Joanna R. Freeland

Applications and Implications of Neutral versus Non-neutral Markers in Molecular Ecology

The field of molecular ecology has expanded enormously in the past two decades, largely because of the growing ease with which neutral molecular genetic data can be obtained from virtually any taxonomic group. However, there is also a growing awareness that neutral molecular data can provide only partial insight into parameters such as genetic diversity, local adaptation, evolutionary potential, effective population size, and taxonomic designations. Here we review some of the applications of neutral versus adaptive markers in molecular ecology, discuss some of the advantages that can be obtained by supplementing studies of molecular ecology with data from non-neutral molecular markers, and summarize new methods that are enabling researchers to generate data from genes that are under selection.

THE MITOCHONDRIAL AND NUCLEAR GENETIC HOMOGENEITY OF THE PHENOTYPICALLY DIVERSE DARWIN'S GROUND FINCHES

The most extensively studied group of Darwins finches is the genus Geospiza, the ground finches, and yet little is known about the evolutionary history and genetic relationships of these birds. Studies using either allozyme or morphological data have been unable to resolve relationships between the six species and numerous populations of ground finches. In this paper we report the results of a study using mitochondrial control region and nuclear internal transcribed spacer (ITS) 1 sequence data. The differentiation of the ground finch species based on morphological data is not reflected in either mitochondrial or nuclear DNA sequence phylogenies. Furthermore, there is little concordance between the mitochondrial haplotypes and ITS alleles found within individuals. We suggest that the absence of species‐specific lineages can be attributed to ongoing hybridization involving all six species of Geospiza. There are no long term selective pressures against hybridization within this genus, and therefore a genetically homogenous genus may be maintained indefinitely. Hybridization has apparently played a role in the adaptive radiation of Darwins finches.

Long-distance dispersal and high genetic diversity are implicated in the invasive spread of the common reed, Phragmites australis (Poaceae), in northeastern North America

PREMISE OF THE STUDY The Eurasian subspecies of the common reed (Phragmites australis subsp. australis, hereafter abbreviated as P. a. australis) was introduced to North America in the late 18(th) century and rapidly expanded its range, posing an ecological threat to wetlands. In this study, we aimed to determine whether admixture among multiple lineages, dispersal mechanisms, and high genetic diversity have contributed to the invasion of P. a. australis in the northeastern part of its range. Understanding mechanisms of the P. a. australis invasion will 1) contribute to a broader understanding of the factors that facilitate plant invasion, and 2) help us to develop effective management strategies for wetlands threatened by P. a. australis invasion. METHODS We used a population genetics approach incorporating nine microsatellite loci to study genetic diversity and population structure in relation to biogeography of introduced North American Phragmites a. australis stands in the northeastern continental region. KEY RESULTS Phragmites a. australis is genetically diverse in the region studied here. Significant population structure exists, and population structure is likely influenced by both long-distance dispersal via major waterways, and short-distance dispersal overland. Different lineages sometimes colonize geographically proximate locations leading to opportunities for admixture. Clonal reproduction likely exaggerates geographical structure among some stands, although high genetic and clonal diversity within some stands implies that sexual reproduction occurs frequently in P. a. australis. CONCLUSIONS A variety of factors, including admixture among multiple lineages, multiple modes of dispersal, and plasticity in reproductive strategy promote the invasion success of Phragmites a. australis. Wetland managers in the St. Lawrence River/Great Lakes region should focus monitoring efforts on the shores of conservation lands to prevent the establishment of propagules from novel lineages.

Community genetics: resource addition has opposing effects on genetic and species diversity in a 150-year experiment.

We used the Park Grass Experiment, begun in 1856, to test alternative hypotheses about the relationship between genetic diversity and plant species diversity. The niche variation hypothesis predicts that populations with few interspecific competitors and hence broader niches are expected to contain greater genetic diversity. The coexistence hypothesis predicts that genetic diversity within species favours coexistence among species and therefore species and genetic diversity should be positively correlated. Amplified Fragment Length Polymorphism (AFLP) markers were used to measure the genetic diversity of populations of Anthoxanthum odoratum growing in 10 plots of differing species richness that lie along resource and soil pH gradients. Genetic diversity in A. odoratum was positively correlated with the number of resources added to a plot, but not correlated with species richness. However, separate analyses have shown a negative correlation between resource addition and species richness at Park Grass and elsewhere, so genetic and species diversity appear to respond in opposite directions.

Selection pressures have caused genome-wide population differentiation of Anthoxanthum odoratum despite the potential for high gene flow

The extent to which divergent selection can drive genome‐wide population differentiation remains unclear. Theory predicts that in the face of ongoing gene flow, population differentiation should be apparent only at those markers that are directly or indirectly (i.e. through linkage) under selection. However, if reproductive barriers limit gene flow, genome‐wide population differentiation may occur even in geographically proximate populations. Some insight into the link between selection and genetic differentiation in the presence of ongoing gene flow can come from long‐term experiments such as The Park Grass Experiment, which has been running for over 150 years, and provides a unique example of a heterogeneous environment with a long and detailed history. Fertilizer treatments applied in the Park Grass Experiment have led to rapid evolutionary change in sweet vernal grass Anthoxanthum odoratum, but until now, nothing was known of how these changes would be reflected in neutral molecular markers. We have genotyped ten A. odoratum populations from the Park Grass Experiment using Amplified Fragment Length Polymorphisms (AFLPs). Our data show that nutrient additions have resulted in genome‐wide divergence among plots despite the high potential for ongoing gene flow. This provides a well‐documented example of concordance between genomes and environmental conditions that has arisen in continuous populations across a time span of fewer than 75 generations.

Extra,pair paternity in willow ptarmigan broods: measuring costs of polygyny to males

Willow ptarmigan are one of only three monogamous grouse species in North America. However, in some populations between 5 and 20% of individuals pair polygynously. It has been suggested that monogamy may be maintained by the high cost of polygyny to males. We have used DNA fingerprinting to assess the actual reproductive success of both monogamous and polygynous adults. We determined whether or not the putative parents were the biological parents of the chicks from 38 broods. Of these clutches 30 were from monogamous matings, and 8 were from bigamous matings. Of the 207 chicks from monogamous matings 96% were within-pair offspring, compared to 67% of the 49 chicks from bigamous matings. All extra-pair offspring chicks resulted from extra-pair fertilizations (EPFs), and there were no instances of intraspecific nest parasitism. Mate guarding by monogamous males seems to be a highly effective method for maintaining genetic monogamy, as the only cases in which EPFs occurred were when the resident female left the territory for a few days or when a second female visited the territory. Our results support the notion that certainty of parentage may be one factor constraining willow ptarmigan males to be monogamous.

Genetic diversity and widespread haplotypes in a migratory dragonfly, the common green darner Anax junius

Abstract.  1. Species that undertake regular two‐way migration may be expected, through population connectivity, to exhibit some level of genetic similarity over broad spatial scales. Although seldom following two‐way migration, highly mobile insect species tend to exhibit either low haplotype diversity and no phylogeographic structuring, or relatively high haplotype diversity and pronounced phylogeographic structuring.

Phylogenetics of Darwin's finches : Paraphyly in the tree-finches, and two divergent lineages in the Warbler finch

The Galapagos Darwins finches (Geospizinae) have been classified as three major groups based on morphology and behavior: ground-finches, tree-finches, and the Warbler Finch (Certhidea olivacea). Little is known about the evolutionary relationships within and among these groups, which is partly due to the lack of a phylogeny based on molecular sequence data. We used mitochondrial sequence data to reconstruct a phylogeny of Darwins finches. These data show that within the tree-finches, only one genus is conclusively monophyletic, and another is conclusively paraphyletic. It may be appropriate to uphold the classification of the tree-finches into two genera. The Warbler Finch complex is paraphyletic, as revealed by two divergent genetic lineages contained within this species. Stochastic lineage sorting within relatively recently diverged species and interspecific and intergeneric hybridization are the two most likely explanations for the sharing of haplotypes among taxa.

Phylogeographic inferences from chloroplast DNA: quantifying the effects of mutations in repetitive and non-repetitive sequences.

Phylogeographic inference can be a powerful tool in reconstructing species’ evolutionary histories; however, although inferred phylogeographic patterns should depend in part on the underlying types and rates of mutations, the effects of different types of mutations have seldom been quantified. In this study we identified two chloroplast minisatellites in the common reed Phragmites australis, and showed that these are more variable than chloroplast microsatellites. We then recreated parsimony networks of the global phylogeography of P. australis based on data that either included or excluded repetitive sequences (minisatellites and microsatellites), thereby illustrating the influence that these repetitive sequences can have on large‐scale phylogeographic inference. The resulting networks differed in the numbers of mutational steps, degrees of uncertainty, and total numbers of haplotypes. In addition, the suggested ancestor‐descendant relationships among lineages changed substantially depending on whether repetitive sequences were included. We therefore caution against the inclusion of repetitive sequences in large‐scale networks because of their high potential for homoplasy. Nevertheless, we advocate the inclusion of repetitive sequences in other analyses: specifically, we show that the ratio of mutations in repetitive vs. non‐repetitive regions can provide insight into the relative ages of lineages.

Gene flow and genetic diversity: a comparison of freshwater bryozoan populations in Europe and North America

We have used microsatellite and mitochondrial sequence data to gain insight into patterns of gene flow and genetic diversity among North American and European populations of the freshwater bryozoan Cristatella mucedo. Mitochondrial sequence data reveal numerous, widely distributed, divergent genetic lineages in North America that can be broadly categorized into two groups, one of which is genetically homogenous and relatively similar to the European haplotypes, the other of which is more diverse. The maximum North American sequence differentiation translates into a divergence time of approximately 1.5 Myr BP. In contrast, European populations contained only three haplotypes that are all closely related. Microsatellite data reveal higher overall levels of genetic diversity in North America than Europe, although levels of within-population genetic variation are similar on the two continents. In North America, two of the three microsatellite loci show bimodal distributions of allele sizes which are significantly associated between the two loci. As a result, two microsatellite lineages are evident, and these are assortatively distributed between the mitochondrial haplotype groupings. The combined mitochondrial and microsatellite data suggest two distinct genetic lineages in North America that may represent cryptic species. Hybridization between the two presumptive species or subspecies may have contributed to the high levels of genetic diversity in North America. The overall lower levels of genetic diversity in Europe can be attributed to postglacial derivation of extant populations from a single mitochondrial lineage, and conformation to a metapopulation structure.