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APPENDIX 3. — Maximum likelihood phylogram inferred from 47 taxa and 3314 in Mucoralean fungi in Thailand: novel species of Absidia from tropical forest soil
APPENDIX 3. — Maximum likelihood phylogram inferred from 47 taxa and 3314 characters based on LSU, SSU and ACT-1 matrix using GTR+G model. ML bootstrap support (≥ 70%) are indicated above the branches or near the nodes. Tree is artificially rooted using Cunninghamella homothallica (CBS 168.53), C. phaeospora (CBS 692.68), and C. bainieri (FSU319). The new species are in black bold and the type species in the dataset are indicated using T. (-) represent bootstrap support lower than 70%. (*) indicates unrecovered branching.
FIG. 7 in Mucoralean fungi in Thailand: novel species of Absidia from tropical forest soil
FIG. 7. — Mycelial growth of A. edaphica V.GHurdeal., E.Gentekaki., H.B.Lee & K.D.Hyde, sp. nov.(MFLUCC 20-0088, ex-type) and A. soli V.GHurdeal., E.Gentekaki., H.B.Lee & K.D.Hyde, sp. nov. (MFLUCC 20-0086, ex-type) in various media at room temperature (around 26°C to 27°C) after two days: A-D, colonies on MEA; E-H, colonies on PDA; I-L, colonies on CMA; M-P, colonies on YMA. The first two rows represent colonies of of A. edaphica sp. nov. and the bottom two rows A. soli sp. nov (obverse (first and third rows) and reverse (second and fourth rows).
FIG. 6 in Mucoralean fungi in Thailand: novel species of Absidia from tropical forest soil
FIG. 6. — Mycelial growth of Absidia edaphica V.GHurdeal., E.Gentekaki., H.B.Lee & K.D.Hyde, sp. nov. and Absidia soli V.GHurdeal., E.Gentekaki., H.B.Lee & K.D.Hyde, sp. nov. in different media at 25°C.
Data from: Vertical differentiation in tropical forest butterflies: a novel mechanism generating insect diversity?
Many tropical fruit-feeding nymphalid butterflies are associated with either the forest canopy or the understory, however, the exceptions offer insights into the origins of tropical diversity. As it occurs in both habitats of tropical forests in Ecuador and Peru, Archaeoprepona demophon is one such exception. We compared patterns of occurrence of A. demophon in the canopy and understory and population genomic variation for evidence of ecological and genetic differentiation between habitats. We found that butterfly occurrences in the canopy were largely uncorrelated with occurrences in the understory at both localities, indicating independent demographic patterns in the two habitats. We also documented modest, significant genome-level differentiation at both localities. Genetic differentiation between habitat types (approximately 20m in elevation) were comparable to levels of differentiation between sampling locations (approximately 1500km). We conclude that canopy and understory populations of A. demophon represent incipient independent evolutionary units. These findings support the hypothesis that divergence between canopy and understory-associated populations might be a mechanism generating insect diversity in the tropics.
Novel climates are already widespread beneath the world's tropical forest canopies.
<p>R code and data to accompany 'Novel climates are already widespread beneath the world’s tropical forest canopies'.</p>
Forest Fire Clustering: A Novel Tool for Identifying Star Members of Clusters
<p>In Tables 4 and 5, the <strong>Cluster</strong> column represents the name of the cluster. </p> <p><strong>Table 4</strong>: The columns <strong>ra</strong>, <strong>dec</strong>, <strong>pmra</strong>, <strong>pmdec</strong>, and <strong>parallax</strong> correspond to the median values for the cluster's position, parallax, and proper motions, respectively. The <strong>[Fe/H]</strong> and <strong>[Fe/H]_err</strong> columns indicate the cluster's [Fe/H] and its associated error. The <strong>logt</strong> and <strong>log_t_err</strong> columns represent the logarithmic age and its error, while the <strong>m-M</strong> and <strong>m-M_err</strong> columns denote the distance modulus and its error. Additionally, the <strong>E(BP-RP)</strong> and <strong>E(BP-RP)_err</strong> columns specify the cluster's reddening and its error, and the <strong>A_V</strong> and <strong>A_V_err</strong> columns represent the extinction and its error.</p> <p><strong>Table 5</strong>: The <strong>rc_pc</strong> and <strong>e_rc_pc</strong> columns indicate the core radius and its error, while the <strong>rt_pc</strong> and <strong>e_rt_pc</strong> columns represent the tidal radius and its error. The <strong>rh_pc</strong> column provides the radius containing half of the total number of stars in the cluster, and the <strong>rhm_pc</strong> column gives the half-mass radius. The <strong>R_J</strong> and <strong>R_J_err</strong> columns represent the Jacobi radius and its error. The <strong>mass</strong> and <strong>mass_err</strong> columns show the total mass of the cluster and its error, and the <strong>fb</strong> column denotes the binary fraction of the cluster. Finally, the <strong>trlx</strong> and <strong>trlx_err</strong> columns represent the relaxation time and its error. The units of<strong> trlx</strong> and <strong>trlx_err</strong> are Myr</p> <p>Note: NULL values for <strong>rc_pc, e_rc_pc, rt_pc, </strong>and <strong>e_rt_pc </strong>indicate the inapplicability of the RDP method. For <strong>Bootes I, NGC 104, NGC 3201, NGC 6121, NGC 6544, </strong>and <strong>NGC 6656</strong>, the parameters listed as “N/A”—including <strong>rhm, rJ, rJ_err, mass, mass_err, fb, trlx_Myr,</strong> and<strong> trlx_err</strong>—cannot be determined using our methods due to their faint magnitudes. This limitation arises because Gaia’s observational capacity extends only to 21 mag.</p> <p> </p>
Data from: Forest passerines as a novel dispersal vector of viable bryophyte propagules
Open the record for dataset details and reuse information.
Data from: Vertical differentiation in tropical forest butterflies: a novel mechanism generating insect diversity?
Open the record for dataset details and reuse information.
PLSS Forests Lost Compared to Modern Forests and Novel Modern Forsets Gained Compared to PLSS Forests, Upper Midwest: Level 1
EuroAmerican land use and its legacies have transformed forest structure and composition across the United States (US). More accurate reconstructions of historical states are critical to understanding the processes governing past, current, and future forest dynamics. Gridded (8x8km) estimates of pre-settlement (1800s) forests from the upper Midwestern US (Minnesota, Wisconsin, and most of Michigan) using 19th Century Public Land Survey System (PLSS) records provide relative composition, biomass, stem density, and basal area for 26 tree genera. This mapping is more robust than past efforts, using spatially varying correction factors to accommodate sampling design, azimuthal censoring, and biases in tree selection. We compare pre-settlement to modern forests using US Forest Service Forest Inventory and Analysis (FIA) data to show the prevalence of lost forests, pre-settlement forests with no current analogue, and novel forests, modern forests with no past analogs. Differences between PLSS and FIA forests are spatially structured as a result of differences in the underlying ecology and land use impacts in the Upper Midwestern United States. Modern biomass is higher than pre-settlement biomass in northern Minnesota, northwestern and south central Wisconsin along the former prairie-forest border through Minnesota that was largely open savanna and the Big Woods of Minnesota. PLSS biomass was higher than today in northern Wisconsin and upper and lower Michigan due to shifts in species composition and, presumably, average stand age. Modern forests are more homogeneous, and ecotonal gradients are more diffuse today than in the past. Novel forest assemblages represent 29% of all FIA cells, while 25% of pre-settlement forests no longer exist in a modern context. Lost forests are centered around the forests of the Tension Zone, particularly in hemlock dominated forests of north-central Wisconsin, and in oak-elm-basswood forests along the forest-prairie boundary in south central
Data from: Can novel pest outbreaks drive ecosystem transitions in northern-boreal birch forest?
1. The boreal biome exhibits distinct alternative ecosystem states with high and low levels of tree-cover. Insect outbreaks facilitated by climate warming could potentially drive transitions from high to low tree-cover states. We investigated whether two key premises for such outbreak-induced transitions – critical thresholds (tipping points) and positive feedbacks that could maintain alternative states – are present in the northern-boreal mountain birch forest of Fennoscandia. Here, climate warming has promoted range expansions of defoliating geometrid moths, resulting in novel, severe multispecies outbreaks, most recently during 2002-2010. 2. We conducted regional-scale field surveys of forest damage and recovery in 280 mountain birch stands in a northeast Norway immediately after the outbreak (2010) and six years later (2016). Satellite-derived time series of the normalized difference vegetation index (NDVI) provided an index of stand defoliation during the outbreak period. 3. The proportion of dead stems per stand displayed a bimodal distribution, with stands generally being either lightly or severely damaged. This was due to a critical threshold in the relationship between defoliation and stem mortality, with mortality rates increasing abruptly in stands experiencing a mean drop in NDVI of more than 4 % during the outbreak. The two key forest regenerative pathways – basal sprouting and sapling production – both displayed positive feedbacks with surviving stems and trees, so that regeneration success declined with increasing damage to the mature tree layer. These feedbacks imply that stands which have been forced across critical defoliation thresholds and suffered collapses of living tree cover may struggle to recover, especially if the loss of positive regenerative feedbacks is compounded by ungulate browsing on birch recruits. 4. Synthesis. The north Fennoscandian mountain birch forest displays critical thresholds and positive feedbacks that conform to theoretical expectations for a system that could be vulnerable to abrupt and persistent changes of state in the face of novel, climatically facilitated insect outbreaks. These findings deepen the understanding of the persistent losses of tree-cover that have occasionally been observed after outbreaks in this system in the past, and adds to the list of mechanisms that could help explain the bistability of tree-cover across the boreal biome.
Data from: Can ecosystem functioning be maintained despite climate-driven shifts in species composition? Insights from novel marine forests
1. Climate change is driving a redistribution of species and reconfiguration of ecological communities at a global scale. Persistent warming in many regions has caused species to extend their geographical ranges into new habitats, with thermally-tolerant species often becoming competitively dominant over species with colder affinities. Although these climate-driven changes in species abundance and diversity are well documented, their ecosystem-level implications are poorly understood, and resolving whether reconfigured communities can maintain fundamental ecosystem functions represents a pressing challenge in an increasingly warmer world. 2. Here, we investigated how climate-driven substitutions of foundation species influence processes associated with carbon and nutrient cycling (biomass production, detritus flow, herbivory, decomposition) by comparing two habitat-forming kelp species with contrasting thermal affinities. We examined the wider consequences of the observed (and predicted) emergence of novel marine forests in the NE Atlantic, which are expected to become more dominated by range-expanding, warm-temperate kelps. 3. Warm-temperate kelps both accumulated and released 80% more biomass than the cold-temperate species despite being taxonomically closely-related and morphologically similar. Furthermore, the warm-temperate species accumulated biomass and released detritus year-round, whereas the cold-temperate species did so during short, discrete periods. The warm-temperate kelps supported higher densities of invertebrate grazers and were a preferred food source. Finally, their detritus decomposed 6.5 times faster, despite supporting comparable numbers of detritivores. Overall, our results indicate an important shift in the cycling of organic matter in kelp forests along parts of the NE Atlantic coastline following climate-driven expansion of a warm-affinity kelp, with novel forests supplying large amounts of temporally-continuous—yet highly labile—organic matter. 4. Synthesis. Collectively, our results show that, like species invasions, climate-driven range expansions and consequent shifts in the identity of dominant species can modify a wide range of important ecosystem processes. However, alterations in overall ecosystem functioning may be relatively limited where foundation species share similar ecological and functional traits.
Data from: Where did all the trees come from? A novel multispecies approach reveals the impacts of biogeographical history and functional diversity on rain forest assembly
Aim: We take advantage of next generation sequencing-based technology to assess how landscape-level dynamics, biogeographical history and functional factors shape the distribution of genetic diversity in rain forest trees. To achieve this, we explore chloroplast genomic diversity and divergence patterns across multiple, co-distributed species from three major centres of rain forest diversity. Location: Subtropical rain forests in south-eastern Australia: Nightcap–Border Ranges, Dorrigo and Washpool. Methods: We assembled chloroplast genomic data from whole-genome shotgun libraries for 71 species collected across three major centres of rain forest diversity. Chloroplast single nucleotide polymorphisms were used to measure genetic variation within and between multiple populations, species and locations, and we used this information to identify patterns related to landscape-level processes, biogeographical origins and functional characteristics. Results: We identified Nightcap–Border Ranges and Dorrigo as containing multiple refugia and Washpool as primarily a recolonized area. We found that rapidly expanding lineages of Indo-Malesian origin exhibit significantly lower levels of genetic diversity than Gondwanan lineages with longer local histories. Functional traits related to persistence and dispersal were the most important in regulating the distribution of genetic diversity. Main conclusions: The distribution and assembly of species reflect interactions and competition between different floristic elements at different stages of continental occupation. Additionally, given the multiple evolutionary origins and histories of the Australian rain forest flora, it is important to avoid treating rain forest communities as single management units.
Data from: Insect herbivory in novel Quercus ilex L. forests: the role of landscape attributes, forest composition and host traits
<p><b><i>Context</i></b> Understanding the intrinsic and extrinsic drivers of herbivory in novel expanding forests is essential to envisage their role for biodiversity conservation.</p> <p><b><i>Aims</i></b>: To analyze the effects of landscape attributes, forest composition, genetic relatedness, ontogeny and leaf traits on insect herbivory in novel <i>Q. ilex</i> forest stands.</p> <p><b><i>Methods: </i></b>In 15 forest patches, we examined effects of patch size and connectivity, forest composition, and tree height, specific leaf area (SLA) and nitrogen content on herbivory. In 3 forest patches, we assessed effects of tree genetic relatedness, ontogeny and spatial distribution.</p> <p><b><i>Results</i></b>: Herbivory was lower in pine-oak than in mixed-oak forests owing to the shorter tree height in the former with no effects of patch size or connectivity. Herbivory increased with SLA whereas nitrogen content had no effect. Within patches, herbivory differed among genetic clusters and was reduced in saplings growing near mature oaks and individuals near the forest edge. </p> <p><b><i>Conclusion </i></b>We illustrate the strong context and scale dependence of tree-herbivore interactions that renders predictions for dynamic systems such as novel oak forests extremely challenging. It implies, however, that the structural heterogeneity of such unmanaged forests allows their function as stepping stones for insect herbivore diversity in fragmented landscapes.</p>
Supplementary material 7 from: Liu QL, Chen SF (2017) Two novel species of Calonectria isolated from soil in a natural forest in China. MycoKeys 26: 25-60. https://doi.org/10.3897/mycokeys.26.14688
Phylogenetic tree of Calonectria species in the Sphaero-Naviculate group based on maximum likelihood (ML) analysis of cmdA gene sequences : Data type: molecular data
Supplementary material 3 from: Liu QL, Chen SF (2017) Two novel species of Calonectria isolated from soil in a natural forest in China. MycoKeys 26: 25-60. https://doi.org/10.3897/mycokeys.26.14688
Phylogenetic tree of Calonectria species in the Prolate group based on maximum likelihood (ML) analysis of cmdA gene sequences : Data type: molecular data
Supplementary material 6 from: Liu QL, Chen SF (2017) Two novel species of Calonectria isolated from soil in a natural forest in China. MycoKeys 26: 25-60. https://doi.org/10.3897/mycokeys.26.14688
Phylogenetic tree of Calonectria species in the Sphaero-Naviculate group based on maximum likelihood (ML) analysis of his3 gene sequences : Data type: molecular data
Supplementary material 2 from: Liu QL, Chen SF (2017) Two novel species of Calonectria isolated from soil in a natural forest in China. MycoKeys 26: 25-60. https://doi.org/10.3897/mycokeys.26.14688
Phylogenetic tree of Calonectria species in the Prolate group based on maximum likelihood (ML) analysis of his3 gene sequences : Data type: molecular data
Supplementary material 1 from: Liu QL, Chen SF (2017) Two novel species of Calonectria isolated from soil in a natural forest in China. MycoKeys 26: 25-60. https://doi.org/10.3897/mycokeys.26.14688
Phylogenetic tree of Calonectria species in the Prolate group based on maximum likelihood (ML) analysis of tef1 gene sequences : Data type: molecular data
Supplementary material 5 from: Liu QL, Chen SF (2017) Two novel species of Calonectria isolated from soil in a natural forest in China. MycoKeys 26: 25-60. https://doi.org/10.3897/mycokeys.26.14688
Phylogenetic tree of Calonectria species in the Sphaero-Naviculate group based on maximum likelihood (ML) analysis of tef1 gene sequences : Data type: molecular data
Supplementary material 4 from: Liu QL, Chen SF (2017) Two novel species of Calonectria isolated from soil in a natural forest in China. MycoKeys 26: 25-60. https://doi.org/10.3897/mycokeys.26.14688
Phylogenetic tree of Calonectria species in the Prolate group based on maximum likelihood (ML) analysis of tub2 gene sequences : Data type: molecular data
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