H. Dawn Marshall

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.

Chloroplast phylogeography and evolution of highly polymorphic microsatellites in lodgepole pine ( Pinus contorta).

Abstract  We employed a novel set of six highly polymophic chloroplastic simple sequence repeat (cpSSR) loci to investigate the phylogeography of lodgepole pine (Pinus contorta Dougl. Ex. Loud.), and to examine aspects of the evolutionary process operating on these repetitive DNA sequences. Chloroplast haplotypes of 500 trees, sampled throughout the range of lodgepole pine, were determined. We found a marked association of genetic distance with physical distance within the scale of 0 to 1,000 km, but no association beyond that range. Likewise, geographic clustering was observed only among recent clades in a dendrogram. These phylogeographic patterns are consistant with a rapid rangewide expansion (”big-bang”) followed by recent, local population differentiation (”galaxy formation”). In support of this expansion, coalescent simulations of the genealogical process gave a long-term effective population size in the low thousands, and a time to common ancestry of about 1,500 generations (12,000 years), consistent with a post-Pleistocene population expansion as documented by previous pollen-sediment analyses. Two lines of evidence (mapping mutational events onto a phylogeny, and evaluation of observed versus expected gene diversity) suggest that five of the cpSSR loci evolve primarily by a stepwise model of evolution of single repeat changes (but with a small proportion of changes involving two or more repeats), and the coalescent simulations point to a mutation rate of about 10–3.

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.

Complete mitochondrial genomes from four subspecies of common chaffinch (Fringilla coelebs): new inferences about mitochondrial rate heterogeneity, neutral theory, and phylogenetic relationships within the order Passeriformes.

We describe whole mitochondrial genome sequences from four subspecies of the common chaffinch (Fringilla coelebs), and compare them to 31 publicly available mitochondrial genome sequences from other Passeriformes. Rates and patterns of mitochondrial gene evolution are analyzed at different taxonomic levels within this avian order, and evidence is adduced for and against the nearly neutral theory of molecular evolution and the role of positive selection in shaping genetic variation of this small but critical genome. We find evidence of mitochondrial rate heterogeneity in birds as in other vertebrates, likely due to differences in mutational pressure across the genome. Unlike in gadine fish and some of the human mitochondrial work we do not observe strong support for the nearly neutral theory of molecular evolution; instead evidence from molecular clocks, distribution of dN/dS ratios at different levels of the taxonomic hierarchy and in different lineages, McDonald-Kreitman tests within Fringillidae, and site-specific tests of selection within Passeriformes, all point to a role for positive selection, especially for the complex I NADH dehydrogenase genes. The protein-coding mitogenome phylogeny of the order Passeriformes is broadly consistent with previously-reported molecular findings, but provides support for a sister relationship between the superfamilies Muscicapoidea and Passeroidea on a short basal internode of the Passerida where relationships have been difficult to resolve. An unexpected placement of the Paridae (represented by Humes groundpecker) within the Muscicapoidea was observed. Consistent with other molecular studies the mtDNA phylogeny reveals paraphyly within the Muscicapoidea and a sister relationship of Fringilla with Carduelis rather than Emberiza.

Microsatellite variation and genetic structure of brook trout (Salvelinus fontinalis) populations in Labrador and neighboring Atlantic Canada: evidence for ongoing gene flow and dual routes of post-Wisconsinan colonization.

In conservation genetics and management, it is important to understand the contribution of historical and contemporary processes to geographic patterns of genetic structure in order to characterize and preserve diversity. As part of a 10-year monitoring program by the Government of Newfoundland and Labrador, Canada, we measured the population genetic structure of the worlds most northern native populations of brook trout (Salvelinus fontinalis) in Labrador to gather baseline data to facilitate monitoring of future impacts of the recently opened Trans-Labrador Highway. Six-locus microsatellite profiles were obtained from 1130 fish representing 32 populations from six local regions. Genetic diversity in brook trout populations in Labrador (average HE= 0.620) is within the spectrum of variability found in other brook trout across their northeastern range, with limited ongoing gene flow occurring between populations (average pairwise FST= 0.139). Evidence for some contribution of historical processes shaping genetic structure was inferred from an isolation-by-distance analysis, while dual routes of post-Wisconsinan recolonization were indicated by STRUCTURE analysis: K= 2 was the most likely number of genetic groups, revealing a separation between northern and west-central Labrador from all remaining populations. Our results represent the first data from the nuclear genome of brook trout in Labrador and emphasize the usefulness of microsatellite data for revealing the extent to which genetic structure is shaped by both historical and contemporary processes.

Mitochondrial DNA diversity and phylogeography of insular Newfoundland red foxes (Vulpes vulpes deletrix)

Abstract As the only native insular Newfoundland, Canada, canid from the extinction of the wolf in the 1930s to the recent arrival of coyotes, the red fox (Vulpes vulpes deletrix) poses interesting questions about genetic distinctiveness and the postglacial colonization history of the islands depauperate mammalian fauna. Here, we characterize genetic variability at the mitochondrial control region in 189 foxes from the island of Newfoundland, Prince Edward Island, and Labrador. We identified 8 haplotypes (3 new to this study) defined by 11 polymorphic sites, with an average pairwise sequence divergence of ∼0.003 and haplotypic diversity of 0.56 among localities. A pairwise distribution of control region sequence differences, rho estimate of divergence time, and tests of neutrality (Fus FS and Tajimas D) are weakly consistent with a population expansion ∼9,000 years ago, correlating with retreat of glacial ice from the region. Haplotype composition reflects primarily the Eastern subclade of Aubry and colleagues and supports Aubrys 2-refugia hypothesis that indigenous red foxes in North America are derived from disparate refugia isolated during the Wisconsinan glaciation. Haplotype identity and pattern of population differentiation suggest recolonization of the island of Newfoundland via a northern glacial refugium via Quebec or Labrador rather than an Atlantic or southern route, but provide no mitochondrial genetic evidence to support differentiation of this population of foxes along subspecies lines. We establish a baseline for continued investigations of population demography, genetic structure, and adaptive genetic diversity in island Newfoundland red foxes, a population of interest from both ecological and wildlife disease perspectives.

Sequence analysis of three pigmentation genes in the Newfoundland population of Canis latrans links the Golden Retriever Mc1r variant to white coat color in coyotes

Three genes, Mc1r, Agouti, and CBD103, interact in a type-switching process that controls much of the pigmentation variation observed in mammals. A deletion in the CBD103 gene is responsible for dominant black color in dogs, while the white-phased black bear (“spirit bear”) of British Columbia, Canada, is the lightest documented color variant caused by a mutation in Mc1r. Rare all-white animals have recently been discovered in a new northeastern population of the coyote in insular Newfoundland and Labrador, Canada. To investigate the causative gene and mutation of white coat in coyotes, we sequenced the three type-switching genes in white and dark-phased animals from Newfoundland. The only sequence variants unambiguously associated with white color were in Mc1r, and one of these variants causes the amino acid variant R306Ter, a premature stop codon also linked to coat color in Golden Retrievers and other dogs with yellow/red coats. The allele carrying R306Ter in coyotes matches that in the Golden Retriever at other variable amino acid sites and hence may have originated in these dogs. Coyotes experienced introgression with wolves and dogs as they colonized northeastern North America, and coyote/Golden Retriever interactions have been observed in Newfoundland. We speculate that natural selection, with or without a founder effect, may contribute to the observed frequency of white coyotes in Newfoundland, as it has contributed to the high frequency of white bears, and of a domestic dog-derived CBD allele in gray wolves.

Sequence analysis of the Ras-MAPK pathway genes SOS1, EGFR & GRB2 in silver foxes (Vulpes vulpes): candidate genes for hereditary hyperplastic gingivitis

Hereditary hyperplastic gingivitis (HHG) is an autosomal recessive disease that presents with progressive gingival proliferation in farmed silver foxes. Hereditary gingival fibromatosis (HGF) is an analogous condition in humans that is genetically heterogeneous with several known autosomal dominant loci. For one locus the causative mutation is in the Son ofsevenless homologue 1 (SOS1) gene. For the remaining loci, the molecular mechanisms are unknown but Ras pathway involvement is suspected. Here we compare sequences for the SOS1 gene, and two adjacent genes in the Ras pathway, growth receptor bound protein 2 (GRB2) and epidermal growth factor receptor (EGFR), between HHG-affected and unaffected foxes. We conclude that the known HGF causative mutation does not cause HHG in foxes, nor do the coding regions or intron–exon boundaries of these three genes contain any candidate mutations for fox gum disease. Patterns of molecular evolution among foxes and other mammals reflect high conservation and strong functional constraints for SOS1 and GRB2 but reveal a lineage-specific pattern of variability in EGFR consistent with mutational rate differences, relaxed functional constraints, and possibly positive selection.

Phylogeographic mitogenomics of Atlantic cod Gadus morhua: Variation in and among trans-Atlantic, trans-Laurentian, Northern cod, and landlocked fjord populations

Abstract The historical phylogeography, biogeography, and ecology of Atlantic cod (Gadus morhua) have been impacted by cyclic Pleistocene glaciations, where drops in sea temperatures led to sequestering of water in ice sheets, emergence of continental shelves, and changes to ocean currents. High‐resolution, whole‐genome mitogenomic phylogeography can help to elucidate this history. We identified eight major haplogroups among 153 fish from 14 populations by Bayesian, parsimony, and distance methods, including one that extends the species coalescent back to ca. 330 kya. Fish from the Barents and Baltic Seas tend to occur in basal haplogroups versus more recent distribution of fish in the Northwest Atlantic. There was significant differentiation in the majority of trans‐Atlantic comparisons (ΦST = .029–.180), but little or none in pairwise comparisons within the Northwest Atlantic of individual populations (ΦST = .000–.060) or defined management stocks (ΦST = .000–.023). Monte Carlo randomization tests of population phylogeography showed significantly nonrandom trans‐Atlantic phylogeography versus absence of such structure within various partitions of trans‐Laurentian, Northern cod (NAFO 2J3KL) and other management stocks, and Flemish Cap populations. A landlocked meromictic fjord on Baffin Island comprised multiple identical or near‐identical mitogenomes in two major polyphyletic clades, and was significantly differentiated from all other populations (ΦST = .153–.340). The phylogeography supports a hypothesis of an eastern origin of genetic diversity ca. 200–250 kya, rapid expansion of a western superhaplogroup comprising four haplogroups ca. 150 kya, and recent postglacial founder populations.

Patterns of MHC-DRB1 polymorphism in a post-glacial island canid, the Newfoundland red fox (Vulpes vulpes deletrix), suggest balancing selection at species and population timescales

As the only native insular Newfoundland canid between the extinction of the wolf in the 1930s and the recent arrival of coyotes, the red fox (Vulpes vulpes deletrix Bangs 1898) poses interesting questions about genetic distinctiveness and the post-glacial colonization history of the island’s depauperate mammalian fauna. Here, we characterized genetic variability at the major histocompatibility complex (MHC) class II DR β1 domain (DRB1) locus in 28 red foxes from six sampling localities island-wide and compared it with mitochondrial control region (CR) diversity and DRB1 diversity in other canids. Our goals were to describe novel DRB1 alleles in a new canid population and to make inferences about the role of selection in maintaining their diversity. As in numerous studies of vertebrates, we found an order-of-magnitude higher nucleotide diversity at the DRB1 locus compared with the CR and significantly positive nonsynonymous-to-synonymous substitution ratios, indicative of selection in the distant past. Although the evidence is weaker, the Ewens-Watterson test of neutrality and the geographical distribution of variation compared with the CR suggest a role for selection over the evolutionary timescale of populations. We report the first genetic data from the DRB1 locus in the red fox and establish baseline information regarding immunogenetic variation in this island canid population which should inform continued investigations of population demography, adaptive genetic diversity, and wildlife disease in red foxes and related species.