Phylogeny, biogeography and ecological diversification of New Caledonian palms (Arecaceae)

BACKGROUND AND AIMS

The geographic origin and evolutionary mechanisms underpinning the rich and distinctive New Caledonian flora remain poorly understood. This is due to the complex geological past of the island and to the scarcity of well-resolved species-level phylogenies. Here, we infer phylogenetic relationships and divergence times of New Caledonian palms, which comprise 40 species. We use this framework to elucidate the biogeography of New Caledonian palm lineages, and to explore how extant species may have formed.

METHODS

A phylogenetic tree including 37 New Caledonian palm species and 77 relatives from tribe Areceae was inferred from 151 nuclear genes obtained by targeted sequencing. Fossil-calibrated divergence times were estimated, and ancestral ranges were inferred. Ancestral and extant ecological preferences in terms of elevation, precipitation and substrate were compared between New Caledonian sister species to explore their possible roles as drivers of speciation.

KEY RESULTS

New Caledonian palms form four well-supported clades, inside which relationships are well resolved. Our results support the current classification, but suggest that Veillonia and Campecarpus should be resurrected, and fail to clarify whether Rhopalostylidinae is sister to or nested in Basseliniinae. New Caledonian palm lineages derive from New Guinean and Australian ancestors, which reached the island through at least three independent dispersal events between the Eocene and Miocene. Palms then dispersed out of New Caledonia at least five times, mainly towards Pacific islands. Geographic and ecological transitions associated with speciation events differed across time and genera. Substrate transitions were more frequently associated with older than younger events.

CONCLUSIONS

Neighbouring areas and a mosaic of local habitats shaped New Caledonia's palm flora, and the island played a significant role in generating palm diversity across the Pacific region. This new spatio-temporal framework will enable population-level ecological and genetic studies to further unpick the mechanisms underpinning New Caledonian palm endemism.

Influence of subsoil and soil volume on the accumulation of nickel by Odontarrhena corsica grown on a serpentine soil

Odontarrhena corsica was grown for three months on Chrome loam topsoil and subsoil from near Reisterstown, MD, to examine the effects of varying soil masses (2.8 and 5.6 kg pot-1) and soil layers (topsoil vs. subsoil) on plant growth and Ni accumulation. The subsoil position effect was simulated by placing a pot of topsoil on top of a pot filled with subsoil. Shoot Ni concentrations were similar for all treatments at 7 g Ni kg-1. Shoot yield was significantly higher in the 5.6 kg treatments compared to the 2.8 kg treatments (>18 g pot-1 vs. ∼12 g pot-1) and also greater in the topsoil treatment compared to the subsoil treatment (24.0 g pot-1 vs. 18.6 g pot-1), resulting in significantly higher phytomining. Soil depth had no statistically significant effect on shoot and root yield. Subsoil fertilization increased yield (25.8 g pot-1 vs. 19.7 g pot-1), enough to suggest that further research is warranted to optimize Ni phytomining. This study confirms the importance of soil volume and root access to the subsoil when evaluating the potential for Ni phytomining by Odontarrhena species. The use of small pots may lead to an underestimation of phytomining potential.

Capture of mammal excreta by Nepenthes is an effective heterotrophic nutrition strategy

BACKGROUND AND AIMS

While isotopic enrichment of nitrogen (15N) and carbon (13C) is often used to determine whether carnivorous plant species capture and assimilate nutrients from supplemental sources such as invertebrate prey or mammal excreta (heterotrophic nutrition), little is known about how successful the different strategies deployed by carnivorous plants are at obtaining supplemental nutrition. The collection of mammalian faeces by Nepenthes (tropical pitcher plants) is the result of a highly specialized biological mutualism that results in heterotrophic nitrogen gain; however, it remains unknown how effective this strategy is in comparison to Nepenthes species not known to collect mammalian faeces.

METHODS

We examined how isotopic enrichment varied in the diverse genus Nepenthes, among species producing pitchers for invertebrate capture and species exhibiting mutualisms for the collection of mammal excreta. Enrichment factors were calculated from δ15N and δ13C values from eight Nepenthes species and naturally occurring hybrids along with co-occurring reference (non-carnivorous) plants from three mountain massifs in Borneo: Mount Kinabalu, Mount Tambuyukon and Mount Trus Madi.

RESULTS

All Nepenthes examined, except N. edwardsiana, were significantly enriched in 15N compared to co-occurring non-carnivorous plants, and 15N enrichment was more than two-fold higher in species with adaptations for the collection of mammal excreta compared with other Nepenthes.

CONCLUSIONS

The collection of mammal faeces clearly represents a highly effective strategy for heterotrophic nitrogen gain in Nepenthes. Species with adaptations for capturing mammal excreta occur exclusively at high elevation (i.e. are typically summit-occurring) where previous studies suggest invertebrate prey are less abundant and less frequently captured. As such, we propose this strategy may maximize nutritional return by specializing towards ensuring the collection and retention of few but higher-value N sources in environments where invertebrate prey may be scarce.

Broomrape Species Parasitizing Odontarrhena lesbiaca (Brassicaceae) Individuals Act as Nickel Hyperaccumulators

The elemental defense hypothesis supports that metal hyperaccumulation in plant tissues serves as a mechanism underpinning plant resistance to herbivores and pathogens. In this study, we investigate the interaction between Odontarrhena lesbiaca and broomrape parasitic species, in the light of the defense hypothesis of metal hyperaccumulation. Plant and soil samples collected from three serpentine sites in Lesbos, Greece were analyzed for Ni concentrations. Phelipanche nowackiana and Phelipanche nana were found to infect O. lesbiaca. In both species, Ni concentration decreased gradually from tubercles to shoots and flowers. Specimens of both species with shoot nickel concentrations above 1000 mg.kg^-1 were found, showing that they act as nickel hyperaccumulators. Low values of parasite to O. lesbiaca leaf or soil nickel quotients were observed. Orobanche pubescens growing on a serpentine habitat but not in association with O. lesbiaca had very low Ni concentrations in its tissues analogous to excluder plants growing on serpentine soils. Infected O. lesbiaca individuals showed lower leaf nickel concentrations relative to the non-infected ones. Elevated leaf nickel concentration of O. lesbiaca individuals did not prevent parasitic plants to attack them and to hyperaccumulate metals to their tissues, contrary to predictions of the elemental defense hypothesis.

Intraspecific Variation in Nickel Tolerance and Hyperaccumulation among Serpentine and Limestone Populations of Odontarrhena serpyllifolia (Brassicaceae: Alysseae) from the Iberian Peninsula

Odontarrhena serpyllifolia (Desf.) Jord. & Fourr. (=Alyssum serpyllifolium Desf.) occurs in the Iberian Peninsula and adjacent areas on a variety of soils including both limestone and serpentine (ultramafic) substrates. Populations endemic to serpentine are known to hyperaccumulate nickel, and on account of this remarkable phenotype have, at times, been proposed for recognition as taxonomically distinct subspecies or even species. It remains unclear, however, to what extent variation in nickel hyperaccumulation within this taxon merely reflects differences in the substrate, or whether the different populations show local adaptation to their particular habitats. To help clarify the physiological basis of variation in nickel hyperaccumulation among these populations, 3 serpentine accessions and 3 limestone accessions were cultivated hydroponically under common-garden conditions incorporating a range of Ni concentrations, along with 2 closely related non-accumulator species, Clypeola jonthlaspi L. and Alyssum montanum L. As a group, serpentine accessions of O. serpyllifolia were able to tolerate Ni concentrations approximately 10-fold higher than limestone accessions, but a continuous spectrum of Ni tolerance was observed among populations, with the least tolerant serpentine accession not being significantly different from the most tolerant limestone accession. Serpentine accessions maintained relatively constant tissue concentrations of Ca, Mg, K, and Fe across the whole range of Ni exposures, whereas in the limestone accessions, these elements fluctuated widely in response to Ni toxicity. Hyperaccumulation of Ni, defined here as foliar Ni concentrations exceeding 1g kg^-1 of dry biomass in plants not showing significant growth reduction, occurred in all accessions of O. serpyllifolia, but the higher Ni tolerance of serpentine accessions allowed them to hyperaccumulate more strongly. Of the reference species, C. jonthlaspi responded similarly to the limestone accessions of O. serpyllifolia, whereas A. montanum displayed by far the lowest degree of Ni tolerance and exhibited low foliar Ni concentrations, which only exceeded 1 g kg^-1 in plants showing severe Ni toxicity. The continuous spectrum of physiological responses among these accessions does not lend support to segregation of the serpentine populations of O. serpyllifolia as distinct species. However, the pronounced differences in degrees of Ni tolerance, hyperaccumulation, and elemental homeostasis observed among these accessions under common-garden conditions argues for the existence of population-level adaptation to their local substrates.

A New Species of Argophyllum (Argophyllaceae) with Notes on the Species from New Caledonia and Nickel Hyperaccumulation

The taxonomy of Argophyllum (Argophyllaceae) in New Caledonia is reviewed here. All names validly published in Argophyllum in this archipelago are discussed and lectotypified when necessary. A new species is described, Argophyllum riparium (The LSID for the name Argophyllum riparium is: 77216335-1) Pillon and Hequet sp. nov. Argophyllum grunowii and A. ellipticum are both species complexes in which several species previously recognized are included here as well. Seven species are recognized in New Caledonia: A. brevipetalum, A. ellipticum, A. grunowii, A. montanum, A. nitidum, A. riparium and A. vernicosum, all endemic. Leaf nickel content of A. riparium can exceed 1000 μg·g^-1, which makes this species a nickel hyperaccumulator. Measurements with a handheld X-Ray Fluorescence (XRF) spectrometer confirmed that this was also the case for all other species from New Caledonia, except A. nitidum. An identification key of New Caledonian species is provided.

Trait-based signatures of cloud base height in a tropical cloud forest

PREMISE

Clouds have profound consequences for ecosystem structure and function. Yet, the direct monitoring of clouds and their effects on biota is challenging especially in remote and topographically complex tropical cloud forests. We argue that known relationships between climate and the taxonomic and functional composition of plant communities may provide a fingerprint of cloud base height, thus providing a rapid and cost-effective assessment in remote tropical cloud forests.

METHODS

To detect cloud base height, we compared species turnover and functional trait values among herbaceous and woody plant communities in an ecosystem dominated by cloud formation. We measured soil and air temperature, soil nutrient concentrations, and extracellular enzyme activity. We hypothesized that woody and herbaceous plants would provide signatures of cloud base height, as evidenced by abrupt shifts in both taxonomic composition and plant function.

RESULTS

We demonstrated abrupt changes in taxonomic composition and the community- weighted mean of a key functional trait, specific leaf area, across elevation for both woody and herbaceous species, consistent with our predictions. However, abrupt taxonomic and functional changes occurred 100 m higher in elevation for herbaceous plants compared to woody ones. Soil temperature abruptly decreased where herbaceous taxonomic and functional turnover was high. Other environmental variables including soil biogeochemistry did not explain the abrupt change observed for woody plant communities.

CONCLUSIONS

We provide evidence that a trait-based approach can be used to estimate cloud base height. We outline how rises in cloud base height and differential environmental requirements between growth forms can be distinguished using this approach.

Bioenergetic constraints on the origin of autotrophic metabolism

Autotrophs form the base of all complex food webs and seemingly have done so since early in Earth history. Phylogenetic evidence suggests that early autotrophs were anaerobic, used CO₂ as both an oxidant and carbon source, were dependent on H₂ as an electron donor, and used iron-sulfur proteins (termed ferredoxins) as a primary electron carrier. However, the reduction potential of H₂ is not typically low enough to efficiently reduce ferredoxin. Instead, in modern strictly anaerobic and H₂-dependent autotrophs, ferredoxin reduction is accomplished using one of several recently evolved enzymatic mechanisms, including electron bifurcating and coupled ion translocating mechanisms. These observations raise the intriguing question of why anaerobic autotrophs adopted ferredoxins as central electron carriers only to have to evolve complex machinery to reduce them. Here, we report calculated reduction potentials for H₂ as a function of observed environmental H₂ concentration, pH and temperature. Results suggest that a combination of alkaline pH and high H₂ concentration yield H₂ reduction potentials low enough to efficiently reduce ferredoxins. Hyperalkaline, H₂ rich environments have existed in discrete locations throughout Earth history where ultramafic minerals are undergoing hydration through the process of serpentinization. These results suggest that serpentinizing systems, which would have been common on early Earth, naturally produced conditions conducive to the emergence of H₂-dependent autotrophic life. The primitive process of hydrogenotrophic methanogenesis is used to examine potential changes in methanogenesis and Fd reduction pathways as these organisms diversified away from serpentinizing environments. This article is part of a discussion meeting issue 'Serpentinite in the earth system'.

Phylogenetic and geographic distribution of nickel hyperaccumulation in neotropical Psychotria

PREMISE

Hyperaccumulation of heavy metals in plants has never been documented from Central America or Mexico. Psychotria grandis, P. costivenia, and P. glomerata (Rubiaceae) have been reported to hyperaccumulate nickel in the Greater Antilles, but they also occur widely across the neotropics. The goals of this research were to investigate the geographic distribution of hyperaccumulation in these species and explore the phylogenetic distribution of hyperaccumulation in this clade by testing related species.

METHODS

Portable x-ray fluorescence (XRF) spectroscopy was used to analyze 565 specimens representing eight species of Psychotria from the Missouri Botanical Garden herbarium.

RESULTS

Nickel hyperaccumulation was found in specimens of Psychotria costivenia ranging from Mexico to Costa Rica and in specimens of P. grandis from Guatemala to Ecuador and Venezuela. Among related species, nickel hyperaccumulation is reported for the first time in P. lorenciana and P. papantlensis, but no evidence of hyperaccumulation was found in P. clivorum, P. flava, or P. pleuropoda. Previous reports of hyperaccumulation in P. glomerata appear to be erroneous, resulting from taxonomic synonymy and specimen misidentification.

CONCLUSIONS

Hyperaccumulation of nickel by Psychotria is now known to occur widely from southern Mexico through Central America to northwestern South America, including some areas not known to have ultramafic soils. Novel aspects of this research include the successful prediction of new hyperaccumulator species based on molecular phylogeny, use of XRF technology to nondestructively obtain elemental data from herbarium specimens, and documentation of previously unknown areas of ultramafic or nickel-rich soil based on such data.

Sporadic Genetic Connectivity among Small Insular Populations of the Rare Geoendemic Plant Caulanthus amplexicaulis var. barbarae (Santa Barbara Jewelflower)

Globally, a small number of plants have adapted to terrestrial outcroppings of serpentine geology, which are characterized by soils with low levels of essential mineral nutrients (N, P, K, Ca, Mo) and toxic levels of heavy metals (Ni, Cr, Co). Paradoxically, many of these plants are restricted to this harsh environment. Caulanthus ampexlicaulis var. barbarae (Brassicaceae) is a rare annual plant that is strictly endemic to a small set of isolated serpentine outcrops in the coastal mountains of central California. The goals of the work presented here were to 1) determine the patterns of genetic connectivity among all known populations of C. ampexlicaulis var. barbarae, and 2) estimate contemporary effective population sizes (Ne), to inform ongoing genomic analyses of the evolutionary history of this taxon, and to provide a foundation upon which to model its future evolutionary potential and long-term viability in a changing environment. Eleven populations of this taxon were sampled, and population-genetic parameters were estimated using 11 nuclear microsatellite markers. Contemporary effective population sizes were estimated using multiple methods and found to be strikingly small (typically Ne < 10). Further, our data showed that a substantial component of genetic connectivity of this taxon is not at equilibrium, and instead showed sporadic gene flow. Several lines of evidence indicate that gene flow between isolated populations is maintained through long-distance seed dispersal (e.g., >1 km), possibly via zoochory.

Magnetic characterizations of nickel hyperaccumulating plants (Planchonella oxyhedra and Rinorea bengalensis) from Halmahera, Indonesia

Magnetic minerals, such as magnetite and hematite, have been reported to be present, in particular, leaves as biogenic particles. The magnetic minerals and properties of Ni hyperaccumulators have not previously been reported in the literature. This study aimed to characterize the magnetic properties of two Ni hyperaccumulating plant species, R. bengalensis and P. oxyhedra, which grow in an ultramafic region on Halmahera Island, Indonesia. For comparison, similar characterization was carried out on two non-hyperaccumulating plant species which grow in the same region. Concentrations of Ni, Fe, and Mn in the leaves of the hyperaccumulating plants were measured using atomic absorption spectroscopy (AAS) and their magnetic properties were characterized using measurements of magnetic susceptibility, low temperature magnetic susceptibility, and hysteresis curves. The results show that, compared to the non-hyperaccumulating plants, the Ni hyperaccumulating plants have higher concentrations of Ni and similar concentration of Fe. The magnetic susceptibilities of hyperaccumulating plants are positive, and those of non-hyperaccumulating plants are negative. This suggests that the abundance of Ni, rather than Fe, may control the magnetic properties of Ni hyperaccumulating plants. This probable connection between Ni concentration and plant magnetic properties could be advantageous for identifying hyperaccumulators, and should, therefore, be explored further.

Recent advances in New Caledonian biogeography

The biota of New Caledonia is one of the most unusual in the world. It displays high diversity and endemism, many peculiar absences, and far-flung biogeographic affinities. For example, New Caledonia is the only place on Earth with both main clades of flowering plants - the endemic Amborella and 'all the rest', and it also has the highest concentration of diversity in conifers. The discovery of Amborella's phylogenetic position led to a surge of interest in New Caledonian biogeography, and new studies are appearing at a rapid rate. This paper reviews work on the topic (mainly molecular studies) published since 2013. One current debate is focused on whether any biota survived the marine transgressions of the Paleocene and Eocene. Total submersion would imply that the entire fauna was derived by long-distance dispersal from continental areas since the Eocene, but only if no other islands (now submerged) were emergent. A review of the literature suggests there is little actual evidence in geology for complete submersion. An alternative explanation for New Caledonia's diversity is that the archipelago acted as a refugium, and that the biota avoided the extinctions that occurred in Australia. However, this is contradicted by the many groups that are anomalously absent or depauperate in New Caledonia, although represented there by a sister group. The anomalous absences, together with the unusual levels of endemism, can both be explained by vicariance at breaks in and around New Caledonia. New Caledonia has always been situated at or near a plate boundary, and its complex geological history includes the addition of new terranes (by accretion), orogeny, and rifting. New Caledonia comprises 'basement' terranes that were part of Gondwana, as well as island arc and forearc terranes that accreted to the basement after it separated from Gondwana. The regional tectonic history helps explain the regional biogeography, as well as distribution patterns within New Caledonia. These include endemics on the basement terranes (for example, the basal angiosperm, Amborella), disjunctions at the West Caledonian fault zone, and great biotic differences between Grande Terre and the Loyalty Islands.

Transcriptome Signatures of Selection, Drift, Introgression, and Gene Duplication in the Evolution of an Extremophile Endemic Plant

Plants on serpentine soils provide extreme examples of adaptation to environment, and thus offer excellent models for the study of evolution at the molecular and genomic level. Serpentine outcrops are derived from ultramafic rock and have extremely low levels of essential plant nutrients (e.g., N, P, K, and Ca), as well as toxic levels of heavy metals (e.g., Ni, Cr, and Co) and low moisture availability. These outcrops provide habitat to a number of endemic plant species, including the annual mustard Caulanthus amplexicaulis var. barbarae (Cab) (Brassicaceae). Its sister taxon, C. amplexicaulis var. amplexicaulis (Caa), is intolerant to serpentine soils. Here, we assembled and annotated comprehensive reference transcriptomes of both Caa and Cab for use in protein coding sequence comparisons. A set of 29,443 reciprocal best Blast hit (RBH) orthologs between Caa and Cab was compared with identify coding sequence variants, revealing a high genome-wide dN/dS ratio between the two taxa (mean = 0.346). We show that elevated dN/dS likely results from the composite effects of genetic drift, positive selection, and the relaxation of negative selection. Further, analysis of paralogs within each taxon revealed the signature of a period of elevated gene duplication (∼10 Ma) that is shared with other species of the tribe Thelypodieae, and may have played a role in the striking morphological and ecological diversity of this tribe. In addition, distribution of the synonymous substitution rate, dS, is strongly bimodal, indicating a history of reticulate evolution that may have contributed to serpentine adaptation.

Feasible metabolisms in high pH springs of the Philippines

A field campaign targeting high pH, H₂-, and CH₄-emitting serpentinite-associated springs in the Zambales and Palawan Ophiolites of the Philippines was conducted in 2012-2013, and enabled description of several springs sourced in altered pillow basalts, gabbros, and peridotites. We combine field observations of pH, temperature, conductivity, dissolved oxygen, and oxidation-reduction potential with analyses of major ions, dissolved inorganic carbon, dissolved organic carbon, and dissolved gas phases in order to model the activities of selected phases important to microbial metabolism, and to rank feasible metabolic reactions based on energy yield. We document changing geochemical inventories in these springs between sampling years, and examine how the environment supports or prevents the function of certain microbial metabolisms. In all, this geochemistry-based assessment of feasible metabolisms indicates methane cycling, hydrogen oxidation, some iron and sulfur metabolisms, and ammonia oxidation are feasible reactions in this continental site of serpentinization.

High pH microbial ecosystems in a newly discovered, ephemeral, serpentinizing fluid seep at Yanartaş (Chimera), Turkey

Gas seeps emanating from Yanartaş (Chimera), Turkey, have been documented for thousands of years. Active serpentinization produces hydrogen and a range of carbon gases that may provide fuel for life. Here we report a newly discovered, ephemeral fluid seep emanating from a small gas vent at Yanartaş. Fluids and biofilms were sampled at the source and points downstream. We describe site conditions, and provide microbiological data in the form of enrichment cultures, Scanning electron microscopy (SEM), carbon and nitrogen isotopic composition of solids, and PCR screens of nitrogen cycle genes. Source fluids are pH 11.95, with a Ca:Mg of ~200, and sediments under the ignited gas seep measure 60°C. Collectively, these data suggest the fluid is the product of active serpentinization at depth. Source sediments are primarily calcite and alteration products (chlorite and montmorillonite). Downstream, biofilms are mixed with montmorillonite. SEM shows biofilms distributed homogeneously with carbonates. Organic carbon accounts for 60% of the total carbon at the source, decreasing downstream to <15% as inorganic carbon precipitates. δ¹³C ratios of the organic carbon fraction of solids are depleted (−25 to −28‰) relative to the carbonates (−11 to −20‰). We conclude that heterotrophic processes are dominant throughout the surface ecosystem, and carbon fixation may be key down channel. δ¹⁵N ratios ~3‰, and absence of nifH in extracted DNA suggest that nitrogen fixation is not occurring in sediments. However, the presence of narG and nirS at most locations and in enrichments indicates genomic potential for nitrate and nitrite reduction. This small seep with shallow run-off is likely ephemeral, but abundant preserved microterracettes in the outflow and the surrounding area suggest it has been present for some time. This site and others like it present an opportunity for investigations of preserved deep biosphere signatures, and subsurface-surface interactions.

Cryptic adaptive radiation in tropical forest trees in New Caledonia

The causes of the species richness of tropical trees are poorly understood, in particular the roles of ecological factors such as soil composition. The nickel(Ni)-hyperaccumulating tree genus Geissois (Cunoniaceae) from the South-west Pacific was chosen as a model of diversification on different substrates. Here, we investigated the leaf element compositions, spatial distributions and phylogeny of all species of Geissois occurring on New Caledonia. We found that New Caledonian Geissois descended from a single colonist and diversified relatively quickly into 13 species. Species on ultramafic and nonultramafic substrates showed contrasting patterns of leaf element composition and range overlap. Those on nonultramafic substrates were largely sympatric but had distinct leaf element compositions. By contrast, species on ultramafic substrates showed similar leaf element composition, but occurred in many cases exclusively in allopatry. Further, earlier work showed that at least three out of these seven species use different molecules to bind Ni. Geissois qualifies as a cryptic adaptive radiation, and may be the first such example in a lineage of tropical forest trees. Variation in biochemical strategies for coping with both typical and adverse soil conditions may help to explain the diversification and coexistence of tropical forest trees on similar soil types.

Genesis of hexavalent chromium from natural sources in soil and groundwater

Naturally occurring Cr(VI) has recently been reported in ground and surface waters. Rock strata rich in Cr(III)-bearing minerals, in particular chromite, are universally found in these areas that occur near convergent plate margins. Here we report experiments demonstrating accelerated dissolution of chromite and subsequent oxidation of Cr(III) to aqueous Cr(VI) in the presence of birnessite, a common manganese mineral, explaining the generation of Cr(VI) by a Cr(III)-bearing mineral considered geochemically inert. Our results demonstrate that Cr(III) within ultramafic- and serpentinite-derived soils/sediments can be oxidized and dissolved through natural processes, leading to hazardous levels of aqueous Cr(VI) in surface and groundwater.