Patterns of DNA Sequence Variation in Plastid Genomes of Species Pairs between Eastern Asia and Eastern North America: An Example From Tulip Trees (Liriodendron)

There exist some species pairs between major continents such as alligators and tulip trees between eastern Asia and eastern North America, and the intercontinental sister species were derived from a common ancestor and separately evolved generating morphological differences and genetic disparities. However, it is unclear about patterns of the disparity between the species at the genome level; for example, are the differences present mostly in introns, intergenic spacers, or protein coding genes? Are there positive or negative selections on certain genes between the two sister species living in different habitats? In this study we obtained plastid genome sequences from multiple individuals of the two tulip trees: Liriodendron tulipifera in eastern North America and L. chinense in China, and examined differences between the two species in various protein coding genes, introns, intergenic spacers, and ribosomal DNAs. Information from the comparative genomic analysis between the species pairs may shed light on the association of changes at gene level with adaptations to their environment

Population Genetic Structures of Two Sister Tulip Tree Species: Implications for the Diversity Anomaly Between Eastern Asia and North America

It has become increasingly evident that biodiversity in the world has been decreasing. In order to face this problem head on we need to understand the underlying mechanisms for the formation of the patterns of biodiversity. A well-known pattern of biodiversity comes from the intercontinental disjunction of plant genera between eastern Asia and North America with unequal species richness. One hypothesis explaining the greater species diversity in eastern Asia than in North America states that faster speciation occurred on the eastern Asian side of the intercontinental disjunction than on the North American side. If this is true, we expect a greater genetic diversity across populations of eastern Asian species than the sister species in North America. In this study, we used tulip tree Liriodendron as our model system to test the hypothesis. Thirty individuals representing nine populations of the North American species (L. tulipifera) and 17 trees from three populations of the eastern Asia species (L. chinense) were included in the study. Sequences of the plastid rpl32-trnL intergenic spacer were obtained from all trees. Phylogenetic analyses using Magnolia species as the outgroup supported the sister relationship of the two species. Both the average number of differences between populations and the number of haplotypes per population were higher in the eastern Asian species than in the North American counterpart. Nonetheless, the short sequences of the rpl32-trnL region (ca. 1400 bp) provided limited information of genetic variation. Therefore, we obtained the entire plastid genome from one tree of the populations sampled, which resulted in over 97,000 bp. This study represents the first comparative genetic analyses of sister species between eastern Asia and North America to gain insights into the formation of the patterns of the species diversity between the two continents

Cross‐Shore Flow and Implications for Carbon Export in the California Current Ecosystem: A Lagrangian Analysis

International audienceEastern Boundary Current Upwelling Systems are regions of elevated primary production and carbon export and thus play a central role in the global carbon cycle. In these regions, nutrient upwelling occurs in a narrow region close to the coast, but primary production and carbon export are typically observed across a broader region. The fact that productive waters reach the open ocean has important consequences for the biological carbon pump, because such transport connects nutrient sources close to the coast to the deep carbon sinks of the offshore ocean. However, many aspects of this offshore transport are still not known. Here we address seasonal and interannual variability of upwelling‐related cross‐shore flows in the California current ecosystem (CCE) by employing Lagrangian diagnostics of horizontal transport inferred from satellite data. We define an advective age as the time a water parcel flowed offshore of the 500 m isobath. We find that the offshore extension of high Chl‐a waters covaries with the age of a coastal water parcel, and is consistent with mesoscale circulation. Interannual variability in the offshore extent of older waters is primarily driven by mesoscale variability and covaries with large scale forcing by both ENSO and the NPGO. The measured ratio of in‐situ new production: carbon export also covaries with water age, and tends to be ≫ 1 in younger and more balanced in older waters. Our results may help to parameterize the role of the finescale on the export of carbon in upwelling regions for climate resolving models

Investigating Particle Size-Flux Relationships and the Biological Pump Across a Range of Plankton Ecosystem States From Coastal to Oligotrophic

International audienceInvestigating Particle Size-Flux Relationships that the particle size-flux relationships may be different within the euphotic zone than in the shallow twilight zone and hypothesize that the changing nature of sinking particles with depth must be considered when investigating the remineralization length scale of sinking particles in the ocean

Lack of host phylogenetic structure in the gut bacterial communities of New Zealand cicadas and their interspecific hybrids

Abstract Host-microbe interactions are intimately linked to eukaryotic evolution, particularly in sap-sucking insects that often rely on obligate microbial symbionts for nutrient provisioning. Cicadas (Cicadidae: Auchenorrhyncha) specialize on xylem fluid and derive many essential amino acids and vitamins from intracellular bacteria or fungi (Hodgkinia, Sulcia, and Ophiocordyceps) that are propagated via transmission from mothers to offspring. Despite the beneficial role of these non-gut symbionts in nutrient provisioning, the role of beneficial microbiota within the gut remains unclear. Here, we investigate the relative abundance and impact of host phylogeny and ecology on gut microbial diversity in cicadas using 16S ribosomal RNA gene amplicon sequencing data from 197 wild-collected cicadas and new mitochondrial genomes across 38 New Zealand cicada species, including natural hybrids between one pair of two species. We find low abundance and a lack of phylogenetic structure and hybrid effects but a significant role of elevation in explaining variation in gut microbiota

The Importance of Mesozooplankton Diel Vertical Migration for Sustaining a Mesopelagic Food Web

We used extensive ecological and biogeochemical measurements obtained from quasi-Lagrangian experiments during two California Current Ecosystem Long-Term Ecosystem Research cruises to analyze carbon fluxes between the epipelagic and mesopelagic zones using a linear inverse ecosystem model (LIEM). Measurement constraints on the model include 14C primary productivity, dilution-based microzooplankton grazing rates, gut pigment-based mesozooplankton grazing rates (on multiple zooplankton size classes), 234Th:238U disequilibrium and sediment trap measured carbon export, and metabolic requirements of micronekton, zooplankton, and bacteria. A likelihood approach (Markov Chain Monte Carlo) was used to estimate the resulting flow uncertainties from a sample of potential flux networks. Results highlight the importance of mesozooplankton active transport (i.e., diel vertical migration) in supplying the carbon demand of mesopelagic organisms and sequestering carbon dioxide from the atmosphere. In nine water parcels ranging from a coastal bloom to offshore oligotrophic conditions, mesozooplankton active transport accounted for 18–84% (median: 42%) of the total carbon transfer to the mesopelagic, with gravitational settling of POC (12–55%; median: 37%), and subduction (2–32%; median: 14%) providing the majority of the remainder. Vertically migrating zooplankton contributed to downward carbon flux through respiration and excretion at depth and via mortality losses to predatory zooplankton and mesopelagic fish (e.g., myctophids and gonostomatids). Sensitivity analyses showed that the results of the LIEM were robust to changes in nekton metabolic demand, rates of bacterial production, and mesozooplankton gross growth efficiency. This analysis suggests that prior estimates of zooplankton active transport based on conservative estimates of standard (rather than active) metabolism are likely too low

Carbon sequestration by multiple biological pump pathways in a coastal upwelling biome

Multiple processes transport carbon into the deep ocean as part of the biological carbon pump, leading to long-term carbon sequestration. However, our ability to predict future changes in these processes is hampered by the absence of studies that have simultaneously quantified all carbon pump pathways. Here, we quantify carbon export and sequestration in the California Current Ecosystem resulting from (1) sinking particles, (2) active transport by diel vertical migration, and (3) the physical pump (subduction + vertical mixing of particles). We find that sinking particles are the most important and export 9.0 mmol C m-2 d-1 across 100-m depth while sequestering 3.9 Pg C. The physical pump exports more carbon from the shallow ocean than active transport (3.8 vs. 2.9 mmol C m-2 d-1), although active transport sequesters more carbon (1.0 vs. 0.8 Pg C) because of deeper remineralization depths. We discuss the implications of these results for understanding biological carbon pump responses to climate change

Data from: Maple phylogeny and biogeography inferred from phylogenomic data

Acer (the maple genus) is one of the diverse tree genera in the Northern Hemisphere with about152 species, most of which are in eastern Asia. There are roughly a dozen of species in Europe/western Asia and a dozen in North America. Several phylogenetic studies of Acer have been conducted since 1998, but none have provided a satisfactory resolution for basal relationships among sections of Acer. Here we report the first well-resolved phylogeny of Acer based on DNA sequences of over 500 nuclear loci generated using the anchored hybrid enrichment method and explore the implications of the robust phylogeny for Acer systematics and biogeography. Our phylogenetic results support the most recent taxonomic treatment of Acer by de Jong with some modifications; section Pentaphylla may be expanded to include section Trifoliata, and A. yangbiense may be included in section Lithocarpa. Sections Spicata, Negundo, Arguta, and Palmata form a clade sister to the rest of the genus where sections Glabra and Parviflora comprise the first clade followed by section Macrantha, sections Ginnala, Lithocarpa, Indivisa, sections Platanoidea and Macrophylla, section Rubra, section Acer, and section Pentaphylla. Monotypic sections Glabra and Macrophylla in North America are sister to the Japanese section Parviflora and Eurasian section Platanoidea, respectively. Ancestral area inferences using S-DIVA (statistical dispersal and vicariance analysis) and DEC (dispersal and extinction cladogenesis) methods suggest that Asia might be the most likely ancestral area of Acer as proposed by Wolfe and Tanai and molecular dating using BEAST (Bayesian evolutionary analysis by sampling trees) indicate that section diversifications of Acer might have completed largely in the late Eocene and the intercontinental disjunctions of Acer between eastern Asia and eastern North America formed mostly in the Miocene