Philippa Kaur

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The richness of Melanesian FrogsApproximately 7.2% (534 out of 7404) of Earth’s recognised frog species occur in Melanesia, a region comprising < 0.7% of the world’s land area. Frog richness in Melanesia, and especially on New Guinea and nearby land-bridge islands (471 species), is higher than in any other tropical insular region (Fig. 1a). New Melanesian frog species have been described at an average rate of nearly 13 species/year since 2000, and the recognised frog fauna has grown by > 50% in that timeframe (Fig. 1b). The authorship of new species has been concentrated, with six authors featuring on 20 or more descriptions since 2000, and one or more of these six authors on every species description since 2000. A small number of species descriptions has included genetic data (31 species), although a higher number of Melanesian frog species have at least one sequence available on GenBank (~38%, or approximately 200 species). This taxonomic work has revealed or emphasised many evolutionary novelties (Fig. 2): multiple apparently independent derivations of extremely miniaturised vertebrates22,23,24, including some of the world’s smallest known tetrapods23,25,26; multiple derivations of complex parental care in different genera27,28; frequent evolutionary shifts between terrestrial, arboreal and scansorial lifecycles22,29; the most extreme sexual size dimorphism yet documented in anurans30; drastic ontogenetic colour change31; a radiation of canopy-dwelling treefrogs32 that show extensive finger webbing and parachuting behaviour convergent with unrelated frog lineages in Asia and the Neotropics; and treefrogs with erectile noses33,34. Taxonomic work has also elucidated novel concentrations of range-restricted endemic taxa, especially in the Milne Bay Region at the far eastern edge of New Guinea21.Fig. 1: Temporal trends in the documentation of the Melanesian frog fauna.a Species accumulation curves for species-rich ( >100 species) insular frog biotas (Species lists from AmphibiaWeb as of 1 October 2021). Separate accumulation curves are given for the entire fauna of Melanesia (including New Guinea), and the fauna of New Guinea and nearby predominantly land-bridge islands. b Species accumulation curve for frogs within Melanesia. Bar at end indicates predicted number of species in each major family based on known, but as yet undescribed candidate species.Full size imageFig. 2: Melanesian frog species described within the last 15 years illustrating the ecological and morphological diversity of the fauna.a Paedophryne titan and b Choerophryne gracilirostris – examples of lineages that have undergone convergent minaturisation; c Choerophryne alpestris – a fossorial species within a largely scansorial lineage; d Xenorhina macrodisca – scansorial species within a largely fossorial lineage; e Cornufer custos and f Oreophryne oviprotector – independent derivations of complex parental care; g Litoria pallidofemora – extensive digital webbing for parachuting; and h Litoria pinocchio – sexually dimorphic and erectile rostral spikes. Photographs F. Kraus (a), S. Richards (b–g), and courtesy of T. Laman (h).Full size imageFrog species richness in Melanesia is highly concentrated into just three families, with Pelodryadidae (137 recognised species, estimated ~200) and especially Microhylidae (317 species, estimated >400) dominating. Melanesian Pelodryadidae are phylogenetically interdigitated with relatives in Australia, suggesting multiple dispersals between the two regions35. In contrast, ancestors of the direct-developing microhylids colonised Melanesia from Asia via trans-marine dispersal likely only once36, radiated across open ecological niches37, and are now the most species-rich insular radiation of frogs in the world. The third major family comprises an ecologically diverse radiation of the direct-developing Ceratobatrachidae (57 species, estimated 66) largely associated with island-arc terranes of East Melanesia and the Philippines, indicating a long history of insular diversification and trans-marine dispersal38. The predominance of direct-developing frogs in Melanesia (~70% of species) mirrors insular faunas in Madagascar (~34%), Sri Lanka (~67%) and the Greater Antilles (~87%). The other four frog families in Melanesia are all relatively species poor (2, 3, 4, and 13 species) (Fig. 1a), centred in New Guinea, and include lineages originating in Asia (Ranidae, Dicroglossidae) or Australia (Myobatrachidae, Limnodynastidae).The described diversity of Melanesian amphibian species remains an underestimate. Survey work and investigation of museum collections by the co-authors identified ~190 additional candidate species distributed across 16 different genera, mostly from Papua New Guinea, suggesting a total richness of over 700 frog species (Fig. 1a, Supplementary Table 1). This estimated percentage of undescribed diversity (~25%) mirrors estimates for the New Guinean flora (~18–22%)7. The majority of candidate species are concentrated in the two most diverse families (Microhylidae and Pelodryadidae), although genetic, morphological, and acoustic evidence indicate the diversity of Melanesian Ranidae is also underestimated (S. Richards and F. Kraus pers. obs.). Most material documenting candidate species has been collected in the last 20 years, and the vast majority is from Papua New Guinea (Supplementary Fig. 1). There is some suggestion of a slowing in the rate of candidate species discovery in the last decade (Supplementary Fig. 2); however, several of the most active field workers in this region have ceased survey work in recent years, which likely accounts for much of this decline. The pervasiveness of complexes of morphologically and/or acoustically cryptic taxa is poorly understood; survey work continues to reveal novelties, and large areas of the region remain unsurveyed or undersampled. In particular, comparisons of area-to-diversity ratios between the better-known eastern portion of New Guinea (Papua New Guinea) with the poorly surveyed western (Indonesian) portion of the island further suggest that, even with candidate species included, diversity in the latter region may be underestimated by as much as 50% (Supplementary Methods and Results, Supplementary Table 2). These trends and patterns all indicate that ~ 700 species is a very conservative minimum estimate of total diversity and support analyses in other taxa showing Melanesia remains a hotspot of unrecognised diversity39,40.Endemism and distributional patternsThe Melanesian frog fauna is highly endemic (97.2%), with tiny proportions of species shared with Australia (2.4%) or with islands farther west in Indonesia (0.6%), indicating that Australia and Melanesia are discrete centres of frog diversification, despite periodic connection via land bridges through the late Tertiary41. The vast majority of Melanesian frog species (471) occur on New Guinea and nearby land-bridge islands (Raja Ampats, Japen and the Milne Bay islands). In comparison, the frog fauna of the much smaller region of Maluku is depauperate (16 species, of which nine are endemic) but also almost certainly underestimated (e.g., there are no Microhylidae recorded from Buru). Most taxa from Maluku are congeneric (and several conspecific) with lineages centred on New Guinea, supporting the biogeographic clustering of Maluku’s amphibians with the main island of New Guinea. In contrast, the frog fauna of East Melanesia is more diverse and highly endemic and dominated by an ecologically diverse radiation of a different family (Ceratobatrachidae) with only four (all pelodryadid treefrogs) out of 56 species shared with nearby New Guinea. East Melanesia and New Guinea appear to be discrete and long-isolated centres of diversification, as expected from their independent geological histories42.Melanesia spans five countries, and this has possibly to some degree masked the exceptional species diversity of the overall region. Papua New Guinea has the highest number of species (398) and endemic species (318). This likely reflects some combination of its slightly larger area (when islands to the north are included), more diverse geological origins, and greater inventory work than seen in neighbouring regions of Indonesia7. Papua, West Papua and Maluku (Indonesia) have many fewer documented species (197), of which a majority (134) is endemic. The boundary between Papua and Papua New Guinea is visible in species-richness maps (Fig. 3a), with lower diversity to the west, indicating that the distribution and diversity of frogs in Indonesia remain less documented in science. The frog faunas of the Solomon Islands (21 species) and Fiji (two species) are more depauperate but include a significant endemic or near-endemic component, whereas the geographically intervening islands of Vanuatu support no native frogs.Fig. 3: Frog species richness in Melanesia based on IUCN distributional maps for all species described by 2019.a All species; b Ceratobatrachidae; c Microhylidae; d Pelodryadidae. Areas of highest estimated diversity correspond to mountain ranges in central and northern New Guinea. The boundaries between Maluku, New Guinea and East Melanesia are indicated. Fiji has only two frog species and is geographically distant from other areas of Melanesia inhabited by frogs and is not visble on this map.Full size imageBased on distribution maps generated for all species recognised by 31 August 2019, the highest regional alpha diversity of frogs occurs along the Central Cordillera of New Guinea (especially in Papua New Guinea) and around the higher mountain ranges along the north coast of Papua New Guinea (Fig. 3a). These centres of diversity correlate with extensive areas of hill and montane forest and broadly correspond with elevational species-richness patterns for mammals and birds in Melanesia43 and for many other taxa elsewhere in the tropics44,45. Large areas of montane forest with lower species richness along the northern versant of the Central Cordillera in Papua New Guinea and in mountain ranges across Papua certainly reflect inadequate sampling. The ceratobatrachid-dominated frog fauna of East Melanesia is richest in Bougainville (Fig. 3d), with attenuating richness towards the west and especially to the east. The two most speciose families both show alpha diversity peaks in mountainous areas of central New Guinea (Fig. 3c–d). In contrast, microhylids are largely absent from the seasonally dry woodlands of the Trans-Fly region in southern New Guinea and exhibit high diversity in northern New Guinea, whereas pelodryadids are much more speciose in the lowlands of southern New Guinea than northern New Guinea. These broad trends may have both ecological (sensitivity of direct-developing microhylids to dry conditions) and historical (Australia as a centre of origin for savanna-adapted Pelodrydidae) underpinnings.The historical and contemporary factors underpinning high frog species diversity in New Guinea remain largely unstudied, especially when compared to other species-rich insular amphibian faunas such as Madagascar46 or the Greater Antilles47. When compared to some areas of the Neotropics, alpha and beta diversities of frogs in lowland forests in the basins of the Sepik and Ramu rivers in New Guinea are unremarkable48. However, the Milne Bay Region has exceptionally high levels of endemism21, so species turnover will be higher in this area. Extent-of-occurrence estimates derived from IUCN maps indicate that direct-developing microhylids have smaller mean and median range sizes than all other families of frogs in Melanesia (Supplementary Table 3). Microhylidae also dominate anuran species diversity in Milne Bay21 and many mountain areas where standing water is very limited49. These data suggest that, as with some areas in the Neotropics50, high beta diversity in lineages with direct development is a key factor underpinning amphibian megadiversity in Melanesia. To address these questions further, synthetic analyses are required to better quantify the extent to which regional megadiversity in Melanesia reflects high community diversity versus species turnover, how elevation and insularity moderates these two parameters, and to what extent emergent patterns may differ from diverse frog communities in other regions such as the Neotropics.The conservation status of Melanesian FrogsThe frog fauna of Melanesia is currently less threatened but more Data Deficient than other comparable insular regions (Fig. 4a). The vast majority of Melanesian frogs are categorised as Least Concern (68%) or Data Deficient (24%). Thirty-one species (6%, or 8% if Data Deficient taxa are excluded) are threatened (Critically Endangered, Endangered, Vulnerable) (Supplementary Table 4), and eight species are considered Near Threatened. No species are assessed as Extinct or Extinct in the Wild. Since the first Global Amphibian Assessment in 2004, the number of Melanesian frog species has grown by 44%, and nearly 60% of the 31 Melanesian frog species now considered threatened were described after 2004 (Fig. 1a). Only one change in status between 2004 and 2019 was considered genuine (Cophixalus sphagnicola), due to the emerging threat of a newly opened mine. All other status changes (for 116 taxa) reflect better information on distribution or changed assessment protocols (Supplementary Table 5). Applying stricter criteria for use of the Data Deficient category in the 2019 IUCN assessment reduced the number of Data Deficient species when compared to 2004 (125 versus 197), but Melanesia still has a higher percentage of Data Deficient taxa than other species-rich tropical insular faunas (Fig. 4a).Fig. 4: The conservation status of Melanesian frogs.a Comparison of number of species in each IUCN threat category across Melanesia, other diverse insular regions, and the nearby continent of Australia. Melanesia has a proportionally low number of threatened taxa but high number of Data Deficient taxa (EX Extinct, CR Critically Endangered, EN Endangered, VU Vulnerable, NT Near Threatened, DD Data Deficient, LC Least Concern, NE Not Evaluated); b Slopes around Mt Simpson, Milne Bay Province, a hotspot of threatened frog diversity due to forest loss through conversion to anthropogenic grasslands; c Choerophryne sanguinopicta from Mt Simpson (Critically Endangered); d Oreophryne ezra from Rossel Island (Critically Endangered) and; e Cornufer citrinospilus from New Britain (Vulnerable). Photographs F. Kraus (b–d), S. Richards (e).Full size imageAll Critically Endangered and Endangered—and most of the Vulnerable—species were listed because of their small extent of occurrence and on-going decline in habitat area and/or quality (criteria B1ab(iii)) (Supplementary Table 6). The key threatening processes were typically forest disturbance or loss due to conversion to plantations or gardens, repeated burning, or mining (Fig. 4b–c). Only two insular species with very localised montane distributions were considered threatened by climatic disturbance and/or climate change alone (Cornufer citrinospilus and Oreophryne ezra) (Fig. 4d–e). No species were currently declining from pathogens, and in particular Batrachochytrium dendrobatidis (Bd), which remains undetected in Melaneisa51. However, the introduction and establishment of Bd has been identified as a severe threat for well over one hundred taxa52, especially for montane pelodryadid treefrogs, a group that has been devastated by this disease in parts of Australia.Although much of New Guinea has historically been considered a ‘wilderness area’ with comparatively little human impact53, the distributions of threatened taxa also highlight areas of conservation concern wherein range-restricted (often single-island endemic) taxa overlap with extensive and increasing anthropogenic impacts (Fig. 5a–b). Nearly half the species identified as threatened (13) are restricted to a recently delineated dramatic centre of herpetofaunal endemism in the Milne Bay Region at the eastern tip of Papua New Guinea21. Three clusters of small-range endemics in this region (all documented in the last two decades) present immediate conservation issues. The first is Mount Simpson, where six microhylids (four named, two awaiting description) with highly restricted ranges are threatened by habitat loss, especially repeated burning and associated conversion of forest to grassland (Fig. 4b). The second is Woodlark Island, where the status of seven endemic microhylids (six named, one undescribed) is likely to worsen rapidly if current, approved proposals to convert large areas of primary forest to oil-palm plantation and/or gold mines proceed21. Finally, Misima Island is home to four endemic microhylids (two considered threatened) with ranges that overlap areas disturbed by mining and forest loss21. Other regions with multiple overlapping threatened taxa are the Adelbert Mountains in Morobe Province (two species), New Britain (two lowland species and one highland species), and Greater Bukida in the Solomon Islands (three lowland species). These clusters of narrow-range taxa highlight important—and in most cases largely overlooked—conservation priorities for Melanesian frogs (and likely other taxa as well21,54). The high percentage of Data Deficient species and low level of survey effort in many areas (especially Papua and West Papua Provinces, Indonesia) also raise the possibility that other threatened hotspots remain overlooked. One area of particular concern may be the island of Biak in Indonesia, which has lost much of its primary vegetation but is home to at least three endemic frogs (one Data Deficient, two Least Concern).Fig. 5: The distribution of threatened frogs in Melanesia.a The estimated distribution of all 31 Melanesian frog species considered Critically Endangered, Endangered or Vulnerable at the end of 2019. Distributional areas are not colour coded by the number of threatened taxa. b Close up of the Milne Bay endemism hotspot. Distributional areas are colour coded by number of taxa, with darker tones indicating more taxa. In both a and b upland areas or islands where the distributions of two or more threatened species overlap are labelled and the number of threatened taxa are indicated in parentheses. Background maps uses the Shuttle Radar Topography Mission (SRTM) 30-meter digital elevation model, accessed from USGS Earth Explorer (https://earthexplorer.usgs.gov/).Full size imageUnderstanding and conserving a megadiverse biotaThe Melanesian flora and frog fauna are both now shown to be megadiverse and highly endemic, yet both also remain poorly known with large areas under-surveyed. An updated comprehensive assessment of threats and taxonomic trends across the frog fauna presented here further highlights that the biota of Melanesia remains relatively intact and less threatened when compared to other biodiverse insular regions. However, a large proportion of the fauna remains Data Deficient or undescribed, and key hotspots of endemism have been overlooked and are increasingly threatened. In both plants and anurans much scientific knowledge of Melanesia’s biota has also been contributed by a relatively small number of productive, but later-career researchers based outside of Melanesia7.Further documenting and conserving the exceptional diversity of Melanesia presents a suite of challenges and opportunities. Recommendations to enable improved documentation of plant megadiversity in Melanesia7 centre around training, capacity-building and support for taxonomy in Melanesia and globally, improving access to specimen collections and diagnostic resources, and ongoing support for survey and collecting within Melanesia. These recommendations apply equally to amphibians. However, addressing these challenges is tempered by the limited career opportunities available to ecologists and taxonomists (both in developed, but especially in developing countries), the variable quality of scientific infrastructure that exists across the region, and the high cost of doing fieldwork in remote areas with limited logistical infrastructure. In the context of these challenges, we hereby focus on suggesting some short-term key priorities and opportunities to build capacity for understanding and conserving frog biodiversity in Melanesia.First, over the last twenty years opportunities to employ Melanesian nationals in survey, monitoring and outreach work have been (and will continue to be) generated predominantly by NGOs, universities and large-scale extractive projects, for example through recent work in the gas fields of the Papua New Guinea Highlands49. While there are diverse perspectives on extractive industries, monitoring and survey work associated with large development projects are a key source of funds to provide training to enable Melanesians to undertake biodiversity work within the region. A key driver of this is strong environmental legislation required by some governments and major lending agencies, in particular the International Finance Corporation under Performance Standard 655. These requirements need to be maintained, enforced and, where possible, exceeded.To further support fieldwork by national scientists there is a need for more readily accessible identification resources for Melanesian researchers, land-owners and managers. An up-to-date comprehensive identification guide to the frog fauna of the whole region would assist and promote taxonomic, ecological and conservation research. However, for many Melanesians, small, regionally focused guides are more usable. These have already been produced for several areas (Supplementary References), providing a model that can be updated and transferred to other regions. Mobile phones are widely used throughout Melanesia, so app- and online-based identification resources may become increasingly accessible. Smartphone-friendly citizen science platforms like iNaturalist56 or even Facebook groups57 also provide potentially powerful resources through which locally collected data can be captured, vetted and disseminated, although their use is currently limited in Melanesia due to patchy internet coverage in many areas. Working with and supporting people from Melanesia to explore and increase the use of these resources could help to ensure longer-term preservation and accessibility of species records and associated data.The latest IUCN assessment for Melanesian frogs also highlights how taxonomic and conservation knowledge is accumulating rapidly. The key geographic areas of threat identified in our study were largely invisible to assessments made less than two decades ago (in 2004) both because the relevant taxonomic work had not been done, and because the situation in Melanesia is changing rapidly. To keep track of these rapid changes it is critical for workers in the region to work together to synthesise and collate new taxonomic, distributional and conservation data. Indeed, since the 2019 IUCN assessment over 20 additional species of Melanesian frogs have been described, and their conservation status should be assessed as a matter of urgency. Preliminary conservation assessments against IUCN criteria are increasingly being included in descriptions, and this trend should be supported and encouraged. More Melanesian nationals need to be involved in conservation assessment processes. Updated comprehensive conservation assessments of other vertebrate groups will also identify complementarity of conservation priorities among taxa in the Melanesian region.Patterns of distribution and threat suggest some geographic priority areas for documenting the diversity of amphibians (and potentially other low-vagility taxa) in Melanesia. First, work in eastern New Guinea has allowed the delineation of geographically localised clusters of threatened taxa that have until now gone unnoticed, perhaps in part because of the designation of much of Melanesia as a sparsely populated and comparatively undisturbed ‘wilderness’ area21. Most threatened frog taxa in these regions are associated with small islands or isolated ‘sky island’ mountains. The degree to which other taxa show endemism in these areas is poorly known. The biotas of potentially comparable islands in Indonesia such as the Raja Ampat Islands, Geelvink Bay and southern Maluku, also remain poorly known, suggesting additional priority areas for survey, taxonomic investigation and conservation assessment. Second, mid-elevation areas show highest alpha diversity, but large areas of this habitat, especially along the northern slopes of the Central Cordillera, remain poorly surveyed. The frog pathogen Bd has devastated montane communities of two Australian frog families that also occur in montane New Guinea (Myobatrachidae and Pelodryadidae)52. In the unfortunate event that Bd colonised New Guinea a wave of rapid declines and extinctions would likely follow52, so a strong baseline of information on montane species diversity, distributions and population status is critical for detecting these impacts. More

Seed sampling and germinationSeed from ten trees from each of 21 native Scottish Scots pine populations (Table 1) were collected in March 2007 and germinated at the James Hutton Institute, Aberdeen (latitude 57.133214, longitude −2.158764) in June 2007. Populations were chosen to represent the species’ native range in Scotland and to include three populations from each of the seven seed zones (Fig. 2). There was no selection of seed-trees on the basis of any traits except for the possession of cones on the date of sampling. Ten seed trees were sampled from each population according to a spatial protocol designed to cover a circle of approximately 1 km in diameter located around a central tree. The sampling strategy identified nine points each in a pre-determined random direction from the central point, whilst stratifying the number sampled with increasing distance from the central point in the ratio 1: 3: 5. This strategy avoids over-sampling the areas close to the centre point. For smaller fragments of woodland, or where only a few trees with cones were present, then the directions of the sampled trees from the central tree were maintained to give a wide coverage of the woodland area, but the distances between trees varied but were never closer than 50 m. To break dormancy, seeds were soaked for 24 hours on the benchtop at room temperature, after which they were stored in wet paper towels and refrigerated in darkness at 3–5 °C for approximately 4 weeks. Seeds were kept moist and transferred to room temperature until germination began (approx. 5–7 days), then transplanted to 8 cm × 8 cm × 9 cm, 0.4 L pots filled with Levington’s C2a compost and 1.5 g of Osmocote Exact 16–18 months slow release fertiliser and kept in an unheated glasshouse. The compost was covered with a layer of grit to reduce moss and liverwort growth. Seedlings from the same mother tree are described as a family and are assumed to be half-siblings.Table 1 Locations and basic environmental data for the populations sampled for seed to establish the trial. See the maternal traits dataset15 for precise data for each mother tree sampled.Full size tableExperimental design: nurseriesThe full collection consisted of 210 families (10 families from each of 21 populations) each consisting of 24 half sibling progeny (total 5,040 individuals); needle tissue was sampled from each seedling and preserved for long term storage, one needle on silica gel, 2–5 needles at −20 °C. After transfer into pots, 8 seedlings per family were moved to one of three nurseries (total 1,680 seedlings per nursery): outdoors at Inverewe Gardens in western Scotland (nursery in the west of Scotland: coded NW, latitude 57.775714, longitude −5.597181, Fig. 2); outdoors in a fruit cage (to minimise browsing) at the James Hutton Institute in Aberdeen (nursery in the east of Scotland: NE); in an unheated glasshouse at the James Hutton Institute in Aberdeen (nursery in a glasshouse: NG). Trees were arranged in 40 randomised trays (blocks) in each nursery. Each block contained two trees per population (total 42 trees). Watering was automatic in NG, and manually as required for NE and NW. No artificial light was used in any of the nurseries. In May 2010 the seedlings from NG were moved outdoors to Glensaugh in Aberdeenshire (latitude 56.893567, longitude −2.535736). In 2010 all plants were repotted into 19 cm (3 L) pots containing Levingtons CNSE Ericaceous compost with added Osmocote STD 16–18 month slow release fertilizer.Experimental design: field sitesIn 2012 the trees were transplanted to one of three field sites: Yair in the Scottish Borders (field site in the south of Scotland: FS, latitude 55.603625, longitude −2.893025); Glensaugh (field site in the east of Scotland: FE); and Inverewe (field site in the west of Scotland: FW). All trees transplanted to FS were raised in the NG and all but four of the trees transplanted to FE were raised locally in the NE (the remainder were grown in NG). In contrast, following mortality and ‘beating up’ (filling gaps where saplings had died), the FW experiment ultimately contained cohorts of trees raised in each of the three nurseries as follows: 290 grown locally in the NW; 132 were grown in the NG; and 82 were grown in the NE.Site historiesThe Yair site (FS) had previously been used for growing Noble fir (Abies procera) for Christmas trees and Lodgepole pine (Pinus contorta), a section of the former were felled and chipped to create a clear area prior to planting. The planting site is also adjacent to a large block of commercial Sitka spruce (Picea sitchensis) forestry, and the Glenkinnon Burn Site of Special Scientific Interest (SSSI NatureScot site code 736; EU site code 135445), an area of mixed broadleaf woodland. Prior to planting, major areas of tall weeds were strimmed. The site was protected by a deer fence. The experiment was planted 8–11 October 2012. The Glensaugh site (FE) is in Forestry Compartment 3 of the Glensaugh Research Station, adjacent to Cleek Loch. It is thought to have been cleared of Scots pine and Larch (Larix decidua) around 1917, after which it reverted to rough grazing. An attempt to reseed part of the site in the 1980s was unsuccessful and it quickly reverted to rough grazing for a second time. The whole site (within which the experimental area is embedded) was deer fenced and re-planted under the Scottish Rural Development Programme (SRDP) in 2012. The experimental plot was planted up 7–9 March 2012. The Inverewe site (FW) had previously been a Sitka spruce and Lodgepole pine plantation (50:50 mix) that had been clear-felled in 2010 following substantial windthrow. The experimental site was deer fenced in early 2012, and the experiment was planted 12–16 March 2012, followed by beating up on 27–28 March 2013 and 22–24 October 2013. There had been minimal preparation of the site in line with current practice for restocking sites. The experimental site is included in the Inverewe Forest Plan, which included deer fencing of a larger area (2014) around the experimental site. Planting of this area was completed in early 2015, funded by NTS (National Trust for Scotland), although natural regeneration is also taking place.At each site, trees were planted in randomised blocks at 3 m × 3 m spacing. There are four randomised blocks in both FS and FE and three in FW. A guard row of Scots pine trees was planted around the periphery of the blocks and between blocks B and C at FS. Each block comprised one individual from each of eight (of the 10 sampled) families per 21 populations (168 trees). Although most families (N = 159) were represented at each of the three sites, families with insufficient trees (N = 9) were replaced in one site (FS) with a different family from the same population. Each experimental site was designed with redundancy such that, if thinning becomes necessary as the trees mature, then the systematic removal of trees (i.e. trees 1,3,5,7, etc of row 1, and 2,4,6,8, etc of row 2, 1,3,5,7,etc of row 3) will maintain a balanced design of the experiment, with sufficient family and population representation to provide an ongoing experiment with full geographic coverage.The field sites generally experience different climates, with FW typically warmer and wetter and with more growing degree days per year and a much longer growing season than both FE and FS (Table 2). The coldest site with the shortest growing season is generally FE.Table 2 Average climatic variables at field sites Glensaugh (FE), Inverewe (FW) and Yair (FS) from planting in 2012 until 2020. Climatic variables are derived from data provided by the Met Office (daily mean, minimum and maximum temperatures and monthly rainfall).Full size tablePhenotype assessmentsMaternal traitsFollowing seed collection, a range of traits were measured in the mother trees in order to control for maternal effects in subsequent measurements of their progeny (Table 3). For each mother tree, measurements of height and diameter at breast height (DBH) were taken, and ten cones were collected and assessed in detail. Cone width and length were measured prior to drying the cones (when they were still closed). Cone weight was measured post-drying. Seed removed from each cone was assessed for total weight (after wings had been removed) and for the count and percentage of seeds which were classed as viable (viable seed were those which had both a wing and an obvious seed). No further seed sorting was applied.Table 3 Traits assessed in mother trees, cones, seeds (dataset: Maternal), nursery seedlings (dataset: Nursery) and field trials (dataset: Field). Within the datasets, traits are recorded in a single column for each year using the format Code-Year (e.g. absolute height in 2008 = HA08) except for the maternal traits datasets which were all measured in 2007.Full size tableNursery traitsSeedling phenotype assessments were performed annually from 2007–2010 for three different trait types: phenology (budburst and growth cessation); form (total number of buds, needle length); cumulative growth (stem diameter and height, canopy width). Measurements of tree form and cumulative growth traits were taken after the end of each growing season. Phenology was assessed weekly during the spring and autumn of 2008 for budburst and growth cessation, respectively. Budburst was defined as the number of days from 31 March 2008 to the time when newly emerged green needles were observed (budburst stage 6: Fig. 3). In some seedlings in 2008, a secondary flush of growth occurred from terminal buds that had formed during the summer of that year. Therefore, growth cessation was defined retrospectively as the number of days from 10 September 2008 to the date when a terminal bud had formed on the leading shoot of the seedling, providing no further growth was observed either on the stem below that bud, nor from the bud itself. Canopy width (widest point) was measured at two perpendicular points in the horizontal plane. Needle length was measured for three needles per tree. Mortality was recorded each year from 2007 to 2010.Fig. 3Phenological stages of bud burst in Pinus sylvestris assessed in field trials. Inset numbers correspond to budburst stage. Budburst stage 1: bud dormant; 2: bud swelling and showing signs of linear expansion; 3: scales open at base revealing green tissue. Remaining bud remains encased by smooth bud scales; 4: scales open along length of shoot revealing green tissue and partially visible needles; 5: white tipped needles visible along length of the shoot; 6: green needles emerging away from the shoot (bottle brush appearance) along its entire length; 7: Needles have separated and next year’s terminal bud is usually formed and clearly visible.Full size imageField traitsTree height was measured in the field in the winter after each growing season from 2013 at FE and FW, and from 2014 to 2020 at all sites. Height was taken as the vertical measurement in cm from top bud straight to the ground. Basal stem diameter was measured at the end of the growing season for trees growing at FE and FW from 2014 to 2020 and for FS in 2020.Phenology assessments were performed in spring at each site from 2015 to 2019. Seven distinct stages of budburst (assessed on the terminal bud) were defined (Fig. 3) although only stages 4 to 6 are included in the dataset and considered for analysis due to high proportions of missing data for the early and late stages. Each tree was assessed for budburst stage at weekly intervals from early spring until budburst was complete. In order to allow comparisons within and among sites and years, the date at which each stage of budburst occurred was considered relative to 31 March of that year. For example, 25 May 2019 is recorded as 55 days since 31 March 2019. The duration of budburst (time taken to reach stage 6 from stage 4) was also estimated.When trees progressed through budburst stages rapidly, skipping a stage between assessments, a mean value was taken from the two assessment dates. For example, if a tree was at stage 4 on day 55 and was recorded as stage 6 at the next assessment on day 62, it is assumed to have reached stage 5 at day 58.5. More

The framework of Swin MSIWe established the first Swin Transformer-based mosquito species identification (Swin MSI) model, with the help of self-constructed image dataset and multi-adjustment-test. Gradient-weighted class activation mapping was used to visualize the identification process (Fig. 1a). The key Swin Transformer block was described on Fig. 1b. Based on practical needs, Swin MSI was additional designed to identify Culex pipiens Complex on the subspecies level (Fig. 1c) and novel mosquito (which was defined as ones beyond 17 species in our dataset) classification attribution (Fig. 1d). Detailed results are shown in the following sections.Figure 1The Framework of Swin MSI. (a)The basic architecture for mosquito features extraction and identification. Attention visualization generated by filters at each layer are shown. (b) Details for Swin Transformer block. (c) For mosquito within our dataset 17 species, output is the top 5 confidence species. (d) For mosquito beyond 17 species (defined as novel species), whether the output is a species or a genus is decided after comparing with confidence threshold.Full size imageMosquito datasetsWe established the highest-definition and most-balanced mosquito image dataset to date. The mosquito image dataset covers 7 genera and 17 species (including 3 morphologically similar subspecies in the Cx. pipiens Complex), which covers the most common and important disease-transmitting mosquitoes at the global scale, with a total of 9,900 mosquito images. The image resolution was 4464 × 2976 pixels. The specific taxonomic status and corresponding images are shown in Fig. 2. Due to the limitation of field collection, Ae. vexans, Coquillettidia ochracea, Mansonia uniformis, An. vagus and Toxorhynchites splendens only have females or only have males. In addition, each mosquito species included 300 images of both sexes, which was large enough and same number for each species, in order to balance the capacity and variety of training sets.Figure 2Taxonomic status and index of mosquito species included in this study Both male and female mosquitoes were photographed from different angles such as dorsal, left side, right side, ventral side, etc. Except for 5 species, each mosquito includes 300 images of both sexes, and the resolution of mosquito photos were 4464 × 2976. Cx. pipiens quinquefasciatus, Cx. pipiens pallens, and Cx. pipiens molestus (subspecies level, in dark gray background) were 3 subspecies in Cx. pipiens Complex (species level).Full size imageWorkflow for mosquito species identificationA three-stage flowchart of building best deep learning model for identification of mosquito species model was adopted (Fig. 3). The first learning stage was conducted by three CNNs (the Mask R-CNN, DenseNet, and YOLOv5) and three transformer models (the Detection Transformer, Vision Transformer, and Swin Transformer). Based on the performance of the first-stage model and the real mosquito labels, the second learning stage involved adjusting the model parameters of the three Swin Transformer variants (T, B, and L) to compare their performances. The third learning stage involved testing the effects of inputting differently sized images (384 × 384 and 224 × 224) to the Swin Transformer-L model; finally, we proposed a deep learning model for mosquito species identification (Swin MSI) to test the recognition effects of different mosquito species. The model was validated on different mosquito species, with a focus on the identification accuracy of three subspecies within the Cx. pipiens Complex and the detection effect of novel mosquito species.Figure 3Flowchart of testing deep learning model for intelligent identification of mosquito species.Full size imageComparison between the CNN model and Transformer model results (1st round of learning)Figure 4a shows the accuracies obtained for the six different computer vision network models tested on the mosquito picture test set. The test results show that the transformer network model had a higher mosquito species discrimination ability than the CNN.Figure 4Comparison of mosquito recognition effects of computer vision network models and variants. (a) Comparison of mosquito identification accuracy between 3 CNNs and 3 Transformer; (b) The best effect CNN (YOLOv5) training set loss curve(blue), validation set loss curve(green) and validation set accuracy curve(orange); (c) The best effect Transformer (Swin Transformer) training set loss curve, validation set loss curve and validation set accuracy curve. (d) Swin-MSI-T test result confusion matrix; (e) Swin-MSI -B test result confusion matrix; (f) Swin-MSI -L test result confusion matrix. Confusion matrix of mosquito labels in which odd numbers represent females and even numbers represent males. The small squares in the confusion matrix represent the recognition readiness rate, from red to green, the recognition readiness rate is getting higher and higher An. sinensis: 1, 2; Cx. pipiens quinquefasciatus: 3, 4; Cx. pipiens pallens: 5, 6; Cx. pipiens molestus: 7,8 Cx. modestus: 9,10; Ae. albopictus: 11, 12 Ae. aegypti: 13, 14; Cx. pallidothorax: 15, 16 Ae. galloisi: 17,18 Ae. vexans: 19, 20; Ae. koreicus: 21, 22 Armigeres subalbatus: 23, 24; Coquillettidia ochracea: 25, 26 Cx. gelidus: 27, 28 Cx. triraeniorhynchus: 29, 30 Mansonia uniformis: 31, 32 An. vagus: 33, 34 Ae. elsaie: 35,36 Toxorhynchites splendens: 37, 38.Full size imageIn the CNN training process (applied to YOLOv5), the validation accuracy requires more than 110 epochs to grow to 0.9, and the validation loss requires 110 epochs to drop to a flat interval; in contrast, during the training step, these losses represent a continuously decreasing process. These results indicate that the deep learning model derived based on the Swin Transformer algorithm was able to achieve a higher recognition accuracy in less time than the rapid convergence ability of the CNN during the iterative process (Fig. 4b).The Swin Transformer model exhibited the highest test accuracy of 96.3%. During the training process, the loss of this model could stabilize after 30 epochs, and its validation accuracy could grow to 0.9 after 20 epochs; during the validation step, the loss can drop to 0.36 after 20 epochs, after which the loss curve fluctuated but did not produce adverse effects (Fig. 4c). Based on the excellent performance of the Swin Transformer model, this model was used as the baseline to carry out the subsequent analyses.Swin Transformer model variant adjustment (2nd round of learning)Following testing performed to clarify the superior performance of the Swin Transformer algorithm, we chose different Drop_path_rate, Embed_dim and Depths parameter settings and labeled the parameter sets as the Swin Transformer-T, Swin Transformer-B, and Swin Transformer-L variants. Drop_path is an efficient regularization method, and an asymmetric Drop_path_rate is beneficial for supervised representation learning when using image classification tasks and Transformer architectures. The Embed_dim parameter represents the image dimensions obtained after the input red–green–blue (RGB) image is calculated by the Swin Transformer block in stage 1. The Depths parameter is the number of Swin Transformer blocks used in the four stages. The parameter information and test results are shown in Table 1. Due to the increase in the Swin Transformer block and Embed_dim parameters in stage 3, the recognition accuracies of the three variants were found to be 95.8%, 96.3%, and 98.2%, Correspondingly, the f1 score were 96.2%, 96.7% and 98.3%; thus, these variants could effectively improve the mosquito species identification ability in a manner similar to the CNN by increasing the number of convolutional channels to extract more features and improve the overall classification ability. In this study, the Swin Transformer-L variant, which exhibited the highest accuracy, was selected as the baseline for the next work.Table 1 Parameters and test accuracy of three variants of Swin Transformer.Full size tableBy plotting a confusion matrix of the test set results derived using the three Swin Transformer variants, we clearly obtained the proportion of correct and incorrect identifications in each category to visually reflect the mosquito species discrimination ability (Fig. 4d–f). In the matrix, the darker diagonal colors indicate higher identification rate accuracies of the corresponding mosquito categories. Among them, five mosquito species were missing because the Ae. vexans, Coquillettidia ochracea, Mansonia uniformis, An. vagus and Toxorhynchites splendens species were represented in the dataset by only females or only males. The confusion matrix shown in Panel C lists the lowest number of mosquito species identification error points and the lowest accuracy level obtained in each category, suggesting that the Swin Transformer-L model has a better classification performance than the Swin Transformer-T and Swin Transformer-B models.Effect of the input image size on the discrimination ability (3rd round of learning)To investigate the relationship between the input image size and mosquito species identification performance, in this study, we conducted a comparison test between input images with sizes of 224 × 224 and 384 × 384, based on the Swin Transformer-L model, and identified 8 categories of mosquito identification accuracy differences. These test results are shown in Table 2. When using an image size of 224 × 224 pixels, the batch_size parameter was set to 16, and when using an image size of 384 × 384 pixels, the batch_size parameter was set to 4; under these conditions, the proportion of utilized video memory accounted for 67%, as shown in Eq. 4, and this was consistent with the description of the relationship between the size of self-attentive operations during the operation of the Swin Transformer model when 384 × 384 pixels images were used. The time required for the Transformer-L model to complete all the training sessions was excessive, reaching 126 h and even exceeding the 124 h required by the YOLOv5 model, which was found to require the highest computation time during the training process in this work. Long-term training process could more fully reflect the performance differences between models. Fortunately and actually, the response speed of the model will not be affected by the training time. Compared to the accuracy of 98.2% obtained for 224 × 224 inputs, the 384 × 384 input image size derived based on the Swin Transformer-L model provided a higher mosquito species identification accuracy of 99.04%, representing an improvement of 0.84%.$$Omega ({text{W}} – {text{MSA}}) = 4{text{HWC}}^{2} + 2{text{M}}^{2} {text{HWC}}$$
(1)
Table 2 Comparison of recognition accuracy for different input image sizes.Full size tableVisualizing and understanding the Swin MSI modelsTo investigate the differences in the attentional features utilized by the Swin MSI and taxonomists for mosquito species identification, we applied the Grad-CAM method to visualize the Swin MSI attentional areas on mosquitoes at different stages. Because the Swin Transformer has different attentional ranges among its multi-head self-attention steps in different stages, different attentional weights can be found on different mosquito positions. In stage 1, the feature dimension of each patch was 4 × 4 × C, thus enabling the Swin Transformer’s multi-head self-attention mechanism to give more attention to the detailed parts of the mosquitoes, such as their legs, wings, antennae, and pronota. In stage 2, the feature dimension of each patch was 8 × 8 × 2C, enabling the Swin Transformer’s multi-head self-attention mechanism to focus on the bodies of the mosquitoes, such as their heads, thoraces, and abdomens. In stage 3, when the feature dimension of each patch was 16 × 16 × 4C, the Swin Transformer’s multi-head self-attention mechanism could focus on most regions of the mosquito, thus forming a global overall attention mechanism for each mosquito (Fig. 5). This attentional focus process is essentially the same as the process used by taxonomists when classifying mosquito morphology, changing from details to localities to the whole mosquito.Figure 5Attention visualization of representative mosquitoes of the genera Ae., Cx., An., Armigeres, Coquillettidia and Mansonia. This is a visualization for identifying the regions in the image that can explain the classification progress. Images of Toxorhynchites contain only males, with obvious differences in morphological characteristics, are not shown.Full size imageAe. aegypti is widely distributed in tropical and subtropical regions around the world and transmits Zika, dengue and yellow fever. A pair of long-stalked sickle-shaped white spots on both shoulder sides of the mesoscutum, with a pair of longitudinal stripes running through the whole mesotergum, is the most important morphological identification feature of this species. This feature was the deepest section in the attention visualization, indicating that the Swin MSI model also recognized it as the principal distinguishing feature. In addition, the abdominal tergum of A. aegypti is black and segments II-VII have lateral silvery white spots and basal white bands; the model also focused on these areas.Cx. triraeniorhynchus is the main vector of Japanese encephalitis; this mosquito has a small body size, a distinctive white ring on the proboscis (its most distinctive morphological feature), and a peppery color on its whole body. Similarly, the model constructed herein focused on both the head and abdominal regions of this species.An. sinensis is the top vector of malaria in China and has no more than three white spots on its anterior wing margin and a distinct white spot on its marginal V5.2 fringe; this feature was observed in Stage 2, at which time the modelstrongly focused on the corresponding area.The most obvious feature of Armigeres subalbatus is the lateral flattening and slightly downward curving of its proboscis; the observation of the attention visualization revealed that the constructed model focused on these regions from Stage 1 to Stage 3. The mesoscutum and abdominal tergum were not critical and were less important for identification than the proboscis, and the attention visualization results correspondingly show that the neural network focused less on these features.Coquillettidia ochracea belongs to the Coquillettidia genus and is golden yellow all over its body, with the most pronounced abdomen among the analyzed species. The model showed a consistent morphological taxonomic focus on the abdomen of this species.Mansonia uniformis is a vector of Malayan filariasis. The abdominal tergum of this species is dark brown, and its abdominal segments II-VII have yellow terminal bands and lateral white spots, which are more obvious than the dark brown feature on proboscis. Through the attention visualization, we determined that the Swin MSI model was more concerned with the abdominal region features than with the proboscis features.Subspecies-level identification tests of mosquitos in the Culex pipiens ComplexFine-grained image classification has been the focus of extensive research in the field of computer vision25,26. Based on the test set (containing 270 images) constructed herein for three subspecies of the Cx. pipiens Complex, the subspecies and sex identification accuracies were 100% when the Swin MSI model was used.The morphological characteristics of Cx. pipiens quinquefasciatus, Cx. pipiens pallens, and Cx. pipiens molestus within the Cx. pipiens Complex are almost indistinguishable, but their host preferences, self-fertility properties, breeding environments, and stagnation overwintering strategies are very different27. Among the existing features available for morphological classification, the stripes on the abdominal tergum of Cx. pipiens quinquefasciatus are usually inverted triangles and are not connected with the pleurosternums, while those of Cx. pipiens pallens are rectangular and are connected with the pleurosternums. Cx. pipiens molestus is morphologically more similar to Cx. pipiens pallens as an ecological subspecies of the Cx. pipiens Complex. However, taxonomists do not recommend using the unstable feature mentioned above as the main taxonomic feature for differentiation. By analyzing the attention visualization results of these three subspecies (last three rows on Fig. 5), we found that the neural networks of Cx. pipiens quinquefasciatus, Cx. pipiens pallens, and Cx. pipiens molestus still focused on the abdominal regions, as shown in dark red. The area of focus of these neural networks differ from that of the human eye, and the results of this study suggest that the Swin MSI model can detect finely granular features among these three mosquito subspecies that are indistinguishable to the naked human eye.Novel mosquito classification attributionAfter we performed a confidence check on the successfully identified mosquito images in the dataset, the lowest confidence value was found to be 85%. A higher confidence threshold mean stricter evaluation criteria, which can better reflect the powerful performance of the model. Therefore, 0.85 was set as the confidence threshold when judging novel mosquitoes. When identifying 10 unknown mosquito species, the highest derived species confidence level was below 85%; when the results were output to the genus level (Fig. 1d), the average probability of obtaining a correct judgment was 96.26%accuracy and 98.09% F1-score (Table 3). The images tested as novel Ae., Cx. and An. mosquito were from Minakshi and Couret et al.28,29.Table 3 Probability of correct attribution of novel species.Full size table More

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Sites overview and characteristicsThis study focused on three regions located in subantarctic, arctic, and subarctic latitudes. The respective latitudinal and longitudinal ranges covered in this study were: 54.95 to 52.08 °S, and 72.03 to 67.34 °W in Patagonia; 67.44 to 67.54 °N, and 86.59 to 86.71 °E in Siberia; 63.21 to 68.63 °N, and −150.79 to −145.98 °W in Alaska (Figs. 1 and 2). The exact coordinates for each sample were included in the submitted dataset. The field campaigns were conducted in 2016, during the summer for each respective region: January-February in Chilean Patagonia, June-July in Alaska and July-August in Siberia.Fig. 1Location of the three areas included in this study (panel a). The permafrost state and the number of sites and samples per region is indicated for each area. General views of 5 sites are provided as examples (b–f). Panel B provides a large view of the ecosystem surrounding the wetland ALP2 (Alaska, exact location indicated by the white circle). Lake PCL1 (panel c) is representative of the lakes on Navarino island (Chilean Patagonia). The glacial lake SIL2 is shown in panel d. At site SIP5, the hollow at first plan is surrounded by palsa (hummock, second plan), characterized by dark organic matter and lichen vegetation (panel e). The PPP3 peatland shown in panel f is dominated by Sphagnum magellanicum, like most peatlands in the area.Full size imageFig. 2Maps of sampling sites in Patagonia, Alaska and Siberia, indicating the ecosystem type (lake, wetland, soil). The tables show the complete- (in white) and the partial- (in grey) characterization sites. The exact coordinates of each sample are provided in the data record (See data records section).Full size imageFor every site included in the present study, a set of nine qualitative environmental and/or ecological site-scale descriptors was selected and adapted from ENVO Environment Ontology40, which included for example permafrost state, biome, environmental feature and vegetation type (Table 1, Fig. 3). Permafrost state was obtained from the NSIDC permafrost map41. The biome, large-scale descriptor based on climate and vegetation criteria, was derived from Olson et al.42. Temperate forest, boreal forest, and tundra biomes were included. The environmental features that were representative for the three regions were considered: lakes, wetlands, broadleaf/coniferous/mixed forest soils, grassland, tundra, and palsa. All the metadata was included in the submitted dataset. Table 2 summarizes the main types of sampled ecosystems and their main characteristics in the three regions, while Supplementary Table S1 provides the details of each sampling site.Table 1 Overview of the dataset contained in Mimarks sheet.Full size tableFig. 3Description of the qualitative environmental/ecological descriptors used to describe every sample, derived from ENVO Environment Ontology40.Full size imageTable 2 Main types of sampled ecosystems in the three studied regions.Full size tableIn Alaska, the studied area ranged from the Alaska Range and Fairbanks area (interior, continental climate, 63–65°N, discontinuous permafrost) up to Toolik Field Station (North Slope, arctic climate, 66–69°N, continuous permafrost; Fig. 2). The physiochemistry and CH4 emissions of lakes ALL1 (Killarney lake), ALL2 (Otto lake), ALL3 (Nutella lake), and ALL4 (Goldstream lake) were previously characterized35. A number of heterogeneous soil and wetland samples were collected around the studied Alaskan lakes and/or from monitored sites, as detailed in Supplementary Table S1. In the Alaska Range and Fairbanks area, soils were mostly covered by mixed or taiga forests, alpine tundra, and bogs or fens wetlands. In the norther Brooks Ranges mountain system, the landscape was piedmont hills with a predominant soil of porous organic peat underlain by silt and glacial till, all in a permafrost state, characterized mainly by Sphagnum and Eriophorum vegetation, as well as dwarf shrubs.In Siberia, the studied area was located in the discontinuous permafrost region surrounding Igarka, on the eastern bank of the Yenisei River (Fig. 2). This region was mainly covered by forest, dominated by larch (Larix Siberica), birch (Betula Pendula), and Siberian pine (Pinus Siberica), and palsa landscapes (frozen peat mounts), the latter being dominated by moss, lichens, Labrador tea and dwarf birch. In degraded areas, thermokarst bogs were dominated by Sphagnum spp. and Eriophorum spp. Land cover was an indicator of permafrost status, since forested areas reflected a deep permafrost table ( >2 m) associated with Pleistocene permafrost, while palsa-dominated landscapes were indicative of the presence of near-surface ( More

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