James Coyer - Academia.edu (original) (raw)

Papers by James Coyer

Genes that were adaptively differentiated between Northern and Southern samples, and enriched in ... more Genes that were adaptively differentiated between Northern and Southern samples, and enriched in biological processes (Tab. S11a) or molecular functions (Tab. S11b). Tab. S11c represents those genes that were not represented in enriched GO-terms. Each row represents one gene with its mapped sequence ID (mRNAID, column A), gene ID (ZosmaID, column B, based on the Zostera marina genome annotation v2.1, GenBank Accession: LFYR00000000), the source (column C) of annotation (inference from homology or top BLAST hit), and the name of the gene (column D). For Tab. S11a and Tab. S11b, the GO-term that each gene represents is represented in column E, and the description for this GO-term in column F.

Journal of Phycology, Dec 1, 2007

Journal of Phycology, Sep 1, 2011

bioRxiv (Cold Spring Harbor Laboratory), Aug 15, 2021

The sex-dependent regulation of gene expression is considered to be an underlying cause of often ... more The sex-dependent regulation of gene expression is considered to be an underlying cause of often extensive, sexually dimorphic traits between males and females. Although the nature and degree of sexbiased gene expression has been well-documented in several animal and plant systems, far less is known about the commonality, conservation, recruitment mechanisms and evolution of sex-biased genes in more distant eukaryotic groups. Brown algae are of particular interest for empirical studies on the evolution of sex-biased gene expression, as they have been evolving independently from animals and plants for over one billion years. Here we focus on two brown algal dioecious species, Fucus serratus and Fucus vesiculosus, where male heterogamety (XX/XY) has recently emerged. Using RNA-seq, we study sex-biased gene expression and discuss different evolutionary forces responsible for the evolution of sexbiased genes. We find that both species evolved masculinized transcriptomes, with sex-biased genes allocated mainly to male reproductive tissue, but virtually absent in vegetative tissues. Conserved malebiased genes were enriched in functions related to gamete production, along with sperm competition and include two flagellar proteins under positive selection. In contrast to female-biased genes, which show high turnover rates, male-biased genes reveal remarkable conservation of bias and expression levels between the two species. As observed in other XY systems, male-biased genes also display accelerated rates of coding sequence evolution compared to female-biased or unbiased genes. Our results imply that evolutionary forces affect male and female sex-biased genes differently on structural and regulatory levels. Similar to evolutionarily distant plant and animal lineages, sex-biased gene expression in Fucus evolved during the transition to dioecy to resolve intra-locus sexual conflict arising from anisogamy. 2 .

Springer eBooks, 2016

Members of the seaweed family Fucaceae have been recurrent models in North Atlantic phylogeograph... more Members of the seaweed family Fucaceae have been recurrent models in North Atlantic phylogeographic research; numerous studies have been published since 2000, and this review synthesizes their major findings. Fucoid species exhibited diverse responses to glacial–interglacial cycles, but evidence indicates there were a few common refugial areas such as north-western Iberia, the Celtic Sea (Brittany/Ireland) region and the North-west Atlantic. In genetically rich refugial areas, pervasive genetic breaks confirmed presently limited gene flow between adjacent distinct genetic groups. In contrast with the maintenance of sharp genetic breaks, most species experienced extensive migration during post-glacial expansion. Poleward migrations in the North-east Atlantic followed routes along north-western Ireland and the transgressing English Channel. These patterns support the role of density-blocking in maintaining sharp genetic breaks at contact zones, and of long-distance dispersal from range edges in mediating expansion into uninhabited regions. The data also indicate that expansions involve mostly the genetic groups located at range edges rather than the entire species’ gene pool, both poleward during interglacials and toward warmer regions during glacial periods. Fucoid expansions have also been linked to introgressive recombination of genomes at (and beyond) contact zones and to gene surfing leading to present large-scale dominance by alleles that were located at the expanding edge. Phylogeographic approaches have also proven useful to identify and track the sources of introductions linked to marine traffic. The integration of environmental niche models with molecular data have further allowed hindcasting southern distributions during glaciation and predicting the potentially negative effects of future climate warming, including the loss of vulnerable, unique trailing-edge lineages, as species’ ranges are predicted to continue shifting northward. Collectively, these studies have contributed greatly to elucidating the links between past and ongoing climatic shifts, range dynamics and geographical patterns of genetic variability in the North Atlantic.

Advances in Marine Biology, 2011

Stress regimes defined as the synchronous or sequential action of abiotic and biotic stresses det... more Stress regimes defined as the synchronous or sequential action of abiotic and biotic stresses determine the performance and distribution of species. The natural patterns of stress to which species are more or less well adapted have recently started to shift and alter under the influence of global change. This was the motivation to review our knowledge on the stress ecology of a benthic key player, the macroalgal genus Fucus. We first provide a comprehensive review of the genus as an ecological model including what is currently known about the major lineages of Fucus species with respect to hybridization, ecotypic differentiation and speciation; as well as life history, population structure and geographic distribution. We then review our current understanding of both extrinsic (abiotic/biotic) and intrinsic (genetic) stress(es) on Fucus species and how they interact with each other. It is concluded that (i) interactive stress effects appear to be equally distributed over additive, antagonistic and synergistic categories at the level of single experiments, but are predominantly additive when averaged over all studies in a meta-analysis of 41 experiments; (ii) juvenile and adult responses to stress frequently differ and (iii) several species or particular populations of Fucus may be relatively unaffected by climate change as a consequence of pre-adapted ecotypes that collectively express wide physiological tolerences. Future research on Fucus should (i) include additional species, (ii) include marginal populations as models for responses to environmental stress; (iii) assess a wider range of stress combinations, including their temporal fluctuations; (iv) better differentiate between stress sensitivity of juvenile versus adult stages; (v) include a functional genomic component in order to better integrate Fucus&#39; ecological and evolutionary responses to stress regimes and (vi) utilize a multivariate modelling approach in order to develop and understand interaction networks.

Molecular Ecology, Sep 22, 2016

Take-down policy If you believe that this document breaches copyright please contact us providing... more Take-down policy If you believe that this document breaches copyright please contact us providing details, and we will remove access to the work immediately and investigate your claim.

Proceedings of The Royal Society B: Biological Sciences, Sep 7, 2002

Historically, the intertidal seaweeds Fucus serratus (Fs) and Fucus evanescens (Fe) were sympatri... more Historically, the intertidal seaweeds Fucus serratus (Fs) and Fucus evanescens (Fe) were sympatric only along the western coast of Norway. In the mid-1890s, Fe (monoecious) was accidentally introduced into the Oslofjord. Putative hybridization with the endemic Fs (dioecious) was observed in Oslofjord by 1977 and in the Kattegat and western Baltic Seas by 1998. At Blushøj, Denmark (Kattegat Sea) putative Fs × Fe hybrids were present only when densities of Fe and Fs exceeded 14 and 2 m Ϫ2 , respectively. All of the 58 putative hybrids that were collected in 1999 were dioecious and intermediate in morphology. Essentially all (57 out of 58) were reproductively mature, but the oogonia possessed fewer and more variably sized eggs than either parent. Examination of each parental species and putative hybrids with nuclear, mitochondrial and chloroplast molecular markers confirmed the occurrence of hybridization. Furthermore, all of the hybrids possessed Fe-type chloroplasts and mitochondria, indicating that only the Fe egg × Fs sperm pairing was successful in the field. The reciprocal cross of Fs egg × Fe sperm was absent in the field and significantly less successful in laboratory crossings. Asymmetrical hybridization has also been reported for several species of plants and animals.

New Phytologist, Jan 22, 2023

Summary Sex‐biased gene expression is considered to be an underlying cause of sexually dimorphic ... more Summary Sex‐biased gene expression is considered to be an underlying cause of sexually dimorphic traits. Although the nature and degree of sex‐biased expression have been well documented in several animal and plant systems, far less is known about the evolution of sex‐biased genes in more distant eukaryotic groups. Here, we investigate sex‐biased gene expression in two brown algal dioecious species, Fucus serratus and Fucus vesiculosus, where male heterogamety (XX/XY) has recently emerged. We find that in contrast to evolutionary distant plant and animal lineages, male‐biased genes do not experience high turnover rates, but instead reveal remarkable conservation of bias and expression levels between the two species, suggesting their importance in sexual differentiation. Genes with consistent male bias were enriched in functions related to gamete production, along with sperm competition and include three flagellar proteins under positive selection. We present one of the first reports, outside of the animal kingdom, showing that male‐biased genes display accelerated rates of coding sequence evolution compared with female‐biased or unbiased genes. Our results imply that evolutionary forces affect male and female sex‐biased genes differently on structural and regulatory levels, resulting in unique properties of differentially expressed transcripts during reproductive development in Fucus algae.

European Journal of Phycology, May 25, 2017

HAL is a multidisciplinary open access archive for the deposit and dissemination of scientific re... more HAL is a multidisciplinary open access archive for the deposit and dissemination of scientific research documents, whether they are published or not. The documents may come from teaching and research institutions in France or abroad, or from public or private research centers. L'archive ouverte pluridisciplinaire HAL, est destinée au dépôt et à la diffusion de documents scientifiques de niveau recherche, publiés ou non, émanant des établissements d'enseignement et de recherche français ou étrangers, des laboratoires publics ou privés.

Molecular Ecology Resources, 2009

Eleven microsatellites were characterized for Semicossyphus pulcher (California sheephead) using ... more Eleven microsatellites were characterized for Semicossyphus pulcher (California sheephead) using an enrichment protocol. The number of alleles varied from three to 14 for a sample of 40 individuals from two populations. Expected heterozygosities ranged from 0.311 to 0.891. All loci but one were in Hardy-Weinberg equilibrium. No evidence for linkage disequilibrium was observed. These polymorphic microsatellites will be useful for genetic diversity and connectivity analyses of S. pulcher.

ZosmaID: gene ID based on the Zostera marina genome annotation v2.1 from the ORCAE database, GenB... more ZosmaID: gene ID based on the Zostera marina genome annotation v2.1 from the ORCAE database, GenBank Accession: LFYR00000000); mRNAID: the mapped sequence ID; name: the gene description; annotation.source: the source of annotation (inference from homology or top BLAST hit); and GO.terms: the associated Gene Ontology terms.

Field courses using scuba allow university students to experience kelp forests and other shallow,... more Field courses using scuba allow university students to experience kelp forests and other shallow, subtidal ecosystems. They are unusually effective for instilling essential scientific values: an appreciation of natural history and an enhanced ability to ask meaningful questions and think holistically. After teaching such courses at six institutions over the past 40 years, we discovered common aspects in how our students developed; how the courses were taught; issues of logistics and safety; and the regulatory obstacles we had to overcome. We highlight the opportunities and the need for getting more students into observing natural history through such field courses, thereby enabling them to better grasp and address the looming crises of the world's ecosystems that support the human population.

Frontiers in Marine Science, Jun 18, 2021

Because Kemp's ridley sea turtles (Lepidochelys kempii) are critically endangered and closely rel... more Because Kemp's ridley sea turtles (Lepidochelys kempii) are critically endangered and closely related to the vulnerable olive ridleys (L. olivacea), it is essential for forensic investigations and conservation efforts to distinguish these species when only skeletal elements remain. DNA extraction and analysis by DNA sequencing of genetic markers is the only method to determine species identity reliably, yet these methods are significantly compromised when DNA becomes degraded. To evaluate the role that time and environment play in obtaining high-quality DNA sequencing data, we placed skeletal elements of a terrestrial mammal (Bos taurus) and L. kempii in a supratidal and subtidal environment for 3 years. Biannual sampling revealed that after 3 years, mitochondrial DNA (mtDNA) consistently identified each species from each environment. Our results show that mtDNA recovery from bone and identification for Kemp's ridley sea turtles was possible up to 3 years in both environments. All sequencing data obtained was accurate and robust, but DNA sequencing results were not consistent after 664-days of exposure. Our findings led us to conclude that if sufficient DNA is extracted from bone samples, then high-quality sequence data can be obtained, and the resulting sequence data accurately reflects the reference sequence for the given gene marker. This study provides evidence that DNA can be extracted and analyzed from challenging biological substrates, like bone, when these substrates are exposed to seasonally dynamic maritime environmental conditions for up to 3-years.

The densities of three species of sea urchins and the giant kelp (Macrocystis pyrifera) were moni... more The densities of three species of sea urchins and the giant kelp (Macrocystis pyrifera) were monitored at a site near Anacapa Island, California. Although the study site had previously supported a dense kelp bed, from 1981-1983 it was dominated by urchins and coralline algae, and Macrocystis was restricted to a narrow band in shallow water. After limited recruitment in 1984, Macrocystis recruited heavily throughout the study site in 1985, resulting in an extensive kelp bed; the recruitment event was not accompanied by a sharp decline in urchin densities. However, high existing urchin densities, accompanied by unusually heavy urchin recruitment in 1985, resulted in the gradual decline of the kelp bed. By 1987, the kelp bed was again restricted to a narrow band in shallow water.

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Ecological interactions among invading species are common and may often be important in facilitat... more Ecological interactions among invading species are common and may often be important in facilitating invasions. Indeed, the presence of one nonindigenous species can act as an agent of disturbance that facilitates the invasion of a second species. However, most studies of nonindigenous species are anecdotal and do not provide substantive evidence that interactions among nonindigenous species have any community-level effects. Here, using a combination of field experiments and observations we examine interactions among introduced species in New England kelp forests and ask whether these interactions have altered paradigms describing subtidal communities in the Gulf of Maine. The green alga Codium fragile was observed at the Isles of Shoals, Maine, USA, in 1983 and has since replaced the native kelp as the dominant seaweed on leeward shores. Experiments manipulating kelp and Codium reveal that Codium does not directly inhibit growth or survival of kelp. Codium does, however, successfully recruit to gaps in the kelp bed and, once established, inhibits recruitment of kelp. A second nonindigenous species, Membranipora membranacea, grows epiphytically on kelp, and experiments reveal that the presence of Membranipora reduces growth and survival of kelp, resulting in defoliation of kelp plants and gap formation in kelp beds. In the absence of Codium, kelp recolonizes these gaps, but when present, Codium colonizes and prevents kelp recolonization. Manipulations of herbivores demonstrate that herbivory will reinforce Codium dominance. Thus, the demise of New England kelp beds appears to result from one invasive species facilitating the spread of a second nonindigenous species.

Ecology, Nov 1, 2002