Quantitative and Molecular Genetic Variation in Captive Cotton-Top Tamarins (Saguinus oedipus)

Most genetic surveys of captive and endangered populations are carried out with single gene characters bearing no direct relationship to life history or other features for which genetic variation needs to be maintained. Quantitative genetic estimates of heritable variation for life-history traits may be a more direct and appropriate measure of genetic variation for some conservation purposes. Furthermore, recent theoretical and empirical results indicate that genetic variation measured on these two levels may not be concordant. We analyzed heterozygosity at 41 allozyme loci and heritability for body weight in captive cotton-top tamarins ( Saguinus oedipus ) from the Marmoset Research Center of the Oak Ridge Associated Universities in order to compare these two levels of genetic variation. Cotton-top tamarins are a highly endangered species native to Colombia. Many animals currently reside in research facilities and zoological parks. A total of 106 animals were used in the isozyme survey, while data on 364 animals contributed to the quantitative genetic study of body weight. We found a very low average heterozygosity ( H = 1%) for this colony. Body weight was moderately and significantly heritable ( h ² = 35%). This heritability is within the normal range for natural animal populations. The finding of biologically significant levels of heritability in a population with abnormally low allozyme heterozygosity illustrates the point that low levels of allozyme heterozygosity should not be taken as an indication of overall lack of genetic variation in important quantitative characters such as life-history traits. Genetic variation required for adaptation of species to future environmental challenges can exist despite low levels of enzyme heterozygosity.     

Population genetics of the family ostreidae. II. Interspecific studies of the genera Crassostrea and Saccostrea

The estimated levels of genetic variation are reported for 6 Crassostrea and 3 Saccostrea species. The estimates are based on examination of 25 to 34 genetic loci. The average heterozygosities ranged from 6 to 22% for the Crassostrea species and from 17 to 19% for the Saccostrea species. A new sibling species (S. manilai) from the Philippines has been identified by means of protein electrophoresis. The genetic similarity and distance between species has been computed for each genus. Also, a pairwise comparison of loci and a dendrogram of the phylogenetic relationship of species has been constructed from the two genera. Some of the taxonomic levels during oyster speciation have been computed from the data of the electrophoretic study of the two lineages. The possibilities of oyster superspecies (e. g. C. gigas, C. virginica and S. cucullata) are discussed based on our population genetic study.     

Conservation Genetics of Potentially Endangered Mutualisms: Reduced Levels of Genetic Variation in Specialist versus Generalist Bees

Abstract:  Oligolectic bees collect pollen from one or a few closely related species of plants, whereas polylectic bees visit a variety of flowers for pollen. Because of their more restricted range of host plants, it maybe expected that specialists exist in smaller, more isolated populations, with lower effective population sizes than generalists. Consequently, we hypothesized that oligolectic bees have reduced levels of genetic variation relative to related polylectic species. To test this hypothesis, we used five phylogenetically independent pairs of species in which one member was oligolectic and the other was polylectic. We assayed genetic variation in our species pairs at an average of 32 allozyme loci. Within each species pair, the oligolectic member had fewer polymorphic loci, lower average allelic richness, and lower average expected heterozygosity than its polylectic relative. Averaged over all species pairs, this corresponds to a 21% reduction in allelic richness, a 72% reduction in the proportion of polymorphic loci, and an 83% reduction in expected heterozygosity in specialists compared with generalists. Our data support the hypothesis of reduced effective population size in oligolectic bees and suggest that they may be more prone to extinction as a result. We suggest that in instances in which bee specialists are involved in mutually codependent relationships with their floral hosts, these mutualisms may be endangered for genetic and ecological reasons.     

Meta-analysis of susceptibility of woody plants to loss of genetic diversity through habitat fragmentation

Shrubs and trees are assumed less likely to lose genetic variation in response to habitat fragmentation because they have certain life-history characteristics such as long lifespans and extensive pollen flow. To test this assumption, we conducted a meta-analysis with data on 97 woody plant species derived from 98 studies of habitat fragmentation. We measured the weighted response of four different measures of population-level genetic diversity to habitat fragmentation with Hedge's d and Spearman rank correlation. We tested whether the genetic response to habitat fragmentation was mediated by life-history traits (longevity, pollination mode, and seed dispersal vector) and study characteristics (genetic marker and plant material used). For both tests of effect size habitat fragmentation was associated with a substantial decrease in expected heterozygosity, number of alleles, and percentage of polymorphic loci, whereas the population inbreeding coefficient was not associated with these measures. The largest proportion of variation among effect sizes was explained by pollination mechanism and by the age of the tissue (progeny or adult) that was genotyped. Our primary finding was that wind-pollinated trees and shrubs appeared to be as likely to lose genetic variation as insect-pollinated species, indicating that severe habitat fragmentation may lead to pollen limitation and limited gene flow. In comparison with results of previous meta-analyses on mainly herbaceous species, we found trees and shrubs were as likely to have negative genetic responses to habitat fragmentation as herbaceous species. We also found that the genetic variation in offspring was generally less than that of adult trees, which is evidence of a genetic extinction debt and probably reflects the genetic diversity of the historical, less-fragmented landscape.     

Founding Lineages and Genic Variability in Plains Bison (Bison bison) from Badlands National Park, South Dakota

Abstract: Starch-gel electrophoresis was used to screen 101 bison from Badlands National Park, South Dakota, for variation at 24 genetic loci. The population was descended from founder groups of about 6 and 3 individuals, separated geographically for a minimum of 64 years. The purpose of this study was (1) to estimate levels of genic variability in this bison population, (2) to assess the extent to which descendents of the two founder groups differ genetically, and (3) to compare the genetic characteristics of the Badlands population with other bison populations. The Badlands herd was found to be polymorphic for only a single locus (MDH–1). Descendents of the founder groups were homogeneous with respect to allelic and genotypic frequencies at this locus. The MDH–1 polymorphism has not been observed in other bison populations, while several polymorphism reported in other bison populations were not detected in the Badlands herd. A mean heterozygosity of 0.012 was observed in the Badlands herd; this value is lower than that typically reported for mammals, though not as low as heterozygosities seen in other populations that have passed through severe bottlenecks in size. These results underscore the need for genetic data in planning breeding programs for species in captivity or managed in isolate reserves.     

Genetic Estimates of Variability and Relatedness for Conservation of an Ozark Cave Crayfish Species Complex

Allozyme-based genetic distances were used to determine the distinctness of six species of cave crayfish from the Ozark Plateau in Missouri, Arkansas, and Oklahoma. One of the cave species is in the subgenus Erebicambarus and the others are in Jugicambarus . Four of the six species are very rare and are found in only one to three known sites each. In addition, most populations of all the species are presumed to be small; rarely are more than a few individuals observed. A chela (claw) was collected from sixty individuals representing the six species, including all known populations of the four rare species. Variability and distance estimates were based on 20 presumptive gene loci. Population samples with identical genotypes were pooled. Thirteen loci were polymorphic, but average heterozygosity was low (H= 1%) compared to epigean crayfish species. Pairwise genetic distances within Jugicambarus ranged from D = 0.051 to 0.522, and mean distance between subgenera was D = 0.676. The underground water systems in Ozark caves are defined by discreet recharge zones. Groundwater pollution threatens the stability of cave ecosystems, including the survival of cave crayfish. If restoration of threatened or extirpated populations becomes necessary, a database of genetic variability and relatedness estimates for known populations of all the species will aid decisions about numbers and sources of individuals for propagation or transfer.     

Genetic Variation for Morphological and Allozyme Variation in Relation to Population Size in Clarkia dudleyana, an Endemic Annual

Abstract: The maintenance of genetic variation within populations is expected to allow species to respond to evolutionary challenges such as selection and environmental stress. Larger populations are generally expected to maintain larger amounts of genetic variation. Although several studies have found a positive relationship between population size and levels of genetic variation for molecular markers such as allozymes, few comparisons have been made between molecular measures of variation and genetic variation that is likely to be ecologically important. Most ecologically important traits require quantitative genetic analyses. I examined the relationship between levels of genetic variation and population size for both allozymes and morphological traits in a California endemic annual plant, Clarkia dudleyana . Levels of genetic variation for allozymes did not show a significant positive relationship with population size. The level of genetic variance for all of the 18 morphological traits exhibited no significant relationship with population size. Further, allozyme heterozygosities were not related to levels of quantitative genetic variation. These results indicate that levels of allozyme variability do not predict levels of genetic variation for morphological traits in C. dudleyana , suggesting that molecular measures of variation, in general, differ from quantitative genetic measures. These results imply that conservation genetic studies should generally focus on aspects other than measuring levels of genetic variation found within populations.     

Genetic Depletion in the European Bison (Bison bonasus) and the Significance of Electrophoretic Heterozygosity for Conservation

Starch gel electrophoresis was used to screen 35 lowland bison from the herd in the Biażlowieża Primeval Forest for genetic variation at 69 presumptive structural loci. Average heterozygosity ( H = 1.2%) proved to be three times lower than that based on 20 loci ( H = 3.5%) reported in a previous study by other authors. These earlier results were interpreted as evidence that the passage of the species through an extreme genetic bottleneck (12 founder genomes) had not had much influence on genetic variation. A comparison of estimates of H and the proportion of polymorphic loci ( P ) among different species or populations of Artiodactyla revealed that P was the only parameter to be significantly reduced in those that had experienced genetic bottlenecks. However, the data also show that, in spite of similar H values in species or populations with or without bottlenecks, average heterozygosity is only useful as an indicator of overall genetic variability in the latter. To draw conclusions about genetic depletion on the basis ofelectrophoretic data, we strongly recommend that H , together with its variance among a large number of loci, and additional parameters such as P and the ratio H:P be taken into account.     

Comparisons of Genetic Diversity in the Endangered Adenophora lobophylla and Its Widespread Congener, A. potaninii

Abstract: Starch-gel electrophoresis was used to examine the levels and distribution of genetic diversity in two Adenophora species: the narrow endangered Adenophora lobophylla and its widespread congener, A. potaninii . Based on allozyme variation at 18 putative loci, we measured high levels of genetic variability both in the endangered and the widespread species, with 83.3% of the loci being polymorphic. The mean expected heterozygosity within populations (   H _ep  ) and within species (   H _es  ) were 0.234 and 0.244 for A. potaninii and were as high as 0.210 and 0.211 for A. lobophylla . There was higher differentiation among populations in A. potaninii (   F _ST = 0.155) than in A. lobophylla (   F _ST = 0.071). The high levels of genetic diversity in the present allozyme survey are consistent with the morphological variation observed in these species and may be attributed to high outcrossing rates in the Adenophora species. In addition, A. lobophylla was identified as a distinct species on the basis of Nei's genetic distances and thus should be given a high priority for protection. It is noteworthy that the endangered A. lobophylla maintains much higher genetic diversity than most endemic or narrowly distributed plant species in spite of its restricted distribution. We hypothesize that A. lobophylla has become endangered for ecological and stochastic reasons, including habitat destruction or environmental changes, mud slides, and human disturbance such as grazing and mowing. Consequently, habitat protection is of particular importance for conserving this endangered species.     

Population structure and genetic variation in two tropical sea anemones (Cnidaria,Actinidae) with different reproductive strategies

Genetic variation and population structure of two tropical sea anemones, Bunodosoma caissarum Correa and Actinia bermudensis McMurrich were related to their different dispersal capabilities and reproductive modes. B. caissarum reproduces sexually and has a long-lived planktotrophic larva; A. bermudensis can reproduce both sexually and asexually, supposedly with short-range dispersal. Both species were sampled along 1150 km of Brazilian coastline between 1990 and 1991 and analyzed by horizontal starch gel electrophoresis for 16 enzyme loci in B. caissarum and 19 in A. bermudensis. B. caissarum had higher levels of heterozygosity (H=0.35) and lower levels of population structuring (F _ST=0.042) than A. bermudensis (H=0.17; F _ST=0.262). At one locality large genetic differences between two sympatric colour morphs of A. bermudensis provide evidence of possible cryptic speciation. Overall levels of genetic variation and heterozygosity in the two species are compatible with their known modes of reproduction.     

Meta-analysis of the differential effects of habitat fragmentation and degradation on plant genetic diversity

Genetic diversity is a key factor for population survival and evolution. However, anthropogenic habitat disturbance can erode it, making populations more prone to extinction. Aiming to assess the global effects of habitat disturbance on plant genetic variation, we conducted a meta-analysis based on 92 case studies obtained from published literature. We compared the effects of habitat fragmentation and degradation on plant allelic richness and gene diversity (equivalent to expected heterozygosity) and tested whether such changes are sensitive to different life-forms, life spans, mating systems, and commonness. Anthropogenic disturbance had a negative effect on allelic richness, but not on gene diversity. Habitat fragmentation had a negative effect on genetic variation, whereas habitat degradation had no effect. When we examined the individual effects in fragmented habitats, allelic richness and gene diversity decreased, but this decrease was strongly dependent on certain plant traits. Specifically, common long-lived trees and self-incompatible species were more susceptible to allelic richness loss. Conversely, gene diversity decreased in common short-lived species (herbs) with self-compatible reproduction. In a wider geographical context, tropical plant communities were more sensitive to allelic richness loss, whereas temperate plant communities were more sensitive to gene diversity loss. Our synthesis showed complex responses to habitat disturbance among plant species. In many cases, the absence of effects could be the result of the time elapsed since the disturbance event or reproductive systems favoring self-pollination, but attention must be paid to those plant species that are more susceptible to losing genetic diversity, and appropriate conservation should be actions taken.     

Biochemical genetic variation and evidence of speciation in Chthamalus barnacles of the tropical eastern Pacific Ocean

Gene-enzyme variation was studied electrophoretically within and between barnacle populations of the genus Chthamalus from 8 intertidal stations from central California to the Pacific coast of Panamá. Horizontal starch-gel electrophoresis separated and resolved 18 enzymes from 512 individual barnacles. A maximum of 25 gene-enzyme systems was interpretable from the resulting zymograms. Electrophoretic phenotypes and patterns of phenotypic variation generally conformed with those observed in other organisms. The amount of genetic variation within barnacle populations varied; average heterozygosity, for example, ranged from a low of 3.4% in a Mexican population of the C. fissus group to a high of 10.4% in C. anisopoma from the Gulf of California. Observed and expected average heterozygosities agreed in all population samples, indicating that these species are outbreeding. In contrast to the prediction stemming from a hypothesis that trophic stability regulates the amount of genetic variation in marine species, average heterozygosity tends to be positively correlated with latitude. Data from these and other barnacle species may support a hybrid environmental heterogeneity-trophic diversity model recently proposed to explain genetic variation in decapod crustaceans. Juxtaposition of individuals from different localities revealed numerous genetic differences among populations of the C. fissus group. At least three partially sympatric sibling species are separated by genetic distances as large as those observed between the C. fissus group and the distinct species C. dalli and C. anisopoma. A cladistic analysis places C. anisopoma close to the Mexican and Panamanian sibling species, with C. fissus from San Diego and C. dalli successively farther removed.     

Interspecific Patterns of Genetic Diversity in Birds: Correlations with Extinction Risk

Abstract:  Birds are frequently used as indicators of ecosystem health and are the most comprehensively studied class in the animal kingdom. Nevertheless, a comprehensive, interspecific assessment of the correlates of avian genetic diversity is lacking, even though indices of genetic diversity are of considerable interest in the conservation of threatened species. We used published data on variation at microsatellite loci from 194 bird species to examine correlates of diversity, particularly with respect to conservation status and population size. We found a significant decline in mean heterozygosity with increasing extinction risk, and showed, by excluding species whose heterozygosity values were calculated with heterospecific primers, that this relationship was not dependent on ascertainment bias. Results of subsequent regression analyses suggested that smaller population sizes of threatened species were largely responsible for this relationship. Thus, bird species at risk of extinction are relatively depauperate in terms of neutral genetic diversity, which is expected to make population recovery more difficult if it reflects adaptive genetic variation. Conservation policy will need to minimize further loss of diversity if the chances of saving threatened species are to be maximized.     

Do dominants have higher heterozygosity? Social status and genetic variation in brown trout, Salmo trutta

A key question of evolutionary importance is what factors influence who becomes dominant. Individual genetic variation has been found to be associated with several fitness traits, including behaviour. Could it also be a factor influencing social dominance? We investigated the association between social status and the amount of intra-individual genetic variation in juvenile brown trout (Salmo trutta). Genetic variation was estimated using 12 microsatellite loci. Dominant individuals had higher mean heterozygosity than subordinates in populations with the longest hatchery background. Heterozygosity–heterozygosity correlations did not find any evidence of inbreeding; however, single-locus analysis revealed four loci that each individually differed significantly between dominant and subordinate fish, thus giving more support to local than general effect as the mechanism behind the observed association between genetic diversity and a fitness-associated trait. We did not find any significant relation between mean d ² and social status, or internal relatedness and social status. Our results suggest that individual genetic variation can influence dominance relations, but manifestation of this phenomenon may depend on the genetic background of the population.     

Limited population structure in Northern and Spotted Wolffishes (<Emphasis Type="Italic">Anarhichas denticulatus</Emphasis> and <Emphasis Type="Italic">A. minor</Emphasis>) despite low apparent dispersal potential

Northern and Spotted Wolffishes (Anarhichas denticulatus and A. minor) are demersal marine fishes listed as “threatened” in Canadian waters. Both species have unusually large benthic eggs and large size at hatch, which should reduce passive dispersal. We examined population differentiation with microsatellite and AFLP loci across the ranges of both species in the North Atlantic Ocean. Although significant population structure was documented, differentiation was less than expected based on knowledge of life history characteristics. Significant differentiation was found in Northern Wolffish between the Barents Sea and other samples based on both microsatellite and AFLP data. In contrast, population structure in the Spotted Wolffish was notably weaker, particularly with microsatellites. Both species were characterized by low genetic diversity for marine fishes and had significantly lower genetic diversity than the congeneric Atlantic Wolffish. This finding was consistent with the conservation status of these three species and suggests potential vulnerability to over-exploitation in Northern and Spotted Wolffishes.     

Genetic variability in bloodworm (Glycera dibranchiata) populations in the Gulf of Maine

Genetic structure of eight Northwest Atlantic populations of the marine polychaeteGlycera dibranchiata Ehlers was examined with starch gel electrophoresis. Samples were collected during summer and fall 1981, and seven polymorphic and four monomorphic loci were consistently scored. Average heterozygosity (0.126) and percent polymorphic loci (59.3) were comparable to the averages reported for marine invertebrates. Minimum genetic distances between populations ranged from 0.003 to 0.093, levels typically associated with local populations of the same species in other taxa. Based on these data, inter- and intra-estuarine migration and gene flow appear to be low. Only two populations, separated by 13 km along the same river in New Brunswick, Canada, were not genetically different from each other. These findings may have relevance for management strategies in bloodworms.     

Genetic variability in the cosmopolitan deep-water ophiuran Ophiomusium lymani

A population of the cosmopolitan deep-sea ophiuran Ophiomusium lymani was studied by gel electrophoresis, and proved to be highly variable genetically; about 53% of the 15 loci studied are polymorphic, and the average individual is heterozygous at about 17% of the loci. This is approximately the same genetic variability displayed by other species, belonging to other phyla or classes, from the same deep-sea trawl. A similarly high level of genetic variation occurs in deep-sea organisms in general, and in a shallow-water tropical species. Both the deep-sea and the tropics are trophically stable environments. On the other hand, low genetic variabilities have been found in marine species from trophically unstable environments. These data suggest that any phylogenetic effects on genetic variability are secondary, and that the trophic regime may be of major importance in determining genetic strategies of adaptation.This study is no. 5 of a series of reports on the results of Expedition Quagmire.     

Heterozygosity,growth, and survival of the hard clam,Mercenaria mercenaria,in seagrass vs sandflat habitats

Populations of the hard clam,Mercenaria mercenaria L., sampled from dissimilar, adjacent habitats (October and November 1987), were used to assess environmental effects on associations among multi-locus heterozygosity, growth, and survival. Individuals were collected from three widely separated localities along the east coast of North America with each consisting of a seagrass bed and an adjacent, unvegetated sandflat. Demographic differences between adjacent populations were attributed to habitat type. Samples from intertidal sandflats at two of the localities were dominated by younger individuals than those from seagrass beds. Differential growth between adjacent populations was detected at only one locality wherein seagrass individuals grew faster than those from the sandflat. Allelic frequencies revealed adjacent populations that were genetically homogeneous. Nearly all of the genetic variance (98%) was within populations, yet a small (1.7%), but significant, portion occurred between localities. Observed and expected heterozygosities revealed a deficiency of heterozygotes in all six samples. Inbreeding and small-scale population subdivision were discounted as causative factors because deficiencies were heterogeneous across loci. Multi-locus heterozygosity was not correlated with growth rate in samples from any locality. Using a consensus test, multilocus heterozygosity was positively associated with ageclass in sandflat, but not seagrass, samples. We suggest that heterozygosity-fitness trait associations in marine bivalves are more likely to occur in populations inhabiting more stressful, fluctuating environments     

Population genetics of the family ostreidae. I. Intraspecific studies of Crassostrea gigas and Saccostrea commercialis

The levels of genetic variation and estimates of genetic similarity and distance were determined for populations of Crassostrea gigas (Thunberg) and Saccostrea commercialis (Iredale and Roughley). The proportion of polymorphic loci in Japanese populations of C. gigas ranged from 0.58 to 0.63, while the individual heterozygosities ranged from 0.20 to 0.22. The proportion of polymorphic loci in Australian populations of S. commercialis ranged from 0.43 to 0.46, the individual heterozygosities from 0.17 to 0.19. The genetic similarity between different geographical populations of both species was approximately 99%. The genetic distance and similarity data derived from this investigation has resulted in some provisional reclassifications. The Portuguese oyster C. angulata (Lamarck) appears to be more appropriately regarded as a recent colonized isolate of C. gigas. The New Zealand oyster S. glomerata (Gould) is considered a subspecies of the eastern Australian rock oyster S. commercialis. The Japanese Kumamoto population of C. gigas warrants reclassification as the non-sibling species C. sikamea.     

Modeling Problems in Conservation Genetics Using Captive Drosophila Populations: Consequences of Equalization of Family Sizes

Equalization of family sizes is recommended for use in captive breeding programs, as it is predicted to double effective population sizes, reduce inbreeding, and slow the loss of genetic variation. The effects of maintaining small captive populations with equalization of family sizes versus random choice of parents on levels of inbreeding genetic variation, reproductive fitness, and effective population sizes ( N _e) were evaluated in 10 lines of each treatment maintained with four pairs of parents per generation. The mean inbreeding coefficient ( F ) increased at a significantly slower rate with equalization than with random choice (means of 0.35 and 0.44 at generation 10). Average heterozygosities at generation 10, based on six polymorphic enzyme loci, were significantly higher with equalization (0.149) than with random choice (0.085), compared to the generation 0 level of 0.188. The competitive index measure of reproductive fitness at generation 11 was more than twice as high with equalization as with random choice, both being much lower than in the outbred base population. There was considerable variation among replicate lines within treatments in all the above measures and considerable overlap between lines from the two treatments. Estimates of N _e for equalization were greater than those for random choice, whether estimated from changes in average heterozygosities or from changes in F. Equalization of family sizes can be unequivocally recommended for use in the genetic management of captive populations.