Genetic Viability Research Articles

Population genetics studies of half-smooth tongue sole Cynoglossus semilaevis using ISSR markers

Inter-simple sequence repeat (ISSR) analysis was performed in order to evaluate the genetic diversity of wild and hatchery samples of half-smooth tongue sole Cynoglossus semilaevis. A group of 200 genotypes belonging to four wild samples, Laizhou (LZ), Weihai (WH), Qingdao (QD), Rizhao (RZ) and one hatchery sample, Mingbo (MB) were screened using 15 different ISSR primers. A total of 137 loci were produced in the five studied samples. 41.80%, 45.26%, 44.27%, 42.86% and 41.59% of these loci were polymorphic over all the genotypes tested in LZ, WH, QD, RZ and MB samples, respectively. The number of polymorphic loci detected by single primer combination ranged from 2 to 7. The average heterozygosity of LZ, WH, QD, RZ and MB samples were 0.0710, 0.0814, 0.0793, 0.0727 and 0.0696, respectively. The WH sample showed a higher genetic diversity including total number of ISSR bands ( P < 0.05), total number of polymorphic bands ( P < 0.05), average heterozygosity ( P < 0.05) and total number of genotypes ( P < 0.05) than all the other samples. Among the five studied samples, the hatchery sample (MB) showed the lowest genetic viability.

Comparison of clonal diversity in mountain and Piedmont populations of Trillium cuneatum (Melanthiaceae‐Trilliaceae), a forest understory species

The balance between clonal and sexual reproduction can vary widely among plant populations, and the extent of clonality may be influenced by the combined effects of historical land use and variation in environmental conditions. We investigated patterns of clonal spread in five Trillium cuneatum populations, two in the Appalachian Mountains characterized by mesic, cooler conditions, and three at lower elevations experiencing warmer, drier conditions and greater disturbance. Using a new measure of the genet effective number and innovative orthogonal contrast methods, we quantified genet structure, contrasting clonal growth in the mountains with that in the Piedmont. Asexual propagation was more common in the Piedmont, where 25% of the sampled ramets were clonally derived, but was much less frequent in the mountains (7% clonal replicates). Hierarchical partitioning of variation in genet diversity showed that the majority (75.8%) of the variation resulted from more vegetative replication in the Piedmont. Most of the remaining variation (21.6%) was attributable to differences between urban and rural Piedmont populations, and a small, statistically nonsignificant fraction of the variation (2.6%) was due to interpopulation differences within the mountains. Higher frequency of cloning may enhance both genetic and demographic population viability in fragmented Piedmont habitats.

Loss of genetic variation and effective population size of Kirikuchi charr: implications for the management of small, isolated salmonid populations

AbstractSmall, isolated populations may face extinction due to a combination of inbreeding depression and other threats. Effective population size (Ne) is one comprehensive measure that allows us to evaluate the genetic status of a population, and to make management decisions regarding genetic viability. We simulated loss of genetic variation and estimated Ne for two small, isolated populations of Kirikuchi charr Salvelinus leucomaenis japonicus, the endangered, southernmost local populations of the genus Salvelinus in the world, using VORTEX, an individual‐based stochastic PVA model. Approximately half of the genetic variation was lost over 200 years regardless of census population size and demographic parameters, and Ne estimates were roughly 50 in each of the two populations, suggesting the possibility of inbreeding depression. The target population size of Ne&gt;500, by securing long‐term viability, is several times that of the present size of each of the populations studied, and no local habitats maintaining such a target number are considered to exist. The results strongly indicate a need for recovering natural connections and potential gene flow among local populations. However, the impending threat to these populations from non‐native charr widely distributed throughout the drainage has prevented the recovery of the connections. Given the small Ne of the two populations, it would be necessary to retain gene flow artificially within or across local populations. This will be true of many other salmonid populations that have been isolated or fragmented recently.

Identification and characterization of a novel gene differentially expressed in zebrafish cross-subfamily cloned embryos

BackgroundCross-species nuclear transfer has been shown to be a potent approach to retain the genetic viability of a certain species near extinction. However, most embryos produced by cross-species nuclear transfer were compromised because that they were unable to develop to later stages. Gene expression analysis of cross-species cloned embryos will yield new insights into the regulatory mechanisms involved in cross-species nuclear transfer and embryonic development.ResultsA novel gene, K31, was identified as an up-regulated gene in fish cross-subfamily cloned embryos using SSH approach and RACE method. K31 complete cDNA sequence is 1106 base pairs (bp) in length, with a 342 bp open reading frame (ORF) encoding a putative protein of 113 amino acids (aa). Comparative analysis revealed no homologous known gene in zebrafish and other species database. K31 protein contains a putative transmembrane helix and five putative phosphorylation sites but without a signal peptide. Expression pattern analysis by real time RT-PCR and whole-mount in situ hybridization (WISH) shows that it has the characteristics of constitutively expressed gene. Sub-cellular localization assay shows that K31 protein can not penetrate the nuclei. Interestingly, over-expression of K31 gene can cause lethality in the epithelioma papulosum cyprinid (EPC) cells in cell culture, which gave hint to the inefficient reprogramming events occurred in cloned embryos.ConclusionTaken together, our findings indicated that K31 gene is a novel gene differentially expressed in fish cross-subfamily cloned embryos and over-expression of K31 gene can cause lethality of cultured fish cells. To our knowledge, this is the first report on the determination of novel genes involved in nucleo-cytoplasmic interaction of fish cross-subfamily cloned embryos.

Identification of differentially expressed genes from the cross-subfamily cloned embryos derived from zebrafish nuclei and rare minnow enucleated eggs

Cross-species nuclear transfer (NT) has been used to retain the genetic viability of a species near extinction. However, unlike intra-species NT, most embryos produced by cross-species NT were unable to develop to later stages due to incompatible nucleo-cytoplasmic interactions between the donor nuclei and the recipient cytoplasm from different species. To study the early nucleo-cytoplasmic interaction in cross-species NT, two laboratory fish species (zebrafish and rare minnow) from different subfamilies were used to generate cross-subfamily NT embryos in the present study. Suppression subtractive hybridization (SSH) was performed to screen out differentially expressed genes from the forward and reverse subtractive cDNA libraries. After dot blot and real-time PCR analysis, 80 of 500 randomly selective sequences were proven to be differentially expressed in the cloned embryos. Among them, 45 sequences shared high homology with 28 zebrafish known genes, and 35 sequences were corresponding to 22 novel expressed sequence tags (ESTs). Based on functional clustering and literature mining analysis, up- and down-regulated genes in the cross-subfamily cloned embryos were mostly relevant to transcription and translation initiation, cell cycle regulation, protein binding, etc. To our knowledge, this is the first report on the determination of genes involved in the early development of cross-species NT embryos of fish.

The genealogy and genetic viability of reintroduced Yellowstone grey wolves

The recovery of the grey wolf in Yellowstone National Park is an outstanding example of a successful reintroduction. A general question concerning reintroduction is the degree to which genetic variation has been preserved and the specific behavioural mechanisms that enhance the preservation of genetic diversity and reduce inbreeding. We have analysed 200 Yellowstone wolves, including all 31 founders, for variation in 26 microsatellite loci over the 10-year reintroduction period (1995-2004). The population maintained high levels of variation (1995 H(0) = 0.69; 2004 H(0) = 0.73) with low levels of inbreeding (1995 F(IS) = -0.063; 2004 F(IS) = -0.051) and throughout, the population expanded rapidly (N(1995) = 21; N(2004) = 169). Pedigree-based effective population size ratios did not vary appreciably over the duration of population expansion (1995 N(e)/N(g) = 0.29; 2000 N(e)/N(g) = 0.26; 2004 N(e)/N(g) = 0.33). We estimated kinship and found only two of 30 natural breeding pairs showed evidence of being related (average r = -0.026, SE = 0.03). We reconstructed the genealogy of 200 wolves based on genetic and field data and discovered that they avoid inbreeding through a wide variety of behavioural mechanisms including absolute avoidance of breeding with related pack members, male-biased dispersal to packs where they breed with nonrelatives, and female-biased subordinate breeding. We documented a greater diversity of such population assembly patterns in Yellowstone than previously observed in any other natural wolf population. Inbreeding avoidance is nearly absolute despite the high probability of within-pack inbreeding opportunities and extensive interpack kinship ties between adjacent packs. Simulations showed that the Yellowstone population has levels of genetic variation similar to that of a population managed for high variation and low inbreeding, and greater than that expected for random breeding within packs or across the entire breeding pool. Although short-term losses in variation seem minimal, future projections of the population at carrying capacity suggest significant inbreeding depression will occur without connectivity and migratory exchange with other populations.

Small effective population sizes of two remnant ocelot populations (Leopardus pardalis albescens) in the United States

Threatened populations are vulnerable to the effects of genetic drift and inbreeding, particularly when gene flow is low and the effective population size is small. Estimates of effective population size (N e ) provide important information on the status of endangered populations that have experienced severe fragmentation and serve as indicators of genetic viability. Genetic data from microsatellite loci were used to estimate N e for the 2 remaining populations of the endangered ocelot (Leopardus pardalis albescens) occurring in the United States. Several methods were used to calculate N e , resulting in estimates ranging from N e = 8.0 (95% CI: 3.2–23.1) to 13.9 (95% CI: 7.7–25.1) for the population located at the Laguna Atascosa Wildlife Refuge in Cameron County, Texas. The ocelot population in Willacy County, Texas, had N e estimates of 2.9 (95% CI: 1.7–5.6) and 3.1 (95% CI: 1.9–13.5), respectively. Estimates of N e in both populations were below the critical value recommended for short-term viability.

Genetic Viability and Population History of the Giant Panda, Putting an End to the “Evolutionary Dead End”?

The giant panda (Ailuropoda melanoleuca) is currently threatened by habitat loss, fragmentation, and human persecution. Its dietary specialization, habitat isolation, and reproductive constraints have led to a perception that this is a species at an "evolutionary dead end," destined for deterministic extinction in the modern world. Here we examine this perception by a comprehensive investigation of its genetic diversity, population structure, and demographic history across its geographic range. We present analysis of 655 base pairs of mitochondrial (mt) control region (CR) DNA and 10 microsatellite loci for samples from its 5 extant mountain populations (Qinling, Minshan, Qionglai, Liangshan, and Lesser Xiangling). Surprisingly, extant populations display average to high levels of CR and microsatellite diversity compared with other bear species. Genetic differentiation among populations was significant in most cases but was markedly higher between Qinling and the other mountain ranges, suggesting, minimally, that the Qinling population should comprise a separate management unit for conservation purposes. Recent demographic inference using microsatellite markers demonstrated a clear genetic signature for population decline starting several thousands years ago or even further back in the past, and being accelerated and enhanced by the expansion of human populations. Importantly, these data suggest that the panda is not a species at an evolutionary "dead end," but in common with other large carnivores, has suffered demographically at the hands of human pressure. Conservation strategies should therefore focus on the restoration and protection of wild habitat and the maintenance of the currently substantial regional genetic diversity, through active management of disconnected populations.

Male dominance linked to size and age, but not to 'good genes' in brown trout (Salmo trutta)

BackgroundMales that are successful in intra-sexual competition are often assumed to be of superior quality. In the mating system of most salmonid species, intensive dominance fights are common and the winners monopolise most mates and sire most offspring. We drew a random sample of mature male brown trout (Salmo trutta) from two wild populations and determined their dominance hierarchy or traits linked to dominance. The fish were then stripped and their sperm was used for in vitro fertilisations in two full-factorial breeding designs. We recorded embryo viability until hatching in both experiments, and juvenile survival during 20 months after release into a natural streamlet in the second experiment. Since offspring of brown trout get only genes from their fathers, we used offspring survival as a quality measure to test (i) whether males differ in their genetic quality, and if so, (ii) whether dominance or traits linked to dominance reveal 'good genes'.ResultsWe found significant additive genetic variance on embryo survival, i.e. males differed in their genetic quality. Older, heavier and larger males were more successful in intra-sexual selection. However, neither dominance nor dominance indicators like body length, weight or age were significantly linked to genetic quality measured as embryo or juvenile survival.ConclusionWe found no evidence that females can improve their offspring's genetic viability by mating with large and dominant males. If there still were advantages of mating with dominant males, they may be linked to non-genetic benefits or to genetic advantages that are context dependent and therefore possibly not revealed under our experimental conditions – even if we found significant additive genetic variation for embryo viability under such conditions.

Genetic diversity and population structure of wolverine (Gulo gulo) populations at the southern edge of their current distribution in North America with implications for genetic viability

The current range of wolverines (Gulo gulo) within the lower 48 states includes small, remnant populations in Idaho, Washington, Wyoming and Montana. The size and trend of each of these populations and connectivity to adjacent populations in the contiguous United States and Canada are poorly understood. In this study, levels of genetic diversity and population genetic structure were examined in three states (Idaho, Wyoming, and Montana) and two Canadian provinces (Alberta and British Columbia) using both mitochondrial (mtDNA) and nuclear microsatellite DNA. Restricted levels of gene flow were detected among these populations with mitochondrial and nuclear DNA and our observations suggest a pattern of male-mediated gene flow. Populations in the United States appear to be receiving migrants from Canada, however, substantial genetic differentiation suggests that gene flow may not be high enough to prevent genetic drift. Our analyses suggest that at least 400 breeding pairs or 1–2 effective migrants per generation would be needed to ensure genetic viability in the long-term for each of the populations in the United States. Significant matrilineal structuring and restricted female gene flow indicates that demographic viability will depend upon the movement of female wolverines into new territories. Results from this study provide guidelines for conservation and management and indicate the need for more ecological data.

Genetic diversity and fitness in peripheral and central populations of the European tree frog Hyla arborea.

Genetic diversity is expected to decrease in small and isolated populations as a consequence of founder effects, bottlenecks, inbreeding and genetic drift. In this study we analyse temporal and spatial effects on genetic variation and progeny viability of the European tree frog (Hyla arborea) at two scales. First, the Swedish distribution has been isolated from the continental distribution for more than 8000 thousand years, and secondly, within Sweden, recent habitat alterations that have taken place during this century have increased isolation between local populations. Genetic variation and progeny survival in relation to isolation was studied within the entire Swedish distribution of the tree frog. Allozyme electrophoresis analysis of froglets, sampled across the Swedish distribution, revealed a low overall genetic variation (1.06 alleles/locus) at the protein level in comparison with continental populations (1.54-1.68 alleles/locus). However, egg hatchability (97%) and early larval survival (95%) were not lower than in other parts of the tree frog distribution or in other anuran species. Within the Swedish distribution, early larval survival was lower in isolated breeding ponds than in more central ones. However, no differences in genetic variation were found in relation to isolation. Polymorphism was detected only at a single locus, and was restricted geographically to the eastern part of the Swedish distribution. Bottlenecks due to climatic changes and fragmentation of suitable habitat (primarily natural pastures with ponds) are suggested as possible causes of the low genetic diversity of the Swedish tree frog population.

General Information &amp; Statistics

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Estimation of the lion (Panthera leo) population in the southwestern Kgalagadi Transfrontier Park using a capture–recapture survey

A previous estimate of the lion (Panthera leo) population in the southwestern Kgalagadi Transfrontier Park (KTP) was made over 20 years ago. This together with increased fears regarding the viability of the population as a result of recent killings of roaming animals, an observed increase in non-violent mortalities during 1996, and possible reduced genetic viability due to suspected isolation, prompted another investigation. Between October 1996 and December 1996,68 lions were captured and marked and subjected to two recapture (resighting) samples. The minimum estimate derived from direct enumeration of marked and unmarked individuals is between 100–103 individuals. Assessment of the adult and subadult population using the Lincoln-Petersen estimator and the software program NOREMARK gives a figure between 92 and 125. The current estimate is below the previous estimate of between 113 and 140 lions. Lion densities of 1.2 adult and subadult lions/100 km>2 in the semi-arid southern Kalahari are considerably lower than those in more mesic regions. Furthermore, there appears to be some demographic variability with the ratio of females to males being twice as high as that recorded 20 years ago.

How important are direct fitness benefits of sexual selection?

Females may choose mates based on the expression of secondary sexual characters that signal direct, material fitness benefits or indirect, genetic fitness benefits. Genetic benefits are acquired in the generation subsequent to that in which mate choice is performed, and the maintenance of genetic variation in viability has been considered a theoretical problem. Consequently, the magnitude of indirect benefits has traditionally been considered to be small. Direct fitness benefits can be maintained without consideration of mechanisms sustaining genetic variability, and they have thus been equated with the default benefits acquired by choosy females. There is, however, still debate as to whether or not males should honestly advertise direct benefits such as their willingness to invest in parental care. We use meta-analysis to estimate the magnitude of direct fitness benefits in terms of fertility, fecundity and two measures of paternal care (feeding rate in birds, hatching rate in male guarding ectotherms) based on an extensive literature survey. The mean coefficients of determination weighted by sample size were 6.3%, 2.3%, 1.3% and 23.6%, respectively. This compares to a mean weighted coefficient of determination of 1.5% for genetic viability benefits in studies of sexual selection. Thus, for several fitness components, direct benefits are only slightly more important than indirect ones arising from female choice. Hatching rate in male guarding ectotherms was by far the most important direct fitness component, explaining almost a quarter of the variance. Our analysis also shows that male sexual advertisements do not always reliably signal direct fitness benefits.

Indirect fitness consequences of mate choice in sticklebacks: offspring of brighter males grow slowly but resist parasitic infections.

'Good genes' models of sexual selection suggest that elaborate male sexual ornaments have evolved as reliable signals of male quality because only males of high genetic viability are able to develop and maintain them. Females benefit from choosing such individuals if quality is heritable. A key prediction is that the offspring of males with elaborate mating displays will perform better than those of less elaborate males, but it has proved difficult to demonstrate such an effect independently of the effects of differences in parental investment. We tested for 'good genes' linked to male ornamentation in the three-spined stickleback Gasterosteus aculeatus using in vitro fertilization to generate maternal half-siblings, which were raised without parental care. Maternal half-siblings sired by brightly coloured males grew less quickly than half-siblings sired by dull males but were more resistant to a controlled disease challenge. Among the offspring that became infected, those with brighter fathers had higher white blood cell counts. This suggests that highly ornamented males confer disease resistance on their offspring. The association with reduced growth suggests a mechanism for the maintenance of heritable variation in both disease resistance and male sexual coloration.

Dynamics of an Isolated Population of Weddell Seals (Leptonychotes weddellii) at White Island, Antarctica

A small population of Weddell seals (Leptonychotes weddellii) was studied at White Island, Antarctica, where it is apparently isolated from other populations of Weddell seals by 18 km of floating glacier ice. The seals at White Island have increased from only nine in 1968–1969 to 26 seals older than pups in 1993–1994, with a concurrent decline in body condition. No evidence of immigration or emigration was found. Higher survival of adult seals, lower fecundity, and higher mortality of pups occurred at White Island relative to seals in an open population only 30 km away in Erebus Bay. High neonatal and preparturient mortality at White Island, including pups with congenital deformities, suggest that genetic viability of this population is questionable. If it remains isolated, the population of Weddell seals at White Island is a model for small populations of endangered seals and possibly for conditions leading to speciation in polar phocids.

Squirrel monkeys in Costa Rica: drifting to extinction

Central American squirrel monkeys Saimiri oerstedii are limited to Costa Rica and Panama, and have never been abundant. The Costa Rican population is now decimated. Based on our survey of squirrel monkeys throughout a large portion of the Costa Rican range of this species in 1996, we can confirm that at least 1246 squirrel monkeys remain in 26 spatially dispersed localities. Despite probable undercounts of squirrel monkeys within sites and potentially missed localities, the total population size should be considered far below a size that would provide longterm genetic viability. Deforestation and habitat fragmentation spurred by agricultural and tourism development are the familiar culprits contributing to this decline. Our strong recommendation is that future conservation efforts be targeted at the level of each specific locality, perhaps recruiting local, national and international sponsors. A focused strategy would allow management efforts to be tailored to the circumstances specific to each site and thus allocate scarce resources more efficiently.

Frequency-Dependent Stability for Two-Species Interactions

Evolutionary game theory is extended to models of two-species interactions where fitnesses are based on individual characteristics (strategies) rather than on a population dynamic that assumes homogeneous species. It is shown that the coevolutionary theories in the literature that combine ecology with genetic viability selection are part of this extended theory and that the dynamic stability resulting from a separation of ecological and evolutionary processes actually follows from game-theoretic solution concepts. The main focus of the paper is to investigate the application of the ESS (evolutionarily stable strategy) solution concept to dynamic stability when fitnesses are given by random interactions between individuals as opposed to viability selection. For two-species frequency-dependent interactions, the ESS criterion that implies stability asserts that, in any system near the ESS, at least one of the species is better off (i.e., more fit) if it evolves towards the ESS. The global stability of a polymorphic two-species ESS that is shown for two-species matrix games gives a powerful tool to predict the course of evolution through static fitness comparisons.

Estimating costs and genetic benefits of various sizes of predator populations: The case of bear, wolf, wolverine and lynx in Sweden

Conservation of endangered species such as the “four big” predators in Sweden—bear (Ursus arctors), wolf (Canis lupus), wolverine (Gulo gulo) and lynx (Lynx lynx)—requires knowledge of the biological needs of the species. Information on the costs of meeting these needs is also of great importance. This paper describes an attempt to estimate such costs. The costs of various sizes of predator populations are seen in relation to their biological “value” in terms of genetic viability after a number of generations. Preliminary analysis indicated that the Swedish government's main expenditure on predators is in the form of compensation paid to owners of livestock killed by predators. Therefore, this study focuses on these costs alone. Historical data on compensation costs, predator populations, and, in some cases, reindeer populations, were used in regression analyses to estimate functions that could be used to predict the compensation costs of various sizes of predator populations. In order to check the plausibility of the regression functions, the maximum cost of the predators' manual meat consumption in terms of reindeer meat equivalents was estimated. The functions obtained from the regression analyses revealed that 500 effective individuals of each predator species would cost society 4 771 310 000 Swedish kronor (SEK) annually. A corresponding estimate based on the predators' maximum annual reindeer meat consumption gave an annual cost of SEK 594 730 000. Thus, the cost estimate based on the regression analyses may be discarded as implausible. The biological benefit of maintaining predator populations at these levels would be a maximum degree of inbreeding of 4–10% after 200 years. The conclusions drawn in this paper are not definitive, since there is some uncertainty in the underlying data. Improved knowledge of predator biology would be useful in future population management, both for ecologists and economists.

Genetic variation in fragmented populations of an Australian rainforest rodent, Melomys cervinipes

Small, isolated populations of an Australian rodent, Melomys cervinipes, occur in rainforest fragments on the Atherton Tableland in northeastern Queensland. We studied the genetic structure of four of these populations: one island (4.3 ha; isolated in 1960), three fragments (2.5, 7.5, 97.5 ha; isolated between 1920 and 1930) and a control population in continuous rainforest. The relative density of M. cervinipes did not differ among the populations, hence population size was approximately proportional to the forest area. Electrophoresis was performed on blood samples taken from the populations. Average heterozygosity (H) was estimated from the allelic distribution of 24 loci for each population and varied from 0.01 to 0.05. The island population had reduced heterozygosity compared to the control population, but the fragment populations were not significantly less heterozygous than the control. Although the fragment populations were markedly different in size, they did not differ in heterozygosity among themselves. The ability of fragment populations to maintain genetic viability is probably due to migration. The rainforest fragments exist in an extensive grassland containing a variety of habitat corridors which could facilitate movement and gene flow. Following the electrophoretic work, spool-and-line and radio tracking and live-trapping were carried out in the corridors; the presence of M. cervinipes in the corridors and its use of the corridors for movement was confirmed. The island population appears to be substantially more isolated than the fragment populations as water is likely to be a much more effective barrier to movement in M. cervinipes than is heterogeneous grassland. The genetic viability of the island population has probably been reduced through drift, leading to fixation of alleles: six of eight polymorphic loci being fixed in the island population. We therefore suggest that retention or establishment of habitat corridors is an important means of sustaining the genetic variability of populations in fragmented systems.