The evolution and phylogenetic placement of invasive Australian Acacia species

A decade of invasive Anopheles stephensi sequence-based identification: toward a global standard

Anopheles stephensi is an invasive malaria vector in Africa that has been implicated in malaria outbreaks in the Horn of Africa. In 10 years, it has been detected as far east as Djibouti and as far west as Ghana. Early detections were mostly incidental, but now active surveillance in Africa has been updated to include An. stephensi. Morphological identification of An. stephensi from native vectors can be challenging, thus, sequence-based assays have been used to confirm identification during initial detections. Methods of sequence-based identification of An. stephensi have varied across initial detections to date. Here, we summarize initial detections, make suggestions that could provide a standardized approach, and discuss how sequences can inform additional genomic studies beyond species identification.

Chromosome-level genome of the transformable northern wattle, Acacia crassicarpa

The genus Acacia is a large group of woody legumes containing an enormous amount of morphological diversity in leaf shape. This diversity is at least in part the result of an innovation in leaf development where many Acacia species are capable of developing leaves of both bifacial and unifacial morphologies. While not unique in the plant kingdom, unifaciality is most commonly associated with monocots, and its developmental genetic mechanisms have yet to be explored beyond this group. In this study, we identify an accession of Acacia crassicarpa with high regeneration rates and isolate a clone for genome sequencing. We generate a chromosome-level assembly of this readily transformable clone, and using comparative analyses, confirm a whole-genome duplication unique to Caesalpinoid legumes. This resource will be important for future work examining genome evolution in legumes and the unique developmental genetic mechanisms underlying unifacial morphogenesis in Acacia.

Characterization of Mineral Composition and Nutritional Value of Acacia Green Pods

The Acacia genus is considered one of the most invasive taxa in some habitats, namely coastal dunes, maritime calcareous soils, fresh lands in the valleys, mountainous areas, and the banks of watercourses and roadsides. In Portugal, the severity risk is very high, so this study aimed to evaluate the nutritional and mineral contents of the green pods as a potential source for livestock feeds and soil fertilizer because, as far as we know, there is no use for this species. The seven different species of Acacia (Acacia mearnsii Link, Acacia longifolia (Andrews) Willd, Acacia melanoxylon R. Br., Acacia pycnantha Bentham, Acacia dealbata Link., Acacia retinodes Schlecht, and Acacia cyclops A. Cunn. ex G. Don fil) were evaluated. The results showed that Acacia green pods have a high protein, fibre and minerals content, especially in potassium (K), calcium (Ca) and magnesium (Mg). All species present a different profile of the studied parameters, suggesting different potentials for their future use. Near-infrared spectroscopy was a potential tool to predict the earlier quality of the Acacia green pods to better select the raw material for the different applications.

Can suitability indices predict plant growth in the invaded range? The case of Acacias species

INTRODUCTION

Forestry in many parts of the world depends on exotic species, making this industry a source of invasions in some countries. Among others, plantations of the genus Pinus, Eucalyptus, Acacia, Populus, and Pseudotsuga underpin the forestry industry and are a vital component of many countries economies. Among woody plants, the cosmopolitan genus Acacia includes some of the most commonly planted trees worldwide. In order to prevent, manage and control invasive plant species, one of the most used tools is species distribution models. The output of these models can also be used to obtain information about population characteristics, such as spatial abundance patterns or species performance. Although ecological theory suggests a direct link between fitness and suitability, this link is often absent. The reasons behind the lack of this relationship are multiple. Chile is one of the countries where Acacia species, in particular, A. dealbata and A. melanoxylon, have become invaders.

METHODS

Here, we used climatic and edaphic variables to predict thepotentially suitable habitats for A. dealbata and A. melanoxylon in continental Chile and evaluate if the suitability indices obtained from these models are associated with the observed performance of the trees along the country.

RESULTS

Our models show that variable importance showed significant similarities between the variables that characterize each species' niche. However, despite the high accuracy of our models, we did not observe an association between suitability and tree growth.

DISCUSSION

This disconnection between suitability and performance can result from multiple causes, from structural limitations, like the lack of biotic interactions in the models, to methodological issues, like the usefulness of the performance metric used. Whatever the scenario, our results suggest that plans to control invasive species should be cautious in assuming this relationship in their design and consider other indicators such as species establishment success.

Newly designed foraminifera primers identify habitat-specific lineages through metabarcoding analyses

Foraminifera include diverse shell-building lineages found in a wide array of aquatic habitats from the deep-sea to intertidal zones to brackish and freshwater ecosystems. Recent estimates of morphological and molecular foraminifera diversity have increased the knowledge of foraminiferal diversity, which is critical as these lineages are used as bioindicators of past and present environmental perturbation. However, a comparative analysis of foraminiferal biodiversity between their major habitats (freshwater, brackish, intertidal, and marine) is underexplored, particularly using molecular tools. Here, we present metabarcoding survey of foraminiferal diversity across different ecosystems using newly designed foraminifera-specific primers that target the hypervariable regions of the foraminifera SSU-rRNA gene (~250-300bp long). We tested these primer sets on four foraminifera species and then across several environments: the intertidal zone, coastal ecosystems, and freshwater vernal pools. We retrieved 655 operational taxonomic units (OTUs); the majority are undetermined taxa that have no closely-matching sequences in the database. Furthermore, we identified 163 OTUs with distinct habitat preferences. Most of the observed OTUs belonged to lineages of single-chambered foraminifera, including poorly explored freshwater foraminifera which encompass a clade of Reticulomyxa-like forms. Our pilot study provides the community with an additional set of newly designed and taxon-specific primers to elucidate foraminiferal diversity across different habitats.

Belowground feedbacks as drivers of spatial self-organization and community assembly

Vegetation patterning in water-limited and other resource-limited ecosystems highlights spatial self-organization processes as potentially key drivers of community assembly. These processes provide insight into predictable landscape-level relationships between organisms and their abiotic environment in the form of regular and irregular patterns of biota and resources. However, two aspects have largely been overlooked; the roles played by plant - soil-biota feedbacks and allelopathy in spatial self-organization, and their potential contribution, along with plant-resource feedbacks, to community assembly through spatial self-organization. Here, we expand the drivers of spatial self-organization from a focus on plant-resource feedbacks to include plant - soil-biota feedbacks and allelopathy, and integrate concepts of nonlinear physics and community ecology to generate a new hypothesis. According to this hypothesis, below-ground processes can affect community assemblages through two types of spatial self-organization, global and local. The former occurs simultaneously across whole ecosystems, leading to self-organized patterns of biota, allelochemicals and resources, and niche partitioning. The latter occurs locally in ecotones, and determines ecotone structure and motion, invasion dynamics, and species coexistence. Studies of the two forms of spatial self-organization are important for understanding the organization of plant communities in drier climates which are likely to involve spatial patterning or re-patterning. Such studies are also important for developing new practices of ecosystem management, based on local manipulations at ecotones, to slow invasion dynamics or induce transitions from transitive to intransitive networks of interspecific interactions which increase species diversity.

Effects of widespread non-native trees on regulating ecosystem services

Tree taxa are often planted beyond their native range to increase the provision of some ecosystem services. Yet, they can disrupt ecosystem processes in their new ranges, causing changes in the provision of other services. Here we review the effects of five widespread tree taxa (Acacia, Ailanthus, Eucalyptus, Pinus and Robinia) on six regulating ecosystem services in areas where they are non-native. We conducted a literature search for pair-wise comparisons between sites dominated by any of the selected taxa and sites with native vegetation. An array of variables were used as indicators for each ecosystem service. Data were analysed using multi-level meta-analyses to compare effects of taxa on each ecosystem service, and effects of the same taxa across contexts. We compiled 857 case studies from 107 source papers. Several taxa tended to increase climate regulation, mostly Eucalyptus. Acacia decreased fire risk prevention. Robinia, Acacia and Ailanthus increased soil fertility, while Eucalyptus and Pinus, tended to decrease it. Soil formation was enhanced by Robinia and Ailanthus. Acacia promoted the increase of water in land pools, while Eucalyptus tended to decrease them. All effects show a large heterogeneity across case studies. Part of this heterogeneity could be attributed to gross climatic differences (i.e. biome), to species differences within each genus, to the structure of the recipient ecosystem, and/or to human management. Managers and policy-makers should consider the context-dependency and the potential effects of non-native trees on a wide range of services to ground their decisions. Our analyses also revealed important gaps of knowledge (e.g. on fire risk prevention, erosion control or water cycle regulation) and some potential publication bias. The methodology used here easily allows for future updates as new information will become available.

New records in vascular plants alien to Tenerife (Spain, Canary Islands)

Background

Recent fieldwork by the author in Tenerife, mostly between 2014 and 2019, yielded new records of alien vascular plants.

New information

Fifteen taxa (Acacia decurrens, A. mearnsii, Caesalpinia pulcherrima, Ensete ventricosum, Eucalyptus camaldulensis subsp. arida, E. cladocalyx, Euryops chrysanthemoides, Ficus elastica, Lippia alba, Pavonia sepioides, Pittosporum tobira, Populus × canadensis, Pyrostegia venusta, Ruellia dipteracanthus and Wigandia kunthii) are reported for the first time from the Canary Islands. All were initially introduced on purpose, mostly as ornamentals, and recently started to escape from cultivation. Most of them are ephemerals or only locally established, but nearly all have the potential to naturalise in the future. Thirteen additional species are reported for the first time from Tenerife: Atriplex nummularia, Bellis perennis, Chenopodium probstii, Coccoloba uvifera, Commelina benghalensis, Cuphea hyssopifolia, Eragrostis virescens, Lemna minuta, Malvastrum corchorifolium, Plerandra elegantissima, Psidium guajava, Thunbergia alata and Urochloa subquadripara. Finally, some miscellaneous notes are provided on the presence of Balanites aegyptiaca, Callistemon viminalis, Grevillea robusta and Passiflora caerulea in Tenerife.

Insights for the Valorization of Biomass from Portuguese Invasive Acacia spp. in a Biorefinery Perspective

Acacia spp. are widespread all over the Portuguese territory, representing a threat to local biodiversity and to the productivity of the forest sector. The measures adopted in some countries for their eradication or to control their propagation are expensive, have been considered unfeasible from practical and economical perspectives, and have generated large amounts of residue that must be valorized in a sustainable way. This review brings together information on the valorization of bark, wood, leaves, flowers, pods, seeds, roots, and exudates from Acacia spp., through the production of high-value bioactive extracts (e.g., antioxidant, antimicrobial, anti-inflammatory, antidiabetic, antiviral, anthelmintic, or pesticidal agents, suitable to be explored by pharmaceutical, nutraceutical, cosmetics, and food and feed industries), its incorporation in innovative materials (e.g., polymers and composites, nanomaterials, low-cost adsorbents), as well as through the application of advanced thermochemical processes (e.g., flash pyrolysis) and pre-treatments to decompose biomass in its structural components, regarding the production of biofuels along with valuable chemicals derived from cellulose, hemicellulose, and lignin. The knowledge of this research is important to encourage an efficient and sustainable valorization of Acacia spp. within a biorefinery concept, which can bring a significant economic return from the valorization of these residues, simultaneously contributing to forest cleaning and management, to reduce the risk of fires, and to improve the social-economic development of rural areas.

Comparative chloroplast genomics between the invasive weed Mikania micrantha and its indigenous congener Mikania cordata: Structure variation, identification of highly divergent regions, divergence time estimation, and phylogenetic analysis

Mikania micrantha and Mikania cordata are the only two species in genus Mikania (Asteraceae) in China. They share very similar morphological and life-history characteristics but occupy quite different habitats. Most importantly, they generate totally different ecological consequences. While M. micrantha has become an exotic invasive weed, M. cordata exists as an indigenous species with no harmful effects on native plants or habitats. As a continuous study of our previously reported M. micrantha chloroplast (cp) genome, in this study we have further sequenced the M. cordata cp genome to (1) conduct a comparative genome analysis to gain insights into the mechanism of invasiveness; (2) develop cp markers to examine the population genetic adaptation of M. micrantha; and (3) screen variable genome regions of phylogenetic utility. The M. cordata chloroplast genome is 151,984 bp in length and displays a typical quadripartite structure. The number and distribution of protein coding genes, tRNA genes, and rRNA genes of M. cordata are identical to those of M. micrantha. The main difference lays in that the pseudogenization of ndhF and a 118-bp palindromic repeat only arises in M. cordata. Fourteen highly divergent regions, 235 base substitutions, and 58 indels were identified between the two cp genomes. Phylogenetic inferences revealed a sister relationship between M. micrantha and M. cordata whose divergence was estimated to occur around 1.78 million years ago (MYA). Twelve cpSSR loci were detected to be polymorphic and adopted to survey the genetic adaptation of M. micrantha populations. No cpSSR loci were found to undergo selection. Our results build a foundation to examine the invasive mechanism of Mikania weed.

Disturbance-dependent invasion of the woody weed, Calotropis procera, in Australian rangelands

Plant invasions are threats to biodiversity and ecosystem processes that have far reaching ecological and economic impacts. Understanding the mechanisms of invasion essentially helps in developing effective management strategies. Rubber bush (Calotropis procera) is an introduced milkweed that invades Australian beef production rangelands. Its establishment is often associated with disturbances caused by pastoral management practices. We examined whether or not rubber bush (1) outcompetes native grasses, (2) can invade intact rangeland, and (3) if disturbance facilitates rubber bush establishment and spread in grassy rangelands. We measured the competitive response of different densities of Mitchell grass (Astrebla pectinata) individuals and the competitive effects of associate rubber bush seedlings in an additive common garden experiment. Replicated field exclosure experiments, under grass-dominated and tropical savanna woodland conditions examined the effect of increasing levels of disturbance on rubber bush seedling emergence. The dominant native Mitchell grass was a stronger competitor than rubber bush when grown together under greenhouse conditions, whereby root and shoot biomass yields were more restricted in rubber bush compared with Mitchell grass. This finding was corroborated in the field exclosure experiments at both sites, where seedling emergence increased 5-fold in seeded and highly disturbed plots where superficial soils were turned over by treatments simulating heavy grazing and trampling by cattle or machinery. Emergence of rubber bush seedlings in seeded plots that were undisturbed, clipped and grazed was minimal and rubber bush seedlings did not survive the seedling stage in these plots. These results demonstrate that disturbance to the superficial soil stratum affects the ability of rubber bush seeds to successfully establish in a microsite, and high levels of soil disturbance substantially increase establishment. Thus, rubber bush is a poor competitor of Mitchell grass and does not invade intact grassland. Consequently, rubber bush invasion is disturbance-dependent in the vast Australian rangelands. The spread of this weed may be arrested by management practices that minimise disturbances to grass cover.

Differential plant invasiveness is not always driven by host promiscuity with bacterial symbionts

Identification of mechanisms that allow some species to outcompete others is a fundamental goal in ecology and invasive species management. One useful approach is to examine congeners varying in invasiveness in a comparative framework across native and invaded ranges. Acacia species have been widely introduced outside their native range of Australia, and a subset of these species have become invasive in multiple parts of the world. Within specific regions, the invasive status of these species varies. Our study examined whether a key mechanism in the life history of Acacia species, the legume-rhizobia symbiosis, influences acacia invasiveness on a regional scale. To assess the extent to which species varying in invasiveness correspondingly differ with regard to the diversity of rhizobia they associate with, we grew seven Acacia species ranging in invasiveness in California in multiple soils from both their native (Australia) and introduced (California) ranges. In particular, the aim was to determine whether more invasive species formed symbioses with a wider diversity of rhizobial strains (i.e. are more promiscuous hosts). We measured and compared plant performance, including aboveground biomass, survival, and nodulation response, as well as rhizobial community composition and richness. Host promiscuity did not differ among invasiveness categories. Acacia species that varied in invasiveness differed in aboveground biomass for only one soil and did not differ in survival or nodulation within individual soils. In addition, acacias did not differ in rhizobial richness among invasiveness categories. However, nodulation differed between regions and was generally higher in the native than introduced range. Our results suggest that all Acacia species introduced to California are promiscuous hosts and that host promiscuity per se does not explain the observed differences in invasiveness within this region. Our study also highlights the utility of assessing potential mechanisms of invasion in species' native and introduced ranges.

The Complete Sequence of the Acacia ligulata Chloroplast Genome Reveals a Highly Divergent clpP1 Gene

Legumes are a highly diverse angiosperm family that include many agriculturally important species. To date, 21 complete chloroplast genomes have been sequenced from legume crops confined to the Papilionoideae subfamily. Here we report the first chloroplast genome from the Mimosoideae, Acacia ligulata, and compare it to the previously sequenced legume genomes. The A. ligulata chloroplast genome is 158,724 bp in size, comprising inverted repeats of 25,925 bp and single-copy regions of 88,576 bp and 18,298 bp. Acacia ligulata lacks the inversion present in many of the Papilionoideae, but is not otherwise significantly different in terms of gene and repeat content. The key feature is its highly divergent clpP1 gene, normally considered essential in chloroplast genomes. In A. ligulata, although transcribed and spliced, it probably encodes a catalytically inactive protein. This study provides a significant resource for further genetic research into Acacia and the Mimosoideae. The divergent clpP1 gene suggests that Acacia will provide an interesting source of information on the evolution and functional diversity of the chloroplast Clp protease complex.

Relatedness defies biogeography: the tale of two island endemics (Acacia heterophylla and A. koa)

Despite the normally strong link between geographic proximity and relatedness of recently diverged taxa, truly puzzling biogeographic anomalies to this expectation exist in nature. Using a dated phylogeny, population genetic structure and estimates of ecological niche overlap, we tested the hypothesis that two geographically very disjunct, but morphologically very similar, island endemics (Acacia heterophylla from Réunion Island and A. koa from the Hawaiian archipelago) are the result of dispersal between these two island groups, rather than independent colonization events from Australia followed by convergent evolution. Our genetic results indicated that A. heterophylla renders A. koa paraphyletic and that the former colonized the Mascarene archipelago directly from the Hawaiian Islands ≤ 1.4 million yr ago. This colonization sequence was corroborated by similar ecological niches between the two island taxa, but not between A. melanoxylon from Australia (a sister, and presumed ancestral, taxon to A. koa and A. heterophylla) and Hawaiian A. koa. It is widely accepted that the long-distance dispersal of plants occurs more frequently than previously thought. Here, however, we document one of the most exceptional examples of such dispersal. Despite c. 18 000 km separating A. heterophylla and A. koa, these two island endemics from two different oceans probably represent a single taxon as a result of recent extreme long-distance dispersal.

Salt- and alkaline-tolerance are linked in Acacia

Saline or alkaline soils present a strong stress on plants that together may be even more deleterious than alone. Australia's soils are old and contain large, sometimes overlapping, areas of high salt and alkalinity. Acacia and other Australian plant lineages have evolved in this stressful soil environment and present an opportunity to understand the evolution of salt and alkalinity tolerance. We investigate this evolution by predicting the average soil salinity and pH for 503 Acacia species and mapping the response onto a maximum-likelihood phylogeny. We find that salinity and alkalinity tolerance have evolved repeatedly and often together over 25 Ma of the Acacia radiation in Australia. Geographically restricted species are often tolerant of extreme conditions. Distantly related species are sympatric in the most extreme soil environments, suggesting lack of niche saturation. There is strong evidence that many Acacia have distributions affected by salinity and alkalinity and that preference is lineage specific.

PhyloJIVE: Integrating biodiversity data with the Tree of Life

MOTIVATION

Rich collections of biodiversity information such as spatial distributions, species descriptions and trait data are now synthesized in publicly available online sources such as GBIF. Also phylogenetic knowledge now provides a sound understanding of the origin of organisms and their place in the tree of life. We demonstrate with PhyloJIVE that any phylogenetic tree can be linked to online biodiversity data in the browser. This evolutionary view of biodiversity data is demonstrated in a case study that suggests that this approach may be useful to scientists and non-experts users.

DNA barcoding for conservation, seed banking and ecological restoration of Acacia in the Midwest of Western Australia

We used DNA barcoding to address an important conservation issue in the Midwest of Western Australia, working on Australia's largest genus of flowering plant. We tested whether or not currently recommended plant DNA barcoding regions (matK and rbcL) were able to discriminate Acacia taxa of varying phylogenetic distances, and ultimately identify an ambiguously labelled seed collection from a mine-site restoration project. Although matK successfully identified the unknown seed as the rare and conservation priority listed A. karina, and was able to resolve six of the eleven study species, this region was difficult to amplify and sequence. In contrast, rbcL was straightforward to recover and align, but could not determine the origin of the seed and only resolved 3 of the 11 species. Other chloroplast regions (rpl32-trnL, psbA-trnH, trnL-F and trnK) had mixed success resolving the studied taxa. In general, species were better resolved in multilocus data sets compared to single-locus data sets. We recommend using the formal barcoding regions supplemented with data from other plastid regions, particularly rpl32-trnL, for barcoding in Acacia. Our study demonstrates the novel use of DNA barcoding for seed identification and illustrates the practical potential of DNA barcoding for the growing discipline of restoration ecology.