Publications by authors named "Nicolas Devos"

25 Publications

  • Page 1 of 1

Exome sequencing of hepatocellular carcinoma in lemurs identifies potential cancer drivers: A pilot study.

Evol Med Public Health 2022 29;10(1):221-230. Epub 2022 Apr 29.

Department of Medicine, Duke University Medical Center, Durham, NC 27710, USA.

Background And Objectives: Hepatocellular carcinoma occurs frequently in prosimians, but the cause of these liver cancers in this group is unknown. Characterizing the genetic changes associated with hepatocellular carcinoma in prosimians may point to possible causes, treatments and methods of prevention, aiding conservation efforts that are particularly crucial to the survival of endangered lemurs. Although genomic studies of cancer in non-human primates have been hampered by a lack of tools, recent studies have demonstrated the efficacy of using human exome capture reagents across primates.

Methodology: In this proof-of-principle study, we applied human exome capture reagents to tumor-normal pairs from five lemurs with hepatocellular carcinoma to characterize the mutational landscape of this disease in lemurs.

Results: Several genes implicated in human hepatocellular carcinoma, including , and , were mutated in multiple lemurs, and analysis of cancer driver genes mutated in these samples identified enrichment of genes involved with degradation and regulation. In addition to these similarities with human hepatocellular carcinoma, we also noted unique features, including six genes that contain mutations in all five lemurs. Interestingly, these genes are infrequently mutated in human hepatocellular carcinoma, suggesting potential differences in the etiology and/or progression of this cancer in lemurs and humans.

Conclusions And Implications: Collectively, this pilot study suggests that human exome capture reagents are a promising tool for genomic studies of cancer in lemurs and other non-human primates.

Lay Summary: Hepatocellular carcinoma occurs frequently in prosimians, but the cause of these liver cancers is unknown. In this proof-of-principle study, we applied human DNA sequencing tools to tumor-normal pairs from five lemurs with hepatocellular carcinoma and compared the lemur mutation profiles to those of human hepatocellular carcinomas.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1093/emph/eoac016DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC9086584PMC
April 2022

A Multidimensional Bioinformatic Platform for the Study of Human Response to Surgery.

Ann Surg 2022 Mar 3. Epub 2022 Mar 3.

Department of Surgery, Duke University; Durham, North Carolina, USA Department of Head and Neck Surgery & Communication Sciences, Duke University; Durham, North Carolina, USA Department of Obstetrics and Gynecology, Duke University; Durham, North Carolina, USA Department of Medicine, Duke University; Durham, North Carolina, USA Duke Molecular Physiology Institute, Duke University; Durham, North Carolina, USA Duke Center for Genomic and Computational Biology, Duke University; Durham, North Carolina, USA Department of Molecular Genetics and Microbiology, Duke University; Durham, North Carolina, USA Department of Electrical and Computer Engineering, Duke University; Durham, North Carolina, USA Department of Biostatistics and Bioinformatics, Duke University; Durham, North Carolina, USA.

Objective: To design and establish a prospective biospecimen repository that integrates multi-omics assays with clinical data to study mechanisms of controlled injury and healing.

Summary Background Data: Elective surgery is an opportunity to understand both the systemic and focal responses accompanying controlled and well-characterized injury to the human body. The overarching goal of this ongoing project is to define stereotypical responses to surgical injury, with the translational purpose of identifying targetable pathways involved in healing and resilience, and variations indicative of aberrant peri-operative outcomes.

Methods: Clinical data from the electronic medical record combined with large-scale biological data sets derived from blood, urine, fecal matter, and tissue samples are collected prospectively through the peri-operative period on patients undergoing fourteen surgeries chosen to represent a range of injury locations and intensities. Specimens are subjected to genomic, transcriptomic, proteomic, and metabolomic assays to describe their genetic, metabolic, immunologic, and microbiome profiles, providing a multidimensional landscape of the human response to injury.

Results: The highly multiplexed data generated includes changes in over 28,000 mRNA transcripts, 100 plasma metabolites, 200 urine metabolites, and 400 proteins over the longitudinal course of surgery and recovery. In our initial pilot dataset, we demonstrate the feasibility of collecting high quality multi-omic data at pre- and post-operative time points and are already seeing evidence of physiologic perturbation between timepoints.

Conclusions: This repository allows for longitudinal, state-of-the-art genomic, transcriptomic, proteomic, metabolomic, immunologic, and clinical data collection and provides a rich and stable infrastructure on which to fuel further biomedical discovery.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1097/SLA.0000000000005429DOI Listing
March 2022

An integrated comparative physiology and molecular approach pinpoints mediators of breath-hold capacity in dolphins.

Evol Med Public Health 2021 28;9(1):420-430. Epub 2021 Oct 28.

Department of Medicine, Duke University Medical Center, Durham, NC, USA.

Background And Objectives: Ischemic events, such as ischemic heart disease and stroke, are the number one cause of death globally. Ischemia prevents blood, carrying essential nutrients and oxygen, from reaching tissues, leading to cell and tissue death, and eventual organ failure. While humans are relatively intolerant to ischemic events, other species, such as marine mammals, have evolved a unique tolerance to chronic ischemia/reperfusion during apneic diving. To identify possible molecular features of an increased tolerance for apnea, we examined changes in gene expression in breath-holding dolphins.

Methodology: Here, we capitalized on the adaptations possesed by bottlenose dolphins () for diving as a comparative model of ischemic stress and hypoxia tolerance to identify molecular features associated with breath holding. Given that signals in the blood may influence physiological changes during diving, we used RNA-Seq and enzyme assays to examine time-dependent changes in gene expression in the blood of breath-holding dolphins.

Results: We observed time-dependent upregulation of the arachidonate 5-lipoxygenase (ALOX5) gene and increased lipoxygenase activity during breath holding. ALOX5 has been shown to be activated during hypoxia in rodent models, and its metabolites, leukotrienes, induce vasoconstriction.

Conclusions And Implications: The upregulation of ALOX5 mRNA occurred within the calculated aerobic dive limit of the species, suggesting that ALOX5 may play a role in the dolphin's physiological response to diving, particularly in a pro-inflammatory response to ischemia and in promoting vasoconstriction. These observations pinpoint a potential molecular mechanism by which dolphins, and perhaps other marine mammals, respond to the prolonged breath holds associated with diving.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1093/emph/eoab036DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8833867PMC
October 2021

Molecular Classification to Prognosticate Response in Medically Managed Endometrial Cancers and Endometrial Intraepithelial Neoplasia.

Cancers (Basel) 2021 Jun 7;13(11). Epub 2021 Jun 7.

Duke Cancer Institute, Duke University Medical Center, Durham, NC 27710, USA.

Background: The aim of this study was to evaluate whether molecular classification prognosticates treatment response in women with endometrial cancers and endometrial intraepithelial neoplasia (EIN) treated with levonorgestrel intrauterine system (LNG-IUS).

Methods: Patients treated with LNG-IUS for endometrial cancer or EIN from 2013 to 2018 were evaluated. Using immunohistochemistry and single gene sequencing of , patients were classified into four groups as per the Proactive Molecular Risk Classifier for Endometrial cancer (ProMisE): -mutated, mismatch repair-deficient (MMRd), p53 wild type (p53wt), and p53-abnormal (p53abn). Groups were assessed relative to the primary outcome of progression or receipt of definitive treatment.

Results: Fifty-eight subjects with endometrioid endometrial cancer or EIN treated with LNG-IUS were included. Of these, 22 subjects (37.9%) had endometrial cancer and 36 subjects (62.1%) had EIN. Per the ProMisE algorithm, 44 patients (75.9%) were classified as p53wt, 6 (10.3%) as MMRd, 4 (6.9%) as p53abn, and 4 (6.9%) as -mutated. Of the 58 patients, 11 (19.0%) progressed or opted for definitive therapy. Median time to progression or definitive therapy was 7.5 months, with p53abn tumors having the shortest time to progression or definitive therapy.

Conclusions: Molecular classification of endometrial cancer and EIN prior to management with LNG-IUS is feasible and may predict patients at risk of progression.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.3390/cancers13112847DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8201008PMC
June 2021

Physiological Fitness and the Pathophysiology of Chronic Lymphocytic Leukemia (CLL).

Cells 2021 05 11;10(5). Epub 2021 May 11.

Division of Medical Oncology, Duke University School of Medicine, Durham, NC 27710, USA.

Chronic lymphocytic leukemia (CLL) is associated with physical dysfunction and low overall fitness that predicts poor survival following the commencement of treatment. However, it remains unknown whether higher fitness provides antioncogenic effects. We identified ten fit (CLL-FIT) and ten less fit (CLL-UNFIT) treatment-naïve CLL patients from 144 patients who completed a set of physical fitness and performance tests. Patient plasma was used to determine its effects on an 5-day growth/viability of three B-cell cell lines (OSU-CLL, Daudi, and Farage). Plasma exosomal miRNA profiles, circulating lipids, lipoproteins, inflammation levels, and immune cell phenotypes were also assessed. CLL-FIT was associated with fewer viable OSU-CLL cells at Day 1 ( = 0.003), Day 4 ( = 0.001), and Day 5 ( = 0.009). No differences between the groups were observed for Daudi and Farage cells. Of 455 distinct exosomal miRNAs identified, 32 miRNAs were significantly different between the groups. Of these, 14 miRNAs had ≤-1 or ≥1 log2 fold differences. CLL-FIT patients had five exosomal miRNAs with lower expression and nine miRNAs with higher expression. CLL-FIT patients had higher HDL cholesterol, lower inflammation, and lower levels of triglyceride components (all < 0.05). CLL-FIT patients had lower frequencies of low-differentiated NKG2+/CD158a/b ( = 0.015 and = 0.014) and higher frequencies of NKG2A/CD158b+ mature NK cells ( = 0.047). The absolute number of lymphocytes, including CD19+/CD5+ CLL-cells, was similar between the groups ( = 0.359). Higher physical fitness in CLL patients is associated with altered CLL-like cell line growth and with altered circulating and cellular factors indicative of better immune functions and tumor control.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.3390/cells10051165DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8151485PMC
May 2021

Prurigo Nodularis Is Characterized by Systemic and Cutaneous T Helper 22 Immune Polarization.

J Invest Dermatol 2021 09 23;141(9):2208-2218.e14. Epub 2021 Mar 23.

Department of Dermatology, School of Medicine, Johns Hopkins University, Baltimore, Maryland, USA. Electronic address:

Prurigo nodularis (PN) is an understudied, chronic inflammatory skin disease that disproportionately affects African Americans and presents with intensely pruritic nodules of unknown etiology. To better characterize the immune dysregulation in PN, PBMCs and skin biopsies were obtained from patients with PN and healthy subjects (majority African American) matched by age, race, and sex. Flow cytometric analysis of functional T-cell response comparing patients with PN with healthy subjects identified increased γδT cells (CD3CD4CD8γδTCR) and Vδ2 γδT enrichment. Activated T cells demonstrated uniquely increased IL-22 cytokine expression in patients with PN compared with healthy controls. CD4+ and CD8+ T cells were identified as the source of increased circulating IL-22. Consistent with these findings, RNA sequencing of lesional PN skin compared with nonlesional PN skin and biopsy site‒matched control skin demonstrated robust upregulation of T helper (Th) 22‒related genes and signaling networks implicated in impaired epidermal differentiation. Th22‒related cytokine upregulation remained significant, with stratifications by race and biopsy site. Importantly, the expression of the IL-22 receptors IL22RA1 and IL22RA2 was significantly elevated in lesional PN skin. These results indicate that both systemic and cutaneous immune responses in patients with PN are skewed toward a Th22/IL-22 profile. PN may benefit from immunomodulatory therapies directed at Th22‒mediated inflammation.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.jid.2021.02.749DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8384659PMC
September 2021

From the Clinic to the Bench and Back Again in One Dog Year: How a Cross-Species Pipeline to Identify New Treatments for Sarcoma Illuminates the Path Forward in Precision Medicine.

Front Oncol 2020 11;10:117. Epub 2020 Feb 11.

Department of Orthopaedic Surgery, Duke University Medical Center, Durham, NC, United States.

Cancer drug discovery is an inefficient process, with more than 90% of newly-discovered therapies failing to gain regulatory approval. Patient-derived models of cancer offer a promising new approach to identify new treatments; however, for rare cancers, such as sarcomas, access to patient samples is limited, which precludes development of patient-derived models. To address the limited access to patient samples, we have turned to pet dogs with naturally-occurring sarcomas. Although sarcomas make up <1% of all human cancers, sarcomas represent 15% of cancers in dogs. Because dogs have similar immune systems, an accelerated pace of cancer progression, and a shared environment with humans, studying pet dogs with cancer is ideal for bridging gaps between mouse models and human cancers. Here, we present our cross-species personalized medicine pipeline to identify new therapies for sarcomas. We explore this process through the focused study of a pet dog, Teddy, who presented with six synchronous leiomyosarcomas. Using our pipeline we identified proteasome inhibitors as a potential therapy for Teddy. Teddy was treated with bortezomib and showed a varied response across tumors. Whole exome sequencing revealed substantial genetic heterogeneity across Teddy's recurrent tumors and metastases, suggesting that intra-patient heterogeneity and tumoral adaptation were responsible for the heterogeneous clinical response. Ubiquitin proteomics coupled with exome sequencing revealed multiple candidate driver mutations in proteins related to the proteasome pathway. Together, our results demonstrate how the comparative study of canine sarcomas offers important insights into the development of personalized medicine approaches that can lead to new treatments for sarcomas in both humans and canines.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.3389/fonc.2020.00117DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7026496PMC
February 2020

Resolution of the ordinal phylogeny of mosses using targeted exons from organellar and nuclear genomes.

Nat Commun 2019 04 2;10(1):1485. Epub 2019 Apr 2.

Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT, 06269, USA.

Mosses are a highly diverse lineage of land plants, whose diversification, spanning at least 400 million years, remains phylogenetically ambiguous due to the lack of fossils, massive early extinctions, late radiations, limited morphological variation, and conflicting signal among previously used markers. Here, we present phylogenetic reconstructions based on complete organellar exomes and a comparable set of nuclear genes for this major lineage of land plants. Our analysis of 142 species representing 29 of the 30 moss orders reveals that relative average rates of non-synonymous substitutions in nuclear versus plastid genes are much higher in mosses than in seed plants, consistent with the emerging concept of evolutionary dynamism in mosses. Our results highlight the evolutionary significance of taxa with reduced morphologies, shed light on the relative tempo and mechanisms underlying major cladogenic events, and suggest hypotheses for the relationships and delineation of moss orders.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1038/s41467-019-09454-wDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6445109PMC
April 2019

Range size heritability and diversification patterns in the liverwort genus Radula.

Mol Phylogenet Evol 2017 01 21;106:73-85. Epub 2016 Sep 21.

Department of Biology, Ecology and Evolution, Institute of Botany, University of Liège, Liège, Belgium; Azorean Biodiversity Group (GBA, CITA-A) and Platform for Enhancing Ecological Research & Sustainability (PEERS), Universidade dos Açores, Angra do Heroísmo, Terceira, Açores, Portugal.

Why some species exhibit larger geographical ranges than others, and to what extent does variation in range size affect diversification rates, remains a fundamental, but largely unanswered question in ecology and evolution. Here, we implement phylogenetic comparative analyses and ancestral area estimations in Radula, a liverwort genus of Cretaceous origin, to investigate the mechanisms that explain differences in geographical range size and diversification rates among lineages. Range size was phylogenetically constrained in the two sub-genera characterized by their almost complete Australasian and Neotropical endemicity, respectively. The congruence between the divergence time of these lineages and continental split suggests that plate tectonics could have played a major role in their present distribution, suggesting that a strong imprint of vicariance can still be found in extant distribution patterns in these highly mobile organisms. Amentuloradula, Volutoradula and Metaradula species did not appear to exhibit losses of dispersal capacities in terms of dispersal life-history traits, but evidence for significant phylogenetic signal in macroecological niche traits suggests that niche conservatism accounts for their restricted geographic ranges. Despite their greatly restricted distribution to Australasia and Neotropics respectively, Amentuloradula and Volutoradula did not exhibit significantly lower diversification rates than more widespread lineages, in contrast with the hypothesis that the probability of speciation increases with range size by promoting geographic isolation and increasing the rate at which novel habitats are encountered. We suggest that stochastic long-distance dispersal events may balance allele frequencies across large spatial scales, leading to low genetic structure among geographically distant areas or even continents, ultimately decreasing the diversification rates in highly mobile, widespread lineages.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.ympev.2016.09.020DOI Listing
January 2017

Organellar phylogenomics of an emerging model system: Sphagnum (peatmoss).

Ann Bot 2016 08 6;118(2):185-96. Epub 2016 Jun 6.

Department of Biology, Duke University, Durham, NC 27708, USA.

Background And Aims: Sphagnum-dominated peatlands contain approx. 30 % of the terrestrial carbon pool in the form of partially decomposed plant material (peat), and, as a consequence, Sphagnum is currently a focus of studies on biogeochemistry and control of global climate. Sphagnum species differ in ecologically important traits that scale up to impact ecosystem function, and sequencing of the genome from selected Sphagnum species is currently underway. As an emerging model system, these resources for Sphagnum will facilitate linking nucleotide variation to plant functional traits, and through those traits to ecosystem processes. A solid phylogenetic framework for Sphagnum is crucial to comparative analyses of species-specific traits, but relationships among major clades within Sphagnum have been recalcitrant to resolution because the genus underwent a rapid radiation. Herein a well-supported hypothesis for phylogenetic relationships among major clades within Sphagnum based on organellar genome sequences (plastid, mitochondrial) is provided.

Methods: We obtained nucleotide sequences (273 753 nucleotides in total) from the two organellar genomes from 38 species (including three outgroups). Phylogenetic analyses were conducted using a variety of methods applied to nucleotide and amino acid sequences. The Sphagnum phylogeny was rooted with sequences from the related Sphagnopsida genera, Eosphagnum and Flatbergium

Key Results: Phylogenetic analyses of the data converge on the following subgeneric relationships: (Rigida (((Subsecunda) (Cuspidata)) ((Sphagnum) (Acutifolia))). All relationships were strongly supported. Species in the two major clades (i.e. Subsecunda + Cuspidata and Sphagnum + Acutifolia), which include >90 % of all Sphagnum species, differ in ecological niches and these differences correlate with other functional traits that impact biogeochemical cycling. Mitochondrial intron presence/absence are variable among species and genera of the Sphagnopsida. Two new nomenclatural combinations are made, in the genera Eosphagnum and Flatbergium

Conclusions: Newly resolved relationships now permit phylogenetic analyses of morphological, biochemical and ecological traits among Sphagnum species. The results clarify long-standing disagreements about subgeneric relationships and intrageneric classification.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1093/aob/mcw086DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4970357PMC
August 2016

Analyses of transcriptome sequences reveal multiple ancient large-scale duplication events in the ancestor of Sphagnopsida (Bryophyta).

New Phytol 2016 07 22;211(1):300-18. Epub 2016 Feb 22.

Department of Biology, Duke University, Durham, NC, 27708, USA.

The goal of this research was to investigate whether there has been a whole-genome duplication (WGD) in the ancestry of Sphagnum (peatmoss) or the class Sphagnopsida, and to determine if the timing of any such duplication(s) and patterns of paralog retention could help explain the rapid radiation and current ecological dominance of peatmosses. RNA sequencing (RNA-seq) data were generated for nine taxa in Sphagnopsida (Bryophyta). Analyses of frequency plots for synonymous substitutions per synonymous site (Ks ) between paralogous gene pairs and reconciliation of 578 gene trees were conducted to assess evidence of large-scale or genome-wide duplication events in each transcriptome. Both Ks frequency plots and gene tree-based analyses indicate multiple duplication events in the history of the Sphagnopsida. The most recent WGD event predates divergence of Sphagnum from the two other genera of Sphagnopsida. Duplicate retention is highly variable across species, which might be best explained by local adaptation. Our analyses indicate that the last WGD could have been an important factor underlying the diversification of peatmosses and facilitated their rise to ecological dominance in peatlands. The timing of the duplication events and their significance in the evolutionary history of peat mosses are discussed.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1111/nph.13887DOI Listing
July 2016

Approximate Bayesian Computation Reveals the Crucial Role of Oceanic Islands for the Assembly of Continental Biodiversity.

Syst Biol 2015 Jul 20;64(4):579-89. Epub 2015 Feb 20.

Department of Biology, Ecology and Evolution, University of Liège, Bât. B22, Boulevard du Rectorat 27, 4000, Liège, Belgium; Department of Plant Biology, University of La Laguna, c/ Astrofísico Francisco Sánches, s/n, 28071, Tenerife, Spain; Azorean Biodiversity Group (GBA, CE3C - Center for Ecology, Evolution and Environmental Changes) and Platform for Enhancing Ecological Research & Sustainability (PEERS), Universidade dos Açores, Rua Capitão João d'Ávila, Pico da Urze, 9700-042 Angra do Heroísmo, Terceira, Açores, Portugal; Plants Division, Department of Life Sciences, The Natural History Museum, Cromwell Road, London, SW7 5BD, UK; Evolutionary Biology and Ecology, Université Libre de Bruxelles (ULB), CP 160/12, av FD Roosevelt 50, 1050, Brussels, Belgium; Department of Biology, Duke University, Box 90338, Durham, NC 27708, USA; and Department of Ecology and Evolution, University of Lausanne, Lausanne, CH-1015, Switzerland Department of Biology, Ecology and Evolution, University of Liège, Bât. B22, Boulevard du Rectorat 27, 4000, Liège, Belgium; Department of Plant Biology, University of La Laguna, c/ Astrofísico Francisco Sánches, s/n, 28071, Tenerife, Spain; Azorean Biodiversity Group (GBA, CE3C - Center for Ecology, Evolution and Environmental Changes) and Platform for Enhancing Ecological Research & Sustainability (PEERS), Universidade dos Açores, Rua Capitão João d'Ávila, Pico da Urze, 9700-042 Angra do Heroísmo, Terceira, Açores, Portugal; Plants Division, Department of Life Sciences, The Natural History Museum, Cromwell Road, London, SW7 5BD, UK; Evolutionary Biology and Ecology, Université Libre de Bruxelles (ULB), CP 160/12, av FD Roosevelt 50, 1050, Brussels, Belgium; Department of Biology, Duke University, Box 90338, Durham, NC 27708, USA; and Department of Ecology and Evolution, University of Lausanne, Lausanne, CH-1015, Switzerland.

The perceived low levels of genetic diversity, poor interspecific competitive and defensive ability, and loss of dispersal capacities of insular lineages have driven the view that oceanic islands are evolutionary dead ends. Focusing on the Atlantic bryophyte flora distributed across the archipelagos of the Azores, Madeira, the Canary Islands, Western Europe, and northwestern Africa, we used an integrative approach with species distribution modeling and population genetic analyses based on approximate Bayesian computation to determine whether this view applies to organisms with inherent high dispersal capacities. Genetic diversity was found to be higher in island than in continental populations, contributing to mounting evidence that, contrary to theoretical expectations, island populations are not necessarily genetically depauperate. Patterns of genetic variation among island and continental populations consistently fitted those simulated under a scenario of de novo foundation of continental populations from insular ancestors better than those expected if islands would represent a sink or a refugium of continental biodiversity. We, suggest that the northeastern Atlantic archipelagos have played a key role as a stepping stone for transoceanic migrants. Our results challenge the traditional notion that oceanic islands are the end of the colonization road and illustrate the significant role of oceanic islands as reservoirs of novel biodiversity for the assembly of continental floras.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1093/sysbio/syv013DOI Listing
July 2015

Efficient purging of deleterious mutations in plants with haploid selfing.

Genome Biol Evol 2014 May 14;6(5):1238-52. Epub 2014 May 14.

Institute of Evolutionary Biology and Environmental Studies, University of Zurich, SwitzerlandSwiss Institute of Bioinformatics, Quartier Sorge-Batiment Genopode, Lausanne, SwitzerlandBioinformatics Institute, Agency for Science, Technology and Research (A*STAR), SingaporeThe Santa Fe Institute, Santa Fe NM.

In diploid organisms, selfing reduces the efficiency of selection in removing deleterious mutations from a population. This need not be the case for all organisms. Some plants, for example, undergo an extreme form of selfing known as intragametophytic selfing, which immediately exposes all recessive deleterious mutations in a parental genome to selective purging. Here, we ask how effectively deleterious mutations are removed from such plants. Specifically, we study the extent to which deleterious mutations accumulate in a predominantly selfing and a predominantly outcrossing pair of moss species, using genome-wide transcriptome data. We find that the selfing species purge significantly more nonsynonymous mutations, as well as a greater proportion of radical amino acid changes which alter physicochemical properties of amino acids. Moreover, their purging of deleterious mutation is especially strong in conserved regions of protein-coding genes. Our observations show that selfing need not impede but can even accelerate the removal of deleterious mutations, and do so on a genome-wide scale.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1093/gbe/evu099DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4041004PMC
May 2014

Integrative taxonomy resolves the cryptic and pseudo-cryptic Radula buccinifera complex (Porellales, Jungermanniopsida), including two reinstated and five new species.

PhytoKeys 2013 30(27):1-113. Epub 2013 Oct 30.

Royal Botanic Gardens and Domain Trust, Mrs Macquaries Road, Sydney, NSW 2000, Australia.

Molecular data from three chloroplast markers resolve individuals attributable to Radula buccinifera in six lineages belonging to two subgenera, indicating the species is polyphyletic as currently circumscribed. All lineages are morphologically diagnosable, but one pair exhibits such morphological overlap that they can be considered cryptic. Molecular and morphological data justify the re-instatement of a broadly circumscribed ecologically variable R. strangulata, of R. mittenii, and the description of five new species. Two species Radula mittenii Steph. and R. notabilis sp. nov. are endemic to the Wet Tropics Bioregion of north-east Queensland, suggesting high diversity and high endemism might characterise the bryoflora of this relatively isolated wet-tropical region. Radula demissa sp. nov. is endemic to southern temperate Australasia, and like R. strangulata occurs on both sides of the Tasman Sea. Radula imposita sp. nov. is a twig and leaf epiphyte found in association with waterways in New South Wales and Queensland. Another species, R. pugioniformis sp. nov., has been confused with Radula buccinifera but was not included in the molecular phylogeny. Morphological data suggest it may belong to subg. Odontoradula. Radula buccinifera is endemic to Australia including Western Australia and Tasmania, and to date is known from south of the Clarence River on the north coast of New South Wales. Nested within R. buccinifera is a morphologically distinct plant from Norfolk Island described as R. anisotoma sp. nov. Radula australiana is resolved as monophyletic, sister to a species occurring in east coast Australian rainforests, and nesting among the R. buccinifera lineages with strong support. The molecular phylogeny suggests several long-distance dispersal events may have occurred. These include two east-west dispersal events from New Zealand to Tasmania and south-east Australia in R. strangulata, one east-west dispersal event from Tasmania to Western Australia in R. buccinifera, and at least one west-east dispersal from Australia to New Zealand in R. australiana. Another west-east dispersal event from Australia to Norfolk Island may have led to the budding speciation of R. anisotoma. In contrast, Radula demissa is phylogeographically subdivided into strongly supported clades either side of the Tasman Sea, suggesting long distance dispersal is infrequent in this species.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.3897/phytokeys.27.5523DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3821098PMC
November 2013

Origins, genetic structure, and systematics of the narrow endemic peatmosses (Sphagnum): S. guwassanense and S. triseriporum (Sphagnaceae).

Am J Bot 2013 Jun 29;100(6):1202-20. Epub 2013 May 29.

Department of Biology, Duke University, Durham, NC 27708, USA.

Unlabelled:

Premise Of The Study: Sphagnum dominates vast expanses of wetland habitats throughout the northern hemisphere and species delimitation within the genus is important because floristic changes associated with a warming global climate may have measureable impacts on large-scale ecological processes. Most northern hemisphere peatmoss species (Sphagnum) have circumboreal ranges, but the Japanese species generally known as S. calymmatophyllum is endemic to Honshu Island. This prompted a population genetic and phylogenetic analysis to resolve the origin(s), population structure, and phylogenetic relationships of this morphologically variable species. •

Methods: Sixty plants collected from Mt. Gassan and Mt. Hakkoda were genotyped for 12 microsatellite loci. Two plastid loci and three anonymous nuclear loci were sequenced in a subset of the plants, plus representatives from 10 closely related species. •

Key Results: Gametophytes exhibited fixed or nearly fixed heterozygosity at 9-10 of the 12 microsatellite loci. Two genetic groups were resolved by the microsatellite data, individuals showed no evidence of admixture, and the two groups of plants differ in morphology. They are heterozygous for different sets of alleles. The two taxa share plastid DNA sequences with two species that are common in Alaska. •

Conclusions: Two taxa were distinguished: S. guwassanense and S. triseriporum. Both are allopolyploids; they originated independently from different but closely related progenitors. The maternal progenitor was likely either S. orientale or S. inexspectatum. The two allopolyploid taxa are heterozygous for (different) private microsatellite alleles, and one progenitor could be extinct.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.3732/ajb.1200630DOI Listing
June 2013

Evolution of sexual systems, dispersal strategies and habitat selection in the liverwort genus Radula.

New Phytol 2011 Oct 7;192(1):225-236. Epub 2011 Jun 7.

Institut de Botanique, Université de Liege, B-22 Sart Tilman, B-4000 Liege, Belgium.

• Shifts in sexual systems are among the most common and important transitions in plants and are correlated with a suite of life-history traits. The evolution of sexual systems and their relationships to gametophyte size, sexual and asexual reproduction, and epiphytism are examined here in the liverwort genus Radula. • The sequence of trait acquisition and the phylogenetic correlations between those traits was investigated using comparative methods. • Shifts in sexual systems recurrently occurred from dioecy to monoecy within facultative epiphyte lineages. Production of specialized asexual gemmae was correlated to neither dioecy nor strict epiphytism. • The significant correlations among life-history traits related to sexual systems and habitat conditions suggest the existence of evolutionary trade-offs. Obligate epiphytes do not produce gemmae more frequently than facultative epiphytes and disperse by whole gametophyte fragments, presumably to avoid the sensitive protonemal stage in a habitat prone to rapid changes in moisture availability. As dispersal ranges correlate with diaspore size, this reinforces the notion that epiphytes experience strong dispersal limitations. Our results thus provide the evolutionary complement to metapopulation, metacommunity and experimental studies demonstrating trade-offs between dispersal distance, establishment ability, and life-history strategy, which may be central to the evolution of reproductive strategies in bryophytes.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1111/j.1469-8137.2011.03783.xDOI Listing
October 2011

Newly resolved relationships in an early land plant lineage: Bryophyta class Sphagnopsida (peat mosses).

Am J Bot 2010 Sep 6;97(9):1511-31. Epub 2010 Aug 6.

Duke University, Department of Biology, Durham, North Carolina 27708 USA.

Unlabelled:

Premise Of The Study: The Sphagnopsida, an early-diverging lineage of mosses (phylum Bryophyta), are morphologically and ecologically unique and have profound impacts on global climate. The Sphagnopsida are currently classified in two genera, Sphagnum (peat mosses) with some 350-500 species and Ambuchanania with one species. An analysis of phylogenetic relationships among species and genera in the Sphagnopsida were conducted to resolve major lineages and relationships among species within the Sphagnopsida. •

Methods: Phylogenetic analyses of nucleotide sequences from the nuclear, plastid, and mitochondrial genomes (11 704 nucleotides total) were conducted and analyzed using maximum likelihood and Bayesian inference employing seven different substitution models of varying complexity. •

Key Results: Phylogenetic analyses resolved three lineages within the Sphagnopsida: (1) Sphagnum sericeum, (2) S. inretortum plus Ambuchanania leucobryoides, and (3) all remaining species of Sphagnum. Sister group relationships among these three clades could not be resolved, but the phylogenetic results indicate that the highly divergent morphology of A. leucobryoides is derived within the Sphagnopsida rather than plesiomorphic. A new classification is proposed for class Sphagnopsida, with one order (Sphagnales), three families, and four genera. •

Conclusions: The Sphagnopsida are an old lineage within the phylum Bryophyta, but the extant species of Sphagnum represent a relatively recent radiation. It is likely that additional species critical to understanding the evolution of peat mosses await discovery, especially in the southern hemisphere.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.3732/ajb.1000055DOI Listing
September 2010

Peatmoss (Sphagnum) diversification associated with Miocene Northern Hemisphere climatic cooling?

Mol Phylogenet Evol 2010 Jun 25;55(3):1139-45. Epub 2010 Jan 25.

Department of Biology, Duke University, Durham, NC 27708, USA.

Global climate changes sometimes spark biological radiations that can feed back to effect significant ecological impacts. Northern Hemisphere peatlands dominated by living and dead peatmosses (Sphagnum) harbor almost 30% of the global soil carbon pool and have functioned as a net carbon sink throughout the Holocene, and probably since the late Tertiary. Before that time, northern latitudes were dominated by tropical and temperate plant groups and ecosystems. Phylogenetic analyses of mosses (phylum Bryophyta) based on nucleotide sequences from the plastid, mitochondrial, and nuclear genomes indicate that most species of Sphagnum are of recent origin (ca. <20 Ma). Sphagnum species are not only well-adapted to boreal peatlands, they create the conditions that promote development of peatlands. The recent radiation that gave rise to extant diversity of peatmosses is temporally associated with Miocene climatic cooling in the Northern Hemisphere. The evolution of Sphagnum has had profound influences on global biogeochemistry because of the unique biochemical, physiological, and morphological features of these plants, both while alive and after death.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.ympev.2010.01.020DOI Listing
June 2010

The ghosts of Gondwana and Laurasia in modern liverwort distributions.

Biol Rev Camb Philos Soc 2010 Aug 15;85(3):471-87. Epub 2010 Dec 15.

Institute of Botany, University of Liège, B22 Sart Tilman, 4000 Liège, Belgium.

Recent advances in phylogenetics and, in particular, molecular dating, indicate that transoceanic dispersal has played an important role in shaping plant and animal distributions, obscuring any effect of tectonic history. Taxonomic sampling in biogeographic studies is, however, systematically biased towards vertebrates and higher plants and the possibility remains that a much stronger signature of ancient vicariance might be evident among other organisms, particularly among basal land plants. Here, an explicit Bayesian model-based approach was used to investigate global-scale biogeographic patterns among liverwort genera and to determine whether the patterns identified are consistent with the expectations of vicariance or dispersal scenarios. The distribution of each genus was mapped onto the phylograms describing the floristic affinities among areas in order to define the synapomorphic transitions supporting the observed groupings. The probabilities of change in a branch were calculated by implementing the Markov model of BayesTraits. The consistent ambiguity in ancestral state reconstructions returned by the unconstrained, two-rate model indicated that the overall signal in the data was weak, leading us to test the performance of competing, explicit models. The analyses resolved clades of geographic areas that are mostly consistent with the kingdoms traditionally identified for plants and animals, but with strikingly lower rates of endemism. The major split observed in the phylograms is into almost entirely Laurasian and Gondwanan clades. Other patterns recovered by the analyses, including Wallace's line and the South Atlantic Disjunction, have also traditionally been interpreted in terms of vicariance. These observations contrast with the idea that, in spore-dispersed organisms like bryophytes and pteridophytes, dispersal obscures evidence of vicariance. However, some discrepancies between the liverwort trees and expectations from a continental drift scenario were observed, such as the sister-group relationship of the Australian and New Zealand floras, which is supported by the co-occurrence of many genera, often endemic to these two areas. Together with an interpretation of the results within a phylogenetic context, our analyses suggest that patterns, which are at first sight consistent with an ancient vicariance hypothesis, may, in fact, conceal a complex mixture of relictual distributions and more recent, asymmetrical dispersal events. Our results provide a framework for testing specific evolutionary hypotheses concerning the extremely low levels of endemism in bryophytes and in particular, the significance of dispersal and cryptic diversification.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1111/j.1469-185X.2009.00111.xDOI Listing
August 2010

And if Engler was not completely wrong? Evidence for multiple evolutionary origins in the moss flora of Macaronesia.

Evolution 2009 Dec 28;63(12):3248-57. Epub 2009 Jul 28.

Institute of Botany, University of Liège, 27 Blvd du Rectorat, B22, Sart Tilman, 4000 Liège, Belgium.

The Macaronesian endemic flora has traditionally been interpreted as a relict of a subtropical element that spanned across Europe in the Tertiary. This hypothesis is revisited in the moss subfamily Helicodontioideae based on molecular divergence estimates derived from two independent calibration techniques either employing fossil evidence or using an Monte Carlo Markov Chain (MCMC) to sample absolute rates of nucleotide substitution from a prior distribution encompassing a wide range of rates documented across land plants. Both analyses suggest that the monotypic Madeiran endemic genus Hedenasiastrum diverged of other Helicodontioideae about 40 million years, that is, well before Macaronesian archipelagos actually emerged, in agreement with the relict hypothesis. Hedenasiastrum is characterized by a plesiomorphic morphology, which is suggestive of a complete morphological stasis over 40 million years. Macaronesian endemic Rhynchostegiella species, whose polyphyletic origin involves multiple colonization events, evolved much more recently, and yet accumulated many more morphological novelties than H. percurrens. The Macaronesian moss flora thus appears as a complex mix of ancient relicts and more recently dispersed, fast-evolving taxa.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1111/j.1558-5646.2009.00787.xDOI Listing
December 2009

Range disjunctions, speciation, and morphological transformation rates in the liverwort genus Leptoscyphus.

Evolution 2009 Mar 19;63(3):779-92. Epub 2008 Dec 19.

Institute of Botany, University of Liège, B22 Sart Tilman, B-4000 Liège, Belgium.

Bryophytes and angiosperms exhibit similar intercontinental disjunct distributions that have traditionally been explained by continental drift. Such disjunct distributions are, however, typically observed at the species level in bryophytes, whereas they occur at much higher taxonomic level in angiosperms. The corollary of this observation is that morphological evolution in bryophytes is exceedingly slow. These hypotheses can now be explicitly tested with the advent of molecular dating. In this article, we show that the trans-Atlantic disjunctions observed in the mostly tropical liverwort genus Leptoscyphus date back to 5.5 Myr, thus largely postdating the opening of the South Atlantic. The temporal calibration of the phylogeny allows us to estimate for the first time the absolute timing of morphological evolution in bryophytes. The time frame necessary for shifts to occur between character states was estimated on average at ca. 4.05+/-1.86 Myr. As opposed to the traditional view that bryophyte evolution has been triggered by episodic shifts in habitat conditions, our analyses furthermore suggest that morphological and molecular divergence gradually accumulated in the genus, which contrasts with the rapid diversification documented in some tropical trees.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1111/j.1558-5646.2008.00567.xDOI Listing
March 2009

Origin and evolution of the northern hemisphere disjunction in the moss genus Homalothecium (Brachytheciaceae).

Am J Bot 2008 Jun;95(6):720-30

Swedish Museum of Natural History, Department of Cryptogamic Botany, Box 50007 SE-104 05 Stockholm, Sweden.

Competing hypotheses that rely either on a stepping-stone dispersal via the North Atlantic or the Bering land bridges, or more recent transoceanic dispersal, have been proposed to explain the disjunct distribution of Mediterranean flora in southern Europe and western North America. These hypotheses were tested with molecular dating using a phylogeny of the moss genus Homalothecium based on ITS, atpB-rbcL, and rpl16 sequence data. The monophyly of two main lineages in Western Palearctic (Europe, central Asia and north Africa) and North America is consistent with the ancient vicariance hypothesis. The monophyly of Madeiran H. sericeum accessions supports the recognition of the Macaronesian endemic H. mandonii. A range of absolute rates of molecular evolution documented in land plants was used as probabilistic calibration prior by a Bayesian inference implementing a relaxed-clock model to derive ages for the nodes of interest. Our age estimates for the divergence of the American and Western Palearctic Homalothecium clade (5.7 Ma, IC 3.52-8.26) and the origin of H. mandonii (2.52 Myr IC 0.86-8.25) are not compatible with the ancient vicariance hypothesis. Age estimates suggests that species distributions result from rare instances of dispersal and subsequent sympatric diversification. The calibrated phylogeny indicates that Homalothecium has undergone a fast radiation during the last 4 Myr, which is consistent with the low levels of morphological divergence among sibling species.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.3732/ajb.2007407DOI Listing
June 2008

The evolution of Dactylorhiza (Orchidaceae) allotetraploid complex: insights from nrDNA sequences and cpDNA PCR-RFLP data.

Mol Phylogenet Evol 2006 Mar 24;38(3):767-78. Epub 2006 Jan 24.

Biodiversity Research Center, Unité d'écologie et de Biogéographie, Université catholique de Louvain, Croix du Sud 4-5, B-1348 Louvain-la-Neuve, Belgium.

Sequence data from a portion of the external transcribed spacer (ETS) and from the internal transcribed spacers (ITS1 and ITS2) of 18S-26S nuclear ribosomal DNA were used together with chloroplast DNA PCR-RFLP data to unravel patterns of allotetraploid speciation within the Western European Dactylorhiza polyploid complex. A maximum likelihood tree based on combined ETS and ITS sequences suggests that the Western European Dactylorhiza allotetraploids have evolved by hybridization between four main diploid lineages. Cloned sequences and the topology of the ITS plus ETS tree indicate that the allotetraploid species D. elata, D. brennensis, and D. sphagnicola have originated from the autotetraploid D. maculata together with the diploid D. incarnata, while D. majalis, D. traunsteineri, and D. angustata seem to have evolved by hybridization between the D. fuchsii s.str and D. incarnata lineages. Finally, the diploid D. saccifera lineage seems to have been involved together with the D. incarnata lineage in the formation of the allotetraploid D. praetermissa. The observed congruence between the chloroplast tree and the ITS/ETS tree suggests a directional evolution of the nrDNA after polyploidization in favor of the maternal genome. Considered together with morphological, biogeographical, and ecological evidence, the molecular analysis leads us to recognize four species within the investigated allotetraploid complex, namely D. majalis, D. praetermissa, D. elata, and D. sphagnicola.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.ympev.2005.11.013DOI Listing
March 2006

Nuclear ribosomal DNA sequence variation and evolution of spotted marsh-orchids (Dactylorhiza maculata group).

Mol Phylogenet Evol 2005 Sep;36(3):568-80

Biodiversity Research Center, Unité d'écologie et de Biogéographie, Université catholique de Louvain, Croix du Sud 4-5, B-1348 Louvain-la-Neuve, Belgium.

Sequences of both internal and external transcribed spacers of nuclear ribosomal DNA were sequenced for four species belonging to the Dactylorhiza maculata group or "spotted marsh-Orchids". These four species are D. fuchsii, D. saccifera, D. foliosa, and D. maculata. Extensive nuclear ribosomal DNA polymorphism was uncovered within the diploid D. fuchsii and the putative autotetraploid D. maculata. Within the phylogenetic trees reconstructed using parsimony and Bayesian analyses, four main lineages (A, B, C, and D) were well supported. While D. saccifera, D. maculata, and D. foliosa were confined to clades B, C, and D, respectively, D. fuchsii accessions were spread over three clades (A, B, and C). Lineage C, which included accessions of the diploid D. fuchsii and the tetraploid D. maculata, was closely related to the lineage of D. foliosa (lineage D), an endemic diploid species from Madeira. Moreover, intra-individual polymorphism was found within accessions of D. maculata, D. fuchsii, and D. saccifera. It is shown that in some instances two lineages, contributed to the observed intra-individual polymorphism (C and A in D. maculata, A and B in D. fuchsii and D. saccifera). Evolutionary scenarios leading to this extensive nuclear ribosomal DNA polymorphism are discussed in the light of results from maternally inherited chloroplast DNA markers and an autopolyploid origin of D. maculata from a D. foliosa-like ancestor is postulated.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.ympev.2005.04.014DOI Listing
September 2005
-->