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Copyright of Conservation Biology is the property of Wiley-Blackwell and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

Fungal diversity drives key processes in terrestrial ecosystems, but remains challenging to measure in the field and to monitor over time. In particular, we lack methods capable of describing both the regional biotas and fungal related conservation values, such as habitats for rare and threatened fungi. Environmental DNA (eDNA) could serve this purpose, once its validity to capture fungal assemblage properties is established. Using three approaches (full‐season eDNA sampling from air, snapshot visual surveys, and eDNA sampling from dead wood), we present the first comparative assessment of fungal diversity at forest stand scale. The focus was on two well‐known fungal groups (lichens and wood inhabiting basidiomycetes) in old hemiboreal forests. Aerial eDNA revealed regional‐scale cryptic diversity not detected in visual surveys, particularly among lichens and including species of conservation concern. However, at the local population scale, both aerial eDNA and eDNA sampled from dead wood often missed visually detected species. In particular, eDNA sampled from dead wood performed only as a supplementary source of species data. The methods differed in detecting the spatial covariance of wood fungal and lichen diversity, with the combined (most complete) dataset indicating the strongest congruence. Synthesis and applications. Neither eDNA approaches nor visual surveys were able to detect full diversity of local fungi and all species of specific conservation value. However, there is clear merit in combined use of these methods, particularly in pairing aerial eDNA with visual observation‐based surveys on selected taxon groups. This approach can be especially valuable in fungal groups that have challenging taxonomy, inhabit partly inaccessible microhabitats, or have overall high diversity (such as lichens). [ABSTRACT FROM AUTHOR]

Molecular methods are increasingly used to identify species that lack conspicuous macro‐ or micromorphological characters. Taxonomic and ecological research teams barcode large numbers of collected voucher specimens annually. In this study we assessed the efficiency of long‐read high throughput sequencing (HTS) as opposed to the traditionally used Sanger method for taxonomic identification of multiple vouchered fungal specimens. We also evaluated whether this method can provide reference information about intraindividual gene polymorphism. We developed a workflow based on a test set of 423 basidiomycete specimens (representing 195 species), the PacBio HTS method, and ribosomal rRNA operon internal transcribed spacer (ITS) and 28S rRNA gene (LSU) markers. The PacBio HTS had a higher success rate than Sanger sequencing at a comparable cost. Species identification based on PacBio reads was usually straightforward, because the dominant operational taxonomic unit (OTU) typically represented the targeted organism. The PacBio HTS also enabled us to detect widespread polymorphism within the ITS marker. We conclude that multiplex DNA barcoding of the fungal ITS and LSU markers using PacBio HTS is a useful tool for taxonomic identification of large amounts of collected voucher specimens at a competitive price. Furthermore, PacBio HTS accurately recovers various alleles and paralogues, which can provide crucial information for species delimitation and population‐level studies. [ABSTRACT FROM AUTHOR]

Questions: In production forest landscapes, threatened species are increasingly confined to fragments of natural forest. Protecting such fragments is a priority to halt further biological degradation, but its effectiveness depends on external impacts on the fragments. In this study, we ask: how does woody vegetation in protected old-forest fragments vary depending on management of their adjacent areas, also in combination with natural site conditions? What are the management impacts on habitat quality of the fragments in the long term? Location: Pinus-dominated and Picea mixed-wood forests in Estonia (hemiboreal Europe). Methods: Forest structure and microclimate were measured at the edge and interior of protected old-forest fragments. Woody vegetation layers, shrub species composition, coarse woody debris, and presence of cut stumps were measured in 107 fragments (adjacent to clearcuts, partial cuts, and unthinned production forests) and in 20 control stands embedded within natural forest. Air temperature and humidity were measured at the edges vs the interior of mixed-woods. Edge age effects were explored along 80 years of post-harvest chronosequences. Results: All edge types studied had multiple, partly forest-type-specific, external effects on stand structure. Some clear-cutting effects on woody layers reversed in later decades, but there was also persistent impoverishment of deadwood pools of the fragments probably related to unreported tree removal. There was a likely indirect pathway of edge effects through overstorey loss, and shrub cover was reduced in the long term. Exotic species were rare. Edges at clear-cut stands influenced humidity regimes rather than temperature regimes. Conclusions: The moderate external effects on stand structure were tightly linked to low overstorey mortality and a lack of exotic species across the forest landscapes studied. Changes in these key factors constitute risks for the future. Protecting setasides from occasional tree cutting, and establishing forest buffers around small fragments and as a precautionary strategy are current priorities in these forest landscapes. [ABSTRACT FROM AUTHOR]

In regions where primeval forests have vanished it is unclear whether forest protection can sustain specialized old-forest biota, and over what time scale. We report on population expansion of an old-growth specific fungus of European conservation concern, Amylocystis lapponica, in the forest reserve network of Estonia. This conspicuous species was known for 40 years from only single records in one old-growth forest and was categorized nationally as Critically Endangered. During the last 10 years A. lapponica has expanded over the eastern half of the country, with nine subpopulations, in 12 localities, now known, all in long-protected old-growth forests and several > 50 km apart. In most of the new localities historical absence of the species can be reliably assessed based on earlier surveys. The historical remnant subpopulation has also increased. The population size (c. 100 mature individuals) in Estonia indicates the species should be recategorized nationally as Endangered. This success story suggests that more than 50 years of non-intervention may be needed even in large old-forest reserves for old-growth specialist species to recover. [ABSTRACT FROM AUTHOR]

• Four tree-scale conservation outcomes of green-tree retention are distinguished. • 38% of retained trees had poor survival combined with low habitat value. • Large aspens had poor survival but supplied valuable dead wood substrate. • Well surviving European nemoral hardwood trees were worth retaining even when small. • Trees likely to develop microhabitats should be facilitated also at thinnings. Retention forestry is a silvicultural approach that can achieve both ecological and economic objectives in various forest ecosystems. It builds largely on the assumption that the live trees left unharvested (the main timber cost) effectively support ecological functioning of post-harvest forest. Such effectiveness can be understood as a combination of the initial ecological value of the tree (that may persist after tree death) and its survival, i.e., the prospect to develop into a high-quality veteran tree in the next forest generation. We assessed those aspects among >3000 live trees actually retained in 103 Estonian harvested sites and monitored over 16 years. We analysed how their survival and habitat value (estimated from tree morphology, confirmed by epiphyte surveys) translate to the veteran-tree perspectives. Only 48% of the trees were still alive after 16 years, and this final survival at the stand-scale was poorly predictable from a few years of monitoring. Only 12% retention trees had both high habitat value and high survival. Most trees (75%) were of low initial habitat value and, combined with low survival, almost 40% of all trees never provided quality habitat for tree-dwelling species. Nevertheless, we found considerable potential for post-harvest development of habitat value; notably in European nemoral hardwood species (such as Fraxinus, Quercus, Ulmus, Acer), which survived well but were usually in subcanopies at the time of the harvest. These findings indicate that retention forestry can improve also highly impoverished (e.g. short-rotation) forests, if analytical tools have been developed and applied to predict tree survival and future habitat quality. [ABSTRACT FROM AUTHOR]

Finding standard cost-effective methods for monitoring biodiversity is challenging due to trade-offs between survey costs (including expertise), specificity, and range of applicability. These trade-offs cause a lack of comparability among datasets collected by ecologists and conservationists, which is most regrettable in taxonomically demanding work on megadiverse inconspicuous taxon groups. We have developed a site-scale survey method for diverse sessile land organisms, which can be analyzed over multiple scales and linked with ecological insights and management. The core idea is that field experts can effectively allocate observation effort when the time, area, and priority sequence of tasks are fixed. We present the protocol, explain its specifications (taxon group; expert qualification; plot size; effort) and applications based on >800 original surveys of four taxon groups; and we analyze its effectiveness using data on polypores in hemiboreal and tropical forests. We demonstrate consistent effort-species richness curves and among-survey variation in contrasting ecosystems, and high effectiveness compared with casual observations both at local and regional scales. Bias related to observer experience appeared negligible compared with typical assemblage variation. Being flexible in terms of sampling design, the method has enabled us to compile data from various projects to assess conservation status and habitat requirements of most species (specifically rarities and including discovery of new species); also, when linked with site descriptions, to complete environmental assessments and select indicator species for management. We conclude that simple rules can significantly improve expert-based biodiversity surveys. Ideally, define (i) a common plot size that addresses multiple taxon groups and management goals; (ii) taxon groups based on field expertise and feasible number of species; (iii) sufficient and practical search time; (iv) a procedure for recording within-plot heterogeneity. Such a framework, combined with freedom to allocate effort on-site, helps utilizing full expertise of observers without losing technical rigor. [ABSTRACT FROM AUTHOR]

Environmental managers often use indicator taxa to monitor full biodiversity and hidden environmental factors. For identifying practical indicators from assemblage data collected in the field, it is crucial to remove irrelevant variation, which unfortunately is not a common practice. We demonstrate, based on field data from Estonian forests, (i) how an attractive indicator group of macrofungi, perennial polypores, loses its apparent indicator value when variation in study effort and conspicuous environmental factors have been reduced; (ii) that simply including survey effort variation is sufficient to create significant covariation between species richness of taxon groups, which has often been taken as a justification for indicator assignment. These results imply that standardizing study effort should become a requirement for any field study that reports indicator taxa based on covariance patterns. We encourage researchers to be explicit and critical about the practical value of indicator taxa when compared with direct measurement of habitat conditions. [ABSTRACT FROM AUTHOR]

Copyright of Folia Cryptogamica Estonica is the property of University of Tartu Press and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

A major question in fungal conservation is why many species are confined to old forests, and how they could be supported by contemporary landscape matrix. Specifically, forestry that retains large biological legacies across landscape could reduce old-forest dependencies to species that require unusual substrate conditions. We sampled polypores in 112 2 ha plots (both old and harvested stands) in a semi-natural forestry context in Estonia and modelled the habitat factors of species confined to old growth. The results confirmed that old-growth assemblages emerged mostly due to diverse and abundant substrate supply (notably downed CWD). Only 10 species (five spruce-dwellers) were confined to old growth; of these, only Fomitopsis rosea and Oxyporus corticola were additionally affected by forest connectivity. The forestry system studied appeared particularly favourable for the species inhabiting deciduous wood. To better address habitat degradation in conservation, expert lists of ‘old-forest (indicator) fungi’ should be replaced with evidence-based focal taxa. [ABSTRACT FROM AUTHOR]

Antrodia is a polyphyletic genus, comprising brown-rot polypores with annual or short-lived perennial resupinate, dimitic basidiocarps. Here we focus on species that are closely related to Antrodia crassa , and investigate their phylogeny and species delimitation using geographic, ecological, morphological and molecular data (ITS and LSU rDNA, tef1 ). Phylogenetic analyses distinguished four clades within the monophyletic group of eleven conifer-inhabiting species (five described herein): (1) A. crassa s. str. (boreal Eurasia), Antrodia cincta sp. nova (North America) and Antrodia cretacea sp. nova (holarctic), all three being characterized by inamyloid skeletal hyphae that dissolve quickly in KOH solution; (2) Antrodia ignobilis sp. nova, Antrodia sitchensis and Antrodia sordida from North America, and Antrodia piceata sp. nova (previously considered conspecific with A. sitchensis ) from Eurasia, possessing amyloid skeletal hyphae; (3) Antrodia ladiana sp. nova from the southern part of the USA, Antrodia pinea from East Asia, and Antrodia ferox – so far known from subtropical North America, but here reported also from Eurasia. These three species have inamyloid hyphae and narrow basidiospores; (4) the North American Antrodia pini-cubensis , sharing similar morphological characters with A. pinea , forming a separate clade. The habitat data indicate that several species are threatened by intensive forestry. [ABSTRACT FROM AUTHOR]

In ecological and biodiversity research, fungal species are traditionally recorded using fruit body sampling, which underestimates mycelial presence of species. We hypothesized that fruit body based species lists are increasingly complete in larger sampling units where fruit bodies can be detected across multiple mycelial occurrences. We compared molecular records (detected with Illumina high-throughput sequencing) and records of fruit bodies of polypores in Estonian wetland pine forests. Of all molecularly detected polypores, 75% were present as conspecific fruit bodies within 30 m (including 24% on the same tree). This distance varied little among study sites. Despite lower costs, fruit body surveys yielded 60 polypore species, while sequencing only detected 13 species. Fruit body surveys of selected macrofungi can be thus efficient for biodiversity assessments. However, combining such surveys with high-throughput sequencing can add a broad description of the whole fungal assemblage even with limited samples (616 OTUs from 30 downed trunks in our study). [ABSTRACT FROM AUTHOR]

Three new species of Hymenochaete from Russian Far East are described based on morphological and ITS rDNA data. Hymenochaete adhaerens sp. nov. is a resupinate species closely related to H. macrospora, from which it differs in having longer basidiospores and setae. The basidiocarps of H. cupulata sp. nov. are effused-reflexed, resembling those of the European H. ulmicola, from which it differs in having setae inflated at the basal part and shorter basidiospores. Both H. adhaerens and H. cupulata inhabit bark of living elm trees ( Ulmus spp.). H. manshurica sp. nov. is resupinate and morphologically similar to the North American H. corticolor, from which it differs in having narrower setae and basidiospores; it has been collected from bark of living Tilia manshurica. [ABSTRACT FROM AUTHOR]

Abstract: Putatively old-forest dependent fungi have acquired a distinct position in biodiversity conservation, acting both as management targets and indicators for other nature values in the forest. Establishing old-forest dependency, however, requires rigorous sampling, taxonomy and identification approaches as exemplified here by a case study on Antrodia crassa. This rarely recorded polypore is considered indicative of old conifer forests in Northern Europe. We demonstrate that the material labelled as A. crassa includes not only frequent misidentifications, but it represents two genetically and ecologically distinct cryptic lineages with partly overlapping distributions. A balanced survey of different successional stages in Estonia indicated that one of those lineages prefers deadwood-rich disturbed habitats, notably clear-cuts, which have been previously undersampled. Because similar problems with cryptic lineages and biased surveys are common in mycological research, lists of ‘old-forest fungi’ should be considered as high-priority working hypotheses for taxonomic and ecological research, rather than well-established management tools. [Copyright &y& Elsevier]

Highlights: [•] Biodiversity consequences of the European ash dieback are hypothetical. [•] We show that the dieback can threaten local populations of ash dependent lichens. [•] Isolated ash-dependent populations of broader significance are of primary concern. [•] Silvicultural diversification is a major tool addressing tree dieback risks. [Copyright &y& Elsevier]

Abstract: The expanding practice of live-tree retention on clear-cuts represents a model case for conservation planning, because the high mortality of those trees requires balancing conflicting management goals in unpredictable conditions over long time frames. We explored the habitat provisioning function of dying retention trees for polypore and epixylic lichen assemblages. We sampled fallen trunks and snags created by known retention-tree deaths during the first post-harvest decade on 46 cut areas in Estonia, hemiboreal Europe. Those trees (particularly large fallen aspens) hosted a species-rich polypore assemblage that included several species of conservation concern. Lichen colonization of wood was slower and most species were found on pine snags. At the tree scale, the total species richness was highest on the trees that had died by trunk breakage creating both a snag and a log. To represent all species at the cutover scale, equal retention of different tree species and dead-wood types was sufficient for common species, but selective retention appeared necessary for species of conservation concern. The most frequent polypore species of conservation concern were either characteristic of specific substrates (notably aspen trunks) or early-successional stand conditions. We conclude that (i) dying retention trees are unlikely to provide dead-wood continuity at the stand scale and this function should be assessed at the landscape scale; (ii) effective habitat provisioning should include predicting and affecting the causes of tree death and linked management decisions based on the diversity, size, and longevity of the trees in specific landscape contexts. [Copyright &y& Elsevier]

• We measure the habitat relationships of wood-inhabiting fungi using DNA metabarcoding. • Old stands had larger species pools, at the landscape but not at the trunk scale. • High landscape-scale forest cover supported trunk scale fungal richness. • Increase in local dead-wood volume increased number of red-listed species per trunk. • Conservation conclusions based on DNA in wood same as in former fruit-body surveys. Understanding the distribution of biodiversity across forest landscapes is a key issue for the spatial planning of conservation management. Obtaining such spatial perspective is challenging because a large part of biodiversity remains hidden to the conventional survey approaches. High-productivity forests are probably the hotspots of hidden biodiversity and, at the same time, under severe timber harvesting pressure. We used DNA-metabarcoding approach to assess habitat quality of successional high productivity forests for wood-inhabiting fungi, focusing on fungal diversity that remains hidden in fruit-body surveys. We sampled a fixed amount of coarse fallen Norway spruce trunks in 40 naturally developing stands ranging from 44 to 140 years of age in hemi-boreal Estonia. We found three main habitat quality patterns. The total number of fungal OTUs in older (>80 years) stands exceeded that in younger stands due to the accumulation of rare fungi. The proportion of trunks hosting highest number of OTUs and trunk-scale richness of rare fungi were greatest in stands surrounded by extensive forest area. The average number of red-listed species per trunk increased mainly along with the volume of fallen dead wood; large volumes provided quality habitats already before the stands had reached 80 years of age. These results support the view that both substrate amount in the forest stand and habitat connectivity on a landscape scale support fungal diversity in dead wood. Earlier studies on wood-inhabiting fungi have reached similar conclusions based on observations of fungal fruit-bodies. Thus, the overall principle of focusing conservation efforts to remaining high quality habitats and landscapes extends to the fungi hidden to the conventional survey methods. [ABSTRACT FROM AUTHOR]

A fundamental problem of sustainability is how to reduce the double complexity of ecological and social systems into simple operational terms. We highlight that the conservation concept of focal species (selected species sensitive to a set of anthropogenic threats to their habitat) links multiple issues of ecological sustainability, and their habitat models can provide a practical tool for solving these issues. A review of the literature shows that most spatial modeling of focal species focuses on vertebrates, lacks the aspect of aquatic and soil habitats, and has been slow in the uptake by actual management planning. We elaborate on a deductive modeling approach that first generalizes the main influential dimensions of habitat change (threats), which are then parameterized as habitat quality estimates for focal species. If built on theoretical understanding and properly scaled, the maps produced with such models can cost-effectively describe the dynamics of ecological qualities across forest landscapes, help set conservation priorities, and reflect on management plans and practices. The models also serve as ecological hypotheses on biodiversity and landscape function. We illustrate this approach based on recent additions to the forest reserve network in Estonia, which addressed the insufficient protection of productive forest types. For this purpose, mostly former production forests that may require restoration were set aside. We distinguished seven major habitat dimensions and their representative taxa in these forests and depicted each dimension as a practical stand-scale decision tree of habitat quality. The model outcomes implied that popular stand-structural targets of active forest restoration would recover passively in reasonable time in these areas, while a critically degraded condition (loss of old trees of characteristic species) required management beyond reserve borders. Another hidden issue revealed was that only a few stands of consistently low habitat quality concentrated in the landscape to allow cost-efficient restoration planning. We conclude that useful habitat models for sustainable forest management have to balance single-species realism with stakeholder expectations of meaningful targets and scales. Addressing such social aspects through the focal species concept could accelerate the adoption of biodiversity distribution modeling in forestry. [ABSTRACT FROM AUTHOR]