The functional stability of ecosystems depends greatly on interspecific differences in responses to environmental perturbation. However, responses to perturbation are not necessarily invariant among populations of the same species, so intraspecific variation in responses might also contribute. Such inter-population response diversity has recently been shown to occur spatially across species ranges, but we lack estimates of the extent to which individual populations across an entire community might have perturbation responses that vary through time. We assess this using 524 taxa that have been repeatedly surveyed for the effects of tropical forest logging at a focal landscape in Sabah, Malaysia. Just 39 % of taxa – all with non-significant responses to forest degradation – had invariant responses. All other taxa (61 %) showed significantly different responses to the same forest degradation gradient across surveys, with 6 % of taxa responding to forest degradation in opposite directions across multiple surveys. Individual surveys had low power (< 80 %) to determine the correct direction of response to forest degradation for one-fifth of all taxa. Recurrent rounds of logging disturbance increased the prevalence of intra-population response diversity, while uncontrollable environmental variation and/or turnover of intraspecific phenotypes generated variable responses in at least 44 % of taxa. Our results show that the responses of individual species to local environmental perturbations are remarkably flexible, likely providing an unrealised boost to the stability of disturbed habitats such as logged tropical forests.### Competing Interest StatementThe authors have declared no competing interest.

Logged and disturbed forests are often viewed as degraded and depauperate environments compared with primary forest. However, they are dynamic ecosystems(1) that provide refugia for large amounts of biodiversity2,3, so we cannot afford to underestimate their conservation value4. Here we present empirically defined thresholds for categorizing the conservation value of logged forests, using one of the most comprehensive assessments of taxon responses to habitat degradation in any tropical forest environment. We analysed the impact of logging intensity on the individual occurrence patterns of 1,681 taxa belonging to 86 taxonomic orders and 126 functional groups in Sabah, Malaysia. Our results demonstrate the existence of two conservation-relevant thresholds. First, lightly logged forests (<29% biomass removal) retain high conservation value and a largely intact functional composition, and are therefore likely to recover their pre-logging values if allowed to undergo natural regeneration. Second, the most extreme impacts occur in heavily degraded forests with more than two-thirds (>68%) of their biomass removed, and these are likely to require more expensive measures to recover their biodiversity value. Overall, our data confirm that primary forests are irreplaceable5, but they also reinforce the message that logged forests retain considerable conservation value that should not be overlooked.

Description: Examining rates at which vertebrate and invertebrate functional groups carry out 3 key ecosystem functions (seed removal, invertebrate predation and scavenging) and whether this changes across the SAFE project forest quality gradient. At second order sites (tree plots) within the SAFE project landscape, bait stations to test these three processes were set up. These consisted of 10 seeds (to test seed removal), live mealworm (to test invertebrate predation) or dead mealworm (to test scavenging). 3 bait stations for each ecosystem process set up in a triangle at the third order point (insect point). These consisted of baits attached to a plastic leaf. Each of these bait stations was assigned vertebrate exclusion treatment (wire cage), invertebrate exclusion (insect glue) or control (no exclusion). Data obtained from LIDAR used as a proxy for forest quality. This should help unravel how ecosystem process rates and the dominant functional group carrying out these processes may change as forests are degraded.Project: This dataset was collected as part of the following SAFE research project: MRes Tropical Forest Ecology Field CourseXML metadata: GEMINI compliant metadata for this dataset is available hereFiles: This consists of 1 file: Ecosystem_Process_Rates.xlsxEcosystem_Process_Rates.xlsxThis file contains dataset metadata and 1 data tables:Rates of Ecosystem Processes (described in worksheet Ecosystem-Process-Rates)Description: Results from ecosystem process rates experiments (described above)Number of fields: 29Number of data rows: 2039Fields: ID: Location of sampling point (Field type: location)ec5_uuid: Entry code on epicollect (Field type: id)created_at: Date and Time (Field type: datetime)created_by: Author email (Field type: id)title: Title of entry on epicollect (Field type: id)X2_Block: Site ID (Field type: id)X3_Tree_plot_ID: Tree plot number (Field type: id)X4_Picture_of_tree_pl: Photo of tree plot tag (Field type: id)X5_Insect_point_ID: Insect point number (Field type: id)X6_Picture_of_insect_: Photo of insect point tag (Field type: id)X7_Repeat: Repeat (Field type: replicate)X8_Treatment: Treatment categories (Field type: categorical)X9_Date: Date (Field type: date)X10_Time: Time (Field type: time)X11_Ecosystem_Process: Ecosystem process (Field type: categorical)X13_Seeds_removed: Number of seeds removed (Field type: numeric)X14_Seeds_partially_e: Number of seeds partially eaten (Field type: numeric)X15_Seeds_untouched: Number of seeds untouched (Field type: numeric)X17_Live_mealworm: Level of consumption of live mealworm (Field type: categorical)X19_Dead_mealworm: Level of consumption of dead mealworm (Field type: categorical)X20_Condition_of_trap: Condition of trap (Field type: categorical)lat_22_GPS: NA (Field type: latitude)long_22_GPS: NA (Field type: longitude)accuracy_22_GPS: GPS accuracy level (Field type: numeric)X23_Observer_initials: Observer identity (Field type: id)X24_Photo_of_plastic_: Photo of bait station - photos stored online at Epicollect5 (Field type: id)X25_Comments: Any additional comments (Field type: comments)Dead_mealworm_binary: Dead mealworm presence (Field type: categorical)Live_mealworm_binary: Live mealworm presence (Field type: categorical)Date range: 2019-02-04 to 2019-02-21Latitudinal extent: 4.6876 to 4.7494Longitudinal extent: 116.9558 to 117.6197

Description: Results from amphibian surveys carried out along riparian transect sites at SAFE project, BorneoProject: This dataset was collected as part of the following SAFE research project: MRes Tropical Forest Ecology Field CourseXML metadata: GEMINI compliant metadata for this dataset is available hereFiles: This consists of 1 file: frogs_data_rob.xlsxfrogs_data_rob.xlsxThis file contains dataset metadata and 3 data tables:Stream Overview (described in worksheet StreamMeasuresParent)Description: Survey overview detailsNumber of fields: 16Number of data rows: 12Fields: ec5_uuid: EpiCollect 5 code (Field type: id)created_at: Date and time of measurement (Field type: date)created_by: Researcher contact email (Field type: id)title: Survey location and visit (Field type: id)2_Stream_ID: Stream idenity code (Field type: location)RiparianWidth: Riparian buffer width (Field type: numeric)lat_3_GPS_Location: Latitude (Field type: numeric)long_3_GPS_Location: Longitude (Field type: numeric)accuracy_3_GPS_Location: Accuracy of GPS location data (Field type: numeric)4_Visit: Visit number (Field type: id)5_Photo_of_stream_la: File ID of photo of river (Field type: id)7_Start_Time: Time sampling started (Field type: time)8_Date_ddMMYYYY: Calendar date of sampling (Field type: date)9_Comments_weather_e: Weather conditions (Field type: comments)11_Surveyors: Identity of surveyors (Field type: id)12_RAs: Identity of research assistants (Field type: id)Stream characteristics (described in worksheet StreamMeasures)Description: Stream characteristics (dimensions, canopy cover and substrate)Number of fields: 19Number of data rows: 105Fields: ec5_parent_uuid: EpiCollect 5 code (Field type: id)created_at: Date and time of measurement (Field type: datetime)created_by: Researcher contact email (Field type: id)StreamID: Stream idenity code (Field type: location)15_Marker_point: Identity of marker point (Field type: id)SiteCode: Location code of site (Field type: location)Width: Width of stream bed (Field type: numeric)17_Upstream_Canopy: Percentage of canopy cover upstream from point (Field type: numeric)18_Downstream_Canopy: Percentage of canopy cover downstream from point (Field type: numeric)19_Left_Canopy: Percentage of canopy cover to left of point (Field type: numeric)20_Right_Canopy: Percentage of canopy cover to right of point (Field type: numeric)20_Large_boulder__co: Percentage coverage by large boulders (Field type: numeric)21_Medium_rock__cove: Percentage coverage by medium rocks (Field type: numeric)22_Small_rock__cover: Percentage coverage by small rocks (Field type: numeric)23_Gravel__cover: Percentage coverage by gravel (Field type: numeric)24_Sand__cover: Percentage coverage by sand (Field type: numeric)25_MudGround__cover: Percentage coverage by mud (Field type: numeric)26_Substrate_cover_o: Percentage coverage by other substrate type (Field type: categorical)27_Water_flow_at_poi: Water flow at point (Field type: categorical)Frog species (described in worksheet FrogData)Description: Recorded frog species and associated body measurementsNumber of fields: 19Number of data rows: 785Fields: Stream_ID: Stream identification code (Field type: location)Date: Date (Field type: date)23_Closest_Marker: Distance along transect at which frog was recorded (Field type: numeric)SiteCode: Location code of recorded frog (Field type: location)24_Horizontal_Distan: Approximate distance of recorded frog from stream bed (Field type: numeric)25_Vertical_Distance: Approximate distance of recorded frog above stream bed (Field type: numeric)27_Substrate: Substrate on which frog was recorded (Field type: categorical)28_Substrate_if_othe: Secondary substrate on which frog was recorded (Field type: categorical)30_Dorsal: EpiCollect 5 code for photograph (dorsal) of recorded frog species (Field type: id)31_Ventral: EpiCollect 5 code for photograph (ventral) of recorded frog species (Field type: id)32_Left_side: EpiCollect 5 code for photograph (left-side) of recorded frog species (Field type: id)33_Right_side: EpiCollect 5 code for photograph (right-side) of recorded frog species (Field type: id)Species: Species or Genus level identity (Field type: taxa)36_Mass_of_frog_in_bag: Combined mass of frog and bag (Field type: numeric)38_Mass_of_empty_bag: Mass of bag alone (Field type: numeric)Mass_of_frog: Mass of frog (Field type: numeric trait)40_SnoutVent_Length: Snout-vent length of frog (Field type: numeric trait)Comment: Comments on frog identity (Field type: comments)Sex: Sex of frog (Field type: categorical trait)Date range: 2019-02-04 to 2019-02-13Latitudinal extent: 4.6498 to 4.7273Longitudinal extent: 117.5413 to 117.6414Taxonomic coverage:All taxon names are validated against the GBIF backbone taxonomy. If a dataset uses a synonym, the accepted usage is shown followed by the dataset usage in brackets. Taxa that cannot be validated, including new species and other unknown taxa, morphospecies, functional groups and taxonomic levels not used in the GBIF backbone are shown in square brackets. - Animalia- - Chordata- - - Amphibia- - - - Anura- - - - - [Other]- - - - - Bufonidae- - - - - - Ansonia- - - - - - - Ansonia spinulifer- - - - - - Phrynoidis- - - - - - - Phrynoidis juxtaspera- - - - - Dicroglossidae- - - - - - Limnonectes- - - - - - - Limnonectes finchi- - - - - - - Limnonectes kuhlii- - - - - - - Limnonectes leporinus- - - - - - - Limnonectes palavanensis- - - - - - Ingerana- - - - - - - Ingerana baluensis (as homotypic_synonym: Occidozyga baluensis)- - - - - - Fejervarya- - - - - - - Fejervarya limnocharis- - - - - - Occidozyga- - - - - - - Occidozyga laevis- - - - - Ranidae- - - - - - Chalcorana- - - - - - - Chalcorana megalonesa- - - - - - - Chalcorana raniceps- - - - - - Meristogenys- - - - - - - Meristogenys orphnocnemis- - - - - - Hylarana- - - - - - - Hylarana picturata (as synonym: Pulchrana picturata)- - - - - - Staurois- - - - - - - Staurois guttatus- - - - - - - Staurois latopalmatus- - - - - Megophryidae- - - - - - Leptolalax- - - - - - - Leptolalax fritinniens- - - - - - - Leptolalax gracilis- - - - - - Leptobrachium- - - - - - - Leptobrachium abbotti- - - - - Rhacophoridae- - - - - - Rhacophorus- - - - - - - Rhacophorus pardalis- - - - - - Polypedates- - - - - - - Polypedates macrotis

Description: Measurements of 24 hour cycles in soil CO2 flux taken from soil collars in the Belian Carbon plot at Maliau. Measurements were taken from 12 subplots over four days at 5-hourly intervals, ensuring good coverage of the complete 24 hour cycle. Air and soil temperatures, soil moisture content and CO2 flux were taken from each plot at each visit. 9 subplots only have a single total soil respiration collar, but 3 subplots also have soil flux partitioning treatments to separate contributions to total respiration from soil organic matter, mycorrhizae and roots.This data was collected by the 2019 cohort of the Tropical Forest Ecology MRes at Imperial College London. Project: This dataset was collected as part of the following SAFE research project: MRes Tropical Forest Ecology Field Course XML metadata: GEMINI compliant metadata for this dataset is available here Files: This dataset consists of 2 files: Carbon_corrected_slopes.xlsx, raw_egm.zip Carbon_corrected_slopes.xlsx This file contains dataset metadata and 2 data tables: 24 hour observations of CO2 flux patterns (described in worksheet Carbon_flux_data) Description: Estimated CO2 flux values, soil moisture and air and soil temperatures from Carbon subplots Number of fields: 14 Number of data rows: 296 Fields: record_no: EGM 'Plot' value - record number on EGM machine for this collar (Field type: ID) plot: Carbon subplot number (Field type: Location) date: Calendar date that measurements taken (Field type: Date) time: Time that measurements taken (Field type: Time) soil_wmc: Soil water moisture content (Field type: Numeric) soil_temp: Soil temperature (Field type: Numeric) air_temp: Air temperature (Field type: Numeric) treatment: Exclusion treatments for partitioning soil respiration components (Field type: Categorical) field_flux: CO2 flux reported in the field by EGM (Field type: Numeric) Source: EGM dat file of source data used for corrected fluxes where available (Field type: File) corrected_flux: Corrected flux measurements using by eye exclusion of raw flux data (Field type: Numeric) n_points: Number of points in EGM record (Field type: Numeric) n_used: Number of points used for corrected slope estimation (Field type: Numeric) flux: Final flux values, using corrected values where available (Field type: Numeric) EGM raw data (described in worksheet EGM_raw_data) Description: Duplicates key information from raw EGM files and indicates points excluded in calculation of corrected flux values Number of fields: 7 Number of data rows: 7114 Fields: Plot: EGM recorder 'plot' code, actually just the record sequence number. (Field type: ID) RecNo: EGM record number - time points of gas measurement at a single plot (Field type: ID) Datetime: Time of gas concentration measurement (Field type: Datetime) CO2.Ref: Measured CO2 (Field type: Numeric) Input.E: EGM internal variable used in slope estimation (Field type: Numeric) Source: Original EGM dat file containing the flux data (Field type: File) ignore: Indicates where points from raw data excluded from corrected slope calculations (Field type: Categorical) raw_egm.zip Description: Zipfile of raw EGM dat files Date range: 2019-02-18 to 2019-02-21 Latitudinal extent: 4.7467 to 4.7480 Longitudinal extent: 116.9693 to 116.9704