Steven M. Carr

Intraspecific Phylogeographic Genomics From Multiple Complete mtDNA Genomes in Atlantic Cod (Gadus morhua): Origins of the “Codmother,” Transatlantic Vicariance and Midglacial Population Expansion

On the basis of multiple complete mitochondrial DNA genome sequences, we describe the temporal phylogeography of Atlantic cod (Gadus morhua), a lineage that has undergone a complex pattern of vicariant evolution, postglacial demographic shifts, and historic sharp population declines due to fishing and/or environmental shifts. Each of 32 fish from four spawning aggregations from the northwest Atlantic and Norway has a unique mtDNA sequence, which differs by 6–60 substitutions. Phylogenetic analysis identifies six major haplogroups that range in age from 37 to 75 KYA. The widespread haplotype identified by previous single-locus analyses at the center of a “star phylogeny” is shown to be a paraphyletic assemblage of genome lineages. The coalescent that includes all cod occurs 162 KYA. The most basal clade comprises two fish from the western Atlantic. The most recent superclade that includes all fish examined from Norway, and which includes 84% of all fish examined, dates to 128 KYA at the Sangamon/Würm interglacial, when ocean depths on continental shelves would have favored transcontinental movement. The pairwise mismatch distribution dates population expansion of this superclade to the middle of the Wisconsinan/Weichsel glaciation 59 KYA, rather than to a postglacial emergence from a marine refugium 12 KYA, or to more recent historic events. We discuss alternative scenarios for the expansion and distribution of the descendants of the “codmother” in the North Atlantic. Mitochondrial phylogenomic analyses generate highly resolved trees that enable fine-scale tests of temporal hypotheses with an accuracy not possible with single-locus methods.

Direction of Introgressive Hybridization between Species of North American Deer (Odocoileus) as Inferred from Mitochondrial-Cytochrome-b Sequences

We used the polymerase chain reaction to amplify a 359-base-pair portion of the mitochondrial-cytochrome-A gene from 157 deer in the genus Odocoileus. The deer examined included Texas white-tailed deer ( Odocoileus virginianus texanus ) and Desert mule deer ( O. hemionus crooki ) from an area of sympatry in west Texas, allopatric populations of both species on either side of the area, and black-tailed deer from California ( O. hemionus columbianus ) and Alaska ( O. hemionus sitkensis ). One moose ( Alces alces ) was included as an outgroup. Direct determination of the DNA sequences revealed 53 variable nucleotide positions that define 11 distinct genotypes. All of the mule deer and a majority of the white-tailed deer within the area of sympatry share a common sequence genotype. Cladistic analysis identifies clades corresponding to populations of O. hemionus and O. virginianus west and east, respectively, of the area of sympatry. The shared sequence is a member of the western, O. hemionus clade, which implies that genetic introgression of mitochondrial DNA has been from mule deer into white-tailed deer. Genotypes found in black-tailed deer from Alaska and one population in northern California form a sister group that is quite divergent (7.5%-sequence difference) from other black-tailed and mule deer. Interspecific sequence divergences are in several cases smaller than intraspecific divergences. Mitochondrial-DNA sequences in O. hemionus appear to be paraphyletic. Possible explanations include sorting of genetic lineages between species, extensive introgression of mitochondrial DNA between subspecies of O. hemionus or between species, or a recent derivation of O. virginianus from O. hemionus.

The clinical and genetic epidemiology of neuronal ceroid lipofuscinosis in Newfoundland

The neuronal ceroid lipofuscinoses (NCLs) are the commonest neurodegenerative disorders of children. The aims of this study were to determine the incidence of NCL in Newfoundland, identify the causative genes, and analyze the relationship between phenotype and genotype. Patients with NCL diagnosed between 1960 and 2005 were ascertained through the provincial genetics and pediatric neurology clinics. Fifty‐two patients from 34 families were identified. DNA was obtained from 28/34 (82%) families; 18 families had mutations in the CLN2 gene, comprising five different mutations of which two were novel. One family had a CLN3 mutation, another had a novel mutation in CLN5, and five families shared the same mutation in CLN6. One family was misdiagnosed, and in two, molecular testing was inconclusive. Disease from CLN2 mutations had an earlier presentation (p = 0.003) and seizure onset (p < 0.001) compared with CLN6 mutation. There was a slower clinical course for those with CLN5 mutation compared with CLN2 mutation. NCL in Newfoundland has a high incidence, 1 in 7353 live births, and shows extensive genetic heterogeneity. The incidence of late infantile NCL, 9.0 per 100,000 (or 1 in 11,161) live births, is the highest reported in the world.

Near Neutrality, Rate Heterogeneity, and Linkage Govern Mitochondrial Genome Evolution in Atlantic Cod (Gadus morhua) and Other Gadine Fish

The mitochondrial DNA (mtDNA) genome figures prominently in evolutionary investigations of vertebrate animals due to a suite of characteristics that include absence of Darwinian selection, high mutation rate, and inheritance as a single linkage group. Given complete linkage and selective neutrality, mtDNA gene trees are expected to correspond to intraspecific phylogenies, and mtDNA diversity will reflect population size. The validity of these assumptions is, however, rarely tested on a genome-wide scale. Here, we analyze rates and patterns of molecular evolution among 32 whole mitochondrial genomes of Atlantic Cod (Gadus morhua) as compared with its sister taxon, the walleye pollock (Gadus [Theragra] chalcogrammus), and genomes of seven other gadine codfish. We evaluate selection within G. morhua, between sister species, and among species and intraspecific measures of linkage disequilibrium and recombination within G. morhua. Strong rate heterogeneity occurs among sites and genes at all levels of hierarchical comparison, consistent with variation in mutation rates across the genome. Neutrality indices (dN/dS) are significantly greater than unity among G. morhua genomes and between sister species, which suggests that polymorphisms within species are slightly deleterious, as expected under the nearly neutral theory of molecular evolution. Among species of gadines, dN/dS ratios are heterogeneous among genes, consistent with purifying selection and variation in functional constraint among genes rather than positive selection. The dN/dS ratio for ND4L is anomalously high across all hierarchical levels. There is no evidence for recombination within G. morhua. These patterns contrast strongly with those reported for humans: genome-wide patterns in other vertebrates should be investigated to elucidate the complex patterns of mtDNA molecular evolution.

A Phylogenetic Perspective on the Evolution of Reproductive Behavior in Pagophilic Seals of the Northwest Atlantic as Indicated by Mitochondrial DNA Sequences

The ice-breeding (pagophilic) habits and relatively short lactation periods of several species of “true” seals (Phocidae) of the Northwest Atlantic, including the harp seal ( Pagophilus ), bearded seal ( Erignathus ), and hooded seal ( Cystophora ), usually are assumed to have evolved in parallel. Current taxonomy regards Pagophilus and ringed seals ( Pusa ) along with harbor seals ( Phoca vitulina ) as subgenera of Phoca , unites Phoca (sensu lato) together with gray seals ( Halichoerus ) and Erignathus in the subfamily Phocinae, and places Cystophora with elephant seals ( Mirounga ) in a separate subfamily, Cystophorinae. Cladistic analysis of variation in the DNA sequence of the mitochondrial cytochrome b gene identifies three clades among northern seals: Phoca-Pusa-Halichoerus, Cystophora-Pagophilus , and Erignathus. Erignathus is the sister group to the other species examined. Each clade may be regarded as a tribe of the subfamily Phocinae (the Phocini, Cystophorini, and Erignathini, respectively). The phylogeny suggests that the ice-breeding habit and associated brief lactation are ancestral characters for the Phocinae and that instances of fast-ice or terrestrial breeding are convergences on the ancestral condition in other phocid subfamilies.

Allozyme and mitochondrial DNA analysis of a hybrid zone between white-tailed deer and mule deer (Odocoileus) in west Texas.

Thirty allozyme loci and 35 mitochondrial DNA (mtDNA) restriction sites were examined in 24 white-tailed deer and 46 mule deer from a hybrid zone in West Texas. A common mtDNA genotype is shared by all of the mule deer with 67% of the white-tailed deer. At the albumin locus, 13% of the white-tailed deer and 24% of the mule deer are heterozygous, sharing alleles that are otherwise species-specific in allopatric populations; 7% of the mule deer are homozygous for the allele that is characteristic of allopatric white-tailed deer. Gene flow appears to have been bidirectional, with greater genetic introgression into mule deer. The mtDNA data suggest that matings between white-tailed and mule deer have occurred in the past. Despite evidence of genetic introgression, analysis of multilocus genotypes indicates that none of the deer examined is an F1 hybrid. Production of such hybrids appears to be generally uncommon in North American deer; management plans that assume otherwise should be reconsidered.

How To Tell a Sea Monster: Molecular Discrimination of Large Marine Animals of the North Atlantic

Abstract. Remains of large marine animals that wash onshore can be difficult to identify due to decomposition and loss of external body parts, and in consequence may be dubbed “sea monsters.” DNA that survives in such carcasses can provide a basis of identification. One such creature washed ashore at St. Bernard’s, Fortune Bay, Newfoundland, in August 2001. DNA was extracted from the carcass and enzymatically amplified by the polymerase chain reaction (PCR): the mitochondrial NADH2 DNA sequence was identified as that of a sperm whale (Physeter catodon). Amplification and sequencing of cryptozoological DNA with “universal” PCR primers with broad specificity to vertebrate taxa and comparison with species in the GenBank taxonomic database is an effective means of discriminating otherwise unidentifiable large marine creatures.

Quantitative Phylogenomics of Within- Species Mitogenome Variation: Monte Carlo and Non-Parametric Analysis of Phylogeographic Structure among Discrete Transatlantic Breeding Areas of Harp Seals (Pagophilus groenlandicus)

Phylogenomic analysis of highly-resolved intraspecific phylogenies obtained from complete mitochondrial DNA genomes has had great success in clarifying relationships within and among human populations, but has found limited application in other wild species. Analytical challenges include assessment of random versus non-random phylogeographic distributions, and quantification of differences in tree topologies among populations. Harp Seals (Pagophilus groenlandicus Erxleben, 1777) have a biogeographic distribution based on four discrete trans-Atlantic breeding and whelping populations located on “fast ice” attached to land in the White Sea, Greenland Sea, the Labrador ice Front, and Southern Gulf of St Lawrence. This East to West distribution provides a set of a priori phylogeographic hypotheses. Outstanding biogeographic questions include the degree of genetic distinctiveness among these populations, in particular between the Greenland Sea and White Sea grounds. We obtained complete coding-region DNA sequences (15,825 bp) for 53 seals. Each seal has a unique mtDNA genome sequence, which differ by 6 ~ 107 substitutions. Six major clades / groups are detectable by parsimony, neighbor-joining, and Bayesian methods, all of which are found in breeding populations on either side of the Atlantic. The species coalescent is at 180 KYA; the most recent clade, which accounts for 66% of the diversity, reflects an expansion during the mid-Wisconsinan glaciation 40 ~ 60 KYA. FST is significant only between the White Sea and Greenland Sea or Ice Front populations. Hierarchal AMOVA of 2-, 3-, or 4-island models identifies small but significant ΦSC among populations within groups, but not among groups. A novel Monte-Carlo simulation indicates that the observed distribution of individuals within breeding populations over the phylogenetic tree requires significantly fewer dispersal events than random expectation, consistent with island or a priori East to West 2- or 3-stepping-stone biogeographic models, but not a simple 1-step trans-Atlantic model. Plots of the cumulative pairwise sequence difference curves among seals in each of the four populations provide continuous proxies for phylogenetic diversification within each. Non-parametric Kolmogorov-Smirnov (K-S) tests of maximum pairwise differences between these curves indicates that the Greenland Sea population has a markedly younger phylogenetic structure than either the White Sea population or the two Northwest Atlantic populations, which are of intermediate age and homogeneous structure. The Monte Carlo and K-S assessments provide sensitive quantitative tests of within-species mitogenomic phylogeography. This is the first study to indicate that the White Sea and Greenland Sea populations have different population genetic histories. The analysis supports the hypothesis that Harp Seals comprises three genetically distinguishable breeding populations, in the White Sea, Greenland Sea, and Northwest Atlantic. Implications for an ice-dependent species during ongoing climate change are discussed.

Conservation genetics of high-arctic Gull species at risk: I. Diversity in the mtDNA control region of circumpolar populations of the Endangered Ivory Gull (Pagophila eburnea)

Abstract The high-arctic Ivory Gull (Pagophila eburnea) has recently undergone a sharp decline in numbers, and in Canada it is listed as “Endangered” under the Species-At-Risk Act. To test for circumpolar genetic distinctiveness, we examined 264 bp of the mtDNA Control Region Domain I from 127 museum specimens collected during the breeding season from northern Canada, Greenland, and Norway, and during the non-breeding season from adjacent overwintering grounds in Canada, Greenland, and a disjunct area in Alaska adjacent to the Bering Sea. Partition of genetic variance according to various phylogeographic and breeding ground models indicates no strong population structure, except that Alaska birds are consistently differentiated from other locations, and there are significant temporal shifts in haplotype frequencies. The evidence suggests that Ivory Gulls in Canada, Greenland, and Norway are a single genetic entity, in contrast to Alaska birds, which may represent a distinctive Siberian population.

Conservation genetics of high-arctic Gull species at risk: II. Diversity in the mtDNA control region of Threatened Ross’s Gull (Rhodostethia rosea)

Abstract Ross’s Gull (Rhodostethia rosea) is the rarest of Canadian high-arctic gulls, and is listed as Threatened under Canada’s Species-At-Risk Act. The large majority of birds breed in Siberia: the origins and affinities of four extremely small breeding colonies observed since 1978 in the Canadian high arctic are unknown. We compared a 515-bp region of the mtDNA Control Region amplified from material in museum collections taken from non-breeding birds in Canada (n = 8) and Alaska (n = 6), the latter passage migrants from the Siberian populations. The Alaskan birds all have distinct haplotypes that differ by as many as six SNPs: Canadian birds taken in the vicinity of the breeding colonies show only two of these. We hypothesize the origins of the Canadian breeding colonies as recent founder events by small numbers of passage migrants from Siberia via Alaska. Ross’s Gull maintains a very tenuous breeding presence in the Canadian high Arctic.