Previous morpho-molecular studies of evolutionary relationships within the economically important... more Previous morpho-molecular studies of evolutionary relationships within the economically important genus of honey bees (Apis), including the Western Honey Bee (A. mellifera L.), have suggested Out of Africa or Asia origins and subsequent spread to Europe. I test these hypotheses by a metaanalysis of complete mitochondrial DNA coding regions (11.0 kbp) from 22 nominal subspecies represented by 78 individual sequences in A. mellifera. Parsimony, distance, and likelihood analyses identify six nested clades: Things Fall Apart with Out of Africa or Asia hypotheses. Molecular clockcalibrated phylogeographic analysis shows instead a basal origin of A. m. mellifera in Europe ~ 780 Kya, and expansion to Southeast Europe and Asia Minor ~ 720 Kya. Eurasian bees spread southward via a Levantine/Nilotic/Arabian corridor into Africa ~ 540 Kya. An African clade re-established in Iberia ~ 100 Kya spread thereafter to westerly Mediterranean islands and back into North Africa. Nominal subspecies within the Asia Minor and Mediterranean clades are less differentiated than are individuals within other subspecies. Names matter: paraphyletic anomalies are artefacts of misreferral in GenBank of sequences to the wrong subspecies, or use of faulty sequences, which are clarified by inclusion of multiple sequences from available subspecies. The genus Apis comprises at least a dozen nominal species of Honey Bees found throughout Asia, Africa, the Middle East, and Europe, including the type species A. mellifera L., the Western Honey Bee (Table ) 1,2 . Although several species are important as traditional local sources of honey, only two cavity-nesting species, A. cerana in India and A. mellifera, have historically been domesticated for this purpose. Apiculture of A. mellifera is documented in Egypt as far back as 2600 BCE 3 . (References to the Levant as "a land of milk and honey" (Exodus 3:8) may refer instead to syrup from wind-and (or) hand-pollinated oasis dates (Phoenix dactylifera) of even greater antiquity 3 ). A. mellifera has been transported by humans around the world as the principal commercial source of honey and beeswax, and is also of particular agricultural importance in the Americas as an introduced pollinator of certain vegetable and fruit crops that are themselves introduced 4 . Competition between introduced generalist honey bees and specialist native insect pollinator (including other non-apine bees) for pollen ("pollen theft") may be detrimental to native plant species 5 . Geographic variation among different local strains or subspecies of A. mellifera is known to contribute to this impact, as it does quality and quantity of honey and other behaviors 6 . Notably, so-called "Africanized" bees have resulted from the escape of African subspecies crossed into domesticated South American hives, where the hybrids combine increased yield of honey with greater aggressiveness, and pose a hazard to humans 7 . Morpho-behavioral taxonomy has recognized three species groups within the genus: Dwarf Honey Bees (A. florea and A. andreniformis), Giant Honey Bees (A. laboriosa, A. dorsata, and A. breviligula), and Cavity-Nesting Honey Bees (A. mellifera together with A. nuluensis, A. nigrocincta, A. cerana (including A. indica), and A. koschevnikovi). A. mellifera is the only species with a native range in Africa and Europe, and includes more than 30 nominal subspecies 2 . These have historically been clustered as four continental groups, designated ACMO for African, Continental, Mellifera, and Oriental distributions 8 . The geographic origin and evolutionary spread of these groups remains controversial, as has their resolution into ancestor-descendant phylogenetic
Canadian Journal of Fisheries and Aquatic Sciences, Aug 1, 1997
Abstract: Greenland halibut (Reinhardtius hippoglossoides) have become of great importance to the... more Abstract: Greenland halibut (Reinhardtius hippoglossoides) have become of great importance to the Canadian fishery since the moratorium on northern cod (Gadus morhua), and an understanding of stock relationships among populations at the northern and southern extremes of their commercial range is crucial for proper management. We compared mitochondrial DNA sequence variation among fish taken from thoughout the Northwest Atlantic (Flemish Pass, the Grand Banks, Davis Strait, and Northwest Greenland) with samples from the Gulf of St. Lawrence, Iceland, and Norway. Within a 401 base pair portion of the cytochrome b gene, 22 genotypes were identified. Three of these occur at frequencies >10% and in the same relative abundances in all samples (except the Gulf of St. Lawrence). Genotype proportions do not differ significantly among samples, and genetic subdivision among samples (measured by the coancestry coefficient q) is nil. Genetic distances among samples are not related to geographic distribution: pairwise differences between the Gulf sample and other western Atlantic samples exceed those for trans-Atlantic comparisons. These data suggest that there is sufficient mixing of Greenland halibut, not only within the NAFO regulatory area, but among sites in the North Atlantic generally, to prevent the development or maintenance of genetically independent stocks.
Phylogenetic analysis of 13 substantially complete mitochondrial DNA genome sequences (14 036 bp)... more Phylogenetic analysis of 13 substantially complete mitochondrial DNA genome sequences (14 036 bp) from 10 taxa of gadine codfishes and pollock provides highly corroborated resolution of outstanding questions on their biogeographic evolution. Of 6 resolvable nodes among species, 4 were supported by >95% of bootstrap replications in parsimony, distance, likelihood, and similarly high posterior probabilities in bayesian analyses, one by 85%-95% according to the method of analysis, and one by 99% by one method and a majority of the other two. The endemic Pacific species, walleye pollock (Theragra chalcogramma), is more closely related to the endemic Atlantic species, Atlantic cod (Gadus macrocephalus), than either is to a second Pacific endemic, Pacific cod (Gadus macrocephalus). The walleye pollock should thus be referred to the genus Gadus as originally described (Gadus chalcogrammus Pallas 1811). Arcto-Atlantic Greenland cod, previously regarded as a distinct species (G. ogac), are a genomically distinguishable subspecies within pan-Pacific G. macrocephalus. Of the 2 endemic Arctic Ocean genera, Polar cod (Boreogadus) as the outgroup to Arctic cod (Arctogadus) and Gadus sensu lato is more strongly supported than a pairing of Boreogadus and Arctogadus as sister taxa. Taking into consideration historical patterns of hydrogeography, we outline a hypothesis of the origin of the 2 endemic Pacific species as independent but simultaneous invasions through the Bering Strait from an Arcto-Atlantic ancestral lineage. In contrast to the genome data, the complete proteome sequence (3830 amino acids) resolved only 3 nodes with >95% confidence, and placed Alaska pollock outside the Gadus clade owing to reversal mutations in the ND5 locus that restore ancestral, non-Gadus, amino acid residues in that species.
Characterization of DNA that remains in seafood products after skin, scales, and shells are remov... more Characterization of DNA that remains in seafood products after skin, scales, and shells are removed is widely used in forensic species identification, however, ordinary methods may be prohibitively expensive or time-consuming if large sample series need to be discriminated. Forensic discrimination of two species of bivalves commercially harvested from the North Atlantic, sea scallops (Placopecten magellanicus) and Icelandic scallops (Chlamys islandica), was made by means of species-specific oligonucleotides (SSOs) in a multiplex polymerase chain reaction (PCR). The test is a simultaneous in vitro amplification of a portion of the mitochondrial Cytochrome Oxidase I locus with a PCR anchor primer for a sequence identical in both species, and two alternative SSOs that selectively amplify either a 619-bp in Placopecten or a 459-bp DNA fragment in Chlamys. Fragment size and thus species identity are determined directly by gel electrophoresis. In the forensic application, analysis of more than 900 scallops from a series of samples seized from two fishing vessels showed significantly variable proportions of the species from the closed and open fisheries (Placopecten versus Chlamys, respectively). The multiplex SSO test provides a direct means of forensic identification of large population sample series, without the necessity of secondary DNA sequencing, RFLP mapping, or fingerprinting, and can be adapted to other loci and species.
The neuronal ceroid lipofuscinoses (NCLs) are the commonest neurodegenerative disorders of childr... more 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 ¼ 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.
Either we do know all the varieties of beings which people our planet, or we do not. If we do not... more Either we do know all the varieties of beings which people our planet, or we do not. If we do not know them all-if Nature has still secrets in the deeps for us, nothing is more conformable to reason than to admit the existence of fishes, or cetaceans of other kinds, or even of new species. .. which an accident of some sort has brought at long intervals to the upper level of the ocean."
We have shown previously that a feed-forward, back propagation neural network model based on comp... more We have shown previously that a feed-forward, back propagation neural network model based on composite n-grams can predict normalized signal strengths of a microarray based DNA sequencing experiment. The microarray comprises a 4xN set of 25-base single-stranded DNA molecule ("oligos"), specific for each of the four possible bases (A, C, G, or T) for Ade-nine, Cytosine, Guanine and Thymine respectively at each of N positions in the experimental DNA. Strength of binding between reference oligos and experimental DNA varies according to base complementarity and the strongest signal in any quartet should `call the base` at that position. Variation in base composition of and (or) order within oligos can affect accuracy and (or) confidence of base calls. To evaluate the effect of order, we present oligos as n-gram neural input vectors of degree 3 and measure their performance. Microarray signal intensity data were divided into training, validation and testing sets. Regression values obtained were >99.80% overall with very low mean square errors that transform to high best validation performance values. Pattern recognition results showed high percentage confusion matrix values along the diagonal and receiver operating characteristic curves were clustered in the upper left corner, both indices of good predictive performance. Higher order n-grams are expected to produce even better predictions.
<b>Copyright information:</b>Taken from "Interspecies hybridization on DNA reseq... more <b>Copyright information:</b>Taken from "Interspecies hybridization on DNA resequencing microarrays: efficiency of sequence recovery and accuracy of SNP detection in human, ape, and codfish mitochondrial DNA genomes sequenced on a human-specific MitoChip"http://www.biomedcentral.com/1471-2164/8/339BMC Genomics 2007;8():339-339.Published online 25 Sep 2007PMCID:PMC2211321. The single minimum-length tree had a length of 2828. All nodes are supported in 100% of 10,000 bootstrap replications, Sequences marked (") are from the present paper. The unmarked sequences are from GenBank ([], [], [], and [revised Cambridge Reference Sequence (rCRS): J01415.1]). The sequence marked (') is from the individual (GenBank ) identified in ref (12) as most divergent from the rCRS.
Question: Are phylogenetic relationships the major determinant of vocal relationships in non-osci... more Question: Are phylogenetic relationships the major determinant of vocal relationships in non-oscine birds (birds that do not have a learning component in the vocalization)? Background: Both environmental variables and phylogenetic affinities can affect vocalizations. Unlearned vocalizations are characteristics of most non-oscine bird families, which have a relatively less-complex syrinx and vocalizations. Organism: A monophyletic group of underground-nesting seabirds (auklets: Aethiini, Alcidae, Charadriiformes) from the Aleutian Islands, Alaska, USA. Methods: We mapped vocal characters (28 acoustic and 10 syringeal) from total repertoires of all members of the tribe Aethiini onto a molecular phylogeny to compare the relative influence of phylogeny and breeding habitat on vocal divergence. Conclusion: Phylogeny, visual display, and ecological factors have contributed to vocal divergence in this clade. Temporal attributes and syringeal attributes of the acoustics of vocalization show...
The advent of so-called NextGen DNA sequencing methods has massively increased the rate at which ... more The advent of so-called NextGen DNA sequencing methods has massively increased the rate at which DNA sequence information can be generated, and the volume and complexity of the data matrices that apply to biological questions, including molecular and organismal evolution and population biology. One such approach is the analysis of complete mitochondrial DNA (mtDNA) genomes from multiple species simultaneously, by means of a “sequencing by hybridization” microarray biotechnology, the “ArkChip”. I review mitogenomic biology and biotechnology, describe some of the known knowns of bioinformatic information content and its computational challenges, outline new computational strategies for known unknowns of evolutionary trees (phylogeny) and population biology structures in time and space (phylogeography), and speculate on future application of Computational Science to biological unknown unknowns.
Tuna fisheries is a growing industry in northeastern Brazil, where the yellowfin tuna (Thunnus al... more Tuna fisheries is a growing industry in northeastern Brazil, where the yellowfin tuna (Thunnus albacares, Bonnaterre 1788) is the most abundant species. The distribution of the populational stock of T. albacares in the equatorial Atlantic Ocean has been considered continuous, however the International Commission for Conservation of the Atlantic Tuna (ICCAT) has worked with a discontinuous population. For practical reasons a “two stock” hypothesis has been used in most assessments and the two stocks are separated at 30° W. In the present paper, a DNA sequencing technique was used to investigate the genetic variation in the T. albacares stock from the southwest equatorial Atlantic Ocean off northeastern Brazil, and the phylogenetic position of this species in the genus Thunnus. Within the 401-bp amplified segment of the cytochrome b gene, a single variable nucleotide site was identified among the 35 sampled individuals of T. albacares. This level of nucleotide sequence divergence is v...
We summarize the results of studies of mitochondrial DNA sequence variation in Atlantic cod (Gadu... more We summarize the results of studies of mitochondrial DNA sequence variation in Atlantic cod (Gadus morhua) from the North Atlantic and adjacent areas. Population genetic structures in the Northwest and Northeast Atlantic and Barents Sea differ markedly. Whereas all populations from the Northwest Atlantic are dominated by a single common genotype and show low haplotype and nucleotide diversity, samples from Norway and the Barents Sea support multiple genotypes at intermediate frequencies and show much higher genetic diversity. Replicate samples taken in the same year at a single location off Newfoundland, or in different years from the Gulf of Maine and Georges Bank, are as dissimilar as samples taken from opposite sides of the Laurentian Channel. Essentially none of the genetic variance in the Northwest Atlantic is attributable to subdivision among samples, whereas a substantial proportion is attributable to trans-Atlantic differentiation. Re-evaluation of comparable microsatellite ...
SALLES, R. et al. Morphometric and mitochondrial DNA analyses of the caribbean red snapper, Lutja... more SALLES, R. et al. Morphometric and mitochondrial DNA analyses of the caribbean red snapper, Lutjanus purpureus (Teleostei, Lutjanidae), in western Atlantic off northern Brazil. Boletim do Instituto de Pesca, Sao Paulo, v. 32, n. 2, p. 115-125, maio 2006.
We examined joint patterns of variation among 11 morphological variables, vertebral counts, and D... more We examined joint patterns of variation among 11 morphological variables, vertebral counts, and DNA sequence variation in the mitochondrial cytochrome h gene among juvenile (0-group) Atlantic cod (Gadus msrhua) from the northeast Newfoundland shelf and the Grand Banks. Canonical discriminant analysis shows that the group centroids of fish on and off the Grand Banks are significantly different and that fish from the most southerly region (30) have a significantly smaller mean vertebral count than fish from the more northerly regions (3K, 3L); however, there is substantial overlap of individuals, and reclassification of fish into their region of origin is successful in less than 50% of cases. Analysis of the distribution of 10 DNA sequence genotypes indicates substantial homogeneity of genotypes within localities and little or no genetic subdivision among regions. The pattern of genetic differentiation is consistent with a model of recent origin of most genetic variation following a b...
The Beothuk were a Native American people who formerly occupied the island of Newfoundland, and w... more The Beothuk were a Native American people who formerly occupied the island of Newfoundland, and who are generally accepted to have become culturally extinct in 1829. The Beothuk succeeded the Maritime Archaic people on the island after a hiatus of ca. 1.4 ka, and were themselves succeeded by the extant Mi’kmaq within historic times. Genetic continuity between ancient and modern Native Americans remains of interest. Complete aDNA mitogenomes from ancient Beothuk and Maritime Archaic were compared with the most closely related modern mitogenomes as obtained by BLAST search of GenBank. Beothuk mitogenomes in five clades are in one case identical to and otherwise differ by minima of three to eight SNPs from the most closely related modern mitogenomes. Maritime Archaic mitogenomes in 12 clades are in one case identical to and otherwise differ by minima of one to nine SNPs from the most similar modern mitogenomes. The single available modern Mi’kmaq mitogenome differs from the most simila...
High-resolution mitogenomics of within-species relationships can answer such phylogeographic ques... more High-resolution mitogenomics of within-species relationships can answer such phylogeographic questions as how species survived the most recent glaciation, as well as identify contemporary factors such as physical barriers, isolation, and gene flow. We examined the mitogenomic population structure of three at-risk species of wolffish: Atlantic (Anarhichas lupus), spotted (A. minor), and northern (A. denticulatus). These species are extensively sympatric across the North Atlantic but exhibit very different life history strategies, a combination that results in concordant and discordant patterns of genetic variation and structure. Wolffish haplogroups were not structured geographically: Atlantic and spotted wolffish each comprised three shallow clades, whereas northern wolffish comprised two deeper but unstructured lineages. We suggest that wolffish species survived in isolation in multiple glacial refugia, either refugia within refugia (Atlantic and spotted wolffish) or more distant r...
Post-glacial origins of woodland caribou (Rangifer tarandus subsp.) on the island of Newfoundland... more Post-glacial origins of woodland caribou (Rangifer tarandus subsp.) on the island of Newfoundland and their relationship to mainland populations have been uncertain. Sequence analysis of 2223 bp of the mitochondrial DNA control region and cytochrome b gene from 233 Newfoundland caribou identified 32 haplotypes in four major clades. Comparison with other Nearctic caribou confirms a closer affinity of the basal Clade A with animals from the mainland, and as an outgroup to Clades B, C, and D that are endemic to the island. This indicates re-entry of caribou to post-glacial Newfoundland across the Strait of Belle Isle from Labrador, rather than from southern coastal refugia. Newfoundland caribou are a distinct subspecies, Rangifer tarandus terranovae (Bangs, 1896). Hierarchical AMOVA shows significant clinal differentiation of the major clades from northwest to southeast across the island. The isolated Avalon Peninsula population in the extreme southeast is genetically depauperate. Foun...
An understanding of population genetic structure, particularly in species threatened with extinct... more An understanding of population genetic structure, particularly in species threatened with extinction, is critical to conservation and preservation of biodiversity. Genetic structure can be influenced by a number of factors including habitat loss, changes to environmental conditions, overexploitation, and the introduction of invasive species (Frankham, 1995; Wilson, 1988). The marine environment has been particularly impacted by overexploitation and environmental change
Previous morpho-molecular studies of evolutionary relationships within the economically important... more Previous morpho-molecular studies of evolutionary relationships within the economically important genus of honey bees (Apis), including the Western Honey Bee (A. mellifera L.), have suggested Out of Africa or Asia origins and subsequent spread to Europe. I test these hypotheses by a metaanalysis of complete mitochondrial DNA coding regions (11.0 kbp) from 22 nominal subspecies represented by 78 individual sequences in A. mellifera. Parsimony, distance, and likelihood analyses identify six nested clades: Things Fall Apart with Out of Africa or Asia hypotheses. Molecular clockcalibrated phylogeographic analysis shows instead a basal origin of A. m. mellifera in Europe ~ 780 Kya, and expansion to Southeast Europe and Asia Minor ~ 720 Kya. Eurasian bees spread southward via a Levantine/Nilotic/Arabian corridor into Africa ~ 540 Kya. An African clade re-established in Iberia ~ 100 Kya spread thereafter to westerly Mediterranean islands and back into North Africa. Nominal subspecies within the Asia Minor and Mediterranean clades are less differentiated than are individuals within other subspecies. Names matter: paraphyletic anomalies are artefacts of misreferral in GenBank of sequences to the wrong subspecies, or use of faulty sequences, which are clarified by inclusion of multiple sequences from available subspecies. The genus Apis comprises at least a dozen nominal species of Honey Bees found throughout Asia, Africa, the Middle East, and Europe, including the type species A. mellifera L., the Western Honey Bee (Table ) 1,2 . Although several species are important as traditional local sources of honey, only two cavity-nesting species, A. cerana in India and A. mellifera, have historically been domesticated for this purpose. Apiculture of A. mellifera is documented in Egypt as far back as 2600 BCE 3 . (References to the Levant as "a land of milk and honey" (Exodus 3:8) may refer instead to syrup from wind-and (or) hand-pollinated oasis dates (Phoenix dactylifera) of even greater antiquity 3 ). A. mellifera has been transported by humans around the world as the principal commercial source of honey and beeswax, and is also of particular agricultural importance in the Americas as an introduced pollinator of certain vegetable and fruit crops that are themselves introduced 4 . Competition between introduced generalist honey bees and specialist native insect pollinator (including other non-apine bees) for pollen ("pollen theft") may be detrimental to native plant species 5 . Geographic variation among different local strains or subspecies of A. mellifera is known to contribute to this impact, as it does quality and quantity of honey and other behaviors 6 . Notably, so-called "Africanized" bees have resulted from the escape of African subspecies crossed into domesticated South American hives, where the hybrids combine increased yield of honey with greater aggressiveness, and pose a hazard to humans 7 . Morpho-behavioral taxonomy has recognized three species groups within the genus: Dwarf Honey Bees (A. florea and A. andreniformis), Giant Honey Bees (A. laboriosa, A. dorsata, and A. breviligula), and Cavity-Nesting Honey Bees (A. mellifera together with A. nuluensis, A. nigrocincta, A. cerana (including A. indica), and A. koschevnikovi). A. mellifera is the only species with a native range in Africa and Europe, and includes more than 30 nominal subspecies 2 . These have historically been clustered as four continental groups, designated ACMO for African, Continental, Mellifera, and Oriental distributions 8 . The geographic origin and evolutionary spread of these groups remains controversial, as has their resolution into ancestor-descendant phylogenetic
Canadian Journal of Fisheries and Aquatic Sciences, Aug 1, 1997
Abstract: Greenland halibut (Reinhardtius hippoglossoides) have become of great importance to the... more Abstract: Greenland halibut (Reinhardtius hippoglossoides) have become of great importance to the Canadian fishery since the moratorium on northern cod (Gadus morhua), and an understanding of stock relationships among populations at the northern and southern extremes of their commercial range is crucial for proper management. We compared mitochondrial DNA sequence variation among fish taken from thoughout the Northwest Atlantic (Flemish Pass, the Grand Banks, Davis Strait, and Northwest Greenland) with samples from the Gulf of St. Lawrence, Iceland, and Norway. Within a 401 base pair portion of the cytochrome b gene, 22 genotypes were identified. Three of these occur at frequencies >10% and in the same relative abundances in all samples (except the Gulf of St. Lawrence). Genotype proportions do not differ significantly among samples, and genetic subdivision among samples (measured by the coancestry coefficient q) is nil. Genetic distances among samples are not related to geographic distribution: pairwise differences between the Gulf sample and other western Atlantic samples exceed those for trans-Atlantic comparisons. These data suggest that there is sufficient mixing of Greenland halibut, not only within the NAFO regulatory area, but among sites in the North Atlantic generally, to prevent the development or maintenance of genetically independent stocks.
Phylogenetic analysis of 13 substantially complete mitochondrial DNA genome sequences (14 036 bp)... more Phylogenetic analysis of 13 substantially complete mitochondrial DNA genome sequences (14 036 bp) from 10 taxa of gadine codfishes and pollock provides highly corroborated resolution of outstanding questions on their biogeographic evolution. Of 6 resolvable nodes among species, 4 were supported by >95% of bootstrap replications in parsimony, distance, likelihood, and similarly high posterior probabilities in bayesian analyses, one by 85%-95% according to the method of analysis, and one by 99% by one method and a majority of the other two. The endemic Pacific species, walleye pollock (Theragra chalcogramma), is more closely related to the endemic Atlantic species, Atlantic cod (Gadus macrocephalus), than either is to a second Pacific endemic, Pacific cod (Gadus macrocephalus). The walleye pollock should thus be referred to the genus Gadus as originally described (Gadus chalcogrammus Pallas 1811). Arcto-Atlantic Greenland cod, previously regarded as a distinct species (G. ogac), are a genomically distinguishable subspecies within pan-Pacific G. macrocephalus. Of the 2 endemic Arctic Ocean genera, Polar cod (Boreogadus) as the outgroup to Arctic cod (Arctogadus) and Gadus sensu lato is more strongly supported than a pairing of Boreogadus and Arctogadus as sister taxa. Taking into consideration historical patterns of hydrogeography, we outline a hypothesis of the origin of the 2 endemic Pacific species as independent but simultaneous invasions through the Bering Strait from an Arcto-Atlantic ancestral lineage. In contrast to the genome data, the complete proteome sequence (3830 amino acids) resolved only 3 nodes with >95% confidence, and placed Alaska pollock outside the Gadus clade owing to reversal mutations in the ND5 locus that restore ancestral, non-Gadus, amino acid residues in that species.
Characterization of DNA that remains in seafood products after skin, scales, and shells are remov... more Characterization of DNA that remains in seafood products after skin, scales, and shells are removed is widely used in forensic species identification, however, ordinary methods may be prohibitively expensive or time-consuming if large sample series need to be discriminated. Forensic discrimination of two species of bivalves commercially harvested from the North Atlantic, sea scallops (Placopecten magellanicus) and Icelandic scallops (Chlamys islandica), was made by means of species-specific oligonucleotides (SSOs) in a multiplex polymerase chain reaction (PCR). The test is a simultaneous in vitro amplification of a portion of the mitochondrial Cytochrome Oxidase I locus with a PCR anchor primer for a sequence identical in both species, and two alternative SSOs that selectively amplify either a 619-bp in Placopecten or a 459-bp DNA fragment in Chlamys. Fragment size and thus species identity are determined directly by gel electrophoresis. In the forensic application, analysis of more than 900 scallops from a series of samples seized from two fishing vessels showed significantly variable proportions of the species from the closed and open fisheries (Placopecten versus Chlamys, respectively). The multiplex SSO test provides a direct means of forensic identification of large population sample series, without the necessity of secondary DNA sequencing, RFLP mapping, or fingerprinting, and can be adapted to other loci and species.
The neuronal ceroid lipofuscinoses (NCLs) are the commonest neurodegenerative disorders of childr... more 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 ¼ 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.
Either we do know all the varieties of beings which people our planet, or we do not. If we do not... more Either we do know all the varieties of beings which people our planet, or we do not. If we do not know them all-if Nature has still secrets in the deeps for us, nothing is more conformable to reason than to admit the existence of fishes, or cetaceans of other kinds, or even of new species. .. which an accident of some sort has brought at long intervals to the upper level of the ocean."
We have shown previously that a feed-forward, back propagation neural network model based on comp... more We have shown previously that a feed-forward, back propagation neural network model based on composite n-grams can predict normalized signal strengths of a microarray based DNA sequencing experiment. The microarray comprises a 4xN set of 25-base single-stranded DNA molecule ("oligos"), specific for each of the four possible bases (A, C, G, or T) for Ade-nine, Cytosine, Guanine and Thymine respectively at each of N positions in the experimental DNA. Strength of binding between reference oligos and experimental DNA varies according to base complementarity and the strongest signal in any quartet should `call the base` at that position. Variation in base composition of and (or) order within oligos can affect accuracy and (or) confidence of base calls. To evaluate the effect of order, we present oligos as n-gram neural input vectors of degree 3 and measure their performance. Microarray signal intensity data were divided into training, validation and testing sets. Regression values obtained were >99.80% overall with very low mean square errors that transform to high best validation performance values. Pattern recognition results showed high percentage confusion matrix values along the diagonal and receiver operating characteristic curves were clustered in the upper left corner, both indices of good predictive performance. Higher order n-grams are expected to produce even better predictions.
<b>Copyright information:</b>Taken from "Interspecies hybridization on DNA reseq... more <b>Copyright information:</b>Taken from "Interspecies hybridization on DNA resequencing microarrays: efficiency of sequence recovery and accuracy of SNP detection in human, ape, and codfish mitochondrial DNA genomes sequenced on a human-specific MitoChip"http://www.biomedcentral.com/1471-2164/8/339BMC Genomics 2007;8():339-339.Published online 25 Sep 2007PMCID:PMC2211321. The single minimum-length tree had a length of 2828. All nodes are supported in 100% of 10,000 bootstrap replications, Sequences marked (") are from the present paper. The unmarked sequences are from GenBank ([], [], [], and [revised Cambridge Reference Sequence (rCRS): J01415.1]). The sequence marked (') is from the individual (GenBank ) identified in ref (12) as most divergent from the rCRS.
Question: Are phylogenetic relationships the major determinant of vocal relationships in non-osci... more Question: Are phylogenetic relationships the major determinant of vocal relationships in non-oscine birds (birds that do not have a learning component in the vocalization)? Background: Both environmental variables and phylogenetic affinities can affect vocalizations. Unlearned vocalizations are characteristics of most non-oscine bird families, which have a relatively less-complex syrinx and vocalizations. Organism: A monophyletic group of underground-nesting seabirds (auklets: Aethiini, Alcidae, Charadriiformes) from the Aleutian Islands, Alaska, USA. Methods: We mapped vocal characters (28 acoustic and 10 syringeal) from total repertoires of all members of the tribe Aethiini onto a molecular phylogeny to compare the relative influence of phylogeny and breeding habitat on vocal divergence. Conclusion: Phylogeny, visual display, and ecological factors have contributed to vocal divergence in this clade. Temporal attributes and syringeal attributes of the acoustics of vocalization show...
The advent of so-called NextGen DNA sequencing methods has massively increased the rate at which ... more The advent of so-called NextGen DNA sequencing methods has massively increased the rate at which DNA sequence information can be generated, and the volume and complexity of the data matrices that apply to biological questions, including molecular and organismal evolution and population biology. One such approach is the analysis of complete mitochondrial DNA (mtDNA) genomes from multiple species simultaneously, by means of a “sequencing by hybridization” microarray biotechnology, the “ArkChip”. I review mitogenomic biology and biotechnology, describe some of the known knowns of bioinformatic information content and its computational challenges, outline new computational strategies for known unknowns of evolutionary trees (phylogeny) and population biology structures in time and space (phylogeography), and speculate on future application of Computational Science to biological unknown unknowns.
Tuna fisheries is a growing industry in northeastern Brazil, where the yellowfin tuna (Thunnus al... more Tuna fisheries is a growing industry in northeastern Brazil, where the yellowfin tuna (Thunnus albacares, Bonnaterre 1788) is the most abundant species. The distribution of the populational stock of T. albacares in the equatorial Atlantic Ocean has been considered continuous, however the International Commission for Conservation of the Atlantic Tuna (ICCAT) has worked with a discontinuous population. For practical reasons a “two stock” hypothesis has been used in most assessments and the two stocks are separated at 30° W. In the present paper, a DNA sequencing technique was used to investigate the genetic variation in the T. albacares stock from the southwest equatorial Atlantic Ocean off northeastern Brazil, and the phylogenetic position of this species in the genus Thunnus. Within the 401-bp amplified segment of the cytochrome b gene, a single variable nucleotide site was identified among the 35 sampled individuals of T. albacares. This level of nucleotide sequence divergence is v...
We summarize the results of studies of mitochondrial DNA sequence variation in Atlantic cod (Gadu... more We summarize the results of studies of mitochondrial DNA sequence variation in Atlantic cod (Gadus morhua) from the North Atlantic and adjacent areas. Population genetic structures in the Northwest and Northeast Atlantic and Barents Sea differ markedly. Whereas all populations from the Northwest Atlantic are dominated by a single common genotype and show low haplotype and nucleotide diversity, samples from Norway and the Barents Sea support multiple genotypes at intermediate frequencies and show much higher genetic diversity. Replicate samples taken in the same year at a single location off Newfoundland, or in different years from the Gulf of Maine and Georges Bank, are as dissimilar as samples taken from opposite sides of the Laurentian Channel. Essentially none of the genetic variance in the Northwest Atlantic is attributable to subdivision among samples, whereas a substantial proportion is attributable to trans-Atlantic differentiation. Re-evaluation of comparable microsatellite ...
SALLES, R. et al. Morphometric and mitochondrial DNA analyses of the caribbean red snapper, Lutja... more SALLES, R. et al. Morphometric and mitochondrial DNA analyses of the caribbean red snapper, Lutjanus purpureus (Teleostei, Lutjanidae), in western Atlantic off northern Brazil. Boletim do Instituto de Pesca, Sao Paulo, v. 32, n. 2, p. 115-125, maio 2006.
We examined joint patterns of variation among 11 morphological variables, vertebral counts, and D... more We examined joint patterns of variation among 11 morphological variables, vertebral counts, and DNA sequence variation in the mitochondrial cytochrome h gene among juvenile (0-group) Atlantic cod (Gadus msrhua) from the northeast Newfoundland shelf and the Grand Banks. Canonical discriminant analysis shows that the group centroids of fish on and off the Grand Banks are significantly different and that fish from the most southerly region (30) have a significantly smaller mean vertebral count than fish from the more northerly regions (3K, 3L); however, there is substantial overlap of individuals, and reclassification of fish into their region of origin is successful in less than 50% of cases. Analysis of the distribution of 10 DNA sequence genotypes indicates substantial homogeneity of genotypes within localities and little or no genetic subdivision among regions. The pattern of genetic differentiation is consistent with a model of recent origin of most genetic variation following a b...
The Beothuk were a Native American people who formerly occupied the island of Newfoundland, and w... more The Beothuk were a Native American people who formerly occupied the island of Newfoundland, and who are generally accepted to have become culturally extinct in 1829. The Beothuk succeeded the Maritime Archaic people on the island after a hiatus of ca. 1.4 ka, and were themselves succeeded by the extant Mi’kmaq within historic times. Genetic continuity between ancient and modern Native Americans remains of interest. Complete aDNA mitogenomes from ancient Beothuk and Maritime Archaic were compared with the most closely related modern mitogenomes as obtained by BLAST search of GenBank. Beothuk mitogenomes in five clades are in one case identical to and otherwise differ by minima of three to eight SNPs from the most closely related modern mitogenomes. Maritime Archaic mitogenomes in 12 clades are in one case identical to and otherwise differ by minima of one to nine SNPs from the most similar modern mitogenomes. The single available modern Mi’kmaq mitogenome differs from the most simila...
High-resolution mitogenomics of within-species relationships can answer such phylogeographic ques... more High-resolution mitogenomics of within-species relationships can answer such phylogeographic questions as how species survived the most recent glaciation, as well as identify contemporary factors such as physical barriers, isolation, and gene flow. We examined the mitogenomic population structure of three at-risk species of wolffish: Atlantic (Anarhichas lupus), spotted (A. minor), and northern (A. denticulatus). These species are extensively sympatric across the North Atlantic but exhibit very different life history strategies, a combination that results in concordant and discordant patterns of genetic variation and structure. Wolffish haplogroups were not structured geographically: Atlantic and spotted wolffish each comprised three shallow clades, whereas northern wolffish comprised two deeper but unstructured lineages. We suggest that wolffish species survived in isolation in multiple glacial refugia, either refugia within refugia (Atlantic and spotted wolffish) or more distant r...
Post-glacial origins of woodland caribou (Rangifer tarandus subsp.) on the island of Newfoundland... more Post-glacial origins of woodland caribou (Rangifer tarandus subsp.) on the island of Newfoundland and their relationship to mainland populations have been uncertain. Sequence analysis of 2223 bp of the mitochondrial DNA control region and cytochrome b gene from 233 Newfoundland caribou identified 32 haplotypes in four major clades. Comparison with other Nearctic caribou confirms a closer affinity of the basal Clade A with animals from the mainland, and as an outgroup to Clades B, C, and D that are endemic to the island. This indicates re-entry of caribou to post-glacial Newfoundland across the Strait of Belle Isle from Labrador, rather than from southern coastal refugia. Newfoundland caribou are a distinct subspecies, Rangifer tarandus terranovae (Bangs, 1896). Hierarchical AMOVA shows significant clinal differentiation of the major clades from northwest to southeast across the island. The isolated Avalon Peninsula population in the extreme southeast is genetically depauperate. Foun...
An understanding of population genetic structure, particularly in species threatened with extinct... more An understanding of population genetic structure, particularly in species threatened with extinction, is critical to conservation and preservation of biodiversity. Genetic structure can be influenced by a number of factors including habitat loss, changes to environmental conditions, overexploitation, and the introduction of invasive species (Frankham, 1995; Wilson, 1988). The marine environment has been particularly impacted by overexploitation and environmental change
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