Michael S. Blouin

DNA-based methods for pedigree reconstruction and kinship analysis in natural populations

The widespread use of microsatellite loci has spurred the recent development of many new statistical methods for inferring kin relationships from molecular data. We now have an unprecedented ability to infer detailed genealogical information about individuals in natural populations, but the best approach for a given problem is not always obvious. Researchers in different fields have also been deriving similar methods independently. Thus, some biologists might not be aware of what is even possible. By adopting these new methods, researchers in ecology and evolution could extract far more pedigree information from natural populations than is currently being exploited.

Use of microsatellite loci to classify individuals by relatedness

This study investigates the use of microsatellite loci for estimating relatedness between individuals in wild, outbred, vertebrate populations. We measured allele frequencies at 20 unlinked, dinucleotide‐repeat microsatellite loci in a population of wild mice (Mus musculus), and used these observed frequencies to generate the expected distributions of pairwise relatedness among full sib, half sib, and unrelated pairs of individuals, as would be estimated from the microsatellite data. In this population one should be able to discriminate between unrelated and full‐sib dyads with at least 97% accuracy, and to discriminate half‐sib pairs from unrelated pairs or from full‐sib pairs with better than 80% accuracy. If one uses the criterion that parent‐offspring pairs must share at least one allele per locus, then only 15% of full‐sib pairs, 2% of half‐sib pairs, and 0% of unrelated pairs in this population would qualify as potential parent‐offspring pairs. We verified that the simulation results (which assume a random mating population in Hardy‐Weinberg and linkage equilibrium) accurately predict results one would obtain from this population in real life by scoring laboratory‐bred full‐ and half‐sib families whose parents were wild‐caught mice from the study population. We also investigated the effects of using different numbers of loci, or loci of different average heterozygosities (He), on misclassification frequencies. Both variables have strong effects on misclassification rate. For example, it requires almost twice as many loci of He= 0.62 to achieve the same accuracy as a given number of loci of He= 0.75. Finally, we tested the ability of UPGMA clustering to identify family groups in our population. Clustering of allele matching scores among the offspring of four sets of independent maternal half sibships (four females, each mated to two different males) perfectly recovered the true family relationships.

Fitness of hatchery-reared salmonids in the wild.

Accumulating data indicate that hatchery fish have lower fitness in natural environments than wild fish. This fitness decline can occur very quickly, sometimes following only one or two generations of captive rearing. In this review, we summarize existing data on the fitness of hatchery fish in the wild, and we investigate the conditions under which rapid fitness declines can occur. The summary of studies to date suggests: nonlocal hatchery stocks consistently reproduce very poorly in the wild; hatchery stocks that use wild, local fish for captive propagation generally perform better than nonlocal stocks, but often worse than wild fish. However, the data above are from a limited number of studies and species, and more studies are needed before one can generalize further. We used a simple quantitative genetic model to evaluate whether domestication selection is a sufficient explanation for some observed rapid fitness declines. We show that if selection acts on a single trait, such rapid effects can be explained only when selection is very strong, both in captivity and in the wild, and when the heritability of the trait under selection is high. If selection acts on multiple traits throughout the life cycle, rapid fitness declines are plausible.

Molecular ecology of parasites: elucidating ecological and microevolutionary processes

We review studies that have used molecular markers to address ecological and microevolutionary processes in parasites. Our goal is to highlight areas of research that may be of particular interest in relation to the parasitic lifestyle, and to draw attention to areas that require additional study. Topics include species identification, phylogeography, host specificity and speciation, population genetic structure, modes of reproduction and transmission patterns, and searching for loci under selection.

Molecular prospecting for cryptic species of nematodes: mitochondrial DNA versus internal transcribed spacer

DNA sequence divergence at internal transcribed spacer regions (ITS-1 and ITS-2) was compared with divergence at mitochondrial cox1 or nad4 loci in pairs of congeneric nematode species. Mitochondrial sequences accumulate substitutions much more quickly than internal transcribed spacer, the difference being most striking in the most closely related species pairs. Thus, mitochondrial DNA may be the best choice for applications in which one is using sequence data on small numbers of individuals to search for potential cryptic species. On the other hand, internal transcribed spacer remains an excellent tool for DNA diagnostics (quickly distinguishing between known species) owing to its lower level of intraspecific polymorphism.

Genetic adaptation to captivity can occur in a single generation

Captive breeding programs are widely used for the conservation and restoration of threatened and endangered species. Nevertheless, captive-born individuals frequently have reduced fitness when reintroduced into the wild. The mechanism for these fitness declines has remained elusive, but hypotheses include environmental effects of captive rearing, inbreeding among close relatives, relaxed natural selection, and unintentional domestication selection (adaptation to captivity). We used a multigenerational pedigree analysis to demonstrate that domestication selection can explain the precipitous decline in fitness observed in hatchery steelhead released into the Hood River in Oregon. After returning from the ocean, wild-born and first-generation hatchery fish were used as broodstock in the hatchery, and their offspring were released into the wild as smolts. First-generation hatchery fish had nearly double the lifetime reproductive success (measured as the number of returning adult offspring) when spawned in captivity compared with wild fish spawned under identical conditions, which is a clear demonstration of adaptation to captivity. We also documented a tradeoff among the wild-born broodstock: Those with the greatest fitness in a captive environment produced offspring that performed the worst in the wild. Specifically, captive-born individuals with five (the median) or more returning siblings (i.e., offspring of successful broodstock) averaged 0.62 returning offspring in the wild, whereas captive-born individuals with less than five siblings averaged 2.05 returning offspring in the wild. These results demonstrate that a single generation in captivity can result in a substantial response to selection on traits that are beneficial in captivity but severely maladaptive in the wild.

Population Biology of Parasitic Nematodes: Applications of Genetic Markers

Publisher Summary This chapter describes genetic approaches to answer a variety of questions in the population biology of parasitic helminths. It lays particular emphasis on nematode parasites. The chapter describes levels of heterozygosity revealed by allozymes and patterns of variation in a variety of different sequence types. It illustrates the ways this variation is distributed in parasite populations, and the ways these patterns can be used to ask questions about the various aspects of nematode biology and epidemiology. It also discusses the interspecific level and describes the way genetic approaches have clarified ideas on nematode speciation and revealed a wealth of sibling species. The chapter presents examples of the use of markers for clarifying life cycles and deals with genes responsible for drug resistance. It also discusses other miscellaneous uses of genetic markers. Much of this section is speculative and describes fields in which genetic markers should see a greater usage in the future.

LIFE CYCLES SHAPE PARASITE EVOLUTION: COMPARATIVE POPULATION GENETICS OF SALMON TREMATODES

Abstract Little is known about what controls effective sizes and migration rates among parasite populations. Such data are important given the medical, veterinary, and economic (e.g., fisheries) impacts of many parasites. The autogenic‐allogenic hypothesis, which describes ecological patterns of parasite distribution, provided the foundation on which we studied the effects of life cycles on the distribution of genetic variation within and among parasite populations. The hypothesis states that parasites cycling only in freshwater hosts (autogenic life cycle) will be more limited in their dispersal ability among aquatic habitats than parasites cycling through freshwater and terrestrial hosts (allogenic life cycle). By extending this hypothesis to the level of intraspecific genetic variation, we examined the effects of host dispersal on parasite gene flow. Our a priori prediction was that for a given geographic range, autogenic parasites would have lower gene flow among subpopulations. We compared intraspecific mitochondrial DNA variation for three described species of trematodes that infect salmonid fishes. As predicted, autogenic species had much more highly structured populations and much lower gene flow among subpopulations than an allogenic species sampled from the same locations. In addition, a cryptic species was identified for one of the autogenic trematodes. These results show how variation in life cycles can shape parasite evolution by predisposing them to vastly different genetic structures. Thus, we propose that knowledge of parasite life cycles will help predict important evolutionary processes such as speciation, coevolution, and the spread of drug resistance.

Carry-over effect of captive breeding reduces reproductive fitness of wild-born descendants in the wild

Supplementation of wild populations with captive-bred organisms is a common practice for conservation of threatened wild populations. Yet it is largely unknown whether such programmes actually help population size recovery. While a negative genetic effect of captive breeding that decreases fitness of captive-bred organisms has been detected, there is no direct evidence for a carry-over effect of captive breeding in their wild-born descendants, which would drag down the fitness of the wild population in subsequent generations. In this study, we use genetic parentage assignments to reconstruct a pedigree and estimate reproductive fitness of the wild-born descendants of captive-bred parents in a supplemented population of steelhead trout (Oncorhynchus mykiss). The estimated fitness varied among years, but overall relative reproductive fitness was only 37 per cent in wild-born fish from two captive-bred parents and 87 per cent in those from one captive-bred and one wild parent (relative to those from two wild parents). Our results suggest a significant carry-over effect of captive breeding, which has negative influence on the size of the wild population in the generation after supplementation. In this population, the population fitness could have been 8 per cent higher if there was no carry-over effect during the study period.

A comparison between mitochondrial DNA and the ribosomal internal transcribed regions in prospecting for cryptic species of platyhelminth parasites

We examined the relative merits of mitochondrial DNA loci and ribosomal DNA internal transcribed spacers for their use in prospecting for cryptic species of platyhelminth parasites. Sequence divergence at ITS1 and ITS2 was compared with divergence at 2 mtDNA loci (NADH dehydrogenase-1 and cytochrome c oxidase I) between closely related species of trematodes and cestodes. Both spacers accumulated substitutions substantially more slowly than mtDNA, which clearly shows a higher level of divergence among species relative to intra-specific variation. Besides a slow rate of substitution, other caveats that may be encountered when using ITS sequences as a prospecting marker are discussed. In particular, we note recent studies that suggest the existence of substantial levels of intra-individual variation in ITS sequences of flatworms. Because it is likely that closely related species share this phenomenon, it may confound the detection of cryptic species, especially if small sample sizes are studied. Although potential limitations of mtDNA are also recognized, the higher rate of evolution and smaller effective population size of this marker increases the probability of detecting diagnostic characters between cryptic species.