( Pan troglodytes schweinfurthii ) at Gombe National Park, Tanzania. DNA samples were collected noninvasively from shed hair and faeces and genotyped using 13‐16 microsatellite loci characterized in humans. All 14 offspring could be assigned to fathers within the community. While there is a positive relationship between male rank and reproductive success, we demonstrate that a range of male mating strategies (possessiveness, opportunistic mating and consortships) can lead to paternity across all male ranks. Several adult females were at risk of breeding with close male relatives. Most successfully avoided close inbreeding but in one case a high-ranking male in the community mated with his mother and produced an offspring. In contrast to recent data on chimpanzees ( P. t. verus ) from the Tai forest, Cote d’Ivoire, no evidence of extra-group paternity was observed in our study. Reanalysis of Tai data using a likelihood approach casts doubt on the occurrence of extra-group paternity in that community as well.

http://uni-landau.de/umwelt/study/content/files/archiv/h.schulz/ws09/populationsgenetik/constable et al 2001.pdf

Noninvasive paternity assignment in Gombe chimpanzees.

Theory predicts widespread loss of genetic diversity from drift and inbreeding in trees subjected to habitat fragmentation, yet empirical support of this theory is scarce. We argue that population genetics theory may be misapplied in light of ecological realities that, when recognized, require scrutiny of underlying evolu- tionary assumptions. One ecological reality is that fragment boundaries often do not represent boundaries for mating populations of trees that benefit from long-distance pollination, sometimes abetted by long-distance seed dispersal. Where fragments do not delineate populations, genetic theory of small populations does not apply. Even in spatially isolated populations, where genetic theory may eventually apply, evolutionary ar- guments assume that samples from fragmented populations represent trees that have had sufficient time to experience drift, inbreeding, and ultimately inbreeding depression, an unwarranted assumption where stands in fragments are living relicts of largely unrelated predisturbance populations. Genetic degradation may not be as important as ecological degradation for many decades following habitat fragmentation.

http://www.srs.fs.usda.gov/pubs/ja/ja_kramer004.pdf

The paradox of forest fragmentation genetics.

Evolutionarily enlightened management

Microsatellite analysis was used to characterize pollen dispersal in a stand of 62 adult bur oaks (Quercus macrocarpa) in northern Illinois. Using PCR amplification of four dinucleotide microsatellite loci, pollen donors of 282 acorns collected from three adult trees located in different parts of the stand were determined by exclusion. Overall at least 57% of the acorns were pollinated by trees outside of the stand, because all adult trees in the stand were excluded from paternity. Average pollination distance for within-stand pollinations was 75 m, and pollen donors for two of the three maternal trees were randomly dispersed throughout the stand. These two trees also received more pollen from 50 m away than from near neighbors. Self-pollination was rare or nonexistent. This study provides direct evidence for high levels of long-distance pollination in a wind-pollinated species, and contradicts traditional models of wind pollination which suggest that clouds of pollen dissipate from the source to ineffectively low densities over short distances. Instead, the mating system of bur oak seems to be extraordinarily efficient at producing highly outbred individuals and ensuring long-range pollen flow, perhaps through pollen competition or mate choice favoring distant pollen sources.

Mary V. Ashley

Papers

Microsatellite analysis of seed dispersal and parentage of saplings in bur oak, Quercus macrocarpa

Noninvasive paternity assignment in Gombe chimpanzees.

The paradox of forest fragmentation genetics.

Evolutionarily enlightened management

High levels of gene flow in bur oak revealed by paternity analysis using microsatellites