Publications by authors named "Madonna L Moss"

7 Publications

  • Page 1 of 1

Functional genetic diversity in an exploited marine species and its relevance to fisheries management.

Proc Biol Sci 2021 02 24;288(1945):20202398. Epub 2021 Feb 24.

School of Aquatic and Fishery Sciences, University of Washington, 1122 NE Boat Street, Seattle WA 98105, USA.

The timing of reproduction influences key evolutionary and ecological processes in wild populations. Variation in reproductive timing may be an especially important evolutionary driver in the marine environment, where the high mobility of many species and few physical barriers to migration provide limited opportunities for spatial divergence to arise. Using genomic data collected from spawning aggregations of Pacific herring () across 1600 km of coastline, we show that reproductive timing drives population structure in these pelagic fish. Within a specific spawning season, we observed isolation by distance, indicating that gene flow is also geographically limited over our study area. These results emphasize the importance of considering both seasonal and spatial variation in spawning when delineating management units for herring. On several chromosomes, we detected linkage disequilibrium extending over multiple Mb, suggesting the presence of chromosomal rearrangements. Spawning phenology was highly correlated with polymorphisms in several genes, in particular , which influences the development of retinal photoreceptors in vertebrates. is probably within a chromosomal rearrangement in Pacific herring and is also associated with spawn timing in Atlantic herring (). The observed genetic diversity probably underlies resource waves provided by spawning herring. Given the ecological, economic and cultural significance of herring, our results support that conserving intraspecific genetic diversity is important for maintaining current and future ecosystem processes.
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http://dx.doi.org/10.1098/rspb.2020.2398DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7934995PMC
February 2021

Archaeological mitogenomes illuminate the historical ecology of sea otters () and the viability of reintroduction.

Proc Biol Sci 2020 12 2;287(1940):20202343. Epub 2020 Dec 2.

Laboratories of Molecular Anthropology and Microbiome Research, Stephenson Research and Technology Center, Norman, OK 73019, USA.

Genetic analyses are an important contribution to wildlife reintroductions, particularly in the modern context of extirpations and ecological destruction. To address the complex historical ecology of the sea otter () and its failed 1970s reintroduction to coastal Oregon, we compared mitochondrial genomes of pre-extirpation Oregon sea otters to extant and historical populations across the range. We sequenced, to our knowledge, the first complete ancient mitogenomes from archaeological Oregon sea otter dentine and historical sea otter dental calculus. Archaeological Oregon sea otters ( = 20) represent 10 haplotypes, which cluster with haplotypes from Alaska, Washington and British Columbia, and exhibit a clear division from California haplotypes. Our results suggest that extant northern populations are appropriate for future reintroduction efforts. This project demonstrates the feasibility of mitogenome capture and sequencing from non-human dental calculus and the diverse applications of ancient DNA analyses to pressing ecological and conservation topics and the management of at-risk/extirpated species.
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http://dx.doi.org/10.1098/rspb.2020.2343DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7739945PMC
December 2020

Specialized sledge dogs accompanied Inuit dispersal across the North American Arctic.

Proc Biol Sci 2019 12 27;286(1916):20191929. Epub 2019 Nov 27.

Holmenkollen Ski Museum, Oslo, Norway.

Domestic dogs have been central to life in the North American Arctic for millennia. The ancestors of the Inuit were the first to introduce the widespread usage of dog sledge transportation technology to the Americas, but whether the Inuit adopted local Palaeo-Inuit dogs or introduced a new dog population to the region remains unknown. To test these hypotheses, we generated mitochondrial DNA and geometric morphometric data of skull and dental elements from a total of 922 North American Arctic dogs and wolves spanning over 4500 years. Our analyses revealed that dogs from Inuit sites dating from 2000 BP possess morphological and genetic signatures that distinguish them from earlier Palaeo-Inuit dogs, and identified a novel mitochondrial clade in eastern Siberia and Alaska. The genetic legacy of these Inuit dogs survives today in modern Arctic sledge dogs despite phenotypic differences between archaeological and modern Arctic dogs. Together, our data reveal that Inuit dogs derive from a secondary pre-contact migration of dogs distinct from Palaeo-Inuit dogs, and probably aided the Inuit expansion across the North American Arctic beginning around 1000 BP.
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http://dx.doi.org/10.1098/rspb.2019.1929DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6939252PMC
December 2019

Intraspecific DNA contamination distorts subtle population structure in a marine fish: Decontamination of herring samples before restriction-site associated sequencing and its effects on population genetic statistics.

Mol Ecol Resour 2019 Sep 17;19(5):1131-1143. Epub 2019 Jun 17.

School of Aquatic and Fishery Sciences, University of Washington, Seattle, Washington.

Wild specimens are often collected in challenging field conditions, where samples may be contaminated with the DNA of conspecific individuals. This contamination can result in false genotype calls, which are difficult to detect, but may also cause inaccurate estimates of heterozygosity, allele frequencies and genetic differentiation. Marine broadcast spawners are especially problematic, because population genetic differentiation is low and samples are often collected in bulk and sometimes from active spawning aggregations. Here, we used contaminated and clean Pacific herring (Clupea pallasi) samples to test (a) the efficacy of bleach decontamination, (b) the effect of decontamination on RAD genotypes and (c) the consequences of contaminated samples on population genetic analyses. We collected fin tissue samples from actively spawning (and thus contaminated) wild herring and nonspawning (uncontaminated) herring. Samples were soaked for 10 min in bleach or left untreated, and extracted DNA was used to prepare DNA libraries using a restriction site-associated DNA (RAD) approach. Our results demonstrate that intraspecific DNA contamination affects patterns of individual and population variability, causes an excess of heterozygotes and biases estimates of population structure. Bleach decontamination was effective at removing intraspecific DNA contamination and compatible with RAD sequencing, producing high-quality sequences, reproducible genotypes and low levels of missing data. Although sperm contamination may be specific to broadcast spawners, intraspecific contamination of samples may be common and difficult to detect from high-throughput sequencing data and can impact downstream analyses.
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http://dx.doi.org/10.1111/1755-0998.12978DOI Listing
September 2019

Archaeological data provide alternative hypotheses on Pacific herring (Clupea pallasii) distribution, abundance, and variability.

Proc Natl Acad Sci U S A 2014 Mar 18;111(9):E807-16. Epub 2014 Feb 18.

Department of Anthropology, University of British Columbia, Vancouver, BC, Canada V6T 1Z1.

Pacific herring (Clupea pallasii), a foundation of coastal social-ecological systems, is in decline throughout much of its range. We assembled data on fish bones from 171 archaeological sites from Alaska, British Columbia, and Washington to provide proxy measures of past herring distribution and abundance. The dataset represents 435,777 fish bones, dating throughout the Holocene, but primarily to the last 2,500 y. Herring is the single-most ubiquitous fish taxon (99% ubiquity) and among the two most abundant taxa in 80% of individual assemblages. Herring bones are archaeologically abundant in all regions, but are superabundant in the northern Salish Sea and southwestern Vancouver Island areas. Analyses of temporal variability in 50 well-sampled sites reveals that herring exhibits consistently high abundance (>20% of fish bones) and consistently low variance (<10%) within the majority of sites (88% and 96%, respectively). We pose three alternative hypotheses to account for the disjunction between modern and archaeological herring populations. We reject the first hypothesis that the archaeological data overestimate past abundance and underestimate past variability. We are unable to distinguish between the second two hypotheses, which both assert that the archaeological data reflect a higher mean abundance of herring in the past, but differ in whether variability was similar to or less than that observed recently. In either case, sufficient herring was consistently available to meet the needs of harvesters, even if variability is damped in the archaeological record. These results provide baseline information prior to herring depletion and can inform modern management.
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http://dx.doi.org/10.1073/pnas.1316072111DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3948274PMC
March 2014

High potential for using DNA from ancient herring bones to inform modern fisheries management and conservation.

PLoS One 2012 30;7(11):e51122. Epub 2012 Nov 30.

Ancient DNA Laboratory, Department of Archaeology, Simon Fraser University, Burnaby, British Columbia, Canada.

Pacific herring (Clupea pallasi) are an abundant and important component of the coastal ecosystems for the west coast of North America. Current Canadian federal herring management assumes five regional herring populations in British Columbia with a high degree of exchange between units, and few distinct local populations within them. Indigenous traditional knowledge and historic sources, however, suggest that locally adapted, distinct regional herring populations may have been more prevalent in the past. Within the last century, the combined effects of commercial fishing and other anthropogenic factors have resulted in severe declines of herring populations, with contemporary populations potentially reflecting only the remnants of a previously more abundant and genetically diverse metapopulation. Through the analysis of 85 archaeological herring bones, this study attempted to reconstruct the genetic diversity and population structure of ancient herring populations using three different marker systems (mitochondrial DNA (mtDNA), microsatellites and SNPs). A high success rate (91%) of DNA recovery was obtained from the extremely small herring bone samples (often <10 mg). The ancient herring mtDNA revealed high haplotype diversity comparable to modern populations, although population discrimination was not possible due to the limited power of the mtDNA marker. Ancient microsatellite diversity was also similar to modern samples, but the data quality was compromised by large allele drop-out and stuttering. In contrast, SNPs were found to have low error rates with no evidence for deviations from Hardy-Weinberg equilibrium, and simulations indicated high power to detect genetic differentiation if loci under selection are used. This study demonstrates that SNPs may be the most effective and feasible approach to survey genetic population structure in ancient remains, and further efforts should be made to screen for high differentiation markers.This study provides the much needed foundation for wider scale studies on temporal genetic variation in herring, with important implications for herring fisheries management, Aboriginal title rights and herring conservation.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0051122PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3511397PMC
May 2013

Paleoindian seafaring, maritime technologies, and coastal foraging on California's Channel Islands.

Science 2011 Mar;331(6021):1181-5

Museum of Natural and Cultural History, University of Oregon, Eugene, OR 97403, USA.

Three archaeological sites on California's Channel Islands show that Paleoindians relied heavily on marine resources. The Paleocoastal sites, dated between ~12,200 and 11,200 years ago, contain numerous stemmed projectile points and crescents associated with a variety of marine and aquatic faunal remains. At site CA-SRI-512 on Santa Rosa Island, Paleocoastal peoples used such tools to capture geese, cormorants, and other birds, along with marine mammals and finfish. At Cardwell Bluffs on San Miguel Island, Paleocoastal peoples collected local chert cobbles, worked them into bifaces and projectile points, and discarded thousands of marine shells. With bifacial technologies similar to those seen in Western Pluvial Lakes Tradition assemblages of western North America, the sites provide evidence for seafaring and island colonization by Paleoindians with a diversified maritime economy.
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http://dx.doi.org/10.1126/science.1201477DOI Listing
March 2011
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