Loss Of Haplotypes Research Articles

Selection and application of four QTLs for grain protein content in modern wheat cultivars

The grain protein content (GPC) is the key parameter for wheat grain nutritional quality. This study conducted a resampling GWAS analysis using 406 wheat accessions across eight environments, and identified four previously reported GPC QTLs. An analysis of 87 landraces and 259 modern cultivars revealed the loss of superior GPC haplotypes, especially in Chinese cultivars. These haplotypes were preferentially adopted in different agroecological zones and had broad effects on wheat yield and agronomic traits. Most GPC QTLs did not significantly reduce yield, suggesting that high GPC can be achieved without a yield penalty. The results of this study provide a reference for future GPC breeding in wheat using the four identified QTLs.

Diversity of mitochondrial DNA in 3 species of great whales before and after modern whaling.

The 20th century commercial whaling industry severely reduced populations of great whales throughout the Southern Hemisphere. The effect of this exploitation on genetic diversity and population structure remains largely undescribed. Here, we compare pre- and post-whaling diversity of mitochondrial DNA (mtDNA) control region sequences for 3 great whales in the South Atlantic, such as the blue, humpback, and fin whale. Pre-whaling diversity is described from mtDNA extracted from bones collected near abandoned whaling stations, primarily from the South Atlantic island of South Georgia. These bones are known to represent the first stage of 20th century whaling and thus pre-whaling diversity of these populations. Post-whaling diversity is described from previously published studies reporting large-scale sampling of living whales in the Southern Hemisphere. Despite relatively high levels of surviving genetic diversity in the post-whaling populations, we found evidence of a probable loss of mtDNA lineages in all 3 species. This is evidenced by the detection of a large number of haplotypes found in the pre-whaling samples that are not present in the post-whaling samples. A rarefaction analysis further supports a loss of haplotypes in the South Atlantic humpback and Antarctic blue whale populations. The bones from former whaling stations in the South Atlantic represent a remarkable molecular archive for further investigation of the decline and ongoing recovery in the great whales of the Southern Hemisphere.

Mitochondrial DNA diversity of the eastern black rhinoceros (Diceros bicornis michaeli) in Tanzania: implications for future conservation

There has been a drastic decline in the number of eastern black rhinoceros (Diceros bicornis michaeli) across Africa, leaving individuals restricted to small, isolated populations that are vulnerable to extinction. Focusing on highly threatened populations in Tanzania, this study investigated the genetic impacts of past management interventions on mitochondrial control region diversity in extant subpopulations, assessed whether there has been evidence of dispersal of females between populations based on haplotype sharing, and related current haplotype diversity to historical patterns. Across extant subpopulations in Tanzania, six maternal haplotypes were identified, with an overall haplotype diversity of h = 0.72 but lower overall nucleotide diversity within populations (π = 0.017) compared to historical populations (π = 0.021). Translocated populations did not share haplotypes with native populations, even though all haplotypes from translocated individuals had been found among historic samples from Kenya. This suggests that translocations have been successful at restoring previous diversity to the region but that the current Intensive Protection Zone (IPZ) management practices have restricted the movement of females between subpopulations. Extant haplotypes were distributed among three East African haplogroups described in previous studies, suggesting that multiple lineages have been preserved despite the loss of historical haplotypes. Our recommendation is to enhance the utilisation of previous translocations by enabling the natural movements of individuals between subpopulations. Such a change in management strategy could be less costly both economically and in terms of animal welfare than the alternative of using genetic data to target specific animals for translocation in order to supplement diversity.

Genetic differences between western and eastern gray whales (Eschrichtius robustus)

Molecular data were used to examine the differentiation between the western and eastern gray whale (Eschrichtius robustus) populations. Control region sequences were generated from samples collected in the western Pacific (n = 45) and eastern Pacific (n = 120). There were 36 unique haplotypes identified. Ten haplotypes were represented in the western samples, and 33 in the eastern samples. Seven of these haplotypes were shared between populations, leaving three haplotypes that were only seen in the western samples and 26 only in the eastern. Although there were no fixed (diagnostic) differences between the western and eastern groups, they were significantly different in their haplotype frequency distributions and should be considered as separate populations. None of the 33 haplotypes found in the eastern samples had a frequency of over 11%, yielding an estimated haplotypic diversity of 0.95. This finding indicates that the reduction in abundance due to whaling may not have had a great effect on the haplotypic diversity of the eastern population, although the loss of rare haplotypes may still have occurred and would be difficult to detect. In contrast, the western group was dominated by two haplotypes, which represented over 77% of all individuals sampled, resulting in a substantially lower haplotypic diversity of 0.70. The lack of fixed differences between the two populations and frequency of shared haplotypes renders these data inappropriate for forensic applications at the population level.

Plasmodium vivax apical membrane antigen 1I-II from Nicaragua (2012-2013): genetic and antigenic polymorphism

Objective. Genetic and antigenic polymorphism of P. vivax apical membrane antigen-1 (pvama1I-II) from Nicaragua was examined. Materials and methods. Infected blood samples from patients were obtained during 2012-2013. A gene fragment comprising domains I-II was amplified and sequenced, and the genetic parameters, haplotype relationships, genetic structure, and amino acid variation in predicted B cell epitopes were analyzed. Results. 65 sequences of pvama1III had 19 nonsynonymous and five synonymous nucleotide changes. Nicaraguan parasites had low diversity, high linkage disequilibrium, and few recombination events. Neutrality tests indicate a positive and divergent selection, and three genetic clusters with loss of haplotypes were demonstrated. Amino acid variation predominated in predicted B cell epitopes and was closely related to that in Latin American parasites. Conclusions. Nicaraguan P. vivax is a moderately differentiated population under contraction and focalization processes, and the antigenic diversity resembles that of Latin American parasites. This information is relevant for vaccine development and epidemiological surveillance.

Museum specimens of a landlocked pinniped reveal recent loss of genetic diversity and unexpected population connections.

The Saimaa ringed seal (Pusa hispida saimensis) is endemic to Lake Saimaa in Finland. The subspecies is thought to have originated when parts of the ringed seal population of the Baltic region were trapped in lakes emerging due to postglacial bedrock rebound around 9000 years ago. During the 20th century, the population experienced a drastic human-induced bottleneck. Today encompassing a little over 400 seals with extremely low genetic diversity, it is classified as endangered. We sequenced sections of the mitochondrial control region from 60 up to 125-years-old museum specimens of the Saimaa ringed seal. The generated dataset was combined with publicly available sequences. We studied how genetic variation has changed through time in this subspecies and how it is phylogenetically related to other ringed seal populations from the Baltic Sea, Lake Ladoga, North America, Svalbard, and the White Sea. We observed temporal fluctuations in haplotype frequencies and loss of haplotypes accompanied by a recent reduction in female effective population size. In apparent contrast with the traditionally held view of the Baltic origin of the population, the Saimaa ringed seal mtDNA variation also shows affinities to North American ringed seals. Our results suggest that the Saimaa ringed seal has experienced recent genetic drift associated with small population size. The results further suggest that extant Baltic ringed seal is not representative of the ancestral population of the Saimaa ringed seal, which calls for re-evaluation of the deep history of this subspecies.

Population genomic transformations induced by isolation of wild bird avian influenza viruses (Orthomyxoviridae) in embryonated chicken eggs.

Isolation and cultivation of wild-type viruses in model organism cells or tissues is standard practice in virology. Oftentimes, the virus host species is distantly related to the species from which the culture system was developed. Thus, virus culture in these tissues and cells basically constitutes a host jump, which can lead to genomic changes through genetic drift and/or adaptation to the culture system. We directly sequenced 70 avian influenza virus (Orthomyxoviridae) genomes from oropharyngeal/cloacal swabs collected from wild bird species and paired virus isolates propagated from the same samples following isolation in specific-pathogen-free embryonated chicken eggs. The data were analyzed using population genetic approaches including evaluation of single nucleotide polymorphism (SNP) frequencies and divergence with pooled-sequencing analyses, consensus sequence placement in neighbor-joining trees, and haplotype reconstruction and networks. We found that propagation of virus in eggs leads to skewed SNP mutation spectra with some SNPs going to fixation. Both synonymous and nonsynonmous SNP frequencies shifted. We found multiple consensus sequences that differed between the swabs and the isolates, with some sequences from the same sample falling into divergent genetic clusters. Twenty of 23 coinfections detected had different dominant subtypes following virus isolation, thus sequences from both the swab and isolate were needed to obtain full subtype data. Haplotype networks revealed haplotype frequency shifts and the appearance or loss of low-frequency haplotypes following isolation. The results from this study revealed that isolation of wild bird avian influenza viruses in chicken eggs leads to skewed populations that are different than the input populations. Consensus sequence changes from virus isolation can lead to flawed phylogenetic inferences, and subtype detection is biased. These results suggest that for genomic studies of wild bird influenza viruses the biological field should move away from chicken egg isolation towards directly sequencing the virus from host samples.

The effect of selection on casein genetic polymorphisms and haplotypes in Italian Holstein cattle

Milk protein genes are known to be highly polymorphic. Several studies have shown the influence of milk proteins genetic variants and casein haplotypes on milk nutritional and technological properties. From 1990, the analysis of caseins polymorphism gained new attention due to the concern about possible negative effects of CSN2*A1 on human health. As a consequence, the CSN2*A2 variant gained interest and milk produced by with A2A2 β-casein cows is now available in different countries. Aim of the present paper was to analyse how casein variants’ and haplotypes’ frequencies changed in the Italian Holstein breed, due to the health ‘claims’ about CSN2*A2, and the possible effects on milk technological properties. Data were compared also with Italian Jersey cattle. A total of 223,655 Holstein and of 622 Jersey were genotyped using Illumina beadchips and data of 62 SNP in the casein cluster were analysed to reconstruct casein genotypes and haplotypes. The results demonstrate that although the selection towards β-casein A2 is not so effective in Italy, an increase of the frequency of this allele to the disadvantage of A1 and B alleles, included in the most favourable genotypes and haplotypes for cheese making, is occurring and should not be forced. Indeed, although a selection for the favourable κ-casein B allele, and against the unfavourable E allele, is occurring and is limiting the general loss of haplotypes associated with good technological properties, the sharp decrease of the favourable B-B and I-B β- κ-haplotypes, is an alert of the risk of losing useful biodiversity. Highlights After the concern about the β-caseinA1 variant on human health, a selection favoring the A2 allele was carried out in different countries. In Italy milk is mostly destined to cheese-making and even without a direct selection for theβ-casein A2 caseins allelic frequencies are changing. Genotyping data should be used to monitor and maybe contrast the reduction of variants associated with milk favorable technological properties.

Recessive Z-linked lethals and the retention of haplotype diversity in a captive butterfly population.

Sex chromosomes are predicted to harbour elevated levels of sexually antagonistic variation due to asymmetries in the heritability of recessive traits in the homogametic versus heterogametic sex. This evolutionary dynamic may manifest as high recessive load specifically affecting the homogametic sex, and the retention of haplotype diversity in small populations. We tested the hypothesis that the Z chromosome in the butterfly Bicyclus anynana carries a high inbred load for male fertility and viability. Homozygosity of Z chromosome blocks was produced by daughter-father backcrosses, and inferred from marker loci positioned via a linkage map. Male sterility was, in general, unrelated to homozygosity in any region of the Z, but there was an extreme deficit of homozygous males within a 2 cM interval in all families. In contrast, no corresponding skew in Z genotype was detected in their (hemizygous) sisters. The same pattern was observed in historically inbred lines, indicating a high frequency of recessive lethals in the ancestral population. Allele-frequency changes between 1993 and 2006 (70 generations at Ne ~ 160) show that, despite the loss of many haplotypes, diversity was retained significantly above the neutral expectation. Effective overdominance in the lethal region can account for this effect locally but not in other parts of the chromosome, that are also associated with persistent linkage disequilibrium. These unexpected patterns suggest the operation of other factors, such as epistatic selection, recombination suppression, assortative mating and meiotic drive. Our results highlight the role of balancing selection in maintaining the inbred load and linked genetic diversity.

Loss of Mitochondrial Genetic Diversity in Overexploited Mediterranean Swordfish (Xiphias gladius, 1759) Population

Intense and prolonged mortality caused by over-exploitation could drive the decay of genetic diversity which may lead to decrease species’ resilience to environmental changes, thus increasing their extinction risk. Swordfish is a high commercial value species, especially in the Mediterranean Sea, where it is affected by high catch levels. Mediterranean swordfish consist of a population genetically and biologically distinct from Atlantic ones and therefore managed as a separate stock. The last Mediterranean swordfish stock assessment reported that in the last forty years Mediterranean swordfish has been overfished and, to date, it is still subject to overfishing. A comparison between an available mitochondrial sequence dataset and a homologous current sample was carried out to investigate temporal genetic variation in the Mediterranean swordfish population over near twenty years. Our study provides the first direct measure of reduced genetic diversity for Mediterranean swordfish during a short period, as measured both in the direct loss of mitochondrial haplotypes and reduction in haplotype diversity. A reduction of the relative females’ effective population size in the recent sample has been also detected. The possible relationship between fishery activities and the loss of genetic diversity in the Mediterranean swordfish population is discussed.

Changes in genetic diversity and differentiation in Red-cockaded woodpeckers (Dryobates borealis) over the past century.

Red‐cockaded woodpeckers (RCW; Dryobates borealis) declined after human activities reduced their fire‐maintained pine ecosystem to <3% of its historical range in the southeastern United States and degraded remaining habitat. An estimated 1.6 million RCW cooperative breeding groups declined to about 3,500 groups with no more than 10,000 birds by 1978. Management has increased RCW population abundances since they were at their lowest in the 1990s. However, no range‐wide study has been undertaken since then to investigate the impacts of this massive bottleneck or infer the effects of conservation management and recent demographic recoveries. We used mitochondrial DNA sequences (mtDNA) and nine nuclear microsatellite loci to determine if range‐wide demographic declines resulted in changes to genetic structure and diversity in RCW by comparing samples collected before 1970 (mtDNA data only), between 1992 and 1995 (mtDNA and microsatellites), and between 2010 and 2014 (mtDNA and microsatellites). We show that genetic diversity has been lost as detected by a reduction in the number of mitochondrial haplotypes. This reduction was apparent in comparisons of pre‐1970 mtDNA data with data from the 1992–1995 and 2010–2014 time points, with no change between the latter two time points in mtDNA and microsatellite analyses. The mtDNA data also revealed increases in range‐wide genetic differentiation, with a genetically panmictic population present throughout the southeastern United States in the pre‐1970s data and subsequent development of genetic structure that has remained unchanged since the 1990s. Genetic structure was also uncovered with the microsatellite data, which like the mtDNA data showed little change between the 1992–1995 and 2010–2014 data sets. Temporal haplotype networks revealed a consistent, star‐like phylogeny, suggesting that despite the overall loss of haplotypes, no phylogenetically distinct mtDNA lineages were lost when the population declined. Our results may suggest that management during the last two decades has prevented additional losses of genetic diversity.

From wild to domestic reindeer – Genetic evidence of a non-native origin of reindeer pastoralism in northern Fennoscandia

The question of how reindeer pastoralism came about has been the subject of recurrent scientific inquiry from many different disciplines. In order to investigate the genetic traces within a Fennoscandian transition from a predominantly hunting economy to reindeer pastoralism, we obtained sequences from the mitochondrial control region from 193 reindeer samples from several archaeological sites dated between 1000 and 1700 CE in Finnmark County, northern Norway. A comparison with similar data from more recent archaeological sites, including extant domestic reindeer, demonstrates that the mitochondrial genome in Finnmark reindeer has gone through massive genetic replacement since medieval times characterized by a significant loss of native mtDNA haplotypes, together with a significant introduction of new haplotypes. Out of a total number of 62 haplotypes identified in both the modern and archaeological samples, only 14 were detected among samples known to represent domestic reindeer, while nine of these haplotypes were completely absent from the more ancient sites. Our documentation of a major genetic shift during the 16th and 17th centuries suggests that non-native animals were introduced during this period, at the same time as the transition to reindeer pastoralism took place.

Abstract NG01: Evolution of neoantigen landscape during immune checkpoint blockade in non-small cell lung cancer

Abstract NG01: Evolution of neoantigen landscape during immune checkpoint blockade in non-small cell lung cancer

Going, going, gone? Loss of genetic diversity in two critically endangered Australian freshwater fishes, Scaturiginichthys vermeilipinnis and Chlamydogobius squamigenus, from Great Artesian Basin springs at Edgbaston, Queensland, Australia

Abstract Artesian springs are particularly sensitive freshwater ecosystems, characterized by specialized flora and fauna which, owing to their isolation, are often endemic. Thus, protection of spring habitats and endemic spring biota is important for biodiversity conservation, particularly because human impacts such as invasive species, habitat destruction, and fragmentation can have such devastating effects. This study investigated the mitochondrial DNA (mtDNA) genetic diversity and structure of two critically endangered (IUCN) freshwater fish species: red‐finned blue‐eye Scaturiginichthys vermeilipinnis, and Edgbaston goby Chlamydogobius squamigenus, with the aim of assisting management agencies to establish relocated populations that conserve the genetic integrity and evolutionary potential of both species. 2862 bp from multiple mtDNA genes were amplified from 111 red‐finned blue‐eye individuals (17 from the 1990s and 94 from 2010), and a 660 bp segment of mtDNA cytochrome b was amplified from 111 Edgbaston goby individuals (from 2010). In total, 14 concatenated mtDNA haplotypes were identified in red‐finned blue‐eye and three cytb haplotypes were identified in Edgbaston goby. Overall assessment of the genetic diversity and structure of the endemic fish fauna from the Edgbaston springs revealed low levels of diversity in both species and a loss of haplotypes in red‐finned blue‐eye over time. In addition, both species displayed significant genetic structure: at the spring scale for red‐finned blue‐eye and at the spring group scale for Edgbaston goby. It is concluded that without the appropriate management of relocated populations, such as considering genetic structure and diversity and selecting high quality habitats, these species are at a severe risk of losing evolutionary potential and becoming extinct. This study provides a valuable example for conservation managers of the contribution that population genetic studies can make regarding the adaptive management of endangered species. Copyright © 2016 John Wiley &amp; Sons, Ltd.

The phylogeographic history of the threatened Diana fritillary, Speyeria diana (Lepidoptera: Nymphalidae): with implications for conservation

The Diana fritillary, Speyeria diana (Cramer 1777) (Lepidoptera: Nymphalidae), is a North American endemic butterfly that disappeared from low elevation sites throughout its range in the twentieth century. It now persists in two geographically isolated mountainous regions, with an 800 km disjunction. Using mitochondrial cytochrome oxidase II DNA sequences from museum and field-sampled specimens, we found greater mtDNA diversity and more widespread differentiation among eastern populations than western ones. In addition, using coalescent-based population divergence models we dated the earliest splitting of eastern and western populations at least 20,000 years ago, during the Last Glacial Maximum. Therefore, the recent range collapse across the center of the historical species distribution may have exacerbated an ancient genetic differentiation between eastern and western populations. Finally, the loss of lowland haplotypes and the relatively large variation among local populations suggests that dispersal is low and lowland populations did not move to higher elevations, perhaps in response to climate change but, rather, appear to have vanished. Our results highlight the value of incorporating genetic data from preserved specimens when investigating the phylogeographic history and conservation status of a threatened species.

The impacts of inbreeding, drift and selection on genetic diversity in captive breeding populations.

The goal of captive breeding programmes is often to maintain genetic diversity until re-introductions can occur. However, due in part to changes that occur in captive populations, approximately one-third of re-introductions fail. We evaluated genetic changes in captive populations using microsatellites and mtDNA. We analysed six populations of white-footed mice that were propagated for 20 generations using two replicates of three protocols: random mating (RAN), minimizing mean kinship (MK) and selection for docility (DOC). We found that MK resulted in the slowest loss of microsatellite genetic diversity compared to RAN and DOC. However, the loss of mtDNA haplotypes was not consistent among replicate lines. We compared our empirical data to simulated data and found no evidence of selection. Our results suggest that although the effects of drift may not be fully mitigated, MK reduces the loss of alleles due to inbreeding more effectively than random mating or docility selection. Therefore, MK should be preferred for captive breeding. Furthermore, our simulations show that incorporating microsatellite data into the MK framework reduced the magnitude of drift, which may have applications in long-term or extremely genetically depauperate captive populations.

Genetic consequences of postglacial range expansion in two codistributed rodents (genus Dipodomys) depend on ecology and genetic locus.

How does range expansion affect genetic diversity in species with different ecologies, and do different types of genetic markers lead to different conclusions? We addressed these questions by assessing the genetic consequences of postglacial range expansion using mitochondrial DNA (mtDNA) and nuclear restriction site-associated DNA (RAD) sequencing in two congeneric and codistributed rodents with different ecological characteristics: the desert kangaroo rat (Dipodomys deserti), a sand specialist, and the Merriam's kangaroo rat (Dipodomys merriami), a substrate generalist. For each species, we compared genetic variation between populations that retained stable distributions throughout glacial periods and those inferred to have expanded since the last glacial maximum. Our results suggest that expanded populations of both species experienced a loss of private mtDNA haplotypes and differentiation among populations, as well as a loss of nuclear single-nucleotide polymorphism (SNP) private alleles and polymorphic loci. However, only D.deserti experienced a loss of nucleotide diversity (both mtDNA and nuclear) and nuclear heterozygosity. For all indices of diversity and differentiation that showed reduced values in the expanded areas, D.deserti populations experienced a greater degree of loss than did D.merriami populations. Additionally, patterns of loss in genetic diversity in expanded populations were substantially less extreme (by two orders of magnitude in some cases) for nuclear SNPs in both species compared to that observed for mitochondrial data. Our results demonstrate that ecological characteristics may play a role in determining genetic variation associated with range expansions, yet mtDNA diversity loss is not necessarily accompanied by a matched magnitude of loss in nuclear diversity.

Museum collections reveal that Buff-breasted Sandpipers (Calidris subruficollis) maintained mtDNA variability despite large population declines during the past 135 years

A principal goal of conservation efforts for threatened and endangered taxa is maintenance of genetic diversity. Modern and historic processes that limit population size can contribute to a loss of genetic variation that can reduce future adaptability of a species. Buff-breasted Sandpipers (Calidris subruficollis) are a Neotropical migratory shorebird that experienced rapid, large-scale declines in population numbers (population bottleneck) due to intensive market hunting at the turn of the 20th century. Market hunting ended shortly after the passage of the Migratory Bird Treaty Act in 1918, but subsequent population losses have occurred due to continued anthropogenic disturbances throughout the species’ migratory range. To assess the impact of population declines on the genetic variation of Buff-breasted Sandpipers, we surveyed two mitochondrial DNA (mtDNA) markers, the control region and cytochrome b, from 209 museum specimens collected between 1874 and 1983 and 460 modern samples collected between 1993 and 2009. Measures of mtDNA variation did not change significantly among individuals sampled before and after the ban on market hunting, nor among four temporal groups (Pre-Act, Early Post-Act, Late Post-Act, and Modern; trend analysis: χ 2 = 0.171, P = 0.679). Similarly, we did not observe loss of common haplotypes, implying that there was no substantial reduction in unique matrilineal units during our 135-year study period. Using Bayesian Skyline reconstruction of temporal changes in effective population size of females (N ef), we concluded that N ef has been stable for the past century. Results of resampling suggest that diversity estimators can be imprecise and we emphasize the importance of a well-rounded analytical approach to addressing conservation genetic hypotheses. Considering all of the evidence it appears that genetic variation and N ef were stable despite the pressures of market hunting early in the 20th century and habitat loss and degradation in the latter half of the 20th century. Conservation efforts should continue to focus on maintaining the population size of Buff-breasted Sandpipers to avoid reaching a threshold where genetic variability is lost.

Living on the edge: reconstructing the genetic history of the Finnish wolf population

BackgroundMany western European carnivore populations became almost or completely eradicated during the last ~200 years, but are now recovering. Extirpation of wolves started in Finland in the 19th century, and for more than 150 years the population size of wolves has remained small. To investigate historical patterns of genetic variation, we extracted DNA from 114 wolf samples collected in zoological museums over the last ~150 years. Fifteen microsatellite loci were used to look at genotypic variation in this historical sample. Additionally, we amplified a 430 bp sequence of mtDNA control region from the same samples. Contemporary wolf samples (N = 298) obtained after the population recovery in the mid-1990s, were used as a reference.ResultsOur analyses of mtDNA revealed reduced variation in the mtDNA control region through the loss of historical haplotypes observed prior to wolf declines. Heterozygosity at autosomal microsatellite loci did not decrease significantly. However, almost 20% of microsatellite alleles were unique to wolves collected before the 1960s. The genetic composition of the population changed gradually with the largest changes occurring prior to 1920. Half of the oldest historical samples formed a distinguishable genetic cluster not detected in the modern-day Finnish or Russian samples, and might therefore represent northern genetic variation lost from today’s gene pool. Point estimates of Ne were small (13.2 and 20.5) suggesting population fragmentation. Evidence of a genetic population bottleneck was also detected.ConclusionsOur genetic analyses confirm changes in the genetic composition of the Finnish wolf population through time, despite the geographic interconnectivity to a much larger population in Russia. Our results emphasize the need for restoration of the historical connectivity between the present wolf populations to secure long-term viability. This might be challenging, however, because the management policies between Western and Eastern Europe often differ greatly. Additionally, wolf conservation is still a rather controversial issue, and anthropogenic pressure towards wolves remains strong.

Japanese chum salmon stock enhancement: current perspective and future challenges

This study reviews the present status of the Japanese chum salmon Oncorhynchus keta stock enhancement program and considers the ecological sustainability of wild populations while providing fishery production, exemplified by the hatchery-based Kitami region set net fishery. The return rate and the number of returns have been historically high in the Sea of Okhotsk, but have decreased in other regions since 2005. Natural spawning of chum salmon occurred in at least 160 rivers in Hokkaido. The genetic diversity of Japanese chum salmon was similar to or higher than that of other Pacific Rim populations. Numbers of alleles were high at microsatellite loci, but the loss of rare haplotypes was observed in all populations. The estimated Ne/N ratio for the Kitami region was >0.15 % including hatchery and wild fish under the present high fishing pressure. Four regional populations were inferred in Hokkaido, however, genetic differentiation was weak and some river-populations were nested. Substantial changes in run timing were observed, but it has recovered gradually owing to the recent practice of escapement. Our analyses highlight the importance of juvenile quality and the vital roles of escapements in enhanced and non-enhanced rivers. New research is needed to minimize the genetic risks associated with hatchery programs.