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The structure of biological communities is strongly driven by climatic conditions (e.g. seasonality) and local factors (e.g. habitat structure). In particular, seasonality affects local communities by altering resource availability and their frequency over seasons, limiting the establishment of many taxa locally. Simultaneously, local conditions (e.g. canopy height), alter the availability of nesting and foraging sites, leading to changes in local patterns of diversity. We hypothesize that rainfall decreases ground-dwelling ant richness and increases species turnover, because the heterogeneity of resources decreases with rainfall affecting ant species activity. Moreover, canopy height should enhance ant richness and beta diversity. Our sampling method involved four primary linear transects, each spaced 100 m apart. Within this framework, we established a grid of 16 collection points for pitfall-trap installation, spaced 200 m from each other while maintaining a minimum distance of 50 m from any forest border. An analysis of covariance was conducted, examining the influence of seasonal variation (dry versus rainy periods) and canopy height (CH) on ant richness and beta diversity components (turnover and nestedness). This 12-month study was conducted in a tropical relictual mountain forest in Northeastern Brazil. Our results partially supported our hypothesis, showing that an increase in rainfall led to a decrease in ant species richness and an increase in the difference in species composition (nestedness) between seasons. Additionally, CH was found to decrease species richness, total beta diversity, and turnover, with no discernible impact on nestedness. In conclusion, our results suggest that seasonal changes and canopy height might play crucial roles in shaping ant community assembly and foraging activities in tropical forest enclaves within the Caatinga biome. [ABSTRACT FROM AUTHOR]

Abstract Marine scientific trawl surveys are commonly used to assess the distribution and population size of fisheries‐related species, yet the method is effort‐intensive and can be environmentally destructive. Sequencing environmental DNA (eDNA) from water samples can reveal the presence of organisms in a community without capturing them; however, we expect the detectability of taxa to differ between eDNA and trawl surveys, and understanding how species traits and population variables contribute to detection differences can help calibrate our expectations from each form of sampling. Here, we coupled eDNA metabarcoding and capture trawl surveys in British Columbia, Canada, to examine species traits that explain recurrent differences in detectability between the two methods, including habitat, body size, and biomass. At the regional scale, 17 of 23 fish species (74%) captured by the trawl were detected by eDNA metabarcoding, and 39 additional species were detected by eDNA sampling only. We found that eDNA metabarcoding disproportionately detected trawl‐caught species with greater local biomass (i.e., greater biomass in the adjacent trawl). Fish detected only in eDNA had a greater range of body lengths and a broader range of habitat preferences outside the trawls' target size and sampling areas. Our results suggest that with our level of sampling, eDNA metabarcoding can adequately recapitulate detection of fish communities detected by trawl surveys, but with a bias toward fish of high population biomass and greater inclusion of fish from outside the trawled area.

The study investigated the microbial carbon metabolic function, functional diversity, and community similarity of six profiles from Luvisols. The Community Level Physiological Profiling (CLPP) technique and the Biolog EcoPlate method based on it were used to determine microbial carbon metabolic function and functional diversity. Soil microbial carbon metabolic function (SMCMF) was found to differ among the six soils, despite all being Luvisols. The sample TA3, under mixed broadleaf vegetation and pH 7.4, showed the highest SMCMF, while the lowest values were observed in sample TA6 under mixed broadleaf and coniferous vegetation and pH 5.1. Carbohydrates were the preferred carbon source for the microbial communities in the studied Luvisols, while the amine/amide group was poorly utilized (only in TA5). The results for functional diversity ranged from 19.35% to 38.71%, with the highest functional diversity found in samples under broadleaf vegetation (TA2, TA3, and TA5). There was a positive correlation (r=0.74) between soil microbial functional diversity and soil organic carbon content, but no such correlation was observed with soil pH. The Simple Matching Coefficient was calculated for the studied soils. TA1 and TA6, with the highest % functional diversity, showed the most similarity finger print (SMC=77%). TA3 and TA5, with the lowest % functional diversity, showed the least similarity (35%). The results of this study confirm the need for further analysis of soil microbial communities, and the importance of considering soil microbial carbon metabolic function, functional diversity and community similarity as separate parameters of the soil microbial community in forest ecosystems. [ABSTRACT FROM AUTHOR]

The concept that microbes associated with macroorganisms evolve as a unit has swept evolutionary ecology. However, this idea is controversial due to factors such as imperfect vertical transmission of microbial lineages and high microbiome variability among conspecific individuals of the same population. Here, we tested several predictions regarding the microbiota of four trematodes (Galactosomum otepotiense, Philophthalmus attenuatus, Acanthoparyphium sp. and Maritrema novaezealandense) that parasitize the same snail host population. We predicted that each parasite species would harbour a distinct microbiota, with microbial composition similarity decreasing with increasing phylogenetic distance among parasite species. We also predicted that trematode species co‐infecting the same individual host would influence each other's microbiota. We detected significant differences in alpha and beta diversity, as well as differential abundance, in the microbiota of the four trematode species. We found no evidence that phylogenetically closely related trematodes had more similar microbiota. We also uncovered indicator bacterial taxa that were significantly associated with each trematode species. Trematode species sharing the same snail host showed evidence of mostly one‐sided bacterial exchanges, with the microbial community of one species approaching that of the other. We hypothesize that natural selection acting on specific microbial lineages may be important to maintain differences in horizontally acquired microbes, with vertical transmission also playing a role. In particular, one trematode species had a more consistent and diverse bacteriota than the others, potentially a result of stronger stabilizing pressures. We conclude that species‐specific processes shape microbial community assembly in different trematodes exploiting the same host population. [ABSTRACT FROM AUTHOR]

The mammal community of the Coastal Range of southern Chile has been little studied even though they inhabit an environment under severe threats due to anthropic disturbance. During the spring-summer seasons of 2020-2021 and 2021-2022, we characterized the communities of wild terrestrial mammals in a native forest (NF) and an exotic plantation of Eucalyptus (PL) of the Coastal Range of Osorno province by phototrapping. We used 1,060 camera-trap days in the NF and 960 camera-trap days in the PL to explore the effect of habitat type on wild mammal diversity in two localities (L-1 and L-2). We quantified the species richness, abundance, community similarity and daily distribution of mammal communities. Species richness was higher in the NF (7-8 spp) than in the PL (3-4 spp). Two community similarity index (CSI) was significantly higher between native forests (CSI = 0.728 ± 0.088) than between Eucalyptus plantations (CSI = 0.211 ± 0.097) (95% CI). Mean abundance was also higher in the NF than in the PL (L-1: 0.011 vs. 0.004 occurrence/camera-trap day (OCT); L-2: 0.008 vs. 0.004 OCT). In L-1, the most abundant mammals in the NF were Leopardus guigna (45.3% of relative occurrence (RO)) and Pudu puda (18.9% RO), and in the PL, they were Lycalopex culpaeus (50% RO) and L. guigna (37.5% RO). In L-2, the highest abundances in the NF were for P. puda (34.5% RO) and Puma concolor (27.6% RO), while in the PL, P. puda was predominant (66.7% RO). In NF of both localities, 22.2% of melanic L. guigna individuals were observed. The highest frequency of occurrences in both locations was between 12:00 and 23:59 hours, with 60% and 76.9% of detections, respectively. The species richness found in native forest is in accordance with studies carried out in other temperate rainforests of southern Chile. In addition, native forests support a richer and more similar community of terrestrial mammals than exotic forest plantations, which indicates that native forests are the main habitat for most mammals detected and that exotic plantations function as a complementary habitat for some species. [ABSTRACT FROM AUTHOR]

Community structure is ubiquitous in various complex networks in nature and is one of the important characteristics of network structure.Community detection can identify useful information in the network,and help to analyze the structure and function of the network.It is widely used in social networks,biology,medicine and other fields.Aiming at the low accuracy of the current community detection algorithm based on local similarity in complex networks,a community detection algorithm based on Markov similarity enhancement and network embedding is proposed.Firstly,inspired by the idea of Markov chain,a Markov similarity enhancement method is proposed,which obtains the steady-state Markov similarity enhancement matrix through the Mar-kov iterative state transition of the initial network.According to the Markov similarity index,the network is divided into initial community structure.Then,a new community similarity index is proposed by combining the network topology and network embedding.The small community in the initial community structure is merged with its closely connected community to obtain the network community structure.On 7 real networks and artificial networks with variable parameters,compared with other 5 well-known community detection algorithms,it is proved that the proposed algorithm has a good community detection effect.

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According to the literature and field based findings at Fanjing, Leigong and Foding Mountains conducted by Tongren University in recent 10 years, list of reptiles has been revised. There are 77 reptile species (including five newly recorded species in Guizhou Province) in the three nature reserves, belonging to two Orders, 17 Families, and 43 Genera, accounting for 15. 07% of the reptile species in China. Fanjing, Leigong and Foding Mts have five, five and four types of distribution patterns of reptiles, respectively. The reptile fauna of Fanjing, Leigong and Foding Mts are mainly Oriental, accounting for 92. 00%, 93. 44% and 91. 11% respectively, with a small number of Palaearctic species. The Jaccard and Sørenson indexes showed that Leigong and Foding Mts had the highest similarity of reptile communities, followed by Fanjing and Foding Mts, and Fanjing and Leigong Mts had the least similarity. [ABSTRACT FROM AUTHOR]

Biomonitoring of plant communities is essential when evaluating outcomes of ecological restoration, but morphology‐based inventories can impede consistency across spatial and temporal scales. The Eden Project botanic garden (Cornwall, UK) offers an opportunity to test whether soil environmental DNA (eDNA) reflects plant species richness, community composition, and diversity. Furthermore, it enables the exploration of whether community complexity, environmental conditions, or sampling scale influence the similarity of soil eDNA‐derived results compared with those derived from classic botanical inventories. Survey plots were established encompassing a mixture of high‐ and low‐complexity plant assemblages, under either hot and humid or cool and dry conditions. Botanical inventories were conducted in quadrats up to 7 m around a soil eDNA sample plot. Soil samples were processed by metabarcoding of trnL p6 loop to determine plant eDNA identity and relative abundance. Differences in diversity and community composition were calculated before determining whether (1) inventory scale; (2) plant assembly complexity; (3) ambient conditions; (4) soil chemistry; (5) bulk root biomass and (6) soil respiration influenced the similarity of soil eDNA and botanical inventory methods. Inventory scale significantly determined the dissimilarity in both diversity and composition, with soil respiration, phosphorus, and C:N ratio also accounting for variation across sites. Our results demonstrate that soil eDNA metabarcoding is an effective approach for quantifying relative diversity in plant communities across broad habitat types and could be integrated into restoration monitoring strategies, but that its application requires an appropriate a priori knowledge of survey sites to best tailor soil eDNA survey implementation. [ABSTRACT FROM AUTHOR]

With the expansion of microbiome sequencing globally, a key challenge is to relate new microbiome samples to the existing space of microbiome samples. Here, we present Microbiome Search Engine (MSE), which enables the rapid search of query microbiome samples against a large, well-curated reference microbiome database organized by taxonomic similarity at the whole-microbiome level. Tracking the microbiome novelty score (MNS) over 8 years of microbiome depositions based on searching in more than 100,000 global 16S rRNA gene amplicon samples, we detected that the structural novelty of human microbiomes is approaching saturation and likely bounded, whereas that in environmental habitats remains 5 times higher. Via the microbiome focus index (MFI), which is derived from the MNS and microbiome attention score (MAS), we objectively track and compare the structural-novelty and attracted-attention scores of individual microbiome samples and projects, and we predict future trends in the field. For example, marine and indoor environments and mother-baby interactions are likely to receive disproportionate additional attention based on recent trends. Therefore, MNS, MAS, and MFI are proposed "alt-metrics" for evaluating a microbiome project or prospective developments in the microbiome field, both of which are done in the context of existing microbiome big data.IMPORTANCE We introduce two concepts to quantify the novelty of a microbiome. The first, the microbiome novelty score (MNS), allows identification of microbiomes that are especially different from what is already sequenced. The second, the microbiome attention score (MAS), allows identification of microbiomes that have many close neighbors, implying that considerable scientific attention is devoted to their study. By computing a microbiome focus index based on the MNS and MAS, we objectively track and compare the novelty and attention scores of individual microbiome samples and projects over time and predict future trends in the field; i.e., we work toward yielding fundamentally new microbiomes rather than filling in the details. Therefore, MNS, MAS, and MFI can serve as "alt-metrics" for evaluating a microbiome project or prospective developments in the microbiome field, both of which are done in the context of existing microbiome big data.

Variations in latitudinal gradients could lead to changes in the performance and ecological effects of invasive plants and thus may affect the species composition, distribution and interspecific substitution of native plant communities. However, variations in structure, similarity and beta (b) diversity within invaded communities across latitudinal gradients in heterogeneous habitats remain unclear. In this study, we conducted a two-year field survey along 21°N to 37°N in China, to examine the differential effects of the amphibious invasive plant Alternanthera philoxeroides on native plant communities in terrestrial and aquatic habitats. We compared the differences in the invasion importance value (IV), species distribution, community similarity (Jaccard index and Sorenson index) and β diversity (Bray--Curtis index and βsim index) between terrestrial and aquatic communities invaded by A. philoxeroides, as well as analyzed their latitudinal trends. We found that the IV of A. philoxeroides and b diversity in aquatic habitatswere all significantly higher than that of terrestrial, while the terrestrial habitat had a higher community similarity values. The aquatic A. philoxeroides IV increasedwith increasing latitude, while the terrestrial IV had no significant latitudinal trend. With increasing latitude, the component proportion of cold- and drought-tolerant species in the terrestrial communities increased, and the dominant accompanying species in the aquatic communities gradually changed fromhygrophytes and floating plants to emerged and submerged plants. In addition, the aquatic communities had lower community similarity values and higher β diversity in higher latitudinal regions, while terrestrial communities had the opposite parameters in these regions. Our study indicates that the bioresistance capacities of the native communities to invasive A. philoxeroides in heterogeneous habitats are different; A. philoxeroides invasion leads to higher community homogenization in terrestrial habitats than in aquatic habitats, and terrestrial communities experience more severe homogenization in higher latitudinal regions. These findings are crucial for predicting the dynamics of invasive plant communities under rapid global change. [ABSTRACT FROM AUTHOR]

Ecological communities change because of both natural and human factors. Distinguishing between the two is critical to ecology and conservation science. One of the most common approaches for modelling species composition changes is calculating beta diversity indices and then relating index changes to environmental changes. The main difficulty with these analyses is that beta diversity indices are paired comparisons, which means indices calculated with the same community are not independent. Mantel tests and generalised dissimilarity modelling (GDM) are two of the most commonly used statistical procedures for analysing such data, employing randomisation tests to consider the data's dependence. Here, we introduce a Bayesian model-based approach called BetaBayes that explicitly incorporates the data dependence. This approach is based on the Bradley–Terry model, which is a widely used approach for modelling paired comparisons that involves building a standard regression model containing two varying intercepts, one for each community involved in the beta diversity index, that capture their respective contributions. We used BetaBayes to analyse a famous dataset collected in Panama that contains information on multiple 1 ha plots from the rain forests of Panama. We calculated the Bray–Curtis index between all pairs of plots, analysed the relationship between the index and two covariates (geographic distance and elevation), and compared the results of BetaBayes with those from the Mantel test and GDM. BetaBayes has two distinctive features. The first is its flexibility, which allows the user to quickly change it to fit the data structure; namely, by adding varying effects, incorporating spatial autocorrelation, and modelling complex nonlinear relationships. The second is that it provides a clear path for performing model validation and model improvement. BetaBayes avoids hypothesis testing, instead focusing on recreating the data generating process and quantifying all the model configurations that are consistent with the observed data. [ABSTRACT FROM AUTHOR]

In order to protect and utilize the Acanthopanax senticosus resources reasonably, taking the typical Acanthopanax senticosus community in Xiaoxing’an Mountains of Heilongjiang Province as the research object, the relationship between the species diversity of Acanthopanax senticosus community and the altitude gradient was explored, and the influence of altitude factors on the species diversity of the community was analyzed. Results showed that: ①With the increasing of the altitude, the species and number of arbors and shrubs in Acanthopanax senticosus community increased first and then decreased, while the species and number of herbs generally decreased. The α diversity index of arbor layer had little change along the altitudinal gradient. The α diversity index of the shrub layer initially increased and then decreased with the increase of altitude gradient. The α diversity index of herb layer showed a downward trend. There was a negative correlation between α diversity index and altitude, and a negative correlation between α diversity index and richness index at 0. 05 level. Species richness contributed the most. ②Cody index βc firstly decreased and then increased with the altitude, and the lowest point was in the middle altitude area (447—469 m). Sorenson index Cs showed a trend of first increasing and then decreasing with the increase of altitude, and the highest peak value still appeared in the middle altitude area (447—469 m). ③The greater the difference of altitude gradient, the lower the community similarity. There were dissimilar levels among Acanthopanax senticosus communities at different altitudes. Within the study scope of Xiaoxing’ an Mountains, species in Acanthopanax senticosus communities with different altitude gradients α diversity, Cody index and Sorenson index all had certain variation rules, which indicated that altitude gradient was one of the important factors affecting the biodiversity of Acanthopanax senticosus community. [ABSTRACT FROM AUTHOR]

The Qinghai-Tibetan Plateau has a booming tourism industry and an increasingly sophisticated road system. There is a paucity of studies quantifying the contributions of anthropogenic and natural factors to microplastic pollution in remote plateau areas. In this study, water and sediment samples were collected from eight lake tourist attractions and four remote lakes in northern and southern regions of the Qinghai-Tibetan Plateau. Microplastics were detected in all samples, with a mean abundance of 0.78 items/L in water and 44.98 items/kg in sediment. The abundance of microplastics in the study area was lower than previously observed in more populated areas of China. Small-sized (<1 mm and 1–2 mm), fiber, and transparent microplastics were predominant, with polyethylene and polypropylene microplastics as the primary polymer types. The compositions of microplastic communities indicated that tourism and road networks were the major sources of microplastics in the lakes. Distance-decay models revealed greater influence of environmental distances on microplastic community similarity than geographic distance. Compared to climate factors, urban spatial impact intensity and traffic flow impact played a leading role in the structuring of microplastic communities in lake water and sediment. Our findings provide novel quantitative insights into the role of various factors in shaping the distribution patterns of microplastic communities in plateau lakes. [Display omitted] ● Microplastic communities in tourist lakes differed from those in other lakes. ● Tourism and road networks were the major sources of microplastics in the lakes. ● Environmental features affected the distance decay of microplastic communities. ● Urban spatial impact intensity and traffic flow shaped lake microplastic communities. [ABSTRACT FROM AUTHOR]

Management and conservation rely on surveys to determine which species are present but some species, such as nocturnal mammals, can be very difficult to detect. Camera trapping, driven transects, and ad hoc records are well-established nocturnal survey methods, but their detection effectiveness has not been tested against known species presence. We tested the effectiveness of these methods with a known assemblage of nocturnal African mammals. We compared camera traps placed at targeted and random locations, driven transects, and informal ad hoc records against one another and the 20 predominately nocturnal medium- and large-sized mammals known to be on site. Species-specific detection patterns, detection curves for each method, and detection effort required per species, were compared to determine the effectiveness of each method. Each of the methods detected at least 60% of known nocturnal mammal species over a 20-month period: driven transects and ad hoc records were the most successful (16/20 80%), followed by targeted camera traps (15/20 75%) and random camera traps (12/20 60%). Jaccard's Coefficients of Community Similarity peaked at 0.78, showing notable differences in the communities sampled with different methods. There was considerable variation in effort required to detect each species for each method, and the number of species detected with specific levels of effort was also highly variable between methods. We suggest that mixing methods, using different camera placement including use of random locations, and incorporating cost-neutral ad hoc records into formal survey efforts can all greatly increase the overall effectiveness and efficiency of species detection. [ABSTRACT FROM AUTHOR]

This study aims to determine the diversity of parasitoids in lowland rice plants in Pidie and Pidie Jaya districts, Aceh Province, Indonesia. The parameters observed included the number of individuals, community structure, wealth index, diversity index and evenness index and parasitoid community similarity. The research was conducted from July to December 2018 in Glumpang Tiga District and Mutiara District, Pidie Regency and Meureudu District and Meurah Dua District, Pidie Jaya Regency using a survey method with a purposive sampling technique. The insect traps used are sweeping net and pit fall trap. The results showed that both Pidie and Pidie Jaya districts indicated that the species richness index, diversity index and evenness index of parasitoid insects increased with increasing age of lowland rice plants. The lowest average species richness index at the age of 30 DAP was 1.51 and the highest was at the age of 60 DAP by 2.05; the lowest average diversity index at the age of 30 DAP was 1.24 and the highest was at the age of 45 DAP at 2.02; The lowest average of the evenness index at the age of 30 DAP was 0.55 and the highest was at the age of 45 DAP at 0.92.

The long-term dynamics of β-diversity of small mammal (SM) communities in the vicinity of a large copper smelter has been analyzed during the periods of high (1990–1997), reduced (1998–2009), and almost terminated emissions (2010–2020). The results show that the β-diversity of communities increases as the smelter is approached, with the level of pollution playing a key role in the formation of community structure (up to 25%). Throughout the 30-year observation period, the background communities have been less variable than the buffer and impact communities; i.e., the more unstable the environment, the higher the community variability. Structural rearrangements in the impact and buffer communities in the period of emission reduction have resulted in the progressive divergence between the communities of background and polluted areas. [ABSTRACT FROM AUTHOR]

Climate has an important role in shaping the composition and structure of woodlands. There is considerable uncertainty regarding how woodlands will respond to climate change over the next hundred years. To better understand likely responses to contemporary climate change, this paper analyses taxonomic richness, evenness and community similarity in palaeoecological data from 31 European woodlands during an abrupt cooling and warming event c. 8200 years ago. Repeated measures ANOVAs demonstrated there was no significant overall difference in richness or community evenness over time. A single significant pairwise contrast was found (richness decreased as climate warmed) but was short-lived, indicating that high-level effects were temporary. However, analysis of species turnover measured using community similarity revealed substantial changes (only 24% of species remained at some sites after climatic change), indicating that the actual species within that community had altered. General(ised) linear models showed variation in the direction and magnitude of community change was not related to the broadscale biogeographical variables of latitude, longitude or altitude. Our research has several important implications for practitioners involved in community ecology research and woodland management. Although site-level richness is largely unaffected, we caution that there will be considerable species turnover in woodlands as the climate warms. As species turnover at individual sites will have a negligible effect if driven by localised random processes, we recommend practitioners to consider long-term gamma diversity wherever possible. This shifts focus towards landscape-scale approaches that span generations rather than the typical 3–5-year span of funding, management plans and political cycles. [ABSTRACT FROM AUTHOR]

Members of the phylum Acidobacteria are among the most abundant soil bacteria on Earth, but little is known about their response to environmental changes. We asked how the relative abundance and biogeographic patterning of this phylum and its subgroups responded to forest-to-pasture conversion in soils of the western Brazilian Amazon. Pyrosequencing of 16S rRNA genes was employed to assess the abundance and composition of the Acidobacteria community across 54 soil samples taken using a spatially nested sampling scheme at the landscape level. Numerically, Acidobacteria represented 20% of the total bacterial community in forest soils and 11% in pasture soils. Overall, 15 different Acidobacteria subgroups of the current 26 subgroups were detected, with Acidobacteria subgroups 1, 3, 5, and 6 accounting together for 87% of the total Acidobacteria community in forest soils and 75% in pasture soils. Concomitant with changes in soil chemistry after forest-to-pasture conversion-particularly an increase in properties linked to soil acidity and nutrient availability-we observed an increase in the relative abundances of Acidobacteria subgroups 4, 10, 17, and 18, and a decrease in the relative abundances of other Acidobacteria subgroups in pasture relative to forest soils. The composition of the total Acidobacteria community as well as the most abundant Acidobacteria subgroups (1, 3, 5, and 6) was significantly more similar in composition across space in pasture soils than in forest soils. These results suggest that preponderant responses of Acidobacteria subgroups, especially subgroups 1, 3, 4, 5, and 6, to forest-to-pasture conversion effects in soils could be used to define management-indicators of agricultural practices in the Amazon Basin. These acidobacterial responses are at least in part through alterations on acidity- and nutrient-related properties of the Amazon soils.

Ecological communities change because of both natural and human factors. Distinguishing between the two is critical to ecology and conservation science. One of the most common approaches for modelling species composition changes is calculating beta diversity indices and then relating index changes to environmental changes. The main difficulty with these analyses is that beta diversity indices are paired comparisons, which means indices calculated with the same community are not independent. Mantel tests and generalised dissimilarity modelling (GDM) are two of the most commonly used statistical procedures for analysing such data, employing randomisation tests to consider the data’s dependence. Here, we introduce a Bayesian model-based approach called BetaBayes that explicitly incorporates the data dependence. This approach is based on the Bradley–Terry model, which is a widely used approach for modelling paired comparisons that involves building a standard regression model containing two varying intercepts, one for each community involved in the beta diversity index, that capture their respective contributions. We used BetaBayes to analyse a famous dataset collected in Panama that contains information on multiple 1 ha plots from the rain forests of Panama. We calculated the Bray–Curtis index between all pairs of plots, analysed the relationship between the index and two covariates (geographic distance and elevation), and compared the results of BetaBayes with those from the Mantel test and GDM. BetaBayes has two distinctive features. The first is its flexibility, which allows the user to quickly change it to fit the data structure; namely, by adding varying effects, incorporating spatial autocorrelation, and modelling complex nonlinear relationships. The second is that it provides a clear path for performing model validation and model improvement. BetaBayes avoids hypothesis testing, instead focusing on recreating the data generating process and quantifying all the model configurations that are consistent with the observed data.

Crop type is one of main factors influencing weed community structure. However, the identity of weed communities associated with the cultivation of different crops in farmlands remains largely unclear. A field survey of weed seed banks was conducted in 2280 fields at 228 sites of 62 locations representing three different types of farmland (95 paddy, 73 summer-ripe, and 60 autumn-ripe farmlands) along the bank of the Yangtze River in Anhui Province, China. A total of 43 families and 174 species of weeds were found in these weed seed banks. A comparison of the composition of weed groups in the seed banks showed that the species number and density percentage of grass, sedge and broadleaf weed groups were similar among the different types of farmland. The seed banks of all three farmland types shared 71 common weed species, accounting for 40.80% of the total number of species. These common weeds, which were both associated and not associated with crops, accounted for 91.71% of the total dominance degree among all farmland types. The crop-associated weed species were distributed in all soil layers of each farmland type. The Shannon-Wiener index H' (description of species diversity which is more sensitive to dense species) and Pielou's evenness index J (description of species evenness) in summer-ripe farmland were similar to those in autumn-ripe farmland but differed from those in paddy farmland. However, the Simpson's index D (description of species diversity which is more sensitive to sparse species) was similar among all three farmland types. The results of similarity comparison indicated that although the aboveground weed community differed among the different cropping patterns, the weed species composition in the soil seed bank was still similar. Consequently, our results demonstrate that after the implementation of long-term monoculture patterns, weed species compositions in the soil seed bank in different farmlands become homogenized regardless of the crop type.

Abstract Change in community similarity (e.g., biotic homogenization) is regulated by different types of introduction and extinction events. However, the spatial patterns and potential drivers of these event types have not yet been addressed to date. Here, we used bird species occurrences on 152 oceanic islands worldwide in both historical (~1500 CE) and current periods with the aim to (1) elucidate the variations of these events among islands and archipelagos and (2) disentangle the effects of biogeographical and environmental factors (e.g., spatial distance, island area, climatic conditions, and/or inter‐island distance). We found that community similarity increased at both island and archipelago scales after species introductions and extinctions. The introduction and extinction of one species to/from only one island (unique introduction and extinction) comprise most events (>94%). Island area has a positive effect on nearly all event types at both island and archipelago scales, while climate difference generally has a negative effect on these events. Conversely, responses to spatial distance and inter‐island distance on different events are more complex than expected. Overall, biogeographical variables (area and distance) seem to explain most of the events followed by climate variables. Yet extinction events at the archipelago level were also highly associated with inter‐island distance as an indicator of dispersal limitation. Our findings provide a solid foundation for understanding the event‐mediated processes of homogenization and present essential insights into how biogeographical and environmental factors affect different events on islands.

Many deforested areas worldwide have been planted with Alnus spp. to protect watersheds and soils. However, the effects of these plantations on biodiversity are little known yet. Contrasting forest types may impose strong environmental filters to some behavioural traits, leading to dissimilar communities. Insectivorous birds are known to be sensitive to changes in habitat structure due to their specialized foraging behaviour. We contrasted species richness, abundance and composition of insectivorous birds, according to functional behaviour groups (foraging strategy and stratum), between secondary forest stands and Andean alder Alnus acuminata plantations, to assess how contrasting forest types affect this bird group in the Colombian Andes. Insectivorous bird species richness and abundance were higher at the Alder plantation rather than at the secondary forest, resulting in dissimilar communities. In this regard, forest plantations act as a positive filter for foliage gleaners and flycatchers, whereas secondary forests act as a positive filter for bark foragers. Secondary forests and alder plantations impose different ecological scenarios to insectivorous birds, related to foraging strategies and foraging stratum, which ultimately leads to a dissimilar species composition. [ABSTRACT FROM AUTHOR]

The conservation challenges facing freshwater ecosystems necessitate broadening our science from understanding individual species loss to anticipating multi-faceted changes to biodiversity. In recent decades, the process of biotic homogenization by which regional biotas become more similar through time has attracted considerable attention. Here, we (1) quantified spatial and temporal changes in taxonomic and functional similarity of fish assemblages among Neotropical reservoirs, (2) determined nonnative species contributions to changes in taxonomic and functional composition, and (3) evaluated relationships between the changes in taxonomic and functional similarity among reservoirs. We did so by considering different spatial scales: inter- and intra-ecoregions. At inter-ecoregion scale, reservoir fish assemblages have become taxonomically homogenized over time, whereas functional trait composition has tended to differentiate. At intra-ecoregion scale, we detected both taxonomic and functional differentiation over time. Despite these overall trends, different ecoregions exhibited considerable variation in patterns of fish faunal homogenization and differentiation. We found a moderate positive relationship between changes in mean taxonomic and functional similarity among reservoirs at inter-ecoregion scale, which was no longer evident within ecoregions. In conclusion, this study demonstrates the strong scale-dependence of perceived patterns in homogenization, and further highlights the magnitude of threats to freshwater biodiversity in the Neotropical ecosystems. [ABSTRACT FROM AUTHOR]

Hydrological connectivity controls the patterns of invertebrate assemblages in wetland ecosystems. With degradation of intertidal wetlands, artificial freshwater release has become an important restoration technique. Hydrological connectivity with tidal creeks is also a key ecological process for intertidal wetlands. However, how hydrologic connectivity affects snail assemblages remains poorly investigated in intertidal wetlands. We studied the differences in snail assemblages in wetlands to understand the effects of hydrological connectivity, wetland to river, and wetland to ocean. We found freshwater connectivity can transform intertidal snail assemblages into freshwater snail assemblages; restored wetlands primarily had freshwater snail species and natural intertidal wetlands mainly supported marine or salt-adapted snail species. Cluster analysis, nMDS plot and ANOSIM analysis showed snail assemblages were influenced strongly by hydrological connectivity. Stenothyra glabra, Oncomelania sp. and Nassarius festivus were indicators of natural intertidal wetlands. Hippeutis cantori, Radix swinhoei and Succinea pfeifferi were indicators of restored wetlands. Our results suggest natural hydrological connectivity with the ocean needs to be maintained when attempting to restore intertidal wetlands. Without this connection, connecting impaired wetlands only to rivers, may not achieve restoration of natural biotic assemblages. [ABSTRACT FROM AUTHOR]

Copyright of Acta Prataculturae Sinica is the property of Acta Prataculturae Sinica Editorial Office 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.)

To clarify the ecology of ant communities of Himalayas, communities from the Diyag and Zanda sections were investigated using a sample-plot method. In total, the 5 355 individuals comprised 7 species belonging to 2 subfamilies and 5 genera of Formicidae. There were 7 species in Diyag section and 3 species in Zanda section. Ant species richness was estimated, the species accumulation curves revealed relatively lower ant species richness of the Diyag and Zanda sections. Ant species numbers, Shannon-Wiener diversity indices, Fisher α indices, and Simpson index on the south slope of the Diyag section displayed a "mid-domain effect" phenomenon, while the individual density displayed a "multi-domain effect" phenomenon. Ant species numbers, individual densities, and Fisher α indices on the south slope of the Zanda section displayed a "multi-domain effect" phenomenon. The similarity analysis revealed a marked dissimilarity of the ant communities among the samples, indicating the existence of differences and similarities in the ant communities along an elevational gradient in this area. The distribution of ant species and diversity were mainly influenced by altitude, while slope direction and vegetation type were important in ant community differentiation. [ABSTRACT FROM AUTHOR]

Joint Species Distribution Modelling (JSDM) is becoming an increasingly popular statistical method for analysing data in community ecology. Hierarchical Modelling of Species Communities (HMSC) is a general and flexible framework for fitting JSDMs. HMSC allows the integration of community ecology data with data on environmental covariates, species traits, phylogenetic relationships and the spatio‐temporal context of the study, providing predictive insights into community assembly processes from non‐manipulative observational data of species communities.The full range of functionality of HMSC has remained restricted to Matlab users only. To make HMSC accessible to the wider community of ecologists, we introduce Hmsc 3.0, a user‐friendly r implementation.We illustrate the use of the package by applying Hmsc 3.0 to a range of case studies on real and simulated data. The real data consist of bird counts in a spatio‐temporally structured dataset, environmental covariates, species traits and phylogenetic relationships. Vignettes on simulated data involve single‐species models, models of small communities, models of large species communities and models for large spatial data. We demonstrate the estimation of species responses to environmental covariates and how these depend on species traits, as well as the estimation of residual species associations. We demonstrate how to construct and fit models with different types of random effects, how to examine MCMC convergence, how to examine the explanatory and predictive powers of the models, how to assess parameter estimates and how to make predictions. We further demonstrate how Hmsc 3.0 can be applied to normally distributed data, count data and presence–absence data.The package, along with the extended vignettes, makes JSDM fitting and post‐processing easily accessible to ecologists familiar with r. [ABSTRACT FROM AUTHOR]

Information centric networking (ICN) has been recently proposed as a prominent solution for content delivery in vehicular ad hoc networks. By caching the data packets in vehicular unused storage space, vehicles can obtain the replicate of contents from other vehicles instead of original content provider, which reduces the access pressure of content provider and increases the response speed of content request. In this paper, we propose a community similarity and population-based cache policy in an ICN vehicle-to-vehicle scenario. First, a dynamic probability caching scheme is designed by evaluating the community similarity and privacy rating of vehicles. Then, a caching vehicle selection method with hop numbers based on content popularity is proposed to reduce the cache redundancy. Moreover, to lower the cache replacement overhead, we put forward a popularity prediction-based cooperative cache replacement mechanism, which predicts and ranks popular content during a period of time. Simulation results show that the performance of our proposed mechanisms is greatly outstanding in reducing the average time delay and increasing the cache hit ratio and the cache hit distance.

Community similarity is often assessed through similarities in species occurrences and abundances (i.e., compositional similarity) or through the distribution of species interactions (i.e., interaction similarity). Unfortunately, the joint empirical evaluation of both is still a challenge. Here, we analyze community similarity in ecological systems in order to evaluate the extent to which indices based exclusively on species composition differ from those that incorporate species interactions. Borrowing tools from graph theory, we compared the classic Jaccard index with the graph edit distance (GED), a metric that allowed us to combine species composition and interactions. We found that similarity measures computed using only taxonomic composition could differ strongly from those that include composition and interactions. We conclude that new indices that incorporate community features beyond composition will be more robust for assessing similitude between natural systems than those purely based on species occurrences. Our results have therefore important conceptual and practical consequences for the analysis of ecological communities.

Copyright of Acta Prataculturae Sinica is the property of Acta Prataculturae Sinica Editorial Office 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.)

Community similarity is often assessed through similarities in species occurrences and abundances (i.e., compositional similarity) or through the distribution of species interactions (i.e., interaction similarity). Unfortunately, the joint empirical evaluation of both is still a challenge. Here, we analyze community similarity in ecological systems in order to evaluate the extent to which indices based exclusively on species composition differ from those that incorporate species interactions. Borrowing tools from graph theory, we compared the classic Jaccard index with the graph edit distance (GED), a metric that allowed us to combine species composition and interactions. We found that similarity measures computed using only taxonomic composition could differ strongly from those that include composition and interactions. We conclude that new indices that incorporate community features beyond composition will be more robust for assessing similitude between natural systems than those purely based on species occurrences. Our results have therefore important conceptual and practical consequences for the analysis of ecological communities. [ABSTRACT FROM AUTHOR]

Assessment and preservation of biodiversity has been a central theme of conservation biology since the discipline's inception. However, when diversity estimates are based purely on measures of presence–absence, or even abundance, they do not directly assess in what way focal habitats support the life history needs of individual species making up biological communities. Here, we move beyond naïve measures of occurrence and introduce the concept of "informed diversity" indices which scale estimates of avian species richness and community assemblage by two critical phases of their life cycle: breeding and molt. We tested the validity of the "informed diversity" concept using bird capture data from multiple locations in northern California and southern Oregon to examine patterns of species richness among breeding, molting, and naïve (based solely on occurrence) bird communities at the landscape and local scales using linear regression, community similarity indices, and a Detrended Correspondence Analysis (DCA). At the landscape scale, we found a striking pattern of increased species richness for breeding, molting, and naïve bird communities further inland and at higher elevations throughout the study area. At the local scale, we found that some sites with species‐rich naïve communities were in fact species‐poor when informed by breeding status, indicating that naïve richness may mask more biologically meaningful patterns of diversity. We suggest that land managers use informed diversity estimates instead of naïve measures of diversity to identify ecologically valuable wildlife habitat. [ABSTRACT FROM AUTHOR]

Many deforested areas worldwide have been planted with Alnus spp. to protect watersheds and soils. However, the effects of these plantations on biodiversity are little known yet. Contrasting forest types may impose strong environmental filters to some behavioural traits, leading to dissimilar communities. Insectivorous birds are known to be sensitive to changes in habitat structure due to their specialized foraging behaviour. We contrasted species richness, abundance and composition of insectivorous birds, according to functional behaviour groups (foraging strategy and stratum), between secondary forest stands and Andean alder Alnus acuminata plantations, to assess how contrasting forest types affect this bird group in the Colombian Andes. Insectivorous bird species richness and abundance were higher at the Alder plantation rather than at the secondary forest, resulting in dissimilar communities. In this regard, forest plantations act as a positive filter for foliage gleaners and flycatchers, whereas secondary forests act as a positive filter for bark foragers. Secondary forests and alder plantations impose different ecological scenarios to insectivorous birds, related to foraging strategies and foraging stratum, which ultimately leads to a dissimilar species composition. [ABSTRACT FROM AUTHOR]

Urbanization is an expanding process worldwide, causing major threats to biodiversity through both species extinction and biotic homogenization. Most studies focusing on urban ecosystems have been conducted in temperate forests of the Northern hemisphere; the ecological and socioeconomic contexts, however, may influence biodiversity responses to urbanization. We ask whether the biomes (here, the humid subtropical forest and the semiarid shrubland) where human settlements and land uses are developed determine bird diversity along urbanization gradients in the southern Neotropics. We propose theoretical responses based on expected variations in vegetation cover along urbanization gradients and fit our data to different models of bird richness from highly developed to non-urban areas and also examine changes in species composition. Species richness was positively correlated to vegetation cover in both human settlements. Results supported some of our predictions. In the city located in the arid biome, the highly developed area supported higher bird richness than the natural habitat, unlike the city from the humid biome; yet, the native bird assemblage was better preserved in the urban area established in the humid biome. Richness in moderately developed areas was either higher than or similar to that in rural or natural areas in the settlement from the arid biome, but lower than or similar to richness in the humid biome. In all the studied urban-rural gradients, bird richness reached a plateau in moderately developed areas, in contrast to urban-natural habitat gradients, where richness either increased (in the humid biome) or declined (in the arid biome). Our study helps to understand how the mechanisms changing biodiversity in urbanized areas may act in different biomes and land uses, and therefore contributes to the search of global explanations of diversity patterns. [ABSTRACT FROM AUTHOR]

The introduction of exotic species to new regions offers opportunities to test fundamental questions in ecology, such as the context-dependency of community structure and assembly. Annual grasslands provide a model system of a major unidirectional introduction of plant species from Europe to North America. We compared the community structure of grasslands in two Mediterranean regions by surveying plots in Spain and in California with similar environmental and management conditions. All species found in Spanish grasslands were native to Spain, and over half of them (74 of 139 species) are known to have colonized California. In contrast, in California, over half of the species (52 of 95 species) were exotic species, all of them native to Spain. Nineteen species were found in multiple plots in both regions (i.e., shared species). The abundance of shared species in California was either similar to (13 species) or greater than (6 species) in Spain. In California, plants considered pests were more likely than non-pest species to have higher abundance. Co-occurring shared species tended to maintain their relative abundance in native and introduced communities, which indicates that pools of exotic species might assemble similarly at home and away. These findings provide interesting insights into community assembly in novel ecosystems. They also highlight an example of startling global and local floristic homogenization.

ABSTRACT With the expansion of microbiome sequencing globally, a key challenge is to relate new microbiome samples to the existing space of microbiome samples. Here, we present Microbiome Search Engine (MSE), which enables the rapid search of query microbiome samples against a large, well-curated reference microbiome database organized by taxonomic similarity at the whole-microbiome level. Tracking the microbiome novelty score (MNS) over 8 years of microbiome depositions based on searching in more than 100,000 global 16S rRNA gene amplicon samples, we detected that the structural novelty of human microbiomes is approaching saturation and likely bounded, whereas that in environmental habitats remains 5 times higher. Via the microbiome focus index (MFI), which is derived from the MNS and microbiome attention score (MAS), we objectively track and compare the structural-novelty and attracted-attention scores of individual microbiome samples and projects, and we predict future trends in the field. For example, marine and indoor environments and mother-baby interactions are likely to receive disproportionate additional attention based on recent trends. Therefore, MNS, MAS, and MFI are proposed “alt-metrics” for evaluating a microbiome project or prospective developments in the microbiome field, both of which are done in the context of existing microbiome big data. IMPORTANCE We introduce two concepts to quantify the novelty of a microbiome. The first, the microbiome novelty score (MNS), allows identification of microbiomes that are especially different from what is already sequenced. The second, the microbiome attention score (MAS), allows identification of microbiomes that have many close neighbors, implying that considerable scientific attention is devoted to their study. By computing a microbiome focus index based on the MNS and MAS, we objectively track and compare the novelty and attention scores of individual microbiome samples and projects over time and predict future trends in the field; i.e., we work toward yielding fundamentally new microbiomes rather than filling in the details. Therefore, MNS, MAS, and MFI can serve as “alt-metrics” for evaluating a microbiome project or prospective developments in the microbiome field, both of which are done in the context of existing microbiome big data.

Dispersal can influence the response of bacterial communities to environmental changes and disturbances. However, the extent to which dispersal contributes to the community response in dependence of the character and strength of the disturbance remains unclear. Here, we conducted a transplant experiment using dialysis bags in which bacterioplankton originating from brackish and marine regions of the Saint Lawrence Estuary were reciprocally incubated in the two environments for 5 days. Dispersal treatments were set-up by subjecting half of the microcosms in each environment to an exchange of cells between the marine and brackish assemblages at a daily exchange rate of 6% (v/v), and the other half of microcosms were kept as the non-dispersal treatments. Bacterial 16S rRNA sequencing was then used to examine the diversity and composition of the active communities. Alpha diversity of the marine communities that were exposed to the brackish environment was elevated greatly by dispersal, but declined in the absence of dispersal. This indicates that dispersal compensated the loss of diversity in the marine communities after a disturbance by introducing bacterial taxa that were able to thrive and coexist with the remaining community members under brackish conditions. On the contrary, alpha diversity of the brackish communities was not affected by dispersal in either environment. Furthermore, dispersal led to an increase in similarity between marine and brackish communities in both of the environments, with a greater similarity when the communities were incubated in the brackish environment. These results suggest that the higher initial diversity in the brackish than in the marine starting community made the resident community less susceptible to dispersing bacteria. Altogether, this study shows that dispersal modifies the diversity and composition of the active communities in response to a salinity disturbance, and enables the local adjustment of specific bacteria under brackish environmental conditions.

Abstract In light of increasing threats to global biodiversity, identifying the patterns in and drivers of variation in species composition along the environmental gradients in understudied regions is crucial for understanding ecosystem vulnerability and resilience. Terrestrial plant communities of interior Alaska are dominated by three major groups of primary producers—vascular plants, mosses, and macrolichens. Recent work has demonstrated broad‐scale positive correlations in species richness patterns among these three functional groups across scales in this region. However, the conspicuous and fundamental differences in reproductive strategies, dispersal ability, and physiological adaptations among these functional groups prompted us to investigate how community composition and species turnover vary across environmental gradients among these disparate groups. We hypothesized that species turnover would be greater in vascular plants than for spore‐producing cryptogam functional groups across gradients of elevation, vegetation type, and distance due to underlying differences in dispersal abilities and the temporal and spatial resolution of habitat preferences among these disparate groups. To address these issues, we compiled a uniquely comprehensive species composition dataset in interior Alaska utilizing a multi‐stage systematic design. We analyzed community similarity using Morisita‐Horn index of multi‐community similarity among all pairs of vegetation types and elevation bands for each functional group and used regression analysis to quantify the rate at which compositional similarity decayed with geographical distance among groups. Our study reveals consistently higher compositional variation (lower similarity) among vascular plants as compared to mosses and macrolichens across landscape gradients and spatial scales in interior Alaska. We also found that the decay of similarity with distance was less for both of the cryptogam groups than for vascular plants. Taken together, our results suggest that differences in functional group dispersal abilities, in combination with varying abilities to utilize fine‐scale temporal and spatial habitat variation, result in reduced turnover among mosses and macrolichens as compared to vascular plants both along landscape gradients and across distance in interior Alaska.

Dispersal can influence the response of bacterial communities to environmental changes and disturbances. However, the extent to which dispersal contributes to the community response in dependence of the character and strength of the disturbance remains unclear. Here, we conducted a transplant experiment using dialysis bags in which bacterioplankton originating from brackish and marine regions of the Saint Lawrence Estuary were reciprocally incubated in the two environments for 5 days. Dispersal treatments were set-up by subjecting half of the microcosms in each environment to an exchange of cells between the marine and brackish assemblages at a daily exchange rate of 6% (v/v), and the other half of microcosms were kept as the non-dispersal treatments. Bacterial 16S rRNA sequencing was then used to examine the diversity and composition of the active communities. Alpha diversity of the marine communities that were exposed to the brackish environment was elevated greatly by dispersal, but declined in the absence of dispersal. This indicates that dispersal compensated the loss of diversity in the marine communities after a disturbance by introducing bacterial taxa that were able to thrive and coexist with the remaining community members under brackish conditions. On the contrary, alpha diversity of the brackish communities was not affected by dispersal in either environment. Furthermore, dispersal led to an increase in similarity between marine and brackish communities in both of the environments, with a greater similarity when the communities were incubated in the brackish environment. These results suggest that the higher initial diversity in the brackish than in the marine starting community made the resident community less susceptible to dispersing bacteria. Altogether, this study shows that dispersal modifies the diversity and composition of the active communities in response to a salinity disturbance, and enables the local adjustment of specific bacteria under brackish environmental conditions. [ABSTRACT FROM AUTHOR]

Urbanization has tremendous impacts on most native species. This is especially true in land snails, which are surprisingly understudied organisms. Due to their low mobility and dispersal potential, land snails are valuable indicators of ecosystem disturbance. For this study, land snails were collected in 54 city parks along an urban gradient to understand impacts of urbanization on snail communities. Sampled parks include small extensively landscaped downtown parks, neighborhood and community parks, district parks, and large nature parks, each with variable vegetation, soil characteristics, disturbance regimes, and human activities. Sampling recovered 12,153 individual snails, representing 20 families, 43 genera, and 95 species. Seven new Tennessee state and 87 new county occurrences were recorded. Five non-native and one extra-limital non-native species were found, four of which are new Tennessee state records. Results show that urbanization greatly alters land snail community structure. Nature and district parks have significantly greater species richness, species diversity and species evenness than community, neighborhood, and downtown parks. Degradation of parks, distance from the park to the commercial city center and percent of coarse woody debris accounted for most of the variation between park types. Non-metric multidimensional scaling and pairwise Jaccard indices indicate that downtown snail communities are more similar whereas snail communities in nature parks are more distinct. This suggests that urbanization promotes homogenization among land snail communities. We also show that this homogenization is thus far driven mainly by synanthropic, broadly adapted native species rather than non-native snail species. [ABSTRACT FROM AUTHOR]

Abstract: Tropical conservation strategies traditionally focus on large tracts of pristine forests but, given rapid primary forest decline, understanding the role of secondary forest remnants for biodiversity maintenance is critical. Until now, the interactive effects of changes in forest amount, configuration and disturbance history (secondary vs. primary forest) on the conservation value of tropical landscapes have remained unknown, hampering the incorporation of these global change drivers into local and global conservation planning. We disentangled effects of landscape‐wide forest amount, fragment size and forest age (old growth vs. secondary forest) on abundance, α‐diversity, β‐diversity (biotic homogenization) and community shifts of bird communities in human‐dominated landscapes of southern Costa Rica. Utilizing two complementary methods, yielding 6,900 individual detections and 223 species, we characterized bird communities in 49 forest fragments representing independent gradients in fragment size (<5 ha vs. >30 ha) and forest amount (5%–80%) in the surrounding landscape (within 1000 m). Abundance and α‐diversity of forest specialists and insectivores declined by half in small fragments, but only in landscapes with little old‐growth forest. Conversely, secondary forest at the landscape scale showed no such compensation effect. Similarly, a null‐model approach indicated significant biotic homogenization in small vs. large fragments, but only in landscapes with little old‐growth forest, suggesting forest amount and configuration interactively affect β‐diversity in tropical human‐dominated landscapes. Finally, dramatic abundance‐based community shifts relative to intact forests are largely a result of landscape‐scale loss of old growth rather than changes in overall forest cover. Policy implications. Our study provides strong evidence that retaining old growth within tropical human‐modified landscapes can simultaneously curb erosion of avian forest specialist α‐diversity, mitigate collapse of β‐diversity (biotic homogenization) and dampen detrimental avian community shifts. However, secondary forests play, at best, a subordinate role to mitigate these processes. To maintain tropical forest biodiversity, retaining old‐growth forest within landscapes should be first priority, highlighting a land‐sparing approach. [ABSTRACT FROM AUTHOR]

In light of increasing threats to global biodiversity, identifying the patterns in and drivers of variation in species composition along the environmental gradients in understudied regions is crucial for understanding ecosystem vulnerability and resilience. Terrestrial plant communities of interior Alaska are dominated by three major groups of primary producers--vascular plants, mosses, and macrolichens. Recent work has demonstrated broad-scale positive correlations in species richness patterns among these three functional groups across scales in this region. However, the conspicuous and fundamental differences in reproductive strategies, dispersal ability, and physiological adaptations among these functional groups prompted us to investigate how community composition and species turnover vary across environmental gradients among these disparate groups. We hypothesized that species turnover would be greater in vascular plants than for spore-producing cryptogam functional groups across gradients of elevation, vegetation type, and distance due to underlying differences in dispersal abilities and the temporal and spatial resolution of habitat preferences among these disparate groups. To address these issues, we compiled a uniquely comprehensive species composition dataset in interior Alaska utilizing a multi-stage systematic design. We analyzed community similarity using Morisita-Horn index of multi-community similarity among all pairs of vegetation types and elevation bands for each functional group and used regression analysis to quantify the rate at which compositional similarity decayed with geographical distance among groups. Our study reveals consistently higher compositional variation (lower similarity) among vascular plants as compared to mosses and macrolichens across landscape gradients and spatial scales in interior Alaska. We also found that the decay of similarity with distance was less for both of the cryptogam groups than for vascular plants. Taken together, our results suggest that differences in functional group dispersal abilities, in combination with varying abilities to utilize fine-scale temporal and spatial habitat variation, result in reduced turnover among mosses and macrolichens as compared to vascular plants both along landscape gradients and across distance in interior Alaska. [ABSTRACT FROM AUTHOR]

Abstract: Question: Is it possible to determine which combination of cluster number and taxon abundance transformation would produce the most effective classification of vegetation data? What is the effect of changing cluster number and taxon abundance weighting (applied simultaneously) on the stability and biological interpretation of vegetation classifications? Locality: Europe, Western Australia, simulated data. Methods: Real data sets representing Hungarian sub‐montane grasslands, European wetlands, and Western Australian kwongan vegetation, as well as simulated data sets were used. The data sets were classified using the partitioning around medoids method. We generated classification solutions by gradually changing the transformation exponent applied to the species projected covers and the number of clusters. The effectiveness of each classification was assessed with a stability index. This index is based on bootstrap resampling of the original data set with subsequent elimination of duplicates. The vegetation types delimited by the most stable classification were compared with other classifications obtained at local maxima of the stability values. The effect of changing the transformation power exponent on the number of clusters, indexed according to their stability, was evaluated. Results: The optimal number of clusters varied with the power exponent in all cases, both with real and simulated data sets. With the real data sets, optimal cluster numbers obtained with different data transformations recovered interpretable biological patterns. Using the simulated data, the optima of stability values identified the simulated number of clusters correctly in most cases. Conclusions: With changing the settings of data transformation and the number of clusters, classifications of different stability can be produced. Highly stable classifications can be obtained from different settings for cluster number and data transformation. Despite similarly high stability, such classifications may reveal contrasting biological patterns, thus suggesting different interpretations. We suggest testing a wide range of available combinations to find the parameters resulting in the most effective classifications. [ABSTRACT FROM AUTHOR]

1. The ability to provide reliable projections for the current and future distribution of land- cover is fundamental if we wish to protect and manage our diminishing natural resources. Two inter- related revolutions make map productions feasible at unprecedented resolutions--the availability of high- resolution remotely sensed data and the development of machine- learning algorithms. However, ground- truthed data needed for training models is in most cases spatially and temporally clustered. Therefore, map production requires extrapolation of models from one place to another and the uncertainty cost of such extrapolation is rarely explored. In other words, the focus has mainly been on projections, and less on quantifying their reliability. 2. Using the concept of "forecast horizon", we suggest that the predictability of landcover classification models should be quantitatively explored as a continuum against distances measured along multiple dimensions--space, time, environmental and spectral. Focusing on ten agricultural sites from England and using models specifically designed to predict multivariate decay- curves, we ask: how does a model's predictive performance decay with distance? More specifically, we explored if we could predict the proficiency (kappa statistics) of a model trained in one site when making predictions in another site based on the spatial, temporal, spectral and environmental distances between sites. 3. We found that model proficiency decays with distance between sites in each dimension. More importantly, we found for the first time, that it is possible to predict the performance a model transferred to or from a novel site will have, based on its distances from known sites. The spectral distance variables were the most important when predicting model transferability. 4. Exploring model transferability as a continuum may have multiple usages including predicting uncertainty values in space and time, prioritisation of strategies for ground- truth data collection, and optimising model characteristics for defined tasks. [ABSTRACT FROM AUTHOR]