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Amphibians are in decline worldwide. However, their patterns of diversity, especially in the tropics, are not well understood, mainly because of incomplete information on taxonomy and distribution. We assess morphological, bioacoustic, and genetic variation of Madagascar's amphibians, one of the first near-complete taxon samplings from a biodiversity hotspot. Based on DNA sequences of 2,850 specimens sampled from over 170 localities, our analyses reveal an extreme proportion of amphibian diversity, projecting an almost 2-fold increase in species numbers from the currently described 244 species to a minimum of 373 and up to 465. This diversity is widespread geographically and across most major phylogenetic lineages except in a few previously well-studied genera, and is not restricted to morphologically cryptic clades. We classify the genealogical lineages in confirmed and unconfirmed candidate species or deeply divergent conspecific lineages based on concordance of genetic divergences with other characters. This integrative approach may be widely applicable to improve estimates of organismal diversity. Our results suggest that in Madagascar the spatial pattern of amphibian richness and endemism must be revisited, and current habitat destruction may be affecting more species than previously thought, in amphibians as well as in other animal groups. This case study suggests that worldwide tropical amphibian diversity is probably underestimated at an unprecedented level and stresses the need for integrated taxonomic surveys as a basis for prioritizing conservation efforts within biodiversity hotspots.

The composition of the human gut microbiota is linked to health and disease, but knowledge of individual microbial species is needed to decipher their biological roles. Despite extensive culturing and sequencing efforts, the complete bacterial repertoire of the human gut microbiota remains undefined. Here we identify 1,952 uncultured candidate bacterial species by reconstructing 92,143 metagenome-assembled genomes from 11,850 human gut microbiomes. These uncultured genomes substantially expand the known species repertoire of the collective human gut microbiota, with a 281% increase in phylogenetic diversity. Although the newly identified species are less prevalent in well-studied populations compared to reference isolate genomes, they improve classification of understudied African and South American samples by more than 200%. These candidate species encode hundreds of newly identified biosynthetic gene clusters and possess a distinctive functional capacity that might explain their elusive nature. Our work expands the known diversity of uncultured gut bacteria, which provides unprecedented resolution for taxonomic and functional characterization of the intestinal microbiota. The known species repertoire of the collective human gut microbiota is substantially expanded with the discovery of 1,952 uncultured bacterial species that greatly improve classification of understudied African and South American samples.

Aim There is an urgent need to explore, characterize, describe and preserve as many species as possible to prevent their decline. Tropical biodiversity hotspots harbour most of the known land diversity and vast amounts of undiscovered and undescribed species. Here, we quantify the taxonomically unassessed amphibian species richness in Madagascar, one of the best‐studied and explored tropical hotspots worldwide, to identify knowledge gaps and conservation implications. Location Madagascar. Time Period Present. Major Taxa Studied Amphibians. Methods We used the Madagascar amphibian fauna as a model to unveil neglected diversity by analysing 10,873 mitochondrial sequences using species delimitation algorithms and incorporating all previously published bioacoustics, distributional, morphological and nuclear data with an integrative approach. Results Besides the currently described 413 species, we identified 408 divergent lineages. Among this, 310 fit the category of candidate species pending a taxonomic assessment, while 98 are considered deep conspecific lineages. These figures suggest that species richness could be twice as high as represented in the current taxonomy. Geographically, most of these candidate species occur in well‐studied areas within the island. Main Conclusions Despite being one of the best‐studied and explored tropical countries worldwide for amphibians, we found that many species are awaiting a taxonomic assessment in Madagascar. Paradoxically, this unassessed diversity concentrates on highly explored regions, emphasizing the importance of exploring and inventorying new areas. Our results highlight the magnitude of the Linnean and Wallacean shortfalls, affecting both species richness estimates and the distribution ranges and biogeographic setting known for this fauna. Current conservation efforts should consider this novel diversity and unexplored areas as they will likely harbour yet many new species to be discovered. We expect similar patterns across less studied tropical realms and encourage researchers to perform such studies in different clades before this neglected biodiversity becomes irremediably lost.

Several recent estimates of global biodiversity have concluded that the total number of species on Earth lies near the lower end of the wide range touted in previous decades. However, none of these recent estimates formally explore the real \"elephant in the room\", namely, what proportion of species are taxonomically invisible to conventional assessments, and thus, as undiagnosed cryptic species, remain uncountable until revealed by multi-gene molecular assessments. Here we explore the significance and extent of so-called \"hyper-cryptic\" species complexes, using the Australian freshwater fish Galaxias olidus as a proxy for any organism whose taxonomy ought to be largely finalized when compared to those in littlestudied or morphologically undifferentiated groups. Our comprehensive allozyme (838 fish for 54 putative loci), mtDNA (557 fish for 605 bp of cytb), and morphological (1963-3389 vouchers for 17-58 characters) assessment of this species across its broad geographic range revealed a 1500% increase in species-level biodiversity, and suggested that additional taxa may remain undiscovered. Importantly, while all 15 candidate species were morphologically diagnosable a posteriori from one another, single-gene DNA barcoding proved largely unsuccessful as an a priori method for species identification. These results lead us to draw two strong inferences of relevance to estimates of global biodiversity. First, hyper-cryptic complexes are likely to be common in many organismal groups. Second, no assessment of species numbers can be considered \"best practice\" in the molecular age unless it explicitly includes estimates of the extent of cryptic and hyper-cryptic biodiversity.

Taxonomy is the cornerstone of extinction risk assessments. Currently, the IUCN Red List treats species complexes either under a single overarching species name-resulting in an unhelpfully broad circumscription and underestimated threat assessment that does not apply to any one species lineage-or omits them altogether-resulting in the omission of species that should be assessed. We argue that taxonomic uncertainty alone, as in species complexes, should be grounds for assessment as Data Deficient (DD). Yet, use of the DD category is currently discouraged, resulting in assessments based on poor data quality and dismissal of the importance of taxonomic confidence in conservation. This policy may be leading to volatile and unwarranted assessments of hundreds of species across the world, and needs to be revised. To illustrate this point, we here present a partial taxonomic revision of torrent frogs from eastern Madagascar in the Mantidactylus subgenus Hylobatrachus. Two named species, Mantidactylus (Hylobatrachus) lugubris and M. (H.) cowanii, and several undescribed candidate species are recognised, but the application of the available names has been somewhat ambiguous. In a recent re-assessment of its conservation status, M. (H.) lugubris was assessed including all complex members except M. (H.) cowanii within its distribution, giving it a status of Least Concern and distribution over most of eastern Madagascar. After describing two of the unnamed lineages as Mantidactylus (Hylobatrachus) atsimo sp. nov. (from southeastern Madagascar) and Mantidactylus (Hylobatrachus) petakorona sp. nov. (from the Marojejy Massif in northeastern Madagascar), we show that Mantidactylus (Hylobatrachus) lugubris is restricted to the central east of Madagascar, highlighting the inaccuracy of its current Red List assessment. We propose to re-assess its status under a more restrictive definition that omits well-defined candidate species, thus representing the actual species to which its assessment refers, to the best of current knowledge. We recommend that for species complexes in general, (1) nominal lineages that can be confidently restricted should be assessed under the strict definition, (2) non-nominal species-level lineages and ambiguous names should be prioritised for taxonomic research, and (3) ambiguous names should be assessed as DD to highlight the deficiency in data on their taxonomic status, which is an impediment to their conservation. This would reduce ambiguity and underestimation of threats involved in assessing species complexes, and place the appropriate emphasis on the importance of taxonomy in anchoring conservation.

Cryptic ecologies, the Wallacean Shortfall of undocumented species’ geographical ranges and the Linnaean Shortfall of undescribed diversity, are all major barriers to conservation assessment. When these factors overlap with drivers of extinction risk, such as insular distributions, the number of threatened species in a region or clade may be underestimated, a situation we term ‘cryptic extinction risk’. The genus Lepidodactylus is a diverse radiation of insular and arboreal geckos that occurs across the western Pacific. Previous work on Lepidodactylus showed evidence of evolutionary displacement around continental fringes, suggesting an inherent vulnerability to extinction from factors such as competition and predation. We sought to (1) comprehensively review status and threats, (2) estimate the number of undescribed species, and (3) estimate extinction risk in data deficient and candidate species, in Lepidodactylus . From our updated IUCN Red List assessment, 60% of the 58 recognized species are threatened (n = 15) or Data Deficient (n = 21), which is higher than reported for most other lizard groups. Species from the smaller and isolated Pacific islands are of greatest conservation concern, with most either threatened or Data Deficient, and all particularly vulnerable to invasive species. We estimated 32 undescribed candidate species and linear modelling predicted that an additional 18 species, among these and the data deficient species, are threatened with extinction. Focusing efforts to resolve the taxonomy and conservation status of key taxa, especially on small islands in the Pacific, is a high priority for conserving this remarkably diverse, yet poorly understood, lizard fauna. Our data highlight how cryptic ecologies and cryptic diversity combine and lead to significant underestimation of extinction risk.

Global biodiversity faces severe anthropogenic threats, with alarming extinction rates projected for the near future. Most of Earth’s diversity remains undescribed, meaning countless species are doomed to extinction before being documented. Since current conservation laws typically consider only described species, the lag time in achieving a representative global biodiversity inventory is a crucial issue impeding effective conservation. Amphibians, the most endangered vertebrate class, exemplify the challenge: while the number of threatened species rises, new species descriptions rapidly increase, and hundreds of candidate species are flagged annually. We analyzed all anuran species described from 2000 to 2023 across four biodiversity-rich tropical regions to investigate the time required to describe new frog species. We quantified the time needed to collect the type series, the number and timing of expeditions, the lag between collection and publication, and the total time. Additionally, we explored temporal trends and the effect of selected abiotic variables. The time-lag from the collection of the first specimen to the formal publication of a frog species description ranged from 0.4 to 125.7 years (median = 7.3, mean = 11.3), type series collection from 0 to 104.9 (median = 0.1, mean = 4.5), and description and publication from 0.2 to 54.6 (median = 4.4, mean = 6.8). Alarmingly, the time required to describe new species is globally increasing. Thirty-six percent of species were named within five years of first collection, highlighting the need for continued collecting, biological collections as reservoirs of undescribed diversity, and calling for specimen revision after expeditions. These results raise concerns about the effectiveness of current taxonomic and conservation practices addressing the biodiversity crisis. We call for a global effort to prioritize taxonomic research and discuss taxonomic and conservation approaches. Under current practices, and given the observed timelines, we will lose the race against extinction for many species.

Selecting suitable species for vegetation restoration presents a notable challenge for land managers and scientists. Recently developed trait‐based approaches may be an effective means of overcoming this challenge. However, we lack a trait‐based species screening model that can be used to select potential species for restoration of degraded ecosystems. Here, we developed a species screening model based on quantitative trait‐based theory and a maximum entropy algorithm. The objective was to select more species that have comparable restoration abilities to the target species that have high survival rates for vegetation restoration based on species' functional traits. Thus, species diversity will be improved to facilitate restoration. We also developed a software platform that can be used to implement the model. We then applied our model and software platform to select species for restoration efforts in a tropical coral island which is part of Hainan Island, China. As a prerequisite, we started with three target species which have high potential for restoring the island. Likewise, 66 non‐native species were selected as the potential species pool. For each species, we identified and measured 28 traits that are strongly associated with harsh environments. Harsh environments are those with drought stress, high temperatures, intensive UV radiation, lack of real soil and nutrients, and high salinity and alkalinity. Then, our software platform was used to run the species selection model. Finally, 12 out of 66 species being identified as suitable species for restoration. We transplanted seedlings of all 66 species to the island to monitor seedlings survival. We found that the 12 species identified from our model had high survival rates, which ranged from 86% to 91%. In contrast, the mean survival rate for species not identified from our model was less than 40%. These results suggest that our species screening procedure was appropriate for selecting candidate species for use in vegetation restoration. We show that by using species natural history information, as well as functional trait data, candidate species for restoration efforts can be successfully identified in a timely manner. Importantly, our proposed method is faster and less costly than more commonly used ‘trial‐and‐error’ method. The most time‐consuming aspect of our approach is the need to measure the functional traits of target and potential species. Ultimately, we provide a protocol for using functional traits to quickly select a large number of suitable species for restoring degraded ecosystems. We expect that this work will be important for future vegetation restoration efforts in tropical islands, and perhaps other ecosystems as well. We also expect that our model will help prevent the invasive species and promote specific ecosystem functions. A free Plain Language Summary can be found within the Supporting Information of this article. 摘要 选择合适的物种进行植被恢复是土地管理者和科学家们面临的一个重大挑战。近年来开发的基于植被功能性状的筛选方法是克服这一挑战的有效手段。然而, 我们缺乏一个基于植被功能性状的, 可用于选择潜在恢复物种的筛选模型。 在本文中, 我们建立了一个基于定量化功能性状理论和最大熵算法的物种筛选模型。模型的目的是根据植物的功能性状特点, 选择更多与已知目标植物相似恢复能力的物种进行植被恢复, 进而改善物种多样性, 以促进恢复。我们同时开发了一个用来实现该模型的软件平台。然后, 我们应用这一模型和软件平台, 在中国海南的一个附属热带珊瑚岛上选择潜在物种进行植被恢复工作。 作为先决条件, 我们已知三个目标物种, 已经证明它们是适合恢复该岛的物种。与此同时, 我们选择了66个非本地物种作为潜在物种库。对于每一个物种, 我们选择并测量了28个与本地恶劣环境密切相关的功能性状。本地的环境特点是干旱胁迫、高温、强烈的紫外线辐射、缺乏真正的土壤和养分、高盐度和高碱度等特定环境。然后, 利用我们的软件平台运行物种选择模型。最后, 66个物种中有12个被确定为适合恢复的潜在物种。 我们把66种植物的幼苗移植到岛上, 以监测幼苗的存活情况。我们发现筛选出的12个物种存活率为86%到91%。相比之下, 未被模型选中的物种平均存活率小于40%。这些结果表明我们的植被筛选模型可以成功选择用于植被恢复的潜在物种。 研究结果表明, 基于植物功能性状数据, 可以准确地筛选出可用于植被恢复的潜在物种。更重要的是, 我们提出的方法比常用的“试错法”更快、成本更低。其中, 该方法最耗时的部分是测量目标物种和潜在物种的功能性状。最后, 我们提供了一个利用功能特性快速选择大量适合恢复退化生态系统的物种的流程。我们预计, 这项工作将对今后热带岛屿以及其他生态系统的植被恢复工作产生重要意义。我们也期望我们的模型在防止入侵物种和提高特定的生态系统功能方面产生重大应用。 A free Plain Language Summary can be found within the Supporting Information of this article.

Amphibians are rapidly vanishing. At the same time, it is most likely that the number of amphibian species is highly underestimated. Recent DNA barcoding work has attempted to define a threshold between intra- and inter-specific genetic distances to help identify candidate species. In groups with high extinction rates and poorly known species boundaries, like amphibians, such tools may provide a way to rapidly evaluate species richness. Here we analyse published and new 16S rDNA sequences from 60 frog species of Amazonia-Guianas to obtain a minimum estimate of the number of undescribed species in this region. We combined isolation by distance, phylogenetic analyses, and comparison of molecular distances to evaluate threshold values for the identification of candidate species among these frogs. In most cases, geographically distant populations belong to genetically highly distinct lineages that could be considered as candidate new species. This was not universal among the taxa studied and thus widespread species of Neotropical frogs really do exist, contrary to previous assumptions. Moreover, the many instances of paraphyly and the wide overlap between distributions of inter- and intra-specific distances reinforce the hypothesis that many cryptic species remain to be described. In our data set, pairwise genetic distances below 0.02 are strongly correlated with geographical distances. This correlation remains statistically significant until genetic distance is 0.05, with no such relation thereafter. This suggests that for higher distances allopatric and sympatric cryptic species prevail. Based on our analyses, we propose a more inclusive pairwise genetic distance of 0.03 between taxa to target lineages that could correspond to candidate species. Using this approach, we identify 129 candidate species, two-fold greater than the 60 species included in the current study. This leads to estimates of around 170 to 460 frog taxa unrecognized in Amazonia-Guianas. As a consequence the global amphibian decline detected especially in the Neotropics may be worse than realised.

Background Species of the genus Bartonella are facultative intracellular alphaproteobacteria with zoonotic potential. Bartonella infections in humans range from mild with unspecific symptoms to life threatening, and can be transmitted via arthropod vectors or through direct contact with infected hosts, although the latter mode of transmission is rare. Among the small mammals that harbour Bartonella spp., rodents are the most speciose group and harbour the highest diversity of these parasites. Human–rodent interactions are not unlikely as many rodent species live in proximity to humans. However, a surprisingly low number of clinical cases of bartonellosis related to rodent-associated Bartonella spp. have thus far been recorded in humans. Methods The main purpose of this review is to determine explanatory factors for this unexpected finding, by taking a closer look at published clinical cases of bartonellosis connected with rodent-associated Bartonella species, some of which have been newly described in recent years. Thus, another focus of this review are these recently proposed species. Conclusions Worldwide, only 24 cases of bartonellosis caused by rodent-associated bartonellae have been reported in humans. Possible reasons for this low number of cases in comparison to the high prevalences of Bartonella in small mammal species are (i) a lack of awareness amongst physicians of Bartonella infections in humans in general, and especially those caused by rodent-associated bartonellae; and (ii) a frequent lack of the sophisticated equipment required for the confirmation of Bartonella infections in laboratories that undertake routine diagnostic testing. As regards recently described Bartonella spp., there are presently 14 rodent-associated Candidatus taxa. In contrast to species which have been taxonomically classified, there is no official process for the review of proposed Candidatus species and their names before they are published. This had led to the use of malformed names that are not based on the International Code of Nomenclature of Prokaryotes. Researchers are thus encouraged to propose Candidatus names to the International Committee on Systematics of Prokaryotes for approval before publishing them, and only to propose new species of Bartonella when the relevant datasets allow them to be clearly differentiated from known species and subspecies. Graphical Abstract