Phillip A. Morin

NOAA National Marine Fisheries Service

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Kelly M. Robertson

National Oceanic and Atmospheric Administration

Andrew D. Foote

University of Oslo

Frederick I. Archer

NOAA National Marine Fisheries Service Southwest Fisheries Science Center

Barbara L. Taylor

NOAA National Marine Fisheries Service

M. Thomas P. Gilbert

Norwegian University of Science and Technology

Robin W. Baird

Cascadia Research Collective

Paul R. Wade

Takeda (United States)

Brittany L. Hancock‐Hanser

NOAA National Marine Fisheries Service Southwest Fisheries Science Center

Karen K. Martien

NOAA National Marine Fisheries Service Southwest Fisheries Science Center

Nicholas J. Davison

University of Glasgow

Cooperative Institutions

NOAA National Marine Fisheries Service

148

National Oceanic and Atmospheric Administration

111

NOAA National Marine Fisheries Service Southwest Fisheries Science Center

103

University of California, San Diego

NOAA National Marine Fisheries Service Alaska Fisheries Science Center

University of St Andrews

University of Washington

University of Copenhagen

University of California, Santa Cruz

Duke University

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Normalization and binning of historical and multi‐source microsatellite data: overcoming the problems of allele size shift with allelogram

Molecular Ecology Resources (2009)

Phillip A. Morin Carl Manaster Sarah L. Mesnick Robert E. Holland

Microsatellite allele data have long been plagued by size shifts that can at best make it difficult to accurately assign genotypes to allele products, and at worse can cause whole batches of data from different instruments, dates or laboratories to be incorrectly assigned. Although modern genotyping technology (capillary electrophoresis) has overcome many of these problems, concern remains regarding the consistency of scores within a laboratory over time and between laboratories when combining data from multiple sources into a single analysis. There remain a large number of laboratories using older technologies or combining data from multiple sources. In addition, thousands of data sets that could potentially be expanded as samples become available are generally regarded as unusable because of the effort that would be required to validate congruence of genotypes from old and new data sets. We present methods to normalize and bin alleles from multiple data sources using a relatively small set of controls and the freely available program allelogram.

Normalization

10.1111/j.1755-0998.2009.02672.x

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Citations (46)

Osteoporosis and Apolipoprotein E Genotype in Older Adults: The

E. Barrett-Connor D. L. Schneider Phillip A. Morin P. Parry

Recent studies reported an association between apolipoprotein E (ApoE) 4 and osteoporosis. We examined the association of ApoE 4 genotype with bone mineral density (BMD), bone loss and fracture risk in 596 men and 332 community-dwelling women aged 45-95 years. Women were postmenopausal and not using estrogen. At the baseline visit, BMD was measured at the ultradistal and midshaft radius using single photon densitometry, and at the hip and lumbar spine using dual-energy X-ray absorptiometry. Hip and lumbar spine BMD levels were remeasured 4 years later. Self-reported fractures were confirmed by radiology reports in 95% of cases. ApoE allele distribution did not vary by age; 25% of men and 20% of women had one ApoE 4 allele. There were no differences in BMD at the lumbar spine, total hip, ultradistal or midshaft radius in men or women with the ApoE 4 allele compared with men or women without the ApoE 4 allele. After an average 4 year interval, there were also no differences in the annualized percent change in BMD at the hip or lumbar spine in men or women with or without an ApoE 4 allele. One or more clinical fractures were reported by 55 men and 109 women. Fewer, not more, clinical fractures were reported in men and women with an ApoE 4 allele; these differences were not statistically significant (p = 0.21 and p = 0.62, respectively). These data do not support the hypotheses that there is an association between ApoE genotype and BMD, bone loss or osteoporotic fractures in older community-dwelling men or women.

Apolipoprotein E

Osteopenia

Source

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Conservation genetics in the new molecular age

Frontiers in Ecology and the Environment (2004)

Robert K. Wayne Phillip A. Morin

Molecular techniques can be used to address questions of conservation significance. At the individual level, these questions concern how kinship affects reproduction, group structure, dispersal, and cooperation which leads to social group assembly rules such that populations can be genetically managed and restored. Furthermore, inbreeding can now be measured at the individual level in natural populations, and, in combination with field studies, can be used to assess fitness declines that might require active management to arrest. We discuss genetic units for conservation and attempt to integrate data on phenotype and the environment into an evaluation that includes genetic data. To a limited extent, genetic surveys can now include genes that may influence fitness, as well as those not under selection. We discuss the use of animal and plant remains to monitor current populations and to determine directly the demographic changes that have occurred in the past.

Conservation Genetics

Inclusive fitness

Genetic Fitness

10.1890/1540-9295(2004)002[0089:cgitnm]2.0.co;2

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Determination of Genealogical Relationships from Genetic Data: A Review of Methods and Applications

Phillip A. Morin

Abstract The concept of kinship has been central to investigating the remarkably varied social structures of primates. Genealogical relationships between individuals are predicted, from the first principles of evolutionary theory, to be critical influences on the nature of social relationships. Sociobiological/socioecological theory in particular predicts that kinship should have primary importance for the cohesion of groups, dominance, inbreeding avoidance, and coalitional behavior (Hamilton 1964, Wrangham 1980, Trivers 1985, Silk 1987).

Sociobiology

Dominance (genetics)

Inclusive fitness

10.1093/oso/9780195148893.003.0002

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A High-Quality Blue Whale Genome, Segmental Duplications, and Historical Demography

Molecular Biology and Evolution (2024)

Yury V. Bukhman Phillip A. Morin Susanne Meyer Li‐Fang Chu Jeff K. Jacobsen

Abstract The blue whale, Balaenoptera musculus, is the largest animal known to have ever existed, making it an important case study in longevity and resistance to cancer. To further this and other blue whale-related research, we report a reference-quality, long-read-based genome assembly of this fascinating species. We assembled the genome from PacBio long reads and utilized Illumina/10×, optical maps, and Hi-C data for scaffolding, polishing, and manual curation. We also provided long read RNA-seq data to facilitate the annotation of the assembly by NCBI and Ensembl. Additionally, we annotated both haplotypes using TOGA and measured the genome size by flow cytometry. We then compared the blue whale genome with other cetaceans and artiodactyls, including vaquita (Phocoena sinus), the world's smallest cetacean, to investigate blue whale's unique biological traits. We found a dramatic amplification of several genes in the blue whale genome resulting from a recent burst in segmental duplications, though the possible connection between this amplification and giant body size requires further study. We also discovered sites in the insulin-like growth factor-1 gene correlated with body size in cetaceans. Finally, using our assembly to examine the heterozygosity and historical demography of Pacific and Atlantic blue whale populations, we found that the genomes of both populations are highly heterozygous and that their genetic isolation dates to the last interglacial period. Taken together, these results indicate how a high-quality, annotated blue whale genome will serve as an important resource for biology, evolution, and conservation research.

Segmental duplication

10.1093/molbev/msae036

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The genome sequence of the white-beaked dolphin, Lagenorhynchus albirostris (Gray, 1846)

Wellcome Open Research (2024)

Nicholas J. Davison Phillip A. Morin

We present a genome assembly from a juvenile female

Gray (unit)

Sequence (biology)

10.12688/wellcomeopenres.23369.1

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Analytical approaches to subspecies delimitation with genetic data

Marine Mammal Science (2017)

Karen K. Martien Matthew S. Leslie Barbara L. Taylor Phillip A. Morin Frederick I. Archer

Abstract The vast and remote distributions and large body size of most cetaceans make it difficult to obtain and maintain morphological collections adequate for advancing sound taxonomic arguments. Consequently, genetic data are playing an increasingly important role in cetacean species and subspecies delimitation. We review seven categories of analytical methods useful in delimiting subspecies based on genetic data. For each category, we summarize its utility in evaluating putative subspecies, the types of markers to which it can be applied, and potential challenges in interpreting results in a taxonomic context. We focus on the utility of each type of method to evaluate the critical features distinguishing subspecies from populations and species: the degree of diagnosability between putative taxa and the extent to which the putative taxa have diverged along separate evolutionary pathways. We conclude that diagnosability is best estimated with either assignment tests or multivariate methods, while evaluating the degree of divergence requires a synthesis of multiple lines of evidence derived from different analytical methods and different data types, including nongenetic data.

Subspecies

Divergence (linguistics)

Genetic data

10.1111/mms.12409

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Citations (23)

No association between the TGF-β1 Leu10Pro polymorphism and osteoporosis among white women in the United States

The American Journal of Medicine (2003)

Elad Ziv Arnold Kahn Jane A. Cauley Phillip A. Morin Robert Saiz

Web of science

10.1016/s0002-9343(02)01393-1

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Citations (20)

Single nucleotide polymorphism (SNP) discovery in mammals: a targeted‐gene approach

Molecular Ecology (2004)

Nicola Aitken Steve Smith C. Schwarz Phillip A. Morin

Abstract Single nucleotide polymorphisms (SNPs) have rarely been exploited in nonhuman and nonmodel organism genetic studies. This is due partly to difficulties in finding SNPs in species where little DNA sequence data exist, as well as to a lack of robust and inexpensive genotyping methods. We have explored one SNP discovery method for molecular ecology, evolution, and conservation studies to evaluate the method and its limitations for population genetics in mammals. We made use of ‘CATS’ (or ‘EPIC’) primers to screen for novel SNPs in mammals. Most of these primer sets were designed from primates and/or rodents, for amplifying intron regions from conserved genes. We have screened 202 loci in 16 representatives of the major mammalian clades. Polymerase chain reaction (PCR) success correlated with phylogenetic distance from the human and mouse sequences used to design most primers; for example, specific PCR products from primates and the mouse amplified the most consistently and the marsupial and armadillo amplifications were least successful. Approximately 24% (opossum) to 65% (chimpanzee) of primers produced usable PCR product(s) in the mammals tested. Products produced generally high but variable levels of readable sequence and similarity to the expected genes. In a preliminary screen of chimpanzee DNA, 12 SNPs were identified from six (of 11) sequenced regions, yielding a SNP on average every 400 base pairs (bp). Given the progress in genome sequencing, and the large numbers of CATS‐like primers published to date, this approach may yield sufficient SNPs per species for population and conservation genetic studies in nonmodel mammals and other organisms.

SNP genotyping

Molecular Inversion Probe

10.1111/j.1365-294x.2004.02159.x

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Citations (180)

Response : Chimpanzee Kinship

Science (1995)

Phillip A. Morin James J. Moore David S. Woodruff

10.1126/science.268.5208.186

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