Fred W. Allendorf

The problems with hybrids: setting conservation guidelines

Abstract Rates of hybridization and introgression are increasing dramatically worldwide because of translocations of organisms and habitat modifications by humans. Hybridization has contributed to the extinction of many species through direct and indirect means. However, recent studies have found that natural hybridization has played an important role in the evolution of many plant and animal taxa. Determining whether hybridization is natural or anthropogenic is crucial for conservation, but is often difficult to achieve. Controversy has surrounded the setting of appropriate conservation policies to deal with hybridization and introgression. Any policy that deals with hybrids must be flexible and must recognize that nearly every situation involving hybridization is different enough that general rules are not likely to be effective. We provide a categorization of hybridization to help guide management decisions

Gene Nomenclature for Protein‐Coding Loci in Fish

Abstract The Fish Genetics Section of the American Fisheries Society established its Nomenclature Committee to develop and promote standardized genetic nomenclatures. Here, following public comments on previously published draft guidelines, we present the committees revised version of a nomenclature for protein-coding loci in fish. This nomenclature closely parallels the one used for human genetics, but improves on it in several respects. The fish system (1) includes standardized abbreviations for commonly analyzed proteins, and provides formal symbols for gene loci encoding these proteins; (2) specifies typographic conventions for distinguishing between genes and proteins and for identifying alleles; (3) provides for multilocus isozyme systems, isoloci, regulatory loci, and pseudogenes; (4) allows important basic information (such as subcellular distributions of gene products, active substrate isomers, recent gene duplicates, and orthologous relationships among loci) to be specified in gene symbols via ...

Genomics and the future of conservation genetics

We will soon have complete genome sequences from thousands of species, as well as from many individuals within species. This coming explosion of information will transform our understanding of the amount, distribution and functional significance of genetic variation in natural populations. Now is a crucial time to explore the potential implications of this information revolution for conservation genetics and to recognize limitations in applying genomic tools to conservation issues. We identify and discuss those problems for which genomics will be most valuable for curbing the accelerating worldwide loss of biodiversity. We also provide guidance on which genomics tools and approaches will be most appropriate to use for different aspects of conservation.

Fluctuating asymmetry as an indicator of stress: Implications for conservation biology

Extinction can be attributed broadly to environmental or genetic stress. The ability to detect such stresses before they seriously affect a population can enhance the effectiveness of conservation programs. Recent studies have shown that within-individual morphological variability may provide a valuable early indicator of environmental and genetic stress.

What can genetics tell us about population connectivity

Genetic data are often used to assess ‘population connectivity’ because it is difficult to measure dispersal directly at large spatial scales. Genetic connectivity, however, depends primarily on the absolute number of dispersers among populations, whereas demographic connectivity depends on the relative contributions to population growth rates of dispersal vs. local recruitment (i.e. survival and reproduction of residents). Although many questions are best answered with data on genetic connectivity, genetic data alone provide little information on demographic connectivity. The importance of demographic connectivity is clear when the elimination of immigration results in a shift from stable or positive population growth to negative population growth. Otherwise, the amount of dispersal required for demographic connectivity depends on the context (e.g. conservation or harvest management), and even high dispersal rates may not indicate demographic interdependence. Therefore, it is risky to infer the importance of demographic connectivity without information on local demographic rates and how those rates vary over time. Genetic methods can provide insight on demographic connectivity when combined with these local demographic rates, data on movement behaviour, or estimates of reproductive success of immigrants and residents. We also consider the strengths and limitations of genetic measures of connectivity and discuss three concepts of genetic connectivity that depend upon the evolutionary criteria of interest: inbreeding connectivity, drift connectivity, and adaptive connectivity. To conclude, we describe alternative approaches for assessing population connectivity, highlighting the value of combining genetic data with capture‐mark‐recapture methods or other direct measures of movement to elucidate the complex role of dispersal in natural populations.

Usefulness of molecular markers for detecting population bottlenecks via monitoring genetic change

It is important to detect population bottlenecks in threatened and managed species because bottlenecks can increase the risk of population extinction. Early detection is critical and can be facilitated by statistically powerful monitoring programs for detecting bottleneck‐induced genetic change. We used Monte Carlo computer simulations to evaluate the power of the following tests for detecting genetic changes caused by a severe reduction in a populations effective size (Ne): a test for loss of heterozygosity, two tests for loss of alleles, two tests for change in the distribution of allele frequencies, and a test for small Ne based on variance in allele frequencies (the ‘variance test’). The variance test was most powerful; it provided an 85% probability of detecting a bottleneck of size Ne = 10 when monitoring five microsatellite loci and sampling 30 individuals both before and one generation after the bottleneck. The variance test was almost 10‐times more powerful than a commonly used test for loss of heterozygosity, and it allowed for detection of bottlenecks before 5% of a populations heterozygosity had been lost. The second most powerful tests were generally the tests for loss of alleles. However, these tests had reduced power for detecting genetic bottlenecks caused by skewed sex ratios. We provide guidelines for the number of loci and individuals needed to achieve high‐power tests when monitoring via the variance test. We also illustrate how the variance test performs when monitoring loci that have widely different allele frequency distributions as observed in five wild populations of mountain sheep (Ovis canadensis).

Genetic effects of harvest on wild animal populations

Human harvest of animals in the wild occurs in terrestrial and aquatic habitats throughout the world and is often intense. Harvest has the potential to cause three types of genetic change: alteration of population subdivision, loss of genetic variation, and selective genetic changes. To sustain the productivity of harvested populations, it is crucial to incorporate genetic considerations into management. Nevertheless, it is not necessary to disentangle genetic and environmental causes of phenotypic changes to develop management plans for individual species. We recommend recognizing that some genetic change due to harvest is inevitable. Management plans should be developed by applying basic genetic principles combined with molecular genetic monitoring to minimize harmful genetic change.

Genome 10K: A Proposal to Obtain Whole-Genome Sequence for 10 000 Vertebrate Species

The human genome project has been recently complemented by whole-genome assessment sequence of 32 mammals and 24 nonmammalian vertebrate species suitable for comparative genomic analyses. Here we anticipate a precipitous drop in costs and increase in sequencing efficiency, with concomitant development of improved annotation technology and, therefore, propose to create a collection of tissue and DNA specimens for 10,000 vertebrate species specifically designated for whole-genome sequencing in the very near future. For this purpose, we, the Genome 10K Community of Scientists (G10KCOS), will assemble and allocate a biospecimen collection of some 16,203 representative vertebrate species spanning evolutionary diversity across living mammals, birds, nonavian reptiles, amphibians, and fishes (ca. 60,000 living species). In this proposal, we present precise counts for these 16,203 individual species with specimens presently tagged and stipulated for DNA sequencing by the G10KCOS. DNA sequencing has ushered in a new era of investigation in the biological sciences, allowing us to embark for the first time on a truly comprehensive study of vertebrate evolution, the results of which will touch nearly every aspect of vertebrate biological enquiry.

Estimation of census and effective population sizes: the increasing usefulness of DNA-based approaches

Population census size (NC) and effective population sizes (Ne) are two crucial parameters that influence population viability, wildlife management decisions, and conservation planning. Genetic estimators of both NC and Ne are increasingly widely used because molecular markers are increasingly available, statistical methods are improving rapidly, and genetic estimators complement or improve upon traditional demographic estimators. We review the kinds and applications of estimators of both NC and Ne, and the often undervalued and misunderstood ratio of effective-to-census size (Ne/NC). We focus on recently improved and well evaluated methods that are most likely to facilitate conservation. Finally, we outline areas of future research to improve Ne and NC estimation in wild populations.

Harnessing genomics for delineating conservation units

Genomic data have the potential to revolutionize the delineation of conservation units (CUs) by allowing the detection of adaptive genetic variation, which is otherwise difficult for rare, endangered species. In contrast to previous recommendations, we propose that the use of neutral versus adaptive markers should not be viewed as alternatives. Rather, neutral and adaptive markers provide different types of information that should be combined to make optimal management decisions. Genetic patterns at neutral markers reflect the interaction of gene flow and genetic drift that affects genome-wide variation within and among populations. This population genetic structure is what natural selection operates on to cause adaptive divergence. Here, we provide a new framework to integrate data on neutral and adaptive markers to protect biodiversity.