Two historical weapon fragments as an aid to estimating the longevity and movements of bowhead whales

The age of bowhead whales captured by Native Alaskan hunters in the Bering, Chukchi and Beaufort Seas has been estimated via chemical analyses of the eye lenses, and other techniques. The racemization-age estimates indicate that bowhead whales (Balaena mysticetus) have a lifespan of more than a century. Stone and ivory weapon fragments recovered from bowhead whales hunted in Wainwright and Barrow (Alaska) in 1981, 1992, 1993 and 1997, provided rough but independent assessments of the whales’ longevity; however, their date of manufacture was unknown. Adding further confirmation of these age estimates, this note describes bomb lance fragments recovered recently (2007) and about 30 years ago (1980) from bowhead whales harvested by Eskimo hunters that were “dateable” and likely manufactured between 1879 and 1885.     

Temporal changes in allele frequencies in two reciprocally selected maize populations

The effects of breeding on allele frequency changes at 82 restriction fragment length polymorphism (RFLP) loci were examined in two maize (Zea mays L.) populations undergoing reciprocal recurrent selection, Iowa Stiff Stalk Synthetic and Iowa Corn Borer Synthetic #1. After 12 cycles of selection, approximately 30% of the alleles were extinct and 10% near fixation in each population. A test of selective neutrality identified several loci in each population whose allele frequency changes cannot be explained by genetic drift; interpopulation mean expected heterozygosity increased for that subset of 28 loci but not for the remaining 54 loci. Mean expected heterozygosity within the two subpopulations decreased 39%, while the between-population component of genetic variation increased from 0.5% to 33.4% of the total. Effective population size is a key parameter for discerning allele frequency changes due to genetic drift versus those resulting from selection and genetic hitchhiking. Empirical estimates of effective population size for each population were within the range predicted by the breeding method. Received: 10 June 1998 / Accepted: 29 April 1999     

The Mitochondrial Genome of the Sperm Whale and a New Molecular Reference for Estimating Eutherian Divergence Dates

Extant cetaceans are systematically divided into two suborders: Mysticeti (baleen whales) and Odontoceti (toothed whales). In this study, we have sequenced the complete mitochondrial (mt) genome of an odontocete, the sperm whale (Physeter macrocephalus), and included it in phylogenetic analyses together with the previously sequenced complete mtDNAs of two mysticetes (the fin and blue whales) and a number of other mammals, including five artiodactyls (the hippopotamus, cow, sheep, alpaca, and pig). The most strongly supported cetartiodactyl relationship was: outgroup,((pig, alpaca),((cow, sheep),(hippopotamus,(sperm whale,(baleen whales))))). As in previous analyses of complete mtDNAs, the sister-group relationship between the hippopotamus and the whales received strong support, making both Artiodactyla and Suiformes (pigs, peccaries, and hippopotamuses) paraphyletic. In addition, the analyses identified a sister-group relationship between Suina (the pig) and Tylopoda (the alpaca), although this relationship was not strongly supported. The paleontological records of both mysticetes and odontocetes extend into the Oligocene, suggesting that the mysticete and odontocete lineages diverged 32–34 million years before present (MYBP). Use of this divergence date and the complete mtDNAs of the sperm whale and the two baleen whales allowed the establishment of a new molecular reference, O/M-33, for dating other eutherian divergences. There was a general consistency between O/M-33 and the two previously established eutherian references, A/C-60 and E/R-50. Cetacean (whale) origin, i.e., the divergence between the hippopotamus and the cetaceans, was dated to ≈55 MYBP, while basal artiodactyl divergences were dated to ≥65 MYBP. Molecular estimates of Tertiary eutherian divergences were consistent with the fossil record. Received: 12 July 1999 / Accepted: 28 February 2000     

Presence and behavior of bowhead whales (Balaena mysticetus) in the Alaskan Beaufort Sea in July 2011

The Western Arctic bowhead whale (Balaena mysticetus) is highly adapted to sea ice and annually migrates through the Bering, Chukchi, and Beaufort seas. While the overall distribution and seasonal movements of bowhead whales are mostly understood, information about their distribution in the Alaskan Beaufort Sea in early to mid-summer has not been well documented. In July 2011, we conducted an exploratory flight in the Alaskan Beaufort Sea, north of Camden Bay (71°N 144°W), near the location of a single satellite-tagged bowhead whale. Eighteen bowhead whales were observed, and behavior consistent with feeding was documented. To our knowledge, this is the first documentation of behavior consistent with feeding north of Camden Bay in mid-July. Few studies have focused on bowhead whale distribution in the Alaskan Beaufort Sea in early to mid-summer, and no long-term, region-wide surveys have been conducted during summer. Bowhead whales are already exposed to anthropogenic disturbance in the Canadian Beaufort Sea in summer, the Alaskan Beaufort Sea in fall, and the Chukchi and Bering seas from fall through spring. The presence of bowhead whale aggregations in the Alaskan Beaufort Sea in summer should be considered when assessing the cumulative effects of human-related activities.     

Stomach contents of bowhead whales (Balaena mysticetus) from four locations in the Canadian Arctic

The stomach contents of four bowhead whales (Balaena mysticetus) harvested between 1994 and 2008 from the Canadian Arctic were examined to assess diet composition. Three samples were collected from bowhead whales of the Eastern Canada–West Greenland (EC–WG) population and represent, according to our knowledge, the first diet analysis from this bowhead whale stock. We also examined the stomach content of one bowhead whale from the Bering-Chukchi-Beaufort (BCB) population hunted in 1996. All four whales had food in their stomachs and their diet varied from exclusively pelagic (BCB whale), with Limnocalanus macrurus being the main prey, to epibenthic and benthic (EC–WG) with Mysis oculata playing an important role. These results indicate broad foraging spectrum of the bowhead whales and add to a basic knowledge of their diet.     

Genetic Structure of the Ancestral Population of Modern Humans

Neutral DNA polymorphisms from an 8-kb segment of the dystrophin gene, previously ascertained in a worldwide sample (n= 250 chromosomes), were used to characterize the population ancestral to the present-day human groups. The ancestral state of each polymorphic site was determined by comparing human variants with their orthologous sites in the great apes. The ``age before fixation' of the underlying mutations was estimated from the frequencies of the new alleles and analyzed in the context of these polymorphisms' distribution among 13 populations from Africa, Europe, Asia, New Guinea, and the Americas (n= 860 chromosomes in total). Seventeen polymorphisms older tan 100,000–200,000 years, which contributed ∼90% to the overall nucleotide diversity, were common to all human groups. Polymorphisms endemic to human groups or continentally restricted were younger than 100,000–200,000 years. Africans (six populations) with 13 such sites stood out from the rest of the world (seven populations), where only 2 population-specific variants were observed. The similarity of the frequencies of the old polymorphisms in Africans and non-Africans suggested a similar profile of genetic variability in the population before the modern human's divergence. This ancestral population was characterized by an effective size of about 10,000 as estimated from the nucleotide diversity; this size may describe the number of breeding individuals over a long time during the Middle Pleistocene or reflect a speciation bottleneck from an initially larger population at the end of this period. Received: 3 February 1998 / Accepted: 9 February 1998     

Sequence-tagged-site (STS) markers of arbitrary genes: the utility of black spruce-derived STS primers in other conifers

 Sequence-tagged-site primers, previously developed based upon black spruce (Picea mariana) cDNA sequences, were tested for their ability to direct specific amplification in two individuals of each of 12 additional conifer species. Nearly all (95–97%) of the primers functioned well in congeneric trials, while a lower proportion (21–33%) scored positively in other Pinaceae genera. Outside of the Pinaceae, amplification of homologous products was not achieved. Products from the various species often differed in size from their homologs in black spruce. In one case a large difference in size was due to the lack of an intron in a jack pine product while in several other cases the differences were due to the presence or absence of large direct repeats in the DNA sequences. Length polymorphism was occasionally evident between the two individuals examined of a given species. We investigated marker polymorphism in detail in a panel of 15 white spruce (Picea glauca) trees. Allelic segregation among haploid megagametophytes was revealed directly at 16 loci by standard agarose-gel electrophoresis without any additional manipulation of amplification products. Polymorphisms observed at 12 of these loci were exclusively co-dominant. For this subset of 12 loci, the average number of alleles was 3.2 and the average observed heterozygosity was 0.37. Received: 10 April 1998 / Accepted: 22 April 1998     

Entanglement‐scar acquisition rates and scar frequency for Bering‐Chukchi‐Beaufort Seas bowhead whales using aerial photography

The Bering‐Chukchi‐Beaufort Seas (BCBS) bowhead whale (Balaena mysticetus) has been considered at low‐risk for entanglement injuries and ship strikes because their range is mainly north of commercial fisheries; nevertheless, changes to their arctic habitat, including a longer open water period and declining sea ice, have resulted in increasing commercial activity and concern about fisheries interactions. We examined interyear matches (between 1985 and 2011) from a photo identification project and identified whales that had acquired entanglement injuries. We estimated the probability of a bowhead acquiring an entanglement injury using two statistical methods: interval censored survival analysis and a simple binomial model. Both methods give similar results, suggesting a 2.2% (95% CI: 1.1%–3.3%) annual probability of acquiring a scar. We also include an entanglement scar frequency analysis of aerial photographs from the 2011 spring and fall surveys near Point Barrow, Alaska, which suggest 12.4% of live bowheads show evidence of entanglement scarring. Entanglement rates for the BCBS bowhead stock are lower than many other large whale stocks, and abundance has increased over the past 35 yr; however, our findings indicate that fishing gear entanglement is a more serious concern for the BCBS bowhead whale population than previously thought.     

FEEDING, SOCIAL AND MIGRATION BEHAVIOR OF BOWHEAD WHALES, BALAENA MYSTICETUS, IN BAFFIN BAY VS. THE BEAUFORT SEA—REGIONS WITH DIFFERENT AMOUNTS OF HUMAN ACTIVITY

This paper compares the behavior of bowhead whales of the Davis Strait/Baffin Bay stock, as observed along the east coast of Baffin Island in 1979–1986, with behavior of the Bering/Chukchi/Beaufort Sea stock observed in the Beaufort Sea in 1980–1986. All data used here were collected during late summer and early autumn in the absence of acute human disturbance. The behavioral repertoires of the two populations were similar. However, quantitative differences were found for whales engaged in all three activities studied: (1) Bowheads feeding in deep water off Isabella Bay, Baffin Island, had longer dives and surfacings, on average, than noted for bowheads feeding in the Beaufort Sea. (2) Among whales socializing in shallow water, we saw sexual interactions more often at Isabella Bay than in the Beaufort Sea. Calls emitted by socializing whales off Baffin Island were similar to those heard in the Chukchi and Beaufort Seas. However, pulsed tonal calls were longer off Baffin Island, and previously undescribed mechanical "crunch" sounds were recorded there near socializing bowheads. (3) During autumn migration, "fluke-out" dives were less common, and dive durations were longer, in the Beaufort Sea than off Baffin Island (P<0.001). Multivariate and other analyses indicated that some but not all differences can be ascribed to regional differences in the natural environment or in whale activities, However, during 1974–1986, Bering/Chukchi/Beaufort bowheads were exposed to more industrial, hunting and other human activity than Davis Strait/Baffin Bay bowheads. The "inconspicuous" behavior during autumn migration in the Beaufort may have been attributable to human activities, but causative links cannot be isolated.     

The MADS-box floral homeotic gene lineages predate the origin of seed plants: Phylogenetic and molecular clock estimates

Flower development in angiosperms is controlled in part by floral homeotic genes, many of which are members of the plant MADS-box regulatory gene family. The evolutionary history of these developmental genes was reconstructed using 74 loci from 15 dicot, three monocot, and one conifer species. Molecular clock estimates suggest that the different floral homeotic gene lineages began to diverge from one another about 450–500 mya, around the time of the origin of land plants themselves. Received: 31 January 1997 / Accepted: 9 April 1997     

Population Genetics of Y-Chromosome Short Tandem Repeats in Humans

Eight human short tandem repeat polymorphisms (STRs) also known as microsatellites—DYS19, DYS388, DYS390, DYS391, DYS392, DYS393, DYS389I, and DYS389II, mapping in the Y chromosome—were analyzed in two Iberian samples (Basques and Catalans). Allele frequency distributions showed significant differences only for DYS392. Fst and gene diversity index (D) were estimated for the Y STRs. The values obtained are comparable to those of autosomal STR if corrections for the smaller effective population size on the Y chromosome are taken into account. This suggests that Y-chromosome microsatellites might be as useful as their autosomal counterparts to both human population genetics and forensics. Our results also reinforce the hypothesis that selective sweeps in the Y chromosome in recent times are unlikely. Haplotypes combining five of the loci were constructed for 71 individuals, showing 29 different haplotypes. A haplotype tree was constructed, from which an estimate of 7,000 to 60,000 years for the age of the Y-chromosome variation in Iberia was derived, in accordance with previous estimates obtained with mtDNA sequences and nuclear markers. Received: 3 January 1997 / Accepted: 25 April 1997     

Variation of Microsatellite Size Homoplasy Across Electromorphs, Loci, and Populations in Three Invertebrate Species

Size homoplasy was analyzed at microsatellite loci by sequencing electromorphs, that is, variants of the same size (base pairs). This study was conducted using five interrupted and/or compound loci in three invertebrate species, the honey bee Apis mellifera, the bumble bee Bombus terrestris, and the freshwater snail Bulinus truncatus. The 15 electromorphs sequenced turned out to hide 31 alleles (i.e., variants identical in sequence). Variation in the amount of size homoplasy was detected among electromorphs and loci. From one to seven alleles were detected per electromorph, and one locus did not show any size homoplasy in both bee species. The amount of size homoplasy was related to the sequencing effort, since the number of alleles was correlated with the number of copies of electromorphs sequenced, but also with the molecular structure of the core sequence at each locus. Size homoplasy within populations was detected only three times, meaning that size homoplasy was detected mostly among populations. We analyzed population structure, estimating F _st and a genetic distance, based on either electromorphs or alleles. Whereas little difference was found in A. mellifera, uncovering size homoplasy led to a more marked population structure in B. terrestris and B. truncatus. We also showed in A. mellifera that the detection of size homoplasy may alter phylogenetic reconstructions. Received: 21 July 1997 / Accepted: 29 January 1998     

Bowhead whales Balaena mysticetus in the Okhotsk Sea

• 1 Little is known about the endangered population of bowhead whales Balaena mysticetus in the Okhotsk Sea (OS). Here, we review existing information about this stock, including much material published in Russian.
• 2 Whaling for OS bowheads began around 1846, was pursued intensively for two decades and continued sporadically until about 1913. Beginning in 1967, whalers from the USSR killed bowheads illegally, although the number of whales taken remains unknown. Estimates of the pre‐exploitation population size have ranged from 3000 to 20000 whales, but all such estimates are based upon untested assumptions and incomplete data.
• 3 Information on historical and current distribution of bowheads comes from whaling records (notably Townsend 1935 ) and from modern (notably Russian/Soviet) marine mammal surveys. Little is known about winter distribution. During spring and summer, known bowhead concentrations occur in Shelikhov Bay and at Shantar. Although historical whaling data show bowheads in Shelikhov Bay during summer and early autumn, there have been no recent sightings later than June. However, extensive 19th century catches were made over much of the northern OS, and the present range and habitat use of the population is probably broader than existing data suggest. There is evidence for age or maturational class segregation between Shantar and Shelikhov Bay; the former hosts immature whales and lactating females, and the latter hosts adults.
• 4 Genetic data indicate that the OS bowhead stock is separate from the Bering‐Chukchi‐Beaufort population, but that the two populations share a common ancestry. There is no evidence that bowheads ever leave the OS.
• 5 Russian observers have put the current size of the OS stock in the low hundreds, but this is not based on quantitative analysis. Overall, the OS bowhead population is very likely to be relatively small; it did not recover from the intensive whaling in the 19th century, and the illegal Soviet catches of the 1960s have further set back its recovery. Dedicated surveys and other research are required to assess the status and conservation needs of the population.

     

Molecular Clock Calibrations and Metazoan Divergence Dates

It has recently been argued that living metazoans diverged over 800 million years ago, based on evidence from 22 nuclear genes for such a deep divergence between vertebrates and arthropods (Gu 1998). Two ``internal' calibration points were used. However, only one fossil divergence date (the mammal–bird split) was directly used to calibrate the molecular clock. The second calibration point (the primate–rodent split) was based on molecular estimates that were ultimately also calibrated by the same mammal–bird split. However, the first tetrapods that can be assigned with confidence to either the mammal (synapsid) lineage or the bird (diapsid) lineage are approximately 288 million years old, while the first mammals that can be assigned with confidence to either the primate or the rodent lineages are 65 million years old, or 85 million years old if ferungulates are part of the primate lineage and zhelestids are accepted as ferungulate relatives. Recalibration of the protein data using these fossil dates indicates that metazoans diverged between 791 and 528 million years ago, a result broadly consistent with the palaeontological documentation of the ``Cambrian explosion.' The third, ``external' calibration point (the metazoan–fungal divergence) was similarly problematic, since it was based on a controversial molecular study (which in turn used fossil dates including the mammal–bird split); direct use of fossils for this calibration point gives the absurd dating of 455 million years for metazoan divergences. Similar calibration problems affect another recent study (Wang et al. 1999), which proposes divergences for metazoans of 1000 million years or more: recalibrations of their clock again yields much more recent dates, some consistent with a ``Cambrian explosion' scenario. Molecular clock studies have persuasively argued for the imperfection of the fossil record but have rarely acknowledged that their inferences are also directly based on this same record. Received: 26 January 1999 / Accepted: 14 April 1999     

Development of 12 novel microsatellite loci in a traditional Chinese medicinal plant, Epimedium brevicornum and cross-amplification in other related taxa

A total of 12 polymorphic microsatellite loci were developed and characterized for a Chinese medicinal plant, Epimedium brevicornum (Berberidaceae). A genomic DNA enrichment protocol was used to isolate microsatellite loci and polymorphism was explored using 38 individuals from one natural population. The observed number of alleles ranged from 2–14. The ranges of observed and expected heterozygosity were 0.00–0.83 and 0.15–0.88, respectively. In addition, successful cross-species amplification of this set of microsatellite markers in other four medicinal Epimedium species suggested that they would provide a useful tool for the genetic and conservation studies of Epimedium species.     

On the Pattern of Polymorphisms at Major Histocompatibility Complex Loci

The pattern of polymorphisms at major histocompatibility complex loci was studied by computer simulations and by DNA sequence analysis. Two types of selection, overdominance plus short-term selection and maternal–fetal incompatibility, were simulated for a gene family with intra- and interlocus gene conversion. Both types of selection were found to be consistent with the observed patterns of polymorphisms. It was also found that the more interlocus conversion occurs, the higher the divergence becomes at both nonsynonymous and synonymous sites. The ratio of nonsynonymous-to-synonymous divergence among alleles decreases as the interlocus conversion rate increases. These results agree with the interpretation that the rate of interlocus conversion is lower in human genes than in genes of other nonprimate mammals. This is because, in the latter, synonymous divergence at the ARS (antigen recognition site) is often higher than that at the non-ARS, whereas in the former, this is not so. Also, the ratio of nonsynonymous to synonymous substitutions at the ARS tends to be higher in human genes than in other mammalian genes. The main difference between overdominance plus short-term selection and maternal–fetal interaction is that the number of alleles and heterozygosity per locus are higher in the latter than in the former under the presumed selection intensities. However, the average divergence among alleles tends to be lower in the latter than in the former under similar conditions. Received: 30 September 1997 / Accepted: 15 December 1997     

Population genetic structure and evolutionary history of North Atlantic beluga whales (Delphinapterus leucas) from West Greenland, Svalbard and the White Sea

Population structure in many Arctic marine mammal species reflects a dynamic interplay between physical isolating mechanisms and the extent to which dispersal opportunities are met. We examined variation within mtDNA and eight microsatellite markers to investigate population structure and demographic history in beluga whales in the North Atlantic. Genetic heterogeneity was observed between Svalbard and West Greenland that reveals limited gene flow over ecological time scales. Differentiation was also recorded between Atlantic belugas and two previously studied populations in the North Pacific, the Beaufort Sea and Gulf of Alaska. However, Bayesian cluster analysis of the nDNA data identified two population clusters that did not correspond to the respective ocean basins, as predicted, but to: (1) Arctic (Svalbard–White Sea–Greenland–Beaufort Sea) and (2) Subarctic (Gulf of Alaska) regions. Similarly, the deepest phylogeographic signal was between the Arctic populations and the Gulf of Alaska. Fitting an isolation-with-migration model yielded genetic abundance estimates that match census estimates and revealed that Svalbard and the Beaufort Sea likely diverged 7,600–35,400 years ago but have experienced recurrent periods with gene flow since then, most likely via the Russian Arctic during subsequent warm periods. Considering current projections of continued sea ice losses in the Arctic, this study identified likely routes of future contact among extant beluga populations, and other mobile marine species, which have implications for genetic introgression, health, ecology and behavior.     

Organization, Structure, and Evolution of the Nonadult Rat β-Globin Gene Cluster

The β-globin gene cluster of Wistar rat was extensively cloned and the embryonic genes were mapped and sequenced. Four overlapping λ Dash recombinant clones cover about 31 kb and contain four nonadult β-globin genes, 5′–ε1–γ1–γ2–ψγ3–3′. The ε1 and γ2 are active genes, since their protein products were detected in the fetal stage of the rat (Iwahara et al., J Biochem 119:360–366, 1996). The γ1 locus might be a pseudogene, since the ATA box in the promoter region is mutated to GTA; however, no other defect is observed. The ψγ3 locus is a truncated pseudogene because a 19-base deletion, which causes a shift of the reading frame, is observed between the second nucleotide of the putative codon 68 and codon 76. A sequence comparison suggests that the ψγ3 might be produced by a gene conversion event of the proto-γ-globin gene set. Possible histories of the evolution of rat nonadult β-globin genes are discussed. Received: 6 August 1998 / Accepted: 12 February 1999     

Freeze-Fracture Analysis of Plasma Membranes of CHO Cells Stably Expressing Aquaporins 1-5

Several studies suggest that aquaporin water channels can be identified in membranes by freeze-fracture electron microscopy. For this report, Chinese Hamster ovary cells were stably transfected with cDNAs encoding aquaporins 1–5. Measurement of the osmotic water permeability of the cells confirmed that functional protein was expressed and delivered to the plasma membrane. By freeze-fracture electron microscopy, a 20% increase in intramembrane particle (IMP) density was found in plasma membranes of cells expressing AQP2, 3 and 5, and a 100% increase was measured in AQP1-expressing cells, when compared to mock-transfected cells. On membranes of cells expressing AQP4, large aggregates of IMPs were organized into orthogonal arrays, which occupied 10–20% of the membrane surface. IMP aggregates were never seen in AQP2-transfected cells. Hexagonally packed IMP clusters were detected in ∼5% of the membranes from AQP3-expressing cells. Particle size-distribution analysis of rotary shadowed IMPs showed a significant shift from 13.5 (control cells) to 8.5 nm or less in AQP-expressing cells; size distribution analysis of unidirectionally shadowed IMPs also showed a significant change when compared to control. Some IMPs in AQP expressing cells had features consistent with the idea that aquaporins are assembled as tetramers. The results demonstrate that in transfected CHO cells, AQP transfection modifies the general appearance and number of IMPs on the plasma membrane, and show that only AQP4 assembles into well-defined IMP arrays. Received: 17 March 1998/Revised: 19 June 1998     

RATE OF INCREASE, 1978–1988, OF BOWHEAD WHALES, BALAENA MYSTICETUS, ESTIMATED FROM ICE-BASED CENSUS DATA

The number of bowhead whales, Balaena mysticetus , passing within viewing range of the ice-based census at Point Barrow, Alaska, during spring migrations from 1978 to 1988 is estimated from the visual census data. The trend in the annual numbers yields an estimated rate of increase of 3.1% per year with a 95% confidence interval ranging from 0.1% to 6.2% for the Bering-Chukchi-Beaufort Seas bowhead stock during this period. Alternative treatments of the data suggest less precise or somewhat lower estimates, but all results indicate that the stock was increasing.