Phylogenomics reveals the evolutionary origin of lichenization in chlorophyte algae

Mutualistic symbioses, such as lichens formed between fungi and green algae or cyanobacteria, have contributed to major transitions in the evolution of life and are at the center of extant ecosystems. However, our understanding of their evolution and function remains elusive in most cases. Here, we investigated the evolutionary history and the molecular innovations at the origin of lichens in green algae. We de novo sequenced the genomes or transcriptomes of 15 lichen-forming and closely-related non-lichen-forming algae and performed comparative phylogenomics with 22 genomes previously generated. We identified more than 350 functional categories significantly enriched in chlorophyte green algae able to form lichens. Among them, functions such as light perception or resistance to dehydration were shared between lichenizing and other terrestrial algae but lost in non-terrestrial ones, indicating that the ability to live in terrestrial habitats is a prerequisite for lichens to evolve. We detected lichen-specific expansions of glycosyl hydrolase gene families known to remodel cell walls, including the glycosyl hydrolase 8 which was acquired in lichenizing Trebouxiophyceae by horizontal gene transfer from bacteria, concomitantly with the ability to form lichens. Mining genome-wide orthogroups, we found additional evidence supporting at least two independent origins of lichen-forming ability in chlorophyte green algae. We conclude that the lichen-forming ability evolved multiple times in chlorophyte green algae, following a two-step mechanism which involves an ancestral adaptation to terrestrial lifestyle and molecular innovations to modify the partners cell walls.

Activation by cleavage of the epithelial Na+ channel α and γ subunits independently coevolved with the vertebrate terrestrial migration

Vertebrates evolved mechanisms for sodium conservation and gas exchange in conjunction with migration from aquatic to terrestrial habitats. Epithelial Na+ channel (ENaC) function is critical to systems responsible for extracellular fluid homeostasis and gas exchange. ENaC is activated by cleavage at multiple specific extracellular polybasic sites, releasing inhibitory tracts from the channel’s α and γ subunits. We found that proximal and distal polybasic tracts in ENaC subunits coevolved, consistent with the dual cleavage requirement for activation observed in mammals. Polybasic tract pairs evolved with the terrestrial migration and the appearance of lungs, coincident with the ENaC activator aldosterone, and appeared independently in the a and g subunits. In summary, sites within ENaC for protease activation developed in vertebrates when renal Na+ conservation and alveolar gas exchange was required for terrestrial survival.

Perspectives in Earthworm Molecular Phylogeny: Recent Advances in Lumbricoidea and Standing Questions

Earthworm systematics have been limited by the small number of taxonomically informative morphological characters and high levels of homoplasy in this group. However, molecular phylogenetic techniques have yielded significant improvements in earthworm taxonomy in the last 15 years. Several different approaches based on the use of different molecular markers, sequencing techniques, and compromises between specimen/taxon coverage and phylogenetic information have recently emerged (DNA barcoding, multigene phylogenetics, mitochondrial genome analysis, transcriptome analysis, targeted enrichment methods, and reduced representation techniques), providing solutions to different evolutionary questions regarding European earthworms. Molecular phylogenetics have led to significant advances being made in Lumbricidae systematics, such as the redefinition or discovery of new genera (Galiciandrilus, Compostelandrilus, Vindoboscolex, Castellodrilus), delimitation and revision of previously existing genera (Kritodrilus, Eophila, Zophoscolex, Bimastos), and changes to the status of subspecific taxa (such as the Allolobophorachaetophora complex). These approaches have enabled the identification of problems that can be resolved by molecular phylogenetics, including the revision of Aporrectodea, Allolobophora, Helodrilus, and Dendrobaena, as well as the examination of small taxa such as Perelia, Eumenescolex, and Iberoscolex. Similar advances have been made with the family Hormogastridae, in which integrative systematics have contributed to the description of several new species, including the delimitation of (formerly) cryptic species. At the family level, integrative systematics have provided a new genus system that better reflects the diversity and biogeography of these earthworms, and phylogenetic comparative methods provide insight into earthworm macroevolution. Despite these achievements, further research should be performed on the Tyrrhenian cryptic complexes, which are of special eco-evolutionary interest. These examples highlight the potential value of applying molecular phylogenetic techniques to other earthworm families, which are very diverse and occupy different terrestrial habitats across the world. The systematic implementation of such approaches should be encouraged among the different expert groups worldwide, with emphasis on collaboration and cooperation.

The evolution of sexual dichromatism in a large radiation of landfowls: re-examining the female-biased selection in Wallace's model

Sexual dichromatism, the colour difference between males and females, has been particularly important for studying the interplay between sexual and natural selection. However, previous studies on the evolutionary forces of sexual dichromatism examing the Darwin's and Wallace's model have produced mixed results. Phasianidae is a species-rich family with worldwide distribution, occupancy in nearly all terrestrial habitats, and a wide diversity of plumage patterns and colourations. Here, we use phylogenetic comparative methods to test the relationship between sexual dichromatism and colour complexity of males and females on both evolutionary direction and tempo including all species in Phasianidae. We show that the evolutionary direction of sexual dichromatism is negatively correlated with colour complexity in females but not males, and the evolutionary rates of sexual dichromatism are positively correlated with the evolutionary rates of colour complexity in both sexes. These results highlight the important role of female colour evolution in shaping sexual dichromatism in the pheasant family, and provide strong empirical supports for Wallace's hypothesis via a mosaic of sexual and natural selection in both sexes.

Fossil Leaves of Meliosma (Sabiaceae) With Associated Pollen and a Eupodid Mite From the Eocene of Maoming Basin, South China

A first occurrence of the genus Meliosma (Sabiaceae) is reported from the upper Eocene of the Maoming Basin of South China. This fossil is one of the oldest reliable records of the genus within its modern center of diversity. Fossil leaves are assigned to a new species, Meliosma eosinica sp. nov. based on leaf morphology and epidermal characters. The leaf epidermal anatomy of fossil Meliosma is illustrated for the first time. We also provide the first SEM observation of pollen grains associated with Meliosma. This study also documents an occurrence of mites within the leaf domatia previously unknown from the fossil record. We presume that the studied mite belongs to the superfamily Eupodoidea (Arthropoda), and probably the family Eupodidae, which comprises very small soft-bodied cosmopolitan mites occupying a wide range of terrestrial habitats. Additionally, we analyze the damage types on the fossil leaves of Meliosma. They exhibit exclusively external foliage feeding damage caused by arthropods and traces of probable fungal infection. A review of currently known fossil occurrences of leaves, fruits, and wood of Meliosma provides evidence for the geological and geographical distribution of the genus.

Host Plant Availability and Nest-Site Selection of the Social Spider Stegodyphus dumicola Pocock, 1898 (Eresidae)

An animals’ habitat defines the resources that are available for its use, such as host plants or food sources, and the use of these resources are critical for optimizing fitness. Spiders are abundant in all terrestrial habitats and are often associated with vegetation, which may provide structure for anchoring capture webs, attract insect prey, or provide protective function. Social spiders construct sedentary communal silk nests on host plants, but we know little about whether and how they make nest-site decisions. We examined host plant use in relation to host plant availability in the social spider Stegodyphus dumicola Pocock, 1898 (Eresidae) across different arid biomes in Namibia and analysed the role of host plant characteristics (height, spines, scent, sturdiness) on nest occurrence. Host plant communities and densities differed between locations. Spider nests were relatively more abundant on Acacia spp., Boscia foetida, Combretum spp., Dichrostachys cinerea, Parkinsonia africana, Tarchonanthus camphoratus, and Ziziphus mucronatus, and nests survived longer on preferred plant genera Acacia, Boscia and Combretum. Spider nests were relatively more abundant on plants higher than 2 m, and on plants with thorns and with a rigid structure. Our results suggest that spiders display differential use of host plant species, and that characteristics such as rigidity and thorns confer benefits such as protection from browsing animals.

Rokubacteria in Northern Peatlands: Habitat Preferences and Diversity Patterns

Rokubacteria is a phylogenetic clade of as-yet-uncultivated prokaryotes, which are detected in diverse terrestrial habitats and are commonly addressed as members of the rare biosphere. This clade was originally described as a candidate phylum; however, based on the results of comparative genome analysis, was later defined as the order-level lineage, Rokubacteriales, within the phylum Methylomirabilota. The physiology and lifestyles of these bacteria are poorly understood. A dataset of 16S rRNA gene reads retrieved from four boreal raised bogs and six eutrophic fens was examined for the presence of the Rokubacteriales; the latter were detected exclusively in fens. Their relative abundance varied between 0.2 and 4% of all bacteria and was positively correlated with pH, total nitrogen content, and availability of Ca and Mg. To test an earlier published hypothesis regarding the presence of methanotrophic capabilities in Rokubacteria, peat samples were incubated with 10% methane for four weeks. No response to methane availability was detected for the Rokubacteriales, while clear a increase in relative abundance was observed for the conventional Methylococcales methanotrophs. The search for methane monooxygenase encoding genes in 60 currently available Rokubacteriales metagenomes yielded negative results, although copper-containing monooxygenases were encoded by some members of this order. This study suggests that peat-inhabiting Rokubacteriales are neutrophilic non-methanotrophic bacteria that colonize nitrogen-rich wetlands.

Competition of insect decomposers over large vertebrate carrion: Necrodes beetles (Silphidae) vs blow flies (Calliphoridae)

Large carrion is inhabited by highly variable and interactive communities of insects. Positive interactions in carrion insect communities have been recently the focus in carrion ecology. By contrast, competition between carrion insects is rather undervalued. Here we provide evidence that blow flies (Calliphoridae) and Necrodes beetles (Silphidae), dominant decomposers of large carcasses in terrestrial habitats, compete over carrion. By reanalysing the results from 90 pig carcasses we demonstrated that the contribution of the flies and the beetles to the decay was negatively related. The greater part of the large carrion pool was monopolised by blow flies, whereas Necrodes beetles abundantly colonized carcasses, on which blow flies were less effective as decomposers. In behavioural assays, we found that adult beetles killed four times more frequently feeding than postfeeding third instar larvae of the flies, with the large decrease in the killing frequency after the larvae reached the age of early third instar. Therefore, adult Necrodes beetles preferentially killed the larvae that were before or in their peak feeding. The study provides evidence that the interaction between blow flies and Necrodes beetles is a combination of indirect exploitative effects of the flies and direct interference effects of the beetles (the mixed competition).

He kete hauora taiao: A Bicultural Ecological Assessment Framework

<p>Ka mau tonu ngā taonga tapu o ngā matua tupuna Koinei ngā taonga i tuku iho, na te ātua Hold fast to the treasures of the ancestors For they are the treasures that have been handed down to us by God’ (Dymond, 2013, p. 274) Ecologists, resource managers, landowners and iwi generally strive to manage biodiversity on their whenua as obliged by legislation. This may include restoration, protection, the mitigation of negative human impacts, or the prevention of further habitat loss. Mainstream ecological science and resource management (ERM) usually guides management decisions and provides evidence of management effectiveness. However, ecological science can struggle with stochastic and complex biological systems. Māori have hundreds of years of environmental knowledge and understanding that could be utilised by mainstream resource managers to enhance society's combined knowledge. An assessment tool that places mātauranga at its core can introduce a Māori perspective, privilege Māori knowledge, enable holistic co-management, re/introduce social values and create a common ground on which the two paradigms can connect. He Kete Hauora Taiao is an environmental assessment framework for terrestrial habitats constructed on Māori ecological health indicators by applying them to quantitative ecological scientific data. He Kete Hauora Taiao is built on the Driver – Pressure – State/Condition – Indicator – Response framework (K. F. D. Hughey, Cullen, Kerr, & Cook, 2004). Māori ecological perspectives or ariā (indicators, perspectives or concepts) are placed at the ‘condition’ level. Ariā include concepts such as mauri, whakapapa, tapu, wairua and mahinga kai which are linked to environmental structures, processes, functions and services. These ecological indicators can then be assessed with recognised qualitative scientific tools, metrics and targets. ESAT, Ecological State Assessment Tool, is a database that accompanies He Kete Hauora Taiao and enables quantitative ecological data to be viewed through a Māori perspective and weighted according to its relevance to management objectives. Creating a new bicultural environmental assessment framework required the exploration of the intersection between Māori ecological knowledge (MEK) and ERM. To my knowledge this is the first MEK based ecological assessment framework created specifically for terrestrial habitats and the first one to attempt to quantify MEK ecological indicators, relate them to ecology and resource management metrics and develop an interface between the two epistemologies. He Kete Hauora Taiao and ESAT (Ecological Statement Assessment Tool) are valuable resource management tools. Together they can create resource management programmes informed by a Māori value framework and are tailored to specific whenua, iwi agendas and political reporting and management requirements. He Kete Hauora Taiao spans the intersection between ERM and MEK, enabling communication and translation. MEK may provide context to scientific data and the scientific data may help augment understanding of MEK. Combined, MEK and ERM may create a powerful force that could vastly improve our resource management and conservation efforts. He Kete Hauora Taiao is a framework that could be engaged with by territorial authorities, iwi kaitiaki and landowners nationwide to automatically build te ao Māori into our management practices.</p>

He kete hauora taiao: A Bicultural Ecological Assessment Framework

<p>Ka mau tonu ngā taonga tapu o ngā matua tupuna Koinei ngā taonga i tuku iho, na te ātua Hold fast to the treasures of the ancestors For they are the treasures that have been handed down to us by God’ (Dymond, 2013, p. 274) Ecologists, resource managers, landowners and iwi generally strive to manage biodiversity on their whenua as obliged by legislation. This may include restoration, protection, the mitigation of negative human impacts, or the prevention of further habitat loss. Mainstream ecological science and resource management (ERM) usually guides management decisions and provides evidence of management effectiveness. However, ecological science can struggle with stochastic and complex biological systems. Māori have hundreds of years of environmental knowledge and understanding that could be utilised by mainstream resource managers to enhance society's combined knowledge. An assessment tool that places mātauranga at its core can introduce a Māori perspective, privilege Māori knowledge, enable holistic co-management, re/introduce social values and create a common ground on which the two paradigms can connect. He Kete Hauora Taiao is an environmental assessment framework for terrestrial habitats constructed on Māori ecological health indicators by applying them to quantitative ecological scientific data. He Kete Hauora Taiao is built on the Driver – Pressure – State/Condition – Indicator – Response framework (K. F. D. Hughey, Cullen, Kerr, & Cook, 2004). Māori ecological perspectives or ariā (indicators, perspectives or concepts) are placed at the ‘condition’ level. Ariā include concepts such as mauri, whakapapa, tapu, wairua and mahinga kai which are linked to environmental structures, processes, functions and services. These ecological indicators can then be assessed with recognised qualitative scientific tools, metrics and targets. ESAT, Ecological State Assessment Tool, is a database that accompanies He Kete Hauora Taiao and enables quantitative ecological data to be viewed through a Māori perspective and weighted according to its relevance to management objectives. Creating a new bicultural environmental assessment framework required the exploration of the intersection between Māori ecological knowledge (MEK) and ERM. To my knowledge this is the first MEK based ecological assessment framework created specifically for terrestrial habitats and the first one to attempt to quantify MEK ecological indicators, relate them to ecology and resource management metrics and develop an interface between the two epistemologies. He Kete Hauora Taiao and ESAT (Ecological Statement Assessment Tool) are valuable resource management tools. Together they can create resource management programmes informed by a Māori value framework and are tailored to specific whenua, iwi agendas and political reporting and management requirements. He Kete Hauora Taiao spans the intersection between ERM and MEK, enabling communication and translation. MEK may provide context to scientific data and the scientific data may help augment understanding of MEK. Combined, MEK and ERM may create a powerful force that could vastly improve our resource management and conservation efforts. He Kete Hauora Taiao is a framework that could be engaged with by territorial authorities, iwi kaitiaki and landowners nationwide to automatically build te ao Māori into our management practices.</p>