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1.
The sequence variation of three exons of the major histocompatibility complex ( Mhc ) was examined in a lake whitefish Coregonus sp., population from the Swiss lake of Hallwil. DNA sequences from the Mhc class I A1 , A2 and class II B1 exons, corresponding to the α1, α2 and β1 domains of the Mhc glycoproteins, were obtained by the polymerase chain reaction followed by cloning and sequencing. The numbers of variable sequences detected for each exon were 15 ( A1 ), 11 ( A2 ) and 20 ( B1 ). Levels of nucleotide similarity ranged from 82 to 99% for the A1 exon, 58–96% for the A2 and 88–99% for the B1 exon. At the A1 and B1 exons, the nonsynonymous substitution rates ( dn ) exceeded synonymous substitution rates ( ds ) greatly within the peptide binding regions, indicating the effect of balancing selection. Sequence diversity at the A2 exon did not seem to be maintained by balancing selection ( ds > dn ). Phylogenetic comparison of whitefish Mhc sequences with sequences from other salmonid species and more distantly related teleosts indicated shared ancestral (trans-species) polymorphism. 相似文献
2.
This study presents the first detailed analysis of the mitochondrial DNA diversity of least cisco Coregonus sardinella in Alaska using a 678 bp segment of the control region (D‐loop) of the mitochondrial genome. Findings suggest that the history of C. sardinella in Alaska differs from that of other species of Coregonus present in the state and surrounding regions. The examined populations of C. sardinella are genetically diverse across Alaska. Sixty‐eight distinct mitochondrial haplotypes were identified among 305 individuals sampled from nine locations. The haplotype minimum spanning network and phylogeny showed a modest level of geographic segregation among haplotypes, suggesting high levels of on‐going or recent connectivity among distant populations. Observed ΦST values and the results of homogeneity and AMOVAs indicate incipient genetic differentiation between aggregations in three broad regional groups. Sites north of the Brooks Range formed one group, sites in the Yukon and Selawik Rivers formed a second group and sites south of the Yukon drainage formed the third group. Overall, the sequence data showed that a large proportion of mtDNA genetic variation in C. sardinella is shared across Alaska, but this variation is not homogeneously distributed across all regions and for all haplotype groups. 相似文献
3.
Yufei Dai Watchara Sakornwimon Rachawadee Chantra Liyuan Zhao Fuxing Wu Reyilamu Aierken Kongkiat Kittiwattanawong Xianyan Wang 《Ecology and evolution》2022,12(5)
The Indo‐Pacific humpback dolphin (Sousa chinensis) is a vulnerable marine mammal species that inhabits shallow, coastal waters from Southeast China, southward throughout Southeast Asia, and westward around the Bay of Bengal to eastern India. Polymorphic microsatellites are useful for elucidating ecological and population genetics‐related questions. Here, 18 new polymorphic microsatellites were developed from S. chinensis genomic DNA by Illumina MiSeq sequencing. Population genetic analyses were conducted on 42 S. chinensis individuals from three geographic locations, including the Xiamen Bay of China, the Western Gulf of Thailand, and Andaman Sea. Our microsatellite data revealed a strong and significant population structure among the three sampling regions (overall F ST = 0.371, p = .001). Pairwise mutual information index also demonstrated high levels of genetic differentiation between different region pairs (values range from 0.272 to 0.339, p < .001). Moreover, Structure analysis inferred three genetic clusters, with the high assignment probabilities of 95.92%, 99.47%, and 99.68%, respectively. Principal coordinate analysis plots of individuals divided entire genotypes into three clusters, indicating high level of genetic differentiation. Our results indicated the strong genetic structure in S. chinensis populations is a result of geographic distances. Other factors such as environmental variables, anthropogenic interference, and social behavior may also have contributed to population differentiation. 相似文献
4.
Stephanie L. Béland Brenna A. Frasier James D. Darling Timothy R. Frasier 《Marine Mammal Science》2020,36(2):398-420
Many species of whales went through recent bottlenecks due to commercial whaling. These declines were rapid and recent relative to the life spans and generation times of these species, raising questions regarding to what degree commercial whaling influenced the genetic characteristics of these populations. We analyzed mitochondrial and nuclear DNA from pre- and postwhaling samples from two populations that have arguably shown the greatest degree of recovery: eastern North Pacific gray and humpback whales. We also compare the performance of different methods to test for historic bottlenecks and infer past demography based on genetic data. We found substantially higher levels of genetic diversity in gray than in humpback whales (for both time periods), likely due to recent connectivity between Atlantic and Pacific gray whale populations. Other than mitochondrial diversity in humpback whales, levels of diversity were not lower in contemporary samples relative to prewhaling samples, indicating that commercial whaling had a minimal impact on metrics of genetic diversity themselves. However, it did have large impacts on the patterns of diversity, as evidenced by all coalescent-based methods showing clear evidence of a bottleneck for both populations, whereas all but one method not based on the coalescent failed to detect a bottleneck. 相似文献
5.
North Pacific humpback whales (Megaptera novaeangliae) migrate annually to foraging grounds in Southeast Alaska that are characterized by semidiurnal tidal cycles. Tidal activity is an important driver of marine mammal behavior on foraging grounds, but is often omitted in studies of acoustic ecology. To better understand the role of sound in this vocal species we investigated the influence of tidal height and direction on humpback whale nonsong calling behavior in Frederick Sound and described new call types for this population. The likelihood of detecting a call from the low‐frequency‐harmonic, pulsed, or noisy‐complex call classes was independent of tidal activity. The likelihood of detecting a call from the tonal call class, and a feeding call in particular, was 2.1 times higher during flood tides than during ebb tides (95% CI 1.1–4.4). This likely reflects an indirect relationship between humpback whale foraging and tides. 相似文献
6.
NORTH PACIFIC HUMPBACK WHALE SONGS: A COMPARISON OF SOUTHEAST ALASKAN FEEDING GROUND SONGS WITH HAWAIIAN WINTERING GROUND SONGS 总被引：1，自引：0，他引：1
Humpback whales sing long, complex songs on their wintering grounds. On 25 August 1979 and 3 September 1981, we made recordings of humpback whale songs in southeastern Alaska, showing that humpback whales also sing on the summer feeding grounds. Both these Alaskan samples are songs in that they are repeating cyclical sound patterns and follow the known structure for humpback whale song. The Alaskan songs contain all the same material sung in the same order as that heard off Mexico and Hawaii in the surrounding wintering seasons. However, song, theme and some phrase durations are abbreviated in the Alaskan songs. The recording of these two songs represents the full sample of song recorded from 155 days over five years of attempting to record humpback whale song in Alaskan waters. 相似文献
7.
David Frei;Salome Mwaiko;Ole Seehausen;Philine G. D. Feulner; 《Evolutionary Applications》2024,17(2):e13617
Genomic diversity is associated with the adaptive potential of a population and thereby impacts the extinction risk of a species during environmental change. However, empirical data on genomic diversity of populations before environmental perturbations are rare and hence our understanding of the impact of perturbation on diversity is often limited. We here assess genomic diversity utilising whole-genome resequencing data from all four species of the Lake Constance Alpine whitefish radiation. Our data covers a period of strong but transient anthropogenic environmental change and permits us to track changes in genomic diversity in all species over time. Genomic diversity became strongly reduced during the period of anthropogenic disturbance and has not recovered yet. The decrease in genomic diversity varies between 18% and 30%, depending on the species. Interspecific allele frequency differences of SNPs located in potentially ecologically relevant genes were homogenized over time. This suggests that in addition to the reduction of genome-wide genetic variation, the differentiation that evolved in the process of adaptation to alternative ecologies between species might have been lost during the ecological disturbance. The erosion of substantial amounts of genomic variation within just a few generations in combination with the loss of potentially adaptive genomic differentiation, both of which had evolved over thousands of years, demonstrates the sensitivity of biodiversity in evolutionary young adaptive radiations towards environmental disturbance. Natural history collections, such as the one used for this study, are instrumental in the assessment of genomic consequences of anthropogenic environmental change. Historical samples enable us to document biodiversity loss against the shifting baseline syndrome and advance our understanding of the need for efficient biodiversity conservation on a global scale. 相似文献
8.
Barbara A. Lagerquist Bruce R. Mate Joel G. Ortega‐Ortiz Martha Winsor Jorge Urbán‐Ramirez 《Marine Mammal Science》2008,24(4):815-830
Humpback whales wintering in the Revillagigedo Archipelago, Mexico, have been considered a different subpopulation from those found off mainland Mexico and Baja California. The primary feeding grounds for Revillagigedo humpbacks remain unknown. In February 2003, we deployed 11 Argos satellite‐monitored radio tags to track movements and surfacings of humpback whales (five adults without calves, five mothers with calves, one calf) off Socorro Island in the Revillagigedo Archipelago. Tracking ranged from 222 to 10,481 km over 4.9–149.1 d. Eight whales left Socorro Island: five visited other Mexican wintering destinations, seven moved north of these areas. Migration routes were primarily offshore (average 444 km). Two whales were tracked to feeding grounds: one to British Columbia (46 d migration), and one to Alaska (49 d migration). Mean travel speeds were 1.2 km/h in wintering areas, 4.0 km/h during migration, and 2.2 km/h in feeding areas. Overall surfacing rates ranged from 21 to 88 surfacings/h. Surfacing rates differed between the calf and all other whales, and between feeding areas and migratory/wintering areas for the calf and an adult without a calf. The calf also showed diel variation in surfacing rates. The offshore habits of tagged whales may explain scarce resightings of Revillagigedo humpbacks outside the Revillagigedo Archipelago. 相似文献
9.
C. Scott Baker Louis M. Herman Anjanette Perry William S. Lawton Janice M. Straley John H. Straley 《Marine Mammal Science》1985,1(4):304-323
A total of 326 humpback whales (Megaptera novaeangliae) were individually identified in southeastern Alaska during five summer seasons (July to September) and four late seasons (November to February) spanning the years 1979 to 1983. Peak numbers of whales were found late in August or early in September. Whales arrived 1–2 wk later in 1982 than in 1981. Whales sighted in both the summer and late seasons of 1981 and 1982 remained about 3.7 mo and one whale remained for at least 4.9 mo. Humpback whales from southeastern Alaska wintered in Hawaiian or Mexican waters, but generally did not travel to other feeding regions. The most rapid migratory transit between Hawaii and southeastern Alaska was 79 d. Based on mark-recapture analyses of the photographic data, we estimate a population of 270–372 whales in the southeastern Alaska feeding herd. 相似文献
10.
This study examined how variability in the abundance and biomass structure of benthic invertebrates affected the feeding choice of the whitefish Coregonus lavaretus on a hard bottom habitat of the brackish Baltic Sea. In general, crustaceans such as Idotea balthica and Gammarus spp. were preferred over molluscs. Although being the most numerous taxon in the invertebrate samples, Mytilus trossulus was the lowest ranking in C. lavaretus food preference. The availability of benthic invertebrate prey set the dietary range of fish but the selectivity largely described fish feeding within this range. There was no clear link between fish predation and the dominance structure of benthic invertebrate communities, suggesting that species composition, abundance and biomass of invertebrate species had no impact on the feeding selectivity of the fish. Thus, while fish predation may not affect the dominant species within a benthic community, due to strong selectivity fish may impose strong pressure on some rarer but highly preferred invertebrate prey species. 相似文献
11.
Andrew Szabo 《Marine Mammal Science》2015,31(2):677-687
Humpbacks whales (Megaptera novaeangliae) have shown a remarkable recovery in the North Pacific, raising concerns regarding their impact on marine communities. In Southeast Alaska, humpbacks feed heavily on euphausiids; however, it remains unclear whether they target immature individuals despite evidence that they do so elsewhere. I evaluate the hypothesis that humpbacks target immature euphausiids in late spring‐summer in Southeast Alaska. Plankton samples were collected at random sites (n = 44) and near whales (n = 53) between 8 June and 9 September 2008 in Frederick Sound and Stephens Passage. The proportion of samples containing immature euphausiids, and immature euphausiid abundance within those samples, were compared between the two sample types. Similar analyses were conducted for adult euphausiids (prey) and calanoid copepods (nonprey) for comparison. I found no statistical difference between the whale and random samples with respect to the occurrence or numerical density of immature euphausiids, which is consistent with the hypothesis that whales did not target them in 2008. Smaller size, insufficient numerical densities and lower energy density of immature euphausiids are suggested as possible reasons. These findings can assist in resolving regional humpback abundance and distribution patterns, and can contribute to an understanding of the trophic interactions characterizing the local ecosystem. 相似文献
12.
Maelle Sevellec Martin Laporte Alex Bernatchez Nicolas Derome Louis Bernatchez 《Ecology and evolution》2019,9(20):11762-11774
Investigating relationships between microbiota and their host is essential toward a full understanding of how animal adapt to their environment. Lake Whitefish offers a powerful system to investigate processes of adaptive divergence where the dwarf, limnetic species evolved repeatedly from the normal, benthic species. We compared the transient intestinal microbiota between both species from the wild and in controlled conditions, including their reciprocal hybrids. We sequenced the 16s rRNA gene V3‐V4 regions to (a) test for parallelism in the transient intestinal microbiota among sympatric pairs, (b) test for transient intestinal microbiota differences among dwarf, normal, and hybrids reared under identical conditions, and (c) compare intestinal microbiota between wild and captive whitefish. A significant host effect on microbiota taxonomic composition was observed when all lakes were analyzed together and in three of the five species pairs. In captive whitefish, host effect was also significant. Microbiota of both reciprocal hybrids fell outside of that observed in the parental forms. Six genera formed a bacterial core which was present in captive and wild whitefish, suggesting a horizontal microbiota transmission. Altogether, our results complex interactions among the host, the microbiota, and the environment, and we propose that these interactions define three distinct evolutionary paths of the intestinal microbiota. 相似文献
13.
Rishi De‐Kayne Stefan Zoller Philine G. D. Feulner 《Molecular ecology resources》2020,20(4):1093-1109
Salmonids are of particular interest to evolutionary biologists due to their incredible diversity of life‐history strategies and the speed at which many salmonid species have diversified. In Switzerland alone, over 30 species of Alpine whitefish from the subfamily Coregoninae have evolved since the last glacial maximum, with species exhibiting a diverse range of morphological and behavioural phenotypes. This, combined with the whole genome duplication which occurred in the ancestor of all salmonids, makes the Alpine whitefish radiation a particularly interesting system in which to study the genetic basis of adaptation and speciation and the impacts of ploidy changes and subsequent rediploidization on genome evolution. Although well‐curated genome assemblies exist for many species within Salmonidae, genomic resources for the subfamily Coregoninae are lacking. To assemble a whitefish reference genome, we carried out PacBio sequencing from one wild‐caught Coregonus sp. “Balchen” from Lake Thun to ~90× coverage. PacBio reads were assembled independently using three different assemblers, falcon , canu and wtdbg2 and subsequently scaffolded with additional Hi‐C data. All three assemblies were highly contiguous, had strong synteny to a previously published Coregonus linkage map, and when mapping additional short‐read data to each of the assemblies, coverage was fairly even across most chromosome‐scale scaffolds. Here, we present the first de novo genome assembly for the Salmonid subfamily Coregoninae. The final 2.2‐Gb wtdbg2 assembly included 40 scaffolds, an N50 of 51.9 Mb and was 93.3% complete for BUSCOs. The assembly consisted of ~52% transposable elements and contained 44,525 genes. 相似文献
14.
Janet L. Neilson Janice M. Straley Christine M. Gabriele Susan Hills 《Journal of Biogeography》2009,36(3):452-464
Aim Entanglement in fishing gear is recognized as a potentially significant source of serious injury and mortality for humpback whales (Megaptera novaeangliae) in some parts of their range. In recent years, the number of humpback whales reported to have been entangled in Alaska has increased. In 2003–04 we quantified the prevalence of non‐lethal entanglements of humpback whales in northern Southeast Alaska (SEAK) with the ultimate goal of informing management discussions of the entanglement issue for the Central North Pacific stock of humpback whales. Location The near‐shore waters of northern Southeast Alaska. Methods We photographed individual humpback whales’ caudal peduncles as they dived and then examined the photographs for scars indicative of a previous entanglement. Results The percentage of whales assessed to have been non‐lethally entangled at some time in their lives ranged from 52% (minimal estimate) to 71% (conditional estimate) to 78% (maximal estimate). Of these, the conditional estimate is recommended because it is based solely on unambiguous scars. Eight per cent of the whales in one portion of the study area (Glacier Bay/Icy Strait) acquired new entanglement scars between 2003 and 2004, although the sample size was small. Calves were less likely than older whales to have entanglement scars, and males may be at higher risk than females. Whales with more photographs and/or photographic coverage may be more likely to be assessed as having been entangled than whales with fewer photographs and/or coverage. Main conclusions Caudal peduncle scars reveal that the majority of humpback whales in northern SEAK have been entangled. Comparison with statistics on reported entanglements suggests that most whales apparently shed the gear on their own, unless humans are disentangling whales much more often than is reported. While cumulative estimates of the percentage of whales with entanglement scars (e.g. the conditional estimate) provide useful baseline information, future efforts should focus on monitoring the annual rate of entanglement scar acquisition as a more powerful measure of contemporary entanglement rates. Our findings indicate that entanglement of humpback whales in fishing gear in SEAK is a management issue warranting increased attention. A proactive approach is needed to address the problem and to identify and implement preventive measures. 相似文献
15.
For a distinct autochthonous Austrian coregonid population called Reinanke Coregonus sp., embryo viability was very low in Zuger jars (mean ± s.d. 36·1 ± 16·1% eyed stage embryos in experiment 1, 15·1 ± 17·0% in experiment 2) but high in vertical flow incubators (63·3 ± 29·0% eyed stage embryos in experiment 1, 57·8 ± 18·9% in experiment 2). Mechanical shock sensitivity is a possible explanation for high embryo mortality. 相似文献
16.
To demonstrate the importance of genetic data for multispecies conservation approaches, we examined the distribution of genetic variation across the range of the mountain whitefish (Prosopium williamsoni) at microsatellite and allozyme loci. The mountain whitefish is a common species that is particularly well suited for accurately revealing historical patterns of genetic structure and differs markedly from previously studied species in habitat requirements and life history characteristics. As such, comparing the population genetic structure of other native fishes to similar data from mountain whitefish could inform management and conservation strategies. Genetic variation for mountain whitefish was hierarchically distributed for both allozymes and microsatellites. We found evidence for a total of five major genetically differentiated assemblages and we observed subdivision among populations within assemblages that generally corresponded to major river basins. We observed little genetic differentiation within major river basins. Geographic patterns of genetic differentiation for mountain whitefish were concordant with other native species in several circumstances, providing information for the designation of conservation units that reflect concordant genetic differentiation of multiple species. Differences in genetic patterns between mountain whitefish and other native fishes reflect either differences in evolutionary histories of the species considered or differences in aspects of their ecology and life history. In addition, mountain whitefish populations appear to exchange genes over a much larger geographic scale than co-occurring salmonids and are likely to be affected differently by disturbances such as habitat fragmentation. 相似文献
17.
Robert C. Lacy 《Zoo biology》1989,8(2):111-123
The concepts of “founder equivalent” and “founder genome equivalent” are introduced to facilitate analysis of the founding stocks of captive or other populations for which pedigrees are available. The founder equivalents of a population are the number of equally contributing founders that would be expected to produce the same genetic diversity as in the population under study. Unequal genetic contributions by founders decrease the founder equivalents, portend greater inbreeding in future generations than would be necessary, and reflect a greater loss of the genetic diversity initially present in the founders. The number of founder genome equivalents of a population is that number of equally contributing founders with no random loss of founder alleles in descendants that would be expected to produce the same genetic diversity as in the population under study. The number of founder genome equivalents is approximately that number of wild-caught animals that would be needed to obtain the same amount of genetic diversity as is in the descendant captive population. Founder equivalents and founder genome equivalents allow comparison of the genetic merits of adding new wild-caught stock vs. further equalizing founder representations in a captive population. 相似文献
18.
19.
C. S. Baker L. Flórez-González B. Abernethy H. C. Rosenbaum R. W. Slade J. Capella J. L. Bannister 《Marine Mammal Science》1998,14(4):721-737
Samples of skin tissue were collected by biopsy darting from humpback whales ( Megaptera novaeangliae ) in six seasonal habitats representing three stocks and four regions: Groups IV (western Australia), V western component (eastern Australia), V eastern component (New Zealand and Tonga) and VI (the Antarctic Peninsula and Gorgona Island, Colombia, South America) of the Southern Hemisphere. A variable section of the mitochondrial DNA control region was amplified and sequenced from 84 of these individuals, distinguishing a total of 48 unique sequences ( i. e. , mtDNA nucleotypes). Phylogenetic reconstructions suggested that these nucleotypes form three clades, corresponding to those previously described in a world-wide survey of humpback whale mtDNA variation, although bootstrap support for two of the clades was relatively low (<50%). An analysis of variance adapted for molecular information showed significant differentiation of nucleotypes among the three Groups (Stocks) and heterogeneity of haplotype diversity among the four regions. A pattern of interchange within and between oceanic basins was demonstrated by the presence of shared identical nucleotypes among humpback whales in regions of the Southern and Northern Hemispheres. 相似文献
20.
Janice M. Straley Terrance J. Quinn II Christine M. Gabriele 《Journal of Biogeography》2009,36(3):427-438
Aim The aim of this study was to use photographs of the unique pattern on the ventral surface of the flukes to estimate the abundance of humpback whales (Megaptera novaeangliae) in a discrete feeding aggregation in northern Southeast Alaska. Location The study was located in northern Southeast Alaska, USA, in the eastern North Pacific Ocean. Methods This study evaluated mark–recapture models, ranging from the simpler models (pooled and stratified, closed Petersen estimators) to more complex multi‐strata models (closed Darroch and open Hilborn). The Akaike Information Criterion, corrected (AICc) was used as a model comparison statistic. Results Our best estimate of whale abundance in northern Southeast Alaska in 2000 is 961 whales [95% confidence interval (657, 1076)]. This estimate comes from the Hilborn open, multi‐strata approach with constant migration over time, time‐dependent capture probabilities by area, and a fixed survival rate of 0.98. The simpler models were problematic owing to several aspects of whale behaviour, including that (1) the whales did not mix randomly throughout the study area, (2) some whales emigrated temporarily outside the study area and were not available for capture, and (3) whales were not equally identifiable because they did not behave in the same way when they showed their flukes upon diving. This led to heterogeneity in capture probability and a bias in the estimates. The more complex models stratified by area, and using migration movements among areas, compensated for some of these issues when estimating population size. Main conclusions We believe that the Hilborn open, multi‐strata model produced the best estimate because: (1) it incorporated the best information about survival, (2) it used detailed information about the various release groups, (3) the analysis provided an integrated environment in which parameters such as migration and capture probabilities are shared, (4) the three strata encompassed a large portion of the areas used by whales, and (5) the Hilborn model selected was superior in terms of model selection criteria and biological realism. These data provide valuable insights into the numbers and movements of humpback whales in three areas of Southeast Alaska. 相似文献