Journal: The Journal of heredity
The difficulties associated with detecting population boundaries have long constrained the conservation and management of highly mobile, wide-ranging marine species, such as killer whales (Orcinus orca). In this study, we use data from 26 nuclear microsatellite loci and mitochondrial DNA sequences (988bp) to test a priori hypotheses about population subdivisions generated from a decade of killer whale surveys across the northern North Pacific. A total of 462 remote skin biopsies were collected from wild killer whales primarily between 2001 and 2010 from the northern Gulf of Alaska to the Sea of Okhotsk, representing both the piscivorous “resident” and the mammal-eating “transient” (or Bigg’s) killer whales. Divergence of the 2 ecotypes was supported by both mtDNA and microsatellites. Geographic patterns of genetic differentiation were supported by significant regions of genetic discontinuity, providing evidence of population structuring within both ecotypes and corroborating direct observations of restricted movements of individual whales. In the Aleutian Islands (Alaska), subpopulations, or groups with significantly different mtDNA and microsatellite allele frequencies, were largely delimited by major oceanographic boundaries for resident killer whales. Although Amchitka Pass represented a major subdivision for transient killer whales between the central and western Aleutian Islands, several smaller subpopulations were evident throughout the eastern Aleutians and Bering Sea. Support for seasonally sympatric transient subpopulations around Unimak Island suggests isolating mechanisms other than geographic distance within this highly mobile top predator.
The Bali (Panthera tigris balica) and Javan (P. t. sondaica) tigers are recognized as distinct tiger subspecies that went extinct in the 1940s and 1980s, respectively. Yet their genetic ancestry and taxonomic status remain controversial. Following ancient DNA procedures, we generated concatenated 1750bp mtDNA sequences from 23 museum samples including 11 voucher specimens from Java and Bali and compared these to diagnostic mtDNA sequences from 122 specimens of living tiger subspecies and the extinct Caspian tiger. The results revealed a close genetic affinity of the 3 groups from the Sunda Islands (Bali, Javan, and Sumatran tigers P. t. sumatrae). Bali and Javan mtDNA haplotypes differ from Sumatran haplotypes by 1-2 nucleotides, and the 3 island populations define a monophyletic assemblage distinctive and equidistant from other mainland subspecies. Despite this close phylogenetic relationship, no mtDNA haplotype was shared between Sumatran and Javan/Bali tigers, indicating litter or no matrilineal gene flow among the islands after they were colonized. The close phylogenetic relationship among Sunda tiger subspecies suggests either recent colonization across the islands, or else a once continuous tiger population that had subsequently isolated into different island subspecies. This supports the hypothesis that the Sumatran tiger is the closest living relative to the extinct Javan and Bali tigers.
Captive breeding and rearing are central elements in conservation, management, and recovery planning for many endangered species including Rio Grande Silvery Minnow, a North American freshwater cyprinid. Traditionally, the sole purpose of hatcheries was to produce as many fish as feasible for stocking and harvest. Production quotas are also an important consideration in hatchery programs for endangered species, but they must also maintain and maximize genetic diversity of fish produced through implementation of best breeding practices. Here, we assessed genetic outcomes and measures of productivity (number of eggs and larval viability) for three replicates of three mating designs that are used for this small, pelagic-spawning fish. These were 1) monogamous mating, 2) hormone-induced communal spawning, and 3) environmentally cued communal spawning. A total of 180 broodstock and 450 progeny were genotyped. Genetic diversity and egg productivity did not differ significantly among spawning designs (H e : F = 0.52, P = 0.67; H o : F = 0.12, P = 0.89; number of eggs: F = 3.59, P = 0.09), and there was evidence for variance in reproductive success among individuals in all three designs. Allelic richness declined from the broodstock to progeny generation in all breeding designs. There was no significant difference in the genetic effective size (regardless of the method used) among designs. Significantly more viable eggs were produced in environmentally cued communal spawn compared to the alternative strategies (F = 5.72, P = 0.04), but this strategy is the most difficult to implement.
Two novel repetitive DNA sequences, VSAREP1 and VSAREP2, were isolated from the water monitor lizard (Varanus salvator macromaculatus, Platynota) and characterized using molecular cytogenetics. The respective lengths and guanine-cytosine (GC) contents of the sequences were 190bp and 57.5% for VSAREP1 and 185bp and 59.7% for VSAREP2, and both elements were tandemly arrayed as satellite DNA in the genome. VSAREP1 and VSAREP2 were each located at the C-positive heterochromatin in the pericentromeric region of chromosome 2q, the centromeric region of chromosome 5, and 3 pairs of microchromosomes. This suggests that genomic compartmentalization between macro- and microchromosomes might not have occurred in the centromeric repetitive sequences of V. salvator macromaculatus. These 2 sequences did only hybridize to genomic DNA of V. salvator macromaculatus, but no signal was observed even for other squamate reptiles, including Varanus exanthematicus, which is a closely related species of V. salvator macromaculatus. These results suggest that these sequences were differentiated rapidly or were specifically amplified in the V. salvator macromaculatus genome.
Many genes are known to have an influence on conformation and performance traits; however, the role of one gene, Myostatin (MSTN), has been highlighted in recent studies on horses. Myostatin acts as a repressor in the development and regulation of differentiation and proliferative growth of skeletal muscle. Several studies have examined the link between MSTN, conformation and performance in racing breeds, but no studies have investigated the relationship in Icelandic horses. Icelandic horses, a highly unique breed, are known both for their robust and compact conformation as well as their additional gaits tölt and pace. Three SNPs (g.65868604G>T [PR8604], g.66493737C>T [PR3737] and g.66495826A>G [PR5826]) flanking or within equine MSTN were genotyped in 195 Icelandic horses. The SNPs and haplotypes were analyzed for association with official estimated breeding values (EBV) for conformation traits (n=11) and gaits (n=5). The EBV for neck, withers and shoulders was significantly associated with both PR8604 and PR3737 (p<0.05). PR8604 was also associated with EBV for total conformation (p=0.05). These associations were all supported by the haplotype analysis. However, while SNP PR5826 showed a significant association with EBVs for leg stance and hooves (p<0.05), haplotype analyses for these traits failed to fully support these associations. This study demonstrates the possible role of MSTN on both the form and function of horses from non-racing breeds. Further analysis of Icelandic horses as well as other non-racing breeds would be beneficial and likely help to completely understand the influence of MSTN on conformation and performance in horses.
Recent advances in genetic and ecological studies of wild animal populations in Chernobyl and Fukushima have demonstrated significant genetic, physiological, developmental, and fitness effects stemming from exposure to radioactive contaminants. The few genetic studies that have been conducted in Chernobyl generally show elevated rates of genetic damage and mutation rates. All major taxonomic groups investigated (i.e., birds, bees, butterflies, grasshoppers, dragonflies, spiders, mammals) displayed reduced population sizes in highly radioactive parts of the Chernobyl Exclusion Zone. In Fukushima, population censuses of birds, butterflies, and cicadas suggested that abundances were negatively impacted by exposure to radioactive contaminants, while other groups (e.g., dragonflies, grasshoppers, bees, spiders) showed no significant declines, at least during the first summer following the disaster. Insufficient information exists for groups other than insects and birds to assess effects on life history at this time. The differences observed between Fukushima and Chernobyl may reflect the different times of exposure and the significance of multigenerational mutation accumulation in Chernobyl compared to Fukushima. There was considerable variation among taxa in their apparent sensitivity to radiation and this reflects in part life history, physiology, behavior, and evolutionary history. Interestingly, for birds, population declines in Chernobyl can be predicted by historical mitochondrial DNA base-pair substitution rates that may reflect intrinsic DNA repair ability.
Mass strandings of whales and dolphins have puzzled biologists since Aristotle. Although environmental factors are often assumed to initiate strandings, social forces must also influence the dynamics of many of these events, particularly for the primary species involved in mass strandings, the long-finned pilot whales (Globicephala melas). Here, we test two hypotheses derived from common assumptions about the social dynamics of long-finned pilot whales by identifying maternal lineages from mtDNA haplotypes and inferring kinship from microsatellite genotypes of 490 individuals from 12 stranding events. Contrary to the “extended matriline” hypothesis, we found that multiple maternal lineages were present in at least 9 of the 12 mass strandings. Contrary to the “kinship cohesion” hypothesis, we found no correlation between spatial distribution and kinship along the stranding beach. Most notably, we documented the spatial disruption of the expected proximity between mothers and their dependent calves. These results challenge the common assumption that kinship-based behavior, such as care-giving, are a primary factor in these mass strandings. We suggest instead that disruption of kinship bonds could result from interactions among unrelated social groups during feeding or mating aggregations, perhaps playing a causal role in these events. Our finding that dependent calves were often spatially separated or absent from their mothers has important implications for humane management of rescue efforts. To improve our understanding of the social causes and consequences of mass strandings, future documentation of strandings should include exhaustive DNA sampling, with accompanying spatial and temporal records.
To evaluate the effects of the Fukushima nuclear accident on the surrounding area, we studied the pale grass blue butterfly Zizeeria maha, the most common butterfly in Japan. We here review our important findings and their implications. We found forewing size reduction, growth retardation, high mortality rates, and high abnormality rates in the field and reared samples. The abnormality rates observed in September 2011 were higher than those observed in May 2011 in almost all localities, implying transgenerational accumulation of genetic damage. Some of the abnormal traits in the F1 generation were inherited by the F2 generation. In a particular cross, the F2 abnormality rate scored 57%. The forewing size reduction and high mortality and abnormality rates were reproduced in external and internal exposure experiments conducted in our laboratory using Okinawa larvae. We observed the possible real-time evolution of radiation resistance in the Fukushima butterflies, which, in retrospect, indicates that field sampling attempts at the very early stages of such accidents are required to understand the ecodynamics of polluted regions. We propose, as the postulates of pollutant-induced biological impacts, that the collection of phenotypic data from the field and their relevant reproduction in the laboratory should be the basis of experimental design to demonstrate the biological effects of environmental pollutants and to investigate the molecular mechanisms responsible for these effects.
Tigers (Panthera tigris), like many large carnivores, are threatened by anthropogenic impacts, primarily habitat loss and poaching. Current conservation plans for tigers focus on population expansion, with the goal of doubling census size in the next 10 years. Previous studies have shown that because the demographic decline was recent, tiger populations still retain a large amount of genetic diversity. Although maintaining this diversity is extremely important to avoid deleterious effects of inbreeding, management plans have yet to consider predictive genetic models. We used coalescent simulations based on previously sequenced mitochondrial fragments (n = 125) from 5 of 6 extant subspecies to predict the population growth needed to maintain current genetic diversity over the next 150 years. We found that the level of gene flow between populations has a large effect on the local population growth necessary to maintain genetic diversity, without which tigers may face decreases in fitness. In the absence of gene flow, we demonstrate that maintaining genetic diversity is impossible based on known demographic parameters for the species. Thus, managing for the genetic diversity of the species should be prioritized over the riskier preservation of distinct subspecies. These predictive simulations provide unique management insights, hitherto not possible using existing analytical methods.
Eritrea has one of the northernmost populations of African elephants. Only about 100 elephants persist in the Gash-Barka administrative zone. Elephants in Eritrea have become completely isolated, with no gene flow from other elephant populations. The conservation of Eritrean elephants would benefit from an understanding of their genetic affinities to elephants elsewhere on the continent and the degree to which genetic variation persists in the population. Using dung samples from Eritrean elephants, we examined 18 species-diagnostic single nucleotide polymorphisms in 3 nuclear genes, sequences of mitochondrial HVR1 and ND5, and genotyped 11 microsatellite loci. The sampled Eritrean elephants carried nuclear and mitochondrial DNA markers establishing them as savanna elephants, with closer genetic affinity to Eastern than to North Central savanna elephant populations, and contrary to speculation by some scholars that forest elephants were found in Eritrea. Mitochondrial DNA diversity was relatively low, with 2 haplotypes unique to Eritrea predominating. Microsatellite genotypes could only be determined for a small number of elephants but suggested that the population suffers from low genetic diversity. Conservation efforts should aim to protect Eritrean elephants and their habitat in the short run, with restoration of habitat connectivity and genetic diversity as long-term goals.