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Understanding the relationship between functional traits and fragmentation is crucial for promoting biodiversity and ecosystem function. Orchid bees (Euglossini) are important pollinators in Neotropical forests, but how body size may be associated with fragmentation and its influence on community organisation remains unexplored. We systematically sampled orchid bee communities across 15 plots in a fragmented area in the Ecuadorian Amazon basin to evaluate how patch size and isolation are associated with body size and abundance. Our samples comprised large‐bodied bees (Eulaema, Euglossa and the parasitic Exaerete), with small Euglossa notably absent. The relative representation of Eulaema species of varying sizes changed across the fragmented landscape, leading to shifts in overall mean body size consistent with the prediction that larger‐bodied pollinators are better at long‐distance movement. Euglossa, the most abundant genus (67% of the total sample), was found across all patches regardless of body size. Euglossa intersecta and Euglossa orellana, the largest Euglossa in the region, were the most common species across the fragmented landscape. The abundance of male euglossines experienced a general decline with decreasing patch size and increasing isolation. However, at the species level, the abundance of some species was not affected at all. Because body size often mediates dispersal ability, thermoregulation, and resource use, we reinforce the importance of assessing body size patterns to understand changes in diversity, abundance and the composition of tropical pollinator communities in fragmented landscapes. [ABSTRACT FROM AUTHOR]

Key Biodiversity Areas (KBAs) are a cornerstone of 21st‐century area‐based conservation targets. In tropical KBAs, biodiversity is potentially at high risk from climate change, because most species reside within or beneath the canopy, where small increases in temperature can lead to novel climate regimes. We quantify novelty in temperature regimes by modeling hourly temperatures below the forest canopy across tropical KBAs between 1990 and 2019. We find that up to 66% of KBAs with tropical forests have recently transitioned to novel temperature regimes. Nevertheless, 34% of KBAs are providing refuge from novelty, 58% of which are not protected. By conducting the first pan‐tropical analyses of changes in below‐canopy temperature conditions in KBAs, we identify KBAs that are acting as climate refugia and should be considered for expansion of the conservation network in response to the post‐2020 Global Biodiversity Framework target to conserve 30% of land area by 2030. [ABSTRACT FROM AUTHOR]

Tropical species richness is threatened by habitat degradation associated with land‐use conversion, yet the consequences for functional diversity remain little understood. Progress has been hindered by difficulties in obtaining comprehensive species‐level trait information to characterize entire assemblages and insufficient appreciation that increasing land‐cover heterogeneity potentially compensates for species loss. We examined the impacts of tropical deforestation associated with land‐use heterogeneity on bird species richness, functional redundancy, functional diversity, and associated components (i.e., alpha diversity, species dissimilarity, and interaction strength of the relationship between abundance and functional dissimilarity). We analyzed over 200 georeferenced bird assemblages in the Atlantic Forest of Brazil. We characterized the functional role of the species of each assemblage and modeled biodiversity metrics as a function of forest cover and land‐cover heterogeneity. Replacement of native Atlantic Forest with a mosaic of land uses (e.g., agriculture, pastures, and urbanization) reduced bird species richness in a nonrandom way. Core forest species, or species considered sensitive to edges, tended to be absent in communities in heterogenous environments. Overall, functional diversity and functional redundancy of bird species were not affected by forest loss. However, birds in highly heterogenous habitats were functionally distinct from birds in forest, suggesting a shift in community composition toward mosaic‐exclusive species led by land‐cover heterogeneity. Threatened species of the Atlantic Forest did not seem to tolerate degraded and heterogeneous environments; they remained primarily in areas with large forest tracts. Our results shed light on the complex effects of native forest transformation to mosaics of anthropogenic landscapes and emphasize the importance of considering the effects of deforestation and land‐use heterogeneity when assessing deforestation effects on Neotropical biodiversity. [ABSTRACT FROM AUTHOR]

Indigenous Peoples are long‐term custodians of their lands, but only recently are their contributions to conservation starting to be recognized in biodiversity policy and practice. Tropical forest loss and degradation are lower in Indigenous lands than unprotected areas, yet the role of Indigenous Peoples' Lands (IPL) in biodiversity conservation has not been properly assessed from regional to global scales. Using species distribution ranges of 11,872 tropical forest‐dependent vertebrates to create area of habitat maps, we identified the overlap of these species ranges with IPL and then compared values inside and outside of IPL for species richness, extinction vulnerability, and range‐size rarity. Of assessed vertebrates, at least 76.8% had range overlaps with IPL, on average overlapping ~25% of their ranges; at least 120 species were found only within IPL. Species richness within IPL was highest in South America, while IPL in Southeast Asia had highest extinction vulnerability, and IPL in Dominica and New Caledonia were important for range‐size rarity. Most countries in the Americas had higher species richness within IPL than outside, whereas most countries in Asia had lower extinction vulnerability scores inside IPL and more countries in Africa and Asia had slightly higher range‐size rarity in IPL. Our findings suggest that IPL provide critical support for tropical forest‐dependent vertebrates, highlighting the need for greater inclusion of Indigenous Peoples in conservation target‐setting and program implementation, and stronger upholding of Indigenous Peoples' rights in conservation policy. [ABSTRACT FROM AUTHOR]

Pemphis acidula is a wild plant in rocky or sandy coastal areas and mangrove ecosystems. Different geographic characteristics may affect plant adaptability and have an impact on the emergence of various genotypes. This study was performed to reveal the phenetic relationship and genetic variation of P. acidula in 3 different areas in Tomini Bay, Gorontalo Province, Indonesia. We took 3 samples from each location and analysed them using 14 morphological characters and molecular approaches based on ISSR markers and ITS gene. The results showed that P. acidula on Olele had bigger sizes in some morphological features compared to the plants in other study areas. The phenetic analysis showed that P. acidula at Biluhu and Dulanga were more closely related, although P. acidula at the 3 locations had 100% similarity. Genetic variation analysis showed the highest genetic similarity based on ISSR markers was found in Dulanga and Biluhu samples (76.8%). Phylogenetic based on ITS gene revealed that Olele samples were in the same clade with P. acidula accession from GenBank (genetic distance 0-0.19%), while Biluhu samples were a sister group (genetic distance 24.97-25.03%) even though their percentage identity corresponds to P. acidula (81.34%). Plant adaptation to different habitat conditions may affect the genetic diversity of P. acidula.

Microbial cellulases are an important industrial enzyme having diverse applications in biotechnology, environmental challenges, industrial products and processes. Extremophiles like thermophillic bacteria are a good source of industrially important cellulases as these can withstand industrially rigorous procedures like paper deinking, fabric material softening, bio stoning, paper and pulp, biopolishing cloth material, animal feed and juice. Identification of novel cellulases or improving them through biotechnological interventions has remained a challenge for researchers. Genetic manipulation of thermophilic bacteria for increased cellulase production or synthetic biology approaches for cellulase gene/gene cluster extraction from thermophilic bacteria and expression in appropriate hosts for improved cellulase synthesis. The classic and high-throughput technologies like genomics, metagenomics and bioinformatics could be exploited to isolate cellulase genes from a variety of thermophilic bacteria and further processing. Keeping in view the ultimate requirement of extremophilic cellulases in industries, present study is a compilation of various aspects related to extremophilic cellulases their sources, production, biotechnological interventions and challenges.

While harboring the bulk of the planet's biodiversity, tropical ecosystems have experienced intense land conversion for agriculture. Studies examining the impacts of land‐use change on tropical biodiversity have primarily focused on forest cover loss but have overlooked the ecological potential of habitats surrounding forest fragments to modulate biodiversity loss. We examined whether small‐mammal communities changed with the land cover surrounding forest fragments, and how functional traits affected responses to land cover. Small mammals were sampled in the Brazilian Cerrado using live‐trap transects. Three landscape types were identified according to the surroundings of the transects (within 750‐m‐radius buffers): forest‐ (≥50% forest cover), pasture‐, and crop‐dominated landscapes (<50% forest cover, with predominance of pastures or crops, respectively). We examined the composition of functional traits across landscape types and used abundance models to analyze the response of small‐mammal communities to land cover. From forest‐dominated to pasture‐ and crop‐dominated landscapes, the abundances and/or species richness of the largest, forest‐specialist, frugivorous/granivorous, and terrestrial species decreased. In forest‐dominated landscapes, abundances and species richness were slightly affected by land cover surrounding forest fragments. In pasture‐ and crop‐dominated landscapes which represent the less‐preserved landscapes, increased proportions of native forests, open formations, and, to some extent, pastures, supported the increased abundance of small mammals. Land cover surrounding forest fragments is critical for maintaining the diversity of species and functional traits within small‐mammal communities. Our results emphasize the need to maintain native vegetation in human‐modified landscapes to maintain biodiversity and ecological functions. [ABSTRACT FROM AUTHOR]

Artisanal and small‐scale gold mining (ASGM), a wealth‐generating industry in many regions, is nonetheless a global challenge for governance and a threat to biodiversity, public health, and ecosystem integrity. In 2019, the Peruvian government mobilized a targeted, large‐scale armed intervention against illegal ASGM, which has caused deforestation and water resource degradation in this Tropical Biodiversity Hotspot. Before the intervention, the extent of waterbodies created by mining (mining ponds) was increasing by 33%–90%/year; after, they decreased by 4%–5%/year in targeted zones. Mining activity indicators showed 70%–90% abandonment. New mining activity accelerated in nearby areas outside the targeted area (pond area increases: 42%–83%; deforestation increases +3–5 km2/year). Far from intervention zones, mining remained stable during the study period. Our analysis demonstrates that targeted, large‐scale government intervention can have positive effects on conservation by stopping illegal mining activity and shifting it to permitted areas, thereby setting the stage for governance. Continued conservation efforts must further address the impacts of informal mining while (1) limiting environmental degradation by legal mining; (2) remediating former mining areas to reduce erosion and enable reforestation or alternative uses of the landscape; and (3) sustaining such efforts, as some miners began to return to intervention areas when enforcement relaxed in 2022. [ABSTRACT FROM AUTHOR]

Franklin ([30]) wrote, "There is also a critical need to integrate biodiversity objectives into management of all our landscapes because preservation of selected tracts of land, even at the largest scale possible, will not by itself achieve the desired goal of maintaining Earth's biodiversity." Recognizing the complex socio-economic nature of the biodiversity crisis, this commentary proposes the expansion of indigenous territories and protected areas, the establishment of a global biodiversity monitoring network, and the training of a new generation of translational ecologists, as potential pathways toward a more promising future. Keywords: conservation outcomes; historical perspective; translational ecology; tropical biodiversity EN conservation outcomes historical perspective translational ecology tropical biodiversity 729 736 8 07/11/23 20230701 NES 230701 This commentary examines the dynamics of tropical conservation science, the translation of scientific insights into practical conservation actions, and the resulting conservation outcomes over the last 35 years, using Biodiversity (Wilson & Peters, 1988) as a point of reference. Biodiversity (Wilson & Peters, 1988) revisited: How has tropical conservation science changed in the last 35 years?. [Extracted from the article]

Abstract Environmental (e)DNA has rapidly become a powerful biomonitoring tool, particularly in aquatic ecosystems. This approach has not been as widely adopted in terrestrial communities where the methods of vertebrate eDNA collection have varied from the use of secondary collectors such as blood feeding parasites and spider webs, to washing surfaces of leaves and soil sampling. Recent studies have demonstrated the potential of direct collection of eDNA from air sampling, but none have tested how effective airborne eDNA sampling might be in a biodiverse environment. We used three prototype samplers to actively sample a mixed neotropical bat community in a partially controlled environment. We assess whether airborne eDNA can accurately characterize a high diversity community with skewed abundances and to determine if filter design impacts DNA collection and taxonomic recovery. Our study provides evidence for the accuracy of airborne eDNA as a detection tool and highlights its potential for monitoring high density, diverse assemblages such as bat roosts. Analysis of air samples recovered >91% of the species present and some limited relationship between species abundance and read count. Our data suggests this method can accurately depict a diverse mixed‐mammal community, particularly when the location is contained (e.g., a roost, den or burrow) but also highlights the potential for secondary transfer of eDNA material on clothing and equipment. Our results also demonstrate that simple, inexpensive, battery‐operated homemade air samplers can collect an abundance of eDNA from the air, opening the opportunity for sampling in remote environments.

The high diversity and limited floral information in tropical forests often pose a challenge for species identification. However, over the past decade, DNA barcoding has been employed in tropical forests, including Sumatran forests, to enhance floristic surveys. This technique facilitates the discrimination of morphologically similar species and addresses the limitations of conventional species identification, which relies on short‐lived reproductive structures. This study aimed to evaluate the efficiency of matK, rbcL, and the combination of both chloroplast markers for species identification in Burseraceae by employing genetic distance and species tree inference. In this study, we collected 197 specimens representing 20 species from five genera of Burseraceae. The highest percentage of specimens' identification (36%) at the species level was obtained using matK + rbcL, followed by matK (31%), and rbcL (7%). The matK dataset presented the highest interspecific divergence with a mean of 0.008. In addition, a lack of barcode gap was observed in both markers, suggesting potential limitations of the core barcodes for distinguishing Sumatran species within Burseraceae. The monophyly test confirmed five species as monophyletic using Bayesian species tree inferences for matK. Overall, our results demonstrate that matK outperforms rbcL in species identification of Burseraceae, whereas their combination did not enhance species delimitation. To improve the molecular species assignments of this family, future studies may consider including more DNA markers in conjuction with matK, and broadening the availability of reference sequences for species that have not yet been included in the databases. The outcomes of molecular species identification vary depending on the taxonomic group under investigation. Implementation of phylogenomics for species delimitation and diagnostic marker development is strongly recommended for tropical biodiversity assessments, especially for poorly studied clades. [ABSTRACT FROM AUTHOR]

Abstract While harboring the bulk of the planet's biodiversity, tropical ecosystems have experienced intense land conversion for agriculture. Studies examining the impacts of land‐use change on tropical biodiversity have primarily focused on forest cover loss but have overlooked the ecological potential of habitats surrounding forest fragments to modulate biodiversity loss. We examined whether small‐mammal communities changed with the land cover surrounding forest fragments, and how functional traits affected responses to land cover. Small mammals were sampled in the Brazilian Cerrado using live‐trap transects. Three landscape types were identified according to the surroundings of the transects (within 750‐m‐radius buffers): forest‐ (≥50% forest cover), pasture‐, and crop‐dominated landscapes (

Abstract Mollinedia (Monimiaceae) presents numerous microendemic species, and its centre of diversity is in the Brazilian Atlantic rainforest, where more than half of the species occur. The taxonomy of microendemic species can be challenging because their morphological and genetic variations can be interpreted as a response to geographic isolation rather than a circumscription for different species. In this paper, we describe Mollinedia pignalii Lírio & Pauli, a microendemic species from the Espírito Santo state, Brazil. Vegetatively, M. pignalii is similar to Mollinedia elegans Tul. and Mollinedia schottiana (Spreng.) Perkins; however, it presents the following differences: white-puberulous leaves, staminate flowers with a flat receptacle and 6 to 14 stamens, white-puberulous pistillate flowers with a cupuliform receptacle and 8 to 22 carpels, and white-puberulous drupelets. Due to the similarity between the three species, M. pignalii has been collected and deposited in herbaria under different names. Here, we describe the new species based on morphology and genome size, a comparison with similar species, and ecological comments in an integrative approach. We also provide its conservation status and an identification key for the species of Monimiaceae occurring in the state of Espírito Santo.

The forest understory experiences temperature variations that are dampened compared to adjacent open areas, allowing the development of a forest microclimate and associated ecological conditions. It is however unclear to what extent forests will maintain this buffering effect under increasing global warming. Providing reliable projections of future forest microclimates is therefore crucial to anticipate climate change impacts on forest biodiversity, and to identify corresponding conservation strategies. Recent empirical studies suggest that the buffering of air temperature extremes in forest understory compared to open land could increase with global warming, albeit at a slower rate than macroclimate temperatures. Here, we investigate the trend of this temperature buffering effect in a high-emission global warming scenario, using the process-based Land Surface Model CLM5.1. We find biome-dependant buffering trends with strongest values in tropical forests where buffering increases for every degree of global warming by 0.1 ^∘ C for maximum soil temperature, and by 0.2 ^∘ C for maximum canopy air temperature. In boreal regions, forest microclimate exhibits a strong seasonality and the effect of global warming is more uncertain. Thus, our results highlight the importance of tropical forest canopies in particular, in maintaining hospitable conditions for understory species while increasing their climate debt under global warming. Our research also illustrates the potential and limitations of Land Surface Models to simulate forest microclimate, and calls for further collaborations between Earth system modelers and ecologists to jointly question climate and biosphere dynamics.

Leucobryum scalare was described in 1904 but its taxonomic status has been disputed, being reduced to a variety of Leucobryum aduncum or synonymized with Leucobryum aduncum. The taxonomic confusion of this taxon has remained unresolved. Hence, we revisited the taxonomic status of the taxon using phylogenetic and morphometric approaches. A total of 27 samples from Leucobryum aduncum var. aduncum and Leucobryum aduncum var. scalare were used to generate data from four markers, including ITS1, ITS2, atpB-rbcL spacer, and trnL-trnF. The concatenated dataset was used to reconstruct a phylogenetic tree. Both qualitative and quantitative morphological characters were measured and analyzed with Principal Component Analysis (PCA) and PERMANOVA. The results showed that the two taxa are closely related but they are reciprocally monophyletic. Both qualitative and quantitative characters could also separate Leucobryum aduncum var. scalare from Leucobryum aduncum var. aduncum as shown with PCA and PERMANOVA. We propose the resurrection of the species rank for Leucobryum scalare as separate from Leucobryum aduncum. This work highlights the need for a more thorough revision of Leucobryum to clarify the actual level of diversity in this genus. [ABSTRACT FROM AUTHOR]

Landscape dynamics are widely thought to govern the tempo and mode of continental radiations, yet the effects of river network rearrangements on dispersal and lineage diversification remain poorly understood. We integrated an unprecedented occurrence dataset of 4,967 species with a newly compiled, time-calibrated phylogeny of South American freshwater fishes—the most species-rich continental vertebrate fauna on Earth—to track the evolutionary processes associated with hydrogeographic events over 100 Ma. Net lineage diversification was heterogeneous through time, across space, and among clades. Five abrupt shifts in net diversification rates occurred during the Paleogene and Miocene (between 30 and 7 Ma) in association with major landscape evolution events. Net diversification accelerated from the Miocene to the Recent (c. 20 to 0 Ma), with Western Amazonia having the highest rates of in situ diversification, which led to it being an important source of species dispersing to other regions. All regional biotic interchanges were associated with documented hydrogeographic events and the formation of biogeographic corridors, including the Early Miocene (c. 23 to 16 Ma) uplift of the Serra do Mar and Serra da Mantiqueira and the Late Miocene (c. 10 Ma) uplift of the Northern Andes and associated formation of the modern transcontinental Amazon River. The combination of high diversification rates and extensive biotic interchange associated with Western Amazonia yielded its extraordinary contemporary richness and phylogenetic endemism. Our results support the hypothesis that landscape dynamics, which shaped the history of drainage basin connections, strongly affected the assembly and diversification of basin-wide fish faunas. [ABSTRACT FROM AUTHOR]

At best, conservation decisions can only be made using the data available at the time. For plants and especially in the tropics, natural history collections remain the best available baseline information upon which to base conservation assessments, in spite of well‐documented limitations in their taxonomic, geographic, and temporal coverage. We explore the extent to which changes to the plant biological record over 20 years have changed our conception of the conservation importance of 931 plant taxa, and 114 vegetation samples, recorded in forest reserves of the southwest Ghana biodiversity hotspot. 36% of species‐level assessments changed as a result of new distribution data. 12% of species accepted in 2016 had no assessment in 1996: of those, 20% are new species publications, 60% are new records for SW Ghana, and 20% are taxonomic resolutions. Apparent species ranges have increased over time as new records are made, but new species publications are overwhelmingly of globally rare species, keeping the balance of perceived rarity in the flora constant over 20 years. Thus, in spite of considerable flux at the species record level, range size rarity scores calculated for 114 vegetation samples of the reserves in 1996 and 2016 are highly correlated with each other: r(112) = 0.84, p <.0005, and showed no difference in mean score over 20 years: paired t(113) = −0.482, p =.631. This consistency in results at the area level allows for worthwhile conservation priority setting over time, and we argue is the better course of action than taking no action at all. [ABSTRACT FROM AUTHOR]

Enhancing connectivity between protected areas is crucial for facilitating species range shifts in response to climate change. Yet spatial planning for this connectivity often overlooks the combined impacts of climate and land-cover change, particularly in tropical regions where habitat loss is a more immediate biodiversity threat. We explore the need for connectivity between protected areas to mitigate the dual impacts of climate- and land-cover change on Borneo. Using habitat suitability models and combined climate and land-cover change forecasts, we develop connectivity models for present and future scenarios, identifying optimal connections between protected areas for 81 species. By considering restoration and opportunity economic costs, we also explore the cost-benefit trade-offs of implementing connectivity plans. Connectivity solutions varied among species, but often converged on the same connections between protected areas, with contemporary connections traversing 6 to 40 km and comprising 67 % forest cover, on average. By the 2080s there were fewer connections, and while many were shorter, they also comprised poorer quality habitat, reflecting reductions in forest cover and species distributions. As a result, the economic cost of creating corridors between protected areas was estimated to be 65 % higher in 2080 than in 2020. Our analysis highlights the urgent need to prioritize connectivity interventions early to maximize long-term benefits for multiple species facing climate-change disruption while minimizing costs. However, conservation planning in tropical regions is complex, given high rates of forest degradation and loss. Implementing our approach at finer spatial scales could help identify cost-effective areas to prioritize landscape connectivity, helping safeguard tropical biodiversity amid changing environmental conditions. [ABSTRACT FROM AUTHOR]

The origin of Dahomey Gap (DG) flora is one of the central biogeographical questions in sub‐Saharan, which has been addressed in several studies. However, floristic evidence based on representative samples from the DG seems to be lacking in the scientific debate. The present study was conducted to fill this gap. Specifically, we assessed Togolese mountain riparian forests as minor forest refugia, examined their contribution to larger sub‐Saharan forest refugia, and discussed the significance of these findings for biogeography and biodiversity conservation. Southwest Togo, West Africa, and sub‐Saharan Upper Guinea Region Floristic data were collected in riparian forests through an intensive botanical inventory (n = 198; 50 × 10 m2). A comparative analysis was performed based on the floristic evidence related to forest refuges. The results showed significantly high species richness (868 species) and a high gamma and beta diversity associated with spatial turnover patterns. They also showed a high affinity between the study forests and large sub‐Saharan forest refugia. Riparian forests share about 60% of their current species richness with large sub‐Saharan forest refugia and contained refuge bio‐indicator species. The floristic evidence, consistent with those of other studies, suggests that Togolese mountains would have very ancient origins and have experienced paleoclimatic events. The studied riparian would have served as refuges during recurrent climatic episodes. Our results support the minimal forest fragmentation hypothesis (network of refugia along rivers). However, they seem to be incompatible with the idea that the DG flora may be essentially a relic of the early Holocene. In sub‐Saharan Africa, where maintaining a vast area of natural forest is difficult due to human pressure, efforts to preserve maximum species diversity should include a focus on the conservation of minor forest refuges, particularly in sub‐humid mountain riparian zone. [ABSTRACT FROM AUTHOR]

Abstract The origin of Dahomey Gap (DG) flora is one of the central biogeographical questions in sub‐Saharan, which has been addressed in several studies. However, floristic evidence based on representative samples from the DG seems to be lacking in the scientific debate. The present study was conducted to fill this gap. Specifically, we assessed Togolese mountain riparian forests as minor forest refugia, examined their contribution to larger sub‐Saharan forest refugia, and discussed the significance of these findings for biogeography and biodiversity conservation. Southwest Togo, West Africa, and sub‐Saharan Upper Guinea Region Floristic data were collected in riparian forests through an intensive botanical inventory (n = 198; 50 × 10 m2). A comparative analysis was performed based on the floristic evidence related to forest refuges. The results showed significantly high species richness (868 species) and a high gamma and beta diversity associated with spatial turnover patterns. They also showed a high affinity between the study forests and large sub‐Saharan forest refugia. Riparian forests share about 60% of their current species richness with large sub‐Saharan forest refugia and contained refuge bio‐indicator species. The floristic evidence, consistent with those of other studies, suggests that Togolese mountains would have very ancient origins and have experienced paleoclimatic events. The studied riparian would have served as refuges during recurrent climatic episodes. Our results support the minimal forest fragmentation hypothesis (network of refugia along rivers). However, they seem to be incompatible with the idea that the DG flora may be essentially a relic of the early Holocene. In sub‐Saharan Africa, where maintaining a vast area of natural forest is difficult due to human pressure, efforts to preserve maximum species diversity should include a focus on the conservation of minor forest refuges, particularly in sub‐humid mountain riparian zone.

Tropical freshwater invertebrate species are becoming extinct without being described, and effective conservation is hampered by a lack of taxonomic and distribution data. DNA metabarcoding is a promising tool for rapid biodiversity assessments that has never been applied to tropical freshwater invertebrates across large spatial and taxonomic scales.Here we use DNA metabarcoding to comprehensively assess the benthic freshwater invertebrate fauna of the Perak River basin, Malaysia. Specific objectives were to: (1) assess performance of two DNA metabarcoding protocols; (2) identify gaps in reference databases; (3) generate new data on species diversity and distribution; and (4) draw conclusions regarding the potential value of DNA metabarcoding in tropical freshwater conservation.Organisms were collected by hand and net at 34 sites and divided into small (retained in 0.5‐mm but passing through 1‐mm mesh) and large (retained in 1‐mm mesh) fractions, and a 313‐bp cytochrome c oxidase subunit I fragment amplified and sequenced using general Metazoa primers.Bioinformatic analysis resulted in 468 operational taxonomic units (~species) from 12 phyla. Only 29% of species could be assigned binominal names through matches to public sequence libraries, indicating varying levels of library completeness across Orders. Extraction of small‐fraction DNA with a soil kit resulted in a significantly higher species count than with a general kit, but this was not even across taxa.Metabarcoding (amplification) success rate, estimated via comparison to morphological identifications of the large‐fraction specimens, was high in most taxa analysed but low, for example, in ampullariid and viviparid gastropods. Conversely, a large proportion of species‐site records for Decapoda and Bivalvia came from metabarcoding only. Species richness averaged 29 ± 16 species per site, dominated by Diptera, Annelida, and Odonata, and was particularly high in tributaries of the mountainous Titiwangsa Range. At least eight species are new records for Malaysia, including the non‐natives Ferrissia fragilis (Gastropoda) and Dugesia notogaea (Platyhelminthes).Our study showed that DNA metabarcoding is generally more effective in detecting tropical freshwater invertebrate species than traditional morphological approaches, and can efficiently improve knowledge of distribution patterns and ranges of native and non‐native species. However, current gaps in reference databases, particularly for bioindicator taxa, such as the Plecoptera, Ephemeroptera, and Coleoptera, need to be addressed urgently. [ABSTRACT FROM AUTHOR]

Understanding the drivers of algal endosymbiont communities hosted by reef corals is a requisite for predicting coral resilience. For the biodiverse reefs of Southeast Asia, few studies have characterised the spatial variability of Symbiodiniaceae communities amongst reefs and investigated species and environmental effects on community structure and diversity. To profile the endosymbionts associated with reef corals inhabiting Southeast Asia, three common species, Pachyseris speciosa, Pocillopora acuta and Diploastrea heliopora, were sampled from 10 reef sites along the coasts of the Malay Peninsula. The nuclear internal transcribed spacer 2 region of Symbiodiniaceae was targeted for high-throughput sequencing, and the SymPortal framework was used to establish the identities of endosymbiont genera and types. Effects of environmental variables on endosymbiont community structure and diversity were then tested. Analyses revealed that Symbiodiniaceae diversity in this region is higher than previously known. Endosymbiont communities are structured significantly by host species and are relatively invariant in D. heliopora, with P. speciosa associating strongly with both Cladocopium and Durusdinium while P. acuta and D. heliopora are dominated by Durusdinium. Environmental parameters influence Symbiodiniaceae communities and diversity distinctly between host species. In particular, higher sea surface temperature (SST) affects endosymbiont diversity positively for P. acuta while higher SST range affects diversity negatively for P. speciosa and D. heliopora. Overall, this study has uncovered the hidden diversity of Symbiodiniaceae types previously unrecorded in the region and established a baseline for future comparative studies on how Southeast Asian reef corals acclimatise and adapt to changing environments through the natural variation of endosymbiont communities. [ABSTRACT FROM AUTHOR]

Anthropogenic‐driven species extinctions are radically changing the biosphere. Biological communities may become increasingly similar to or dissimilar from one another via the processes of biotic homogenisation or heterogenisation. A key question is how the conversion of native forests to agriculture may influence these processes by driving changes in the occurrence patterns of restricted‐range endemic species versus wide‐ranging generalists. We examined biotic homogenisation and heterogenisation in bird communities on the Southeast Asian islands of Borneo, Sulawesi, Seram, Buru, Talaud and Sangihe. Each island is characterised by high levels of avian endemism and unique spatial configuration of forest conversion to agriculture. Forest conversion to agriculture influenced the patterns of biotic homogenisation on five islands. Bird communities became increasingly dissimilar to forest reference communities relative to localised patterns of deforestation. Turnover led to species with larger global range‐sizes dominating communities at the expense of island endemics and ecological specialists. Within islands, forest conversion did not result in clear changes to β‐diversity, whereas between‐island communities became increasingly similar with greater deforestation, implying that patterns of forest conversion profoundly affect biotic homogenisation. Our findings elucidate how continued conversion of forests is causing the replacement of endemic species by a small cohort of shared ubiquitous species with potentially strong negative consequences for ecosystem functioning and resilience. Halting reorganisation of the biosphere via the loss of range‐restricted species and spread of wide‐ranged generalists will require improved efforts to reduce the impacts of deforestation, particularly in regions with high endemism. [ABSTRACT FROM AUTHOR]

Hopea odorata Roxb. is a forest plant from Dipterocarpaceae family that has important economic and ecological functions in the ecosystem. Generative propagation of H. odorata is limited because of its recalcitrant seed that cannot be stored for long periods at room temperature or even at low temperature. Cryopreservation is a seed storage technique that has the potential to prolong the shelf life of recalcitrant seeds. The aim of this study was to evaluate the effect of cryoprotectant and cryopreservation treatment on seed viability and biochemical change (electrolyte leakage, total malondialdehyde, total phenol) of H. odorata seeds. Fresh seeds of H. odorata were treated with two types of cryoprotectans namely PVS1 as non penetrating cryoprotectant and PVS2 as penetrating cryoprotectant, each type of cryoprotectant with four different concentrations (25, 50, 75 or 100%(w/v)) and four different immersion times (30, 60, 90 or 120 mins). Seeds were then stored in two different temperatures, at room temperature (28±2⁰C) or in liquid nitrogen (-196±2⁰C) for 24 hours to evaluate the cryoprotectant toxicity. The results showed that H. odorata seeds stored at room temperature and immersed either in 100%, 75% or 50% of PVS1 possess a higher viability as well as germination percentage, germination rate, vigour index and maximum growth potensial. In addition, they have lower value of electrolyte leakage, total malondialdehyde and total phenol compared to those seeds treated with PVS2. Meanwhile, both type of cryoprotectants and cryopreservation treatment in this study have not been able yet to increase seed viability of H. odorata. Cryopreservation treatments caused an increase in the total of malondialdehyde and electrolyte leakageas and these leads the inability of H. odorata seeds to germinate. PVS1 cryoprotectant seems to cause less toxic effects on H. odorata seeds but it can not prevent the negative impact of cryopreservation treatment.

Seed dispersal by animals is one of the most important ecological processes in tropical forests, entailing millions of years of evolutionary adaptations of plants and frugivorous animals forming networks of interactions that, ultimately, contribute to the resilience of such forests. We analyze 29 seed dispersal networks in the threatened Atlantic Forest biodiversity hotspot, with data on the frequency of feeding visits by birds to fruiting plants to answer: 1) which are the effects of forest cover and landscape connectivity on the maintenance of phylogenetic diversity (PD) of interacting birds and plants and the evolutionary distinctiveness of the interactions (EDi) between them; and 2) how EDi and plant/bird PD affects the robustness of the interaction networks? We found that forest cover positively influences both plant and bird PD and EDi. Landscape connectivity is an important predictor of bird PD, but not plant PD, suggesting that the spatial arrangement of forest remnants is essential for guaranteeing bird movement among forest fragments. Furthermore, interaction networks of areas with higher PD and EDi had great robustness to the simulated extinction of species, which underscore the importance of larger forest blocks for conserving evolutionary information and, consequently, the health and natural resistance of seed dispersal networks against environmental change. [ABSTRACT FROM AUTHOR]

The Malay Archipelago, also known as Malesia, is customarily divided into nine ecogeographical regions. In any comparison between these regions, Borneo usually stands out with the highest number of species, but if the number of species is divided by land area to obtain a regional species intensity index, the Malay Peninsula stands out prominently, not only for plants but also for mammals, reptiles, amphibians and fish. This striking pattern across the taxonomic spectrum suggests that the forces driving speciation have been more intense in the Malay Peninsula than in other regions of the Archipelago. The Malay Peninsula also stands out in comparison with countries in continental South-East Asia. Possible contributory factors to the intensity of speciation may be the height and structure of dipterocarp forests, the rate of tree turnover and the phenomenon of mass flowering. [ABSTRACT FROM AUTHOR]

The study examines the gross morphology of giant bamboo (Dendrocalamus asper) relative to varying elevation, temperature, and relative humidity in five forest areas of Bukidnon province in the Philippines. Results revealed that variations in leaf sizes and the number of nodes and internodes among elevation ranges were not significant. However, the culm length of giant bamboo was significantly higher in the mid-elevation range (644-892 m asl) and lower elevation range (344-447 m asl) compared to culms in higher elevations. In addition, differences in culm diameter and culm thickness were significant showing larger diameter and thicker culms in the mid-elevation range (644-892 m asl) as compared to the higher (1117-1124 m asl) and lower (344-347 m asl) elevation range. The level of phosphorus and nitrogen was the highest in the mid and lower elevation range while potassium level was abundant in the highest elevations. Correlation analysis showed a negative relationship between culm lengths to elevation and relative humidity while mid and top section diameters were negatively correlated to temperature until 892 m asl. Leaf area and leaf width were strongly influenced by phosphorus level. The canonical correspondence analysis showed culm lengths were affected by relative humidity and elevation while the number of nodes and internodes, top and mid-section culm thickness, average diameter and basal section diameters were affected by temperature. Non-metric multidimensional scaling revealed that variation in bamboo morphology occured at the lowest and highest elevation while overall similarity was observed at 600-900 m asl elevation, suggesting an optimal growth for giant bamboo might be within the range. [ABSTRACT FROM AUTHOR]

The North Maluku waters is one of tropical waters, place of distribution and spread of anguillid eels (Anguilla spp.) in Indonesia. The structure of molecule of eel species and composition of its population inhabiting the waters is important to be observed to determine the management of supply of eel species seedlings. The aim of this study is to do molecular identification, analyse the genetic distance and phylogenic tree of eel based upon the partial Displacement Loop and Cytochrom b genes as the genetic marker. This study used 14 eel samples collected from 3 locations in North Maluku (Bacan, Tidore and West Gane). Partial D-Loop and Cyt b genes were amplified using the primary partial D-Loop and Cyt-b genes and then the similarities of the sequencing results were analyzed using Blastn NCBI. The analysis of genetic distance and phylogenic tree were conducted by means of Kimura-2-Parameter method using MEGA X (Molecular Evolutionary Genetic Analysis) program. The results showed two types of anguillid species identified: Anguilla marmorata (97-100%) and Anguilla interioris (100%). Anguilla marmorata is a species with high spreading rate, and it can be found in all locations. Meanwhile, Anguilla interioris is the species with limited spreading and it can be only found in West Gane. The average of genetic distance between populations had a medium value (0.33), indicating that there was a variety of genetics. Based upon the analysis of phylogenic tree, Anguilla marmorata spread in North Maluku is considered to come from the different breeds but has mixed in nature in view of migration process. [ABSTRACT FROM AUTHOR]

The exceptional concentration of vertebrate diversity in continental freshwaters has been termed the “freshwater fish paradox,” with > 15,000 fish species representing more than 20% of all vertebrate species compressed into tiny fractions of the Earth’s land surface area (

The Unionidae represent an excellent model taxon for unravelling the drivers of freshwater diversity, but, phylogeographic studies on Southeast Asian taxa are hampered by lack of a comprehensive phylogeny and mutation rates for this fauna. We present complete female- (F) and male-type (M) mitogenomes of four genera of the Southeast Asian clade Contradentini+Rectidentini. We calculate substitution rates for the mitogenome, the 13 protein-coding genes, the two ribosomal units and three commonly used fragments (co1, nd1 and 16S) of both F- and M-mtDNA, based on a fossil-calibrated, mitogenomic phylogeny of the Unionidae. Phylogenetic analyses, including an M+F concatenated dataset, consistently recovers a monophyletic Gonideinae. Subfamily-level topology is congruent with that of a previous nuclear genomic study and with patterns in mitochondrial gene order, suggesting Unionidae F-type 2 as a synapomorphy of the Gonideinae. Our phylogeny indicates that the clades Contradentini+Rectidentini and Lamprotulini+Pseudodontini+Gonideini split in the early Cretaceous (~125 Mya), and that the crown group of Contradentini+Rectidentini originated in the late Cretaceous (~79 Mya). Most gonideine tribes originated during the early Palaeogene. Substitution rates were comparable to those previously published for F-type co1 and 16S for certain Unionidae and Margaritiferidae species (pairs). [ABSTRACT FROM AUTHOR]

The diversity of native oysters in many regions is overshadowed by the global dominance of a few economically important species. Here we describe the Muar Oyster, Crassostrea (Magallana) saidii sp. nov., first reported as an established local fishery renowned for exceptional and distinctive flavour over 160 years ago by British colonial officials in Malaysia, but as yet never formally named or described as a species. This new species has a subtle but clear morphological diagnosis dependent on three-dimensional characters, which has long been recognised by local fishers to differentiate the new species from co-occurring C. (M.) belcheri (G. B. Sowerby II, 1871). The Indo-Pacific clade Magallana Salvi & Mariottini, 2016 in Salvi and Mariottini 2017 is a phylogenetically distinct group that nonetheless cannot be morphologically separated from the broader genus Crassostrea Sacco, 1897. Fossils or species known only from shell specimens, though morphologically distinct species, cannot be classified as Magallana, Talonostrea Li & Qi, 1994, or Crassostrea s.s.; therefore, we revise these groups as sub-genera within Crassostrea. Our analysis of the COI barcoding fragment from previously published sequences of all available Magallana species found that gene is not sufficient to separate several economically important species, and revealed more than 5% of sequences in GenBank represent identification errors. The new species Crassostrea (Magallana) saidii sp. nov., which is genetically, morphologically, and gastronomically distinct, is known from only one population under potential threat from urbanisation. Many more global species of Magallana remain undescribed. The systematics of this group is critical to understand the diversity of global oysters, and to understand the sustainable use of species grown worldwide for centuries as our food. [ABSTRACT FROM AUTHOR]

Petungkriyono forest is a tropical rainforest with high biodiversity. The increasing tourism activities in Petungkriyono lead to land conversion. Dragonfly (order Odonata) is a good bioindicator for aquatic and terrestrial. This study aimed to compare the community structure of Odonata in natural forests and tourist sites. The method of collecting imago Odonata was done by direct searching, samples were captured using sweep netting. The results showed that the dragonflies found in all locations consisted of the same family, 2 families (Gomphidae and Libellulidae) from the suborder Anisoptera and 6 families (Calopterygidae, Chlorocyphidae, Coenagrionidae, Euphaidae Platycnemididae, and Platystictidae) from the suborder Zygoptera. The total species of dragonflies found in Sokokembang were 15 species with a total of 293 individuals, Tirta Muncar 13 species of 287 individuals, Karanggondang 17 species of 276 individuals, and Curug Lawe 14 species of 242 individuals. The highest relative abundance of individuals was in the natural forest of Sokokembang is Drepanosticta spatulifera (26.28%) and in Karanggondang Vestalis luctuosa (24.64%), while in the tourist forests of Tirta Muncar and Curug Lawe were Euphaea variegata (34.84% and 28.51 %). The structure of the Odonata community is based on the Shannon-Wiener diversity index in the natural forests of Sokokembang (2.18) and Karanggondang (2.21) at the tourist sites of Tirta Muncar (1.84) and Curug Lawe (2.11). The results showed that the structure of the Odonata community based on the level of the diversity index value, evenness index, and dominance index in natural forests and tourist sites in Petungkriyono forest was not significantly different.

The Amazon River Basin, one of the world’s most threatened ecosystems, has an enormous diversity of fish species, a result of temporally and spatially complex habitat containing biogeochemically different river systems. The annual hydrologic cycle results in floodplain lakes during low water and inundates forests during high water, exposing fish to different resources and environmental conditions. The two principal river systems in the central Brazilian Amazon are blackwater, with nutrient-poor acidic water, and nutrient-rich whitewater. Although species-rich, the Amazon Basin is data-poor in terms of comparative studies on a regional scale. We analyzed data sets from independent sampling studies of pelagic fish in 16 floodplain lakes, nine whitewater (Rio Solimões) and seven blackwater (Rio Negro), in the central Amazon Basin of Brazil. Our findings suggest striking similarities in pelagic fish diversity patterns. Species richness was virtually equal (165 in whitewater and 168 in blackwater). Both species richness, and number of migratory species, per lake increased toward the confluence of the rivers in both systems in our study. The proportion of unique species was also similar in whitewater lakes and blackwater (41 and 43%, respectively), boosting total regional richness to 237 species. However, species composition in whitewater lakes was more homogenous (lower β diversity), and species composition was associated with conductivity and pH in whitewater, but with dissolved oxygen and transparency in blackwater. Therefore, regional fish diversity cannot be represented by sampling one lake or even one drainage system, but must include multiple lakes from both systems. These two systems may differ in sensitivity to anthropogenic stressors such as damming and deforestation.

Emerging large-scale datasets coupled with statistical advances have provided new insights into the processes that generate the latitudinal diversity gradient (LDG). But many of these studies run into an old, if often underappreciated, problem: The interpretation of the data critically depends on the consistent application of criteria to define what constitutes a species. This is particularly pernicious for the LDG because good species have been easier to recognize in temperate than in tropical regions. We provide evidence that this latitudinal taxonomy gradient exists, discuss how this potentially impacts inferences about latitudinal variation in ecoevolutionary processes such as population differentiation and speciation, and provide a roadmap for how to mitigate taxonomic biases in the study of biodiversity patterns. Phylogenetic data has revealed, among other things, that recent speciation rates appear to be faster in the temperate regions than in the more biodiverse tropics, but that tropical species harbor more population substructure and within-species genetic diversity. These findings have upended conventional explanations for the existence of the latitudinal diversity gradient. These inferences are, however, critically dependent on species' being defined in a consistent way across latitudes. Evidence from case studies suggests that this assumption is not met. Instead, many good tropical species are not (yet) recognized, creating a taxonomic debt in the tropics. Understanding the ecological and evolutionary processes that generate the latitudinal diversity gradient will require engaging seriously with taxonomic practice and developing strategies to mitigate the biases that it may create. [ABSTRACT FROM AUTHOR]

Understanding the interactions among microbial communities, plant communities and soil properties following deforestation could provide insights into the long-term effects of land-use change on ecosystem functions, and may help identify approaches that promote the recovery of degraded sites. We combined high-throughput sequencing of fungal rDNA and molecular barcoding of plant roots to estimate fungal and plant community composition in soil sampled across a chronosequence of deforestation. We found significant effects of land-use change on fungal community composition, which was more closely correlated to plant community composition than to changes in soil properties or geographic distance, providing evidence for strong links between above- and below-ground communities in tropical forests.

Despite evidence that species' traits affect rates of bird diversification, biogeographic studies tend to prioritise earth history in Neotropical bird speciation. Here we compare mitochondrial genetic differentiation among 56 co‐distributed Neotropical bird species with varying ecologies. The trait 'diet' best predicted divergence, with plant‐dependent species (mostly frugivores and nectivores) showing lower levels of genetic divergence than insectivores or mixed‐diet species. We propose that the greater vagility and demographic instability of birds whose diets rely on fruit, seeds, or nectar  known to vary in abundance seasonally and between years  relative to birds that eat primarily insects, drives episodic re‐unification of otherwise isolated populations, resetting the divergence 'clock'. Testing this prediction using coalescent simulations, we find that plant‐dependent species show stronger signals of recent demographic expansion compared to insectivores or mixed‐diet species, consistent with this hypothesis. Our study provides evidence that localised ecological phenomena scale up to generate larger macroevolutionary patterns. [ABSTRACT FROM AUTHOR]

Sedimentary ancient DNA has been proposed as a key methodology for reconstructing biodiversity over time. Yet, despite the concentration of Earth’s biodiversity in the tropics, this method has rarely been applied in this region. Moreover, the taphonomy of sedimentary DNA, especially in tropical environments, is poorly understood. This study elucidates challenges and opportunities of sedimentary ancient DNA approaches for reconstructing tropical biodiversity. We present shotgun-sequenced metagenomic profiles and DNA degradation patterns from multiple sediment cores from Mubwindi Swamp, located in Bwindi Impenetrable Forest (Uganda), one of the most diverse forests in Africa. We describe the taxonomic composition of the sediments covering the past 2200 years and compare the sedimentary DNA data with a comprehensive set of environmental and sedimentological parameters to unravel the conditions of DNA degradation. Consistent with the preservation of authentic ancient DNA in tropical swamp sediments, DNA concentration and mean fragment length declined exponentially with age and depth, while terminal deamination increased with age. DNA preservation patterns cannot be explained by any environmental parameter alone, but age seems to be the primary driver of DNA degradation in the swamp. Besides degradation, the presence of living microbial communities in the sediment also affects DNA quantity. Critically, 92.3% of our metagenomic data of a total 81.8 million unique, merged reads cannot be taxonomically identified due to the absence of genomic references in public databases. Of the remaining 7.7%, most of the data (93.0%) derive from Bacteria and Archaea, whereas only 0–5.8% are from Metazoa and 0–6.9% from Viridiplantae, in part due to unbalanced taxa representation in the reference data. The plant DNA record at ordinal level agrees well with local pollen data but resolves less diversity. Our animal DNA record reveals the presence of 41 native taxa (16 orders) including Afrotheria, Carnivora, and Ruminantia at Bwindi during the past 2200 years. Overall, we observe no decline in taxonomic richness with increasing age suggesting that several-thousand-year-old information on past biodiversity can be retrieved from tropical sediments. However, comprehensive genomic surveys of tropical biota need prioritization for sedimentary DNA to be a viable methodology for future tropical biodiversity studies.

Abstract Introduction A decline in direct experience with nature can lead to disaffection of natural environments, wildlife, and public indifference towards biodiversity conservation. This study measured on affective attitude towards wildlife (i.e., preferences for and willingness to coexist with 22 animal species) and examined the relationships between these attitudes and childhood experiences with nature. Methods A face to face interview was carried out in rapidly urbanizing Malaysia for both urban and suburban 357 adults (age > 20 years old). Results It found that Malaysian people liked several insects and squirrels, but disliked mammals generally. Mediation analysis, with controlling sociodemographic factors (gender, age and ethnicity), showed that childhood nature experience was positively associated with preference for wild animals (standardized path coefficient = 0.18; p

The description of a new species is a key step in cataloguing the World's flora. However, this is only a preliminary stage in a long process of understanding what that species represents. We investigated how long the species discovery process takes by focusing on three key stages: 1, the collection of the first specimen; 2, the publication of the species name; and 3, the date when a minimum number of 15 accurately named specimens are available. We quantified the time lags associated with these stages for several groups of plants with different numbers of species and from different regions, including the 20 most species-rich Angiosperm families. Our analyses reveal that it takes decades to accumulate a minimum number of specimens to allow subsequent studies of any kind. The time lag between stages 1 and 3 is consistently over 70 years with groups such as the tropical genus Aframomum reflecting an average time lag of over 100 years. In light of our results, we suggest that species discovery is most accurately characterized as a lengthy process of knowledge accumulation, often spanning decades, rather than a one-off event. [ABSTRACT FROM AUTHOR]

Insect parasitoids may be an exception to the typical biogeographic pattern of increasing species richness at lower latitudes exhibited by most taxa. Evidence for this 'anomalous' latitudinal gradient has been derived from observations of hymenopteran parasitoids and it has been argued that other parasitoid groups should show a similar pattern of diversity. Several mechanisms have been proposed to explain this disparity, most notably the nasty host and resource fragmentation hypotheses.We review and evaluate these hypotheses with respect to tachinid flies (Diptera: Tachinidae), and bring to the argument evidence from eight trapping surveys from temperate and tropical regions in the Americas including the United States, Costa Rica, and Ecuador. We find no evidence that tachinid fly diversity is lower in the tropics than in the temperate region. Our results, along with other lines of evidence, rather suggest that New World Tachinidae likely conform to the same negative relationship between latitude and richness as their largely phytophagous host taxa.We discuss geographic patterns of tachinid diversity in relation to ecological and evolutionary processes, and why they may differ from their hymenopteran parasitoid counterparts. Parasitoid taxa appear to vary strongly in their diversity responses to latitude and we concur with previous researchers that more survey data are necessary to reach strong conclusions about parasitoid latitudinal diversity patterns. [ABSTRACT FROM AUTHOR]

Aim: To quantify evolutionary transitions between tropical evergreen rain forest and seasonally dry biomes, to test whether biome transitions affect lineage diversification and to examine the robustness of these results to methodological choices. Location: The tropics. Time period: The Cenozoic. Major taxa studied: The plant subfamily Bombacoideae (Malvaceae). Methods: We inferred ancestral biomes based on a fossil‐dated molecular phylogeny of 103 species (59% of the clade) and recorded the number of transitions among biomes using biogeographical stochastic mapping based on the dispersal‐extinction‐cladogenesis model. We then estimated diversification rates using state‐specific speciation and extinction rate (SSE) methods. Furthermore, we tested the sensitivity of the results to model choice, phylogenetic uncertainty, measurement error and biome definition. Results: We found numerous transitions from evergreen rain forest to seasonally dry biomes, and fewer in the opposite direction. These results were robust to methodological choices. Biome type did not influence diversification rates, although this result was subject to uncertainty, especially related to model choice and biome definition. Main conclusions: Our results contradict the idea of evolutionary biome conservatism in Bombacoideae, and support previous findings that evergreen rain forests serve as a source for the flora of seasonally dry biomes. The impact of biome classification and biome definition on the results suggest caution when using a biome concept for biogeographical reconstruction and diversification rate analysis. [ABSTRACT FROM AUTHOR]

Rain forests on Borneo support exceptional concentrations of endemic insect biodiversity, but many of these forest‐dependent species are threatened by land‐use change. Totally protected areas (TPAs) of forest are key for conserving biodiversity, and we examined the effectiveness of the current TPA network for conserving range‐restricted butterflies in Sabah (Malaysian Borneo). We found that mean diurnal temperature range and precipitation of the wettest quarter of the year were the most important predictors of butterfly distributions (N = 77 range‐restricted species), and that species richness increased with elevation and aboveground forest carbon. On average across all species, TPAs were effective at conserving ~43% of species' ranges, but encompassed only ~40% of areas with high species richness (i.e., containing at least 50% of our study species). The TPA network also included only 33%–40% of areas identified as high priority for conserving range‐restricted species, as determined by a systematic conservation prioritization analysis. Hence, the current TPA network is reasonably effective at conserving range‐restricted butterflies, although considerable areas of high species richness (6,565 km2) and high conservation priority (11,152–12,531 km2) are not currently protected. Sabah's remaining forests, and the range‐restricted species they support, are under continued threat from agricultural expansion and urban development, and our study highlights important areas of rain forest that require enhanced protection. Abstract in Malay is available with online material. [ABSTRACT FROM AUTHOR]

The bulk of the world’s biodiversity is found in tropical regions, which are increasingly threatened by the human-led degradation of natural habitats. Yet, little is known about tropical biodiversity responses to habitat loss and fragmentation. Here we review all available literature assessing landscape effects on gene flow in tropical species, aiming to help unravel the factors underpinning functional connectivity in the tropics. We map and classify studies by focus species, the molecular markers employed, statistical approaches to assess landscape effects on gene flow, and the evaluated landscape and environmental variables. We then compare qualitatively and quantitatively landscape effects on gene flow across species and units of analysis. We found 69 articles assessing landscape effects on gene flow in tropical organisms, most of which were published in the last five years, were concentrated in the Americas, and focused on amphibians or mammals. Most studies employed population-level approaches, microsatellites were the preferred type of markers, and Mantel and partial Mantel tests the most common statistical approaches used. While elevation, land cover and forest cover were the most common gene flow predictors assessed, habitat suitability was found to be a common predictor of gene flow. A third of all surveyed studies explicitly assessed the effect of habitat degradation, but only 14 of these detected a reduced gene flow with increasing habitat loss. Elevation was responsible for most significant microsatellite-based isolation by resistance effects and a single study reported significant isolation by non-forested areas in an ant. Our study reveals important knowledge gaps on the study of landscape effects on gene flow in tropical organisms, and provides useful guidelines on how to fill them.

To meet a global demand for timber, tree plantations were established in South America during the first half of the 20th century. Extensive plantings of non-native species now are found in Brazil, Chile, Argentina, and Uruguay. In Colombia, miscellaneous plantations were established in the 1950s, during a period of intensive local logging, when policies to limit deforestation in native Quercus humboldtii forests were established. One unforeseen consequence of planting non-native trees was the simultaneous introduction and subsequent persistence of ectomycorrhizal fungi. We sought to document the origins and spread of the introduced Amanita muscaria found in Colombian plantations of the Mexican species Pinus patula, North American species P. taeda, and Australian species Acacia melanoxylon and Eucalyptus globulus. In Colombia, Amanita muscaria is establishing a novel association with native Q. humboldtii and has spread to local Q. humboldtii forests. According to a Bayesian phylogeny and haplotype analysis based on the nuclear rDNA internal transcribed spacer region ITS1-5.8-ITS2 (ITS barcode), A. muscaria individuals found in four exotic plant species, and those colonizing Q. humboldtii roots, have a Eurasian origin and belong to two Eurasian haplotypes. This is the first time the spread of an introduced mutualist fungus into native Colombian Q. humboldtii forests is reported. To arrest its spread, we suggest the use of local inocula made up of native fungi, instead of inocula of introduced fungi. [ABSTRACT FROM AUTHOR]

Bivalved gastropods (family Juliidae) are a pan-tropical group of small, green, extraordinary gastropods with a symmetrical clam-like shell. Only a single species of Juliidae has been reported in Malaysia, Berthelinia singaporensis Jensen, 2015, feeding on multiple species of siphonous green algae in the genus Caulerpa. In spite of a baseline expectation for megadiversity in this region, including 13 recorded species in the genus Caulerpa from two small field sites studied here, B. singaporensis appears to be a relative generalist without preferences among available Caulerpa spp. that occur in suitable (micro)habitats. The life cycle of Juliidae includes univalve, coiled larvae that transform to bivalved adults. In the presence of Caulerpa, swimming veligers rapidly settle and begin feeding; in a later, terminal metamorphosis, the larval operculum is shed, and the teleoconch shell field splits to form a second, right valve of the adult bivalved form. By three days after hatching, settled larvae achieve a fully functional bivalved shell with a working hinge. Both veligers and adults produce an unusual elastic mucous tether to maintain attachment to the substratum or food plant. These animals are dependent on Caulerpa for their entire life cycle; so, adults occupy environments where dislodgement may be a substantial risk. In the adult, bivalved, form, the gastropod can withdraw completely into its shell and close the valves while maintaining the byssus-like tether. This arrangement, enabling the gastropod to be simultaneously anchored to the food plant and protected within the shell, suggests that being able to use a byssus is the most plausible adaptive explanation for the evolution of the bivalved form within gastropods. [ABSTRACT FROM AUTHOR]

Dispersal is important for biodiversity maintenance in both neutral and niche theories. However, little is known about the potential role of Allee effect at the community level. In the present study, we developed neutral models for quantifying the separate and joint influences of the Allee effect and dispersal process, respectively, on species abundance distribution (SAD) patterns. Tree census data from Barro Colorado Island (BCI), Panama were used as the case to compare different neutral SAD models. Results showed that Allee effects were not detected in the BCI tree SAD curve. By contrast, the neutral models with the incorporation of dispersal process (including both immigration and emigration) can remarkably improve the fitting power of neutral models on the BCI tree SAD curve. Finally, even though the influence is not detectable, the Allee effect-based SAD models still might be alternative SAD models for model comparison and null hypothesis testing. • Influence of Allee effect on species abundance distribution was evaluated. • Different models incorporating Allee effect and dispersal process were compared. • Signal of Allee effect was not detected when fitted onto an empirical dataset. • By contrast, dispersal was found to be important empirically. [ABSTRACT FROM AUTHOR]

ABSTRACT The bulk of the world's biodiversity is found in tropical regions, which are increasingly threatened by the human-led degradation of natural habitats. Yet, little is known about tropical biodiversity responses to habitat loss and fragmentation. Here we review all available literature assessing landscape effects on gene flow in tropical species, aiming to help unravel the factors underpinning functional connectivity in the tropics. We map and classify studies by focus species, the molecular markers employed, statistical approaches to assess landscape effects on gene flow, and the evaluated landscape and environmental variables. We then compare qualitatively and quantitatively landscape effects on gene flow across species and units of analysis. We found 69 articles assessing landscape effects on gene flow in tropical organisms, most of which were published in the last five years, were concentrated in the Americas, and focused on amphibians or mammals. Most studies employed population-level approaches, microsatellites were the preferred type of markers, and Mantel and partial Mantel tests the most common statistical approaches used. While elevation, land cover and forest cover were the most common gene flow predictors assessed, habitat suitability was found to be a common predictor of gene flow. A third of all surveyed studies explicitly assessed the effect of habitat degradation, but only 14 of these detected a reduced gene flow with increasing habitat loss. Elevation was responsible for most significant microsatellitebased isolation by resistance effects and a single study reported significant isolation by non-forested areas in an ant. Our study reveals important knowledge gaps on the study of landscape effects on gene flow in tropical organisms, and provides useful guidelines on how to fill them. [ABSTRACT FROM AUTHOR]