Population genetic research is a critical tool for the conservation and management of marine mamm... more Population genetic research is a critical tool for the conservation and management of marine mammals and other species. The bowhead whale (Balaena mysticetus) is subject to aboriginal subsistence hunting in Alaska, Canada, Chukotka, and Greenland and managed by the International Whaling Commission for all those countries except Canada. Genetic studies support conservation management plans and the determination of safe hunting quotas by providing information on levels of genetic diversity, estimates of abundance and effective population size, and stock separation. Because bowhead populations are monitored in several countries, including genetic monitoring, there is a need for methods that can be consistently used in multiple labs that provide comparable data that can be publicly shared and built upon by successive studies. Here we present a new panel of single nucleotide polymorphisms (SNPs), derived from multiple bowhead populations, that meet those criteria. We describe the us...
The taxonomic history of bats of the tribe Lasiurini (Chiroptera: Vespertilionidae) has undergone... more The taxonomic history of bats of the tribe Lasiurini (Chiroptera: Vespertilionidae) has undergone significant changes over time. Authors at different times have recognized various numbers of genera and subgenera within the tribe. The most recent proposed change to generic level taxonomy (that there should be three genera recognized instead of a single genus) has been debated in the literature. We reviewed papers that commented on the recent changes to lasiurine generic taxonomy, as well as those that have adopted the new taxonomy and the ones that have not. We also reviewed the relevant taxonomic literature from 1942 to the present that shows the fluid taxonomic history of these bats. The literature review shows that the recently proposed taxonomic change recognizing the three groups of lasiurine bats as distinct genera is the only taxonomy that differentiates the tribe from the genera. Examination of times to most recent common ancestor (TMRCA) of 24 vespertilionid genera shows Las...
Previous studies on genetics of hoary bats produced differing conclusions on the timing of their ... more Previous studies on genetics of hoary bats produced differing conclusions on the timing of their colonization of the Hawaiian Islands and whether or not North American (Aeorestes cinereus) and Hawaiian (A. semotus) hoary bats are distinct species. One study, using mtDNA COI and nuclear Rag2 and CMA1, concluded that hoary bats colonized the Hawaiian Islands no more than 10,000 years ago based on indications of population expansion at that time using Extended Bayesian Skyline Plots. The other study, using 3 mtDNA and 1 Y-chromosome locus, concluded that the Hawaiian Islands were colonized about 1 million years ago. To address the marked inconsistencies between those studies, we examined DNA sequences from 4 mitochondrial and 2 nuclear loci in lasiurine bats to investigate the timing of colonization of the Hawaiian Islands by hoary bats, test the hypothesis that Hawaiian and North American hoary bats belong to different species, and further investigate the generic level taxonomy within...
I t is well documented that rates of chromosomal evolution and the kinds of rearrangements involv... more I t is well documented that rates of chromosomal evolution and the kinds of rearrangements involved vary markedly among taxa. This has led to the formulation of models that seek to identify biological factors that promote rapid chro-mosomal evolution. For the most part, these models focus on population genetic parameters under which a newly arisen chromosomal mutation would have a finite probability of becoming established. Most models assume that rearrangements of the chromosomes do not affect the function of genes and thus have no effect on the phenotype of the organism. They also assume that some degree of sterility is produced in the heterozygote due to an impairment of normal meiosis. Under these conditions, chromosomal evolution will be most rapid in species that possess small d e m e sizes because sampling errors due to stochastic events are what drive t h e rearrangement to fixation through the heterozygosity bottleneck. There is a finite probability of this occurring only in small demes. This may result not only in chromosomal evolution, but also in speciation (termed stasipatric spe-ciation). We will collectively term these models the deme size model and note that they derive from the population genetics of Sewell Wright. Among the most important contributors to the development of the deme size model are M. J. D. Still another model of chromosomal evolution (White, 1978b) is based largely on work done by E. Capanna, A. Gropp, and their colleagues (see references in White, 1978b) on Italian and Swiss populations of mice of the Mus musculus complex. The model, termed "chain processes in chromosomal speciation," is an explanation of why some groups of animals have acquired numerous rearrangements , apparently during stasipatric spe-ciation. Several populations of Mus are known to differ from the primitive 2n = 40 karyotype (all acrocentric autosomes) by as many as 9 and as few as 3 fusions. White considers this group of animals to exhibit a phenomenon known as area effects in which populations possess co-adapted gene complexes that differ from other populations. Chromosomal rearrangements spread throughout the area effect population in spite of reducing the fertility of heterozygous individuals. Once the population'has become fixed for the rearrangements, however, it will be more "fit" because its coadapted gene complex will be protected from the dis-ruptive effects of introgression from neighboring populations. This model is quite different from the deme size models mentioned above in that it considers …
Mammals vary dramatically in lifespan, by at least two-orders of magnitude, but the molecular bas... more Mammals vary dramatically in lifespan, by at least two-orders of magnitude, but the molecular basis for this difference remains largely unknown. The bowhead whale Balaena mysticetus is the longest-lived mammal known, with an estimated maximal lifespan in excess of two hundred years. It is also one of the two largest animals and the most cold-adapted baleen whale species. Here, we report the first genome-wide gene expression analyses of the bowhead whale, based on the de novo assembly of its transcriptome. Bowhead whale or cetacean-specific changes in gene expression were identified in the liver, kidney and heart, and complemented with analyses of positively selected genes. Changes associated with altered insulin signaling and other gene expression patterns could help explain the remarkable longevity of bowhead whales as well as their adaptation to a lipid-rich diet. The data also reveal parallels in candidate longevity adaptations of the bowhead whale, naked mole rat and Brandt'...
Proceedings of the National Academy of Sciences, 1986
Fixation of centric fusions in natural populations often encounters minimal meiotic problems due ... more Fixation of centric fusions in natural populations often encounters minimal meiotic problems due to the ability of trivalents to segregate normally; therefore, little sterility barrier is achieved between a founder population and the parental stock. However, a strong sterility barrier can develop between different founder populations fixed for centric fusions that are monobrachially homologous in the resulting biarmed chromosomes (one arm is homologous but the other is nonhomologous). Hybridization through secondary contact then results in complex multivalents, which encounter problems in segregation and produce unbalanced gametes. Speciation mediated by centric fusions is a peripatric speciation model that does not postulate populational phenomena atypical of those characteristic of most mammals. The model appears applicable to a diversity of mammalian taxa such as bats of the Rhogeessa tumida-parvula complex, shrews of the Sorex araneus complex, and rodents of the Mus musculus and...
Many studies use genetic markers to explore population structure and variability within species. ... more Many studies use genetic markers to explore population structure and variability within species. However, only a minority use more than one type of marker and, despite increasing evidence of a link between heterozygosity and individual fitness, few ask whether diversity correlates with population trajectory. To address these issues, we analysed data from the Steller's sea lion, Eumetiopias jubatus, where three stocks are distributed over a vast geographical range and where both genetic samples and detailed demographic data have been collected from many diverse breeding colonies. To previously published mitochondrial DNA (mtDNA) and microsatellite data sets, we have added new data for amplified fragment length polymorphism (AFLP) markers, comprising 238 loci scored in 285 sea lions sampled from 23 natal rookeries. Genotypic diversity was low relative to most vertebrates, with only 37 loci (15.5%) being polymorphic. Moreover, contrasting geographical patterns of genetic diversity ...
Mitochondrial DNA sequence data were used to examine the phylogeographic history of Steller's... more Mitochondrial DNA sequence data were used to examine the phylogeographic history of Steller's sea lions (Eumetopias jubatus) in relation to the presence of Plio‐Pleistocene insular refugia. Cytochrome b and control region sequences from 336 Steller's sea lions reveal phylogenetic lineages associated with continental refugia south of the ice sheets in North America and Eurasia. Phylogenetic analysis suggests the genetic structure of E. jubatus is the result of Pleistocene glacial geology, which caused the elimination and subsequent reappearance of suitable rookery habitat during glacial and interglacial periods. The cyclic nature of geological change produced a series of independent population expansions, contractions and isolations that had analogous results on Steller's sea lions and other marine and terrestrial species. Our data show evidence of four glacial refugia in which populations of Steller's sea lions diverged. These events occurred from approximately 60 00...
Although direct DNA sequencing is now readily available, restriction enzyme analyses are still wi... more Although direct DNA sequencing is now readily available, restriction enzyme analyses are still widely used in population genetics and molecular systematics studies. These analyses provide cheaper and faster ways to assay patterns of nucleotide differentiation across a large number of individuals. In this paper, we introduce a new approach to restriction enzyme analyses in which high-resolution restriction site maps are obtained from partial digestions of PCR products. This procedure increases the level of resolution at least an order of magnitude over the double-digestion method for restriction enzyme mapping, can target specific DNA regions with the use of specific primers, and, because it uses chemiluminescent detection of DNA, can be easily implemented in laboratories that lack the necessary setups to handle radioactive substances.
Genome size (the amount of DNA per cell) was measured by flow-cytometric analysis in seven specie... more Genome size (the amount of DNA per cell) was measured by flow-cytometric analysis in seven species of a chromosomally variable rodent genus: Ctenomys boliviensis, C. conoveri, C. frater, C. leucodon, C. lewisi, C. opimus, and C. steinbachi. The mean genome size of these species was 7.19 pg DNA and little inter- and intra-specific variation was observed. Genome size was not correlated with diploid number, suggesting that chromosomal evolution at this level is independent of total DNA content. A hypothetical taxonomic unit optimization procedure was carried out using genome size change on a Wagner tree derived from allozyme data. Allozyme evolution and genome size change are linked by a weak, but significant, negative correlation suggestive of preferential genie evolution in the absence of genome size evolution.Key words: genome size, Ctenomyidae, chromosomal evolution.
Population genetic research is a critical tool for the conservation and management of marine mamm... more Population genetic research is a critical tool for the conservation and management of marine mammals and other species. The bowhead whale (Balaena mysticetus) is subject to aboriginal subsistence hunting in Alaska, Canada, Chukotka, and Greenland and managed by the International Whaling Commission for all those countries except Canada. Genetic studies support conservation management plans and the determination of safe hunting quotas by providing information on levels of genetic diversity, estimates of abundance and effective population size, and stock separation. Because bowhead populations are monitored in several countries, including genetic monitoring, there is a need for methods that can be consistently used in multiple labs that provide comparable data that can be publicly shared and built upon by successive studies. Here we present a new panel of single nucleotide polymorphisms (SNPs), derived from multiple bowhead populations, that meet those criteria. We describe the us...
The taxonomic history of bats of the tribe Lasiurini (Chiroptera: Vespertilionidae) has undergone... more The taxonomic history of bats of the tribe Lasiurini (Chiroptera: Vespertilionidae) has undergone significant changes over time. Authors at different times have recognized various numbers of genera and subgenera within the tribe. The most recent proposed change to generic level taxonomy (that there should be three genera recognized instead of a single genus) has been debated in the literature. We reviewed papers that commented on the recent changes to lasiurine generic taxonomy, as well as those that have adopted the new taxonomy and the ones that have not. We also reviewed the relevant taxonomic literature from 1942 to the present that shows the fluid taxonomic history of these bats. The literature review shows that the recently proposed taxonomic change recognizing the three groups of lasiurine bats as distinct genera is the only taxonomy that differentiates the tribe from the genera. Examination of times to most recent common ancestor (TMRCA) of 24 vespertilionid genera shows Las...
Previous studies on genetics of hoary bats produced differing conclusions on the timing of their ... more Previous studies on genetics of hoary bats produced differing conclusions on the timing of their colonization of the Hawaiian Islands and whether or not North American (Aeorestes cinereus) and Hawaiian (A. semotus) hoary bats are distinct species. One study, using mtDNA COI and nuclear Rag2 and CMA1, concluded that hoary bats colonized the Hawaiian Islands no more than 10,000 years ago based on indications of population expansion at that time using Extended Bayesian Skyline Plots. The other study, using 3 mtDNA and 1 Y-chromosome locus, concluded that the Hawaiian Islands were colonized about 1 million years ago. To address the marked inconsistencies between those studies, we examined DNA sequences from 4 mitochondrial and 2 nuclear loci in lasiurine bats to investigate the timing of colonization of the Hawaiian Islands by hoary bats, test the hypothesis that Hawaiian and North American hoary bats belong to different species, and further investigate the generic level taxonomy within...
I t is well documented that rates of chromosomal evolution and the kinds of rearrangements involv... more I t is well documented that rates of chromosomal evolution and the kinds of rearrangements involved vary markedly among taxa. This has led to the formulation of models that seek to identify biological factors that promote rapid chro-mosomal evolution. For the most part, these models focus on population genetic parameters under which a newly arisen chromosomal mutation would have a finite probability of becoming established. Most models assume that rearrangements of the chromosomes do not affect the function of genes and thus have no effect on the phenotype of the organism. They also assume that some degree of sterility is produced in the heterozygote due to an impairment of normal meiosis. Under these conditions, chromosomal evolution will be most rapid in species that possess small d e m e sizes because sampling errors due to stochastic events are what drive t h e rearrangement to fixation through the heterozygosity bottleneck. There is a finite probability of this occurring only in small demes. This may result not only in chromosomal evolution, but also in speciation (termed stasipatric spe-ciation). We will collectively term these models the deme size model and note that they derive from the population genetics of Sewell Wright. Among the most important contributors to the development of the deme size model are M. J. D. Still another model of chromosomal evolution (White, 1978b) is based largely on work done by E. Capanna, A. Gropp, and their colleagues (see references in White, 1978b) on Italian and Swiss populations of mice of the Mus musculus complex. The model, termed "chain processes in chromosomal speciation," is an explanation of why some groups of animals have acquired numerous rearrangements , apparently during stasipatric spe-ciation. Several populations of Mus are known to differ from the primitive 2n = 40 karyotype (all acrocentric autosomes) by as many as 9 and as few as 3 fusions. White considers this group of animals to exhibit a phenomenon known as area effects in which populations possess co-adapted gene complexes that differ from other populations. Chromosomal rearrangements spread throughout the area effect population in spite of reducing the fertility of heterozygous individuals. Once the population'has become fixed for the rearrangements, however, it will be more "fit" because its coadapted gene complex will be protected from the dis-ruptive effects of introgression from neighboring populations. This model is quite different from the deme size models mentioned above in that it considers …
Mammals vary dramatically in lifespan, by at least two-orders of magnitude, but the molecular bas... more Mammals vary dramatically in lifespan, by at least two-orders of magnitude, but the molecular basis for this difference remains largely unknown. The bowhead whale Balaena mysticetus is the longest-lived mammal known, with an estimated maximal lifespan in excess of two hundred years. It is also one of the two largest animals and the most cold-adapted baleen whale species. Here, we report the first genome-wide gene expression analyses of the bowhead whale, based on the de novo assembly of its transcriptome. Bowhead whale or cetacean-specific changes in gene expression were identified in the liver, kidney and heart, and complemented with analyses of positively selected genes. Changes associated with altered insulin signaling and other gene expression patterns could help explain the remarkable longevity of bowhead whales as well as their adaptation to a lipid-rich diet. The data also reveal parallels in candidate longevity adaptations of the bowhead whale, naked mole rat and Brandt'...
Proceedings of the National Academy of Sciences, 1986
Fixation of centric fusions in natural populations often encounters minimal meiotic problems due ... more Fixation of centric fusions in natural populations often encounters minimal meiotic problems due to the ability of trivalents to segregate normally; therefore, little sterility barrier is achieved between a founder population and the parental stock. However, a strong sterility barrier can develop between different founder populations fixed for centric fusions that are monobrachially homologous in the resulting biarmed chromosomes (one arm is homologous but the other is nonhomologous). Hybridization through secondary contact then results in complex multivalents, which encounter problems in segregation and produce unbalanced gametes. Speciation mediated by centric fusions is a peripatric speciation model that does not postulate populational phenomena atypical of those characteristic of most mammals. The model appears applicable to a diversity of mammalian taxa such as bats of the Rhogeessa tumida-parvula complex, shrews of the Sorex araneus complex, and rodents of the Mus musculus and...
Many studies use genetic markers to explore population structure and variability within species. ... more Many studies use genetic markers to explore population structure and variability within species. However, only a minority use more than one type of marker and, despite increasing evidence of a link between heterozygosity and individual fitness, few ask whether diversity correlates with population trajectory. To address these issues, we analysed data from the Steller's sea lion, Eumetiopias jubatus, where three stocks are distributed over a vast geographical range and where both genetic samples and detailed demographic data have been collected from many diverse breeding colonies. To previously published mitochondrial DNA (mtDNA) and microsatellite data sets, we have added new data for amplified fragment length polymorphism (AFLP) markers, comprising 238 loci scored in 285 sea lions sampled from 23 natal rookeries. Genotypic diversity was low relative to most vertebrates, with only 37 loci (15.5%) being polymorphic. Moreover, contrasting geographical patterns of genetic diversity ...
Mitochondrial DNA sequence data were used to examine the phylogeographic history of Steller's... more Mitochondrial DNA sequence data were used to examine the phylogeographic history of Steller's sea lions (Eumetopias jubatus) in relation to the presence of Plio‐Pleistocene insular refugia. Cytochrome b and control region sequences from 336 Steller's sea lions reveal phylogenetic lineages associated with continental refugia south of the ice sheets in North America and Eurasia. Phylogenetic analysis suggests the genetic structure of E. jubatus is the result of Pleistocene glacial geology, which caused the elimination and subsequent reappearance of suitable rookery habitat during glacial and interglacial periods. The cyclic nature of geological change produced a series of independent population expansions, contractions and isolations that had analogous results on Steller's sea lions and other marine and terrestrial species. Our data show evidence of four glacial refugia in which populations of Steller's sea lions diverged. These events occurred from approximately 60 00...
Although direct DNA sequencing is now readily available, restriction enzyme analyses are still wi... more Although direct DNA sequencing is now readily available, restriction enzyme analyses are still widely used in population genetics and molecular systematics studies. These analyses provide cheaper and faster ways to assay patterns of nucleotide differentiation across a large number of individuals. In this paper, we introduce a new approach to restriction enzyme analyses in which high-resolution restriction site maps are obtained from partial digestions of PCR products. This procedure increases the level of resolution at least an order of magnitude over the double-digestion method for restriction enzyme mapping, can target specific DNA regions with the use of specific primers, and, because it uses chemiluminescent detection of DNA, can be easily implemented in laboratories that lack the necessary setups to handle radioactive substances.
Genome size (the amount of DNA per cell) was measured by flow-cytometric analysis in seven specie... more Genome size (the amount of DNA per cell) was measured by flow-cytometric analysis in seven species of a chromosomally variable rodent genus: Ctenomys boliviensis, C. conoveri, C. frater, C. leucodon, C. lewisi, C. opimus, and C. steinbachi. The mean genome size of these species was 7.19 pg DNA and little inter- and intra-specific variation was observed. Genome size was not correlated with diploid number, suggesting that chromosomal evolution at this level is independent of total DNA content. A hypothetical taxonomic unit optimization procedure was carried out using genome size change on a Wagner tree derived from allozyme data. Allozyme evolution and genome size change are linked by a weak, but significant, negative correlation suggestive of preferential genie evolution in the absence of genome size evolution.Key words: genome size, Ctenomyidae, chromosomal evolution.
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Papers by John Bickham