Undescribed species have higher extinction risk than known species

Reply to Pitogo et al.: No single silver bullet to simply understand war-biodiversity conflict in the Philippines

Sociopolitical conflicts have significant but often overlooked impacts on biodiversity. In our reply, we reaffirm key findings from our previous work and directly address the Matters Arising raised by Pitogo and colleagues. Additionally, we present fine-scale analyses that further support our original conclusions. We emphasise the need for continued research to fully unravel the complex relationship between conflict and environmental impacts.

Undescribed and imperiled vertebrate biodiversity near an American urban center

Urban expansion threatens biodiversity hotspots and endemic species. In this study, we describe two imperiled new species of fishes belonging to the vermilion darter (Etheostoma chermocki) complex. These new species are restricted to individual stream systems surrounding the city of Birmingham, Alabama, USA, and are at risk of extinction due to anthropogenic development. Genomic species delimitation reveals that members of this species complex, which differ subtly but consistently in meristic counts and coloration, show high levels of genomic divergence and little gene flow among them. These brilliantly coloured species, whose diversification tied to the erosional dynamics of the Black Warrior River basin, exemplify the imperiled, yet undescribed, species diversity within an urban landscape in the southeastern North American biodiversity hotspot.

Psychrophilic fungi from the world's roof, II: Species delimitation within an integrative taxonomic framework

Southeast Qinghai-Tibet Plateau, which harbors large numbers of marine glaciers and spans across two worldwide "biodiversity hotspots," is facing massive habitat loss in the context of global warming, and the biodiversity of coldadapted fungi in this unique area is also suffering drastic reduction. In this study, we selected 23 fungal isolates that represented the most commonly encountered psychrophilic taxa isolated from soil or water samples of marine glaciers in the southeast Qinghai-Tibet Plateau for detailed taxonomic studies. Incorporating morphological characteristics, multilocus phylogenetic analyses, and the results of four widely used molecular species delimitation methods, including two distance-based: Automatic Barcode Gap Discovery (ABGD) and Assemble Species by Automatic Partitioning (ASAP), and two tree-based: Bayesian Poisson Tree Processes (bPTP) and generalized mixed Yule coalescent model (GMYC), seven Gelida (formerly Psychrophila) species, including six new species, and two Tetracladium species, including one new species, were described. As the genus name Psychrophila is an illegitimate later homonym of a plant genus, we proposed the new name Gelida as a replacement for Psychrophila and transferred four illegitimate Psychrophila species to Gelida as new combinations. Our study provides a valuable perspective on how to delimit robust and accurate species boundaries within an integrative taxonomic framework, which is especially important for efficient biodiversity assessment and conservation of the fungal groups that are facing serious habitat loss.

Cryptic species conservation: a review

Cryptic species are groups of two or more taxa that were previously classified as single nominal species. Being almost morphologically indistinguishable, cryptic species have historically been hard to detect. Only through modern morphometric, genetic, and molecular analyses has the hidden biodiversity of cryptic species complexes been revealed. Cryptic diversity is now widely acknowledged, but unlike more recognisable, charismatic species, scientists face additional challenges when studying cryptic taxa and protecting their wild populations. Demographical and ecological data are vital to facilitate and inform successful conservation actions, particularly at the individual species level, yet this information is lacking for many cryptic species due to their recent taxonomic description and lack of research attention. The first part of this article summarises cryptic speciation and diversity, and explores the numerous barriers and considerations that conservation biologists must navigate to detect, study and manage cryptic species populations effectively. The second part of the article seeks to address how we can overcome the challenges associated with efficiently and non-invasively detecting cryptic species in-situ, and filling vital knowledge gaps that are currently inhibiting applied conservation. The final section discusses future directions, and suggests that large-scale, holistic, and collaborative approaches that build upon successful existing applications will be vital for cryptic species conservation. This article also acknowledges that sufficient data to implement effective species-specific conservation will be difficult to attain for many cryptic animals, and protected area networks will be vital for their conservation in the short term.

One-quarter of freshwater fauna threatened with extinction

Freshwater ecosystems are highly biodiverse1 and important for livelihoods and economic development2, but are under substantial stress3. To date, comprehensive global assessments of extinction risk have not included any speciose groups primarily living in freshwaters. Consequently, data from predominantly terrestrial tetrapods4,5 are used to guide environmental policy6 and conservation prioritization7, whereas recent proposals for target setting in freshwaters use abiotic factors8-13. However, there is evidence14-17 that such data are insufficient to represent the needs of freshwater species and achieve biodiversity goals18,19. Here we present the results of a multi-taxon global freshwater fauna assessment for The IUCN Red List of Threatened Species covering 23,496 decapod crustaceans, fishes and odonates, finding that one-quarter are threatened with extinction. Prevalent threats include pollution, dams and water extraction, agriculture and invasive species, with overharvesting also driving extinctions. We also examined the degree of surrogacy of both threatened tetrapods and freshwater abiotic factors (water stress and nitrogen) for threatened freshwater species. Threatened tetrapods are good surrogates when prioritizing sites to maximize rarity-weighted richness, but poorer when prioritizing based on the most range-restricted species. However, they are much better surrogates than abiotic factors, which perform worse than random. Thus, although global priority regions identified for tetrapod conservation are broadly reflective of those for freshwater faunas, given differences in key threats and habitats, meeting the needs of tetrapods cannot be assumed sufficient to conserve freshwater species at local scales.

This is the way the world ends; not with a bang but a whimper: Estimating the number and ongoing rate of extinctions of Australian non-marine invertebrates

Biodiversity is in rapid decline, but the extent of loss is not well resolved for poorly known groups. We estimate the number of extinctions for Australian non-marine invertebrates since the European colonisation of the continent. Our analyses use a range of approaches, incorporate stated uncertainties and recognise explicit caveats. We use plausible bounds for the number of species, two approaches for estimating extinction rate, and Monte Carlo simulations to select combinations of projected distributions from these variables. We conclude that 9,111 (plausible bounds of 1,465 to 56,828) Australian species have become extinct over this 236-year period. These estimates dwarf the number of formally recognised extinctions of Australian invertebrates (10 species) and of the single invertebrate species listed as extinct under Australian legislation. We predict that 39-148 species will become extinct in 2024. This is inconsistent with a recent pledge by the Australian government to prevent all extinctions. This high rate of loss is largely a consequence of pervasive taxonomic biases in community concern and conservation investment. Those characteristics also make it challenging to reduce that rate of loss, as there is uncertainty about which invertebrate species are at the most risk. We outline conservation responses to reduce the likelihood of further extinctions.

The small and inconspicuous majority: Revealing the megadiversity and historical biogeography of the Pristimantis unistrigatus species group (Anura, Strabomantidae)

With more than 600 recognized species, the genus Pristimantis is already the most diverse among vertebrates, but described species only represent a fraction of the actual diversity in this clade. This genus is widely distributed throughout the Neotropics and represents an interesting model for biogeographic studies because Pristimantis spp. are direct developing and generally have narrow ecological niches and low dispersal abilities. The P. unistrigatus species group is one of the most important components in the genus (ca. 200 recognized species) and has been supported by morphological but not by molecular evidence. We assessed the species boundaries and distribution in the P. unistrigatus species group and infer spatiotemporal patterns of diversification related to historical landscape changes in the Neotropics. We gathered three mitochondrial, and two nuclear DNA loci from 416 specimens throughout the range of the group, and including 68 nominal species. We redefine the group based on the obtained phylogeny and found 151 candidate species that composes it, with 83 of these remaining undescribed. We recovered 11 major clades within the group that diverged before 13 Ma. The diversification of the group started during the early Miocene most likely in northwestern South America, currently corresponding to western Amazonia and northern Andes. The other neotropical areas subsequently acted as sinks, receiving lineages mostly during the last 10 Ma, after the demise of the Pebas System and the setup of the modern Amazonian hydrographic system.

The diversity of ignorance and the ignorance of diversity: origins and implications of "shadow diversity" for conservation biology and extinction

Biodiversity shortfalls and taxonomic bias can lead to inaccurate assessment of conservation priorities. Previous literature has begun to explore practical reasons why some species are discovered sooner or are better researched than others. However, the deeper socio-cultural causes for undiscovered and neglected biodiversity, and the value of collectively analysing species at risk of unrecorded, or "dark", extinction, are yet to be fully examined. Here, we argue that a new label (we propose "shadow diversity") is needed to shift our perspective from biodiversity shortfalls to living, albeit unknown, species. We suggest this linguistic shift imparts intrinsic value to these species, beyond scientific gaze and cultural systems. We review research on undiscovered, undetected and hidden biodiversity in the fields of conservation biology, macroecology and genetics. Drawing on philosophy, geography, history and sociology, we demonstrate that a range of socio-cultural factors (funding, education and historical bias) combine with traditional, practical impediments to limit species discovery and detection. We propose using a spectrum of shadow diversity which enables a complex, non-binary and comprehensive approach to biodiversity unknowns. Shadow diversity holds exciting potential as a tool to increase awareness, appreciation and support for the conservation of traditionally less studied wildlife species and sites, from soil microbes to less charismatic habitat fragments. We advocate for a shift in how the conservation community and wider public see biodiversity and an increase in popular support for conserving a wider range of life forms. Most importantly, shadow diversity provides appropriate language and conceptual frameworks to discuss species absent from conservation assessment and at potential risk of dark extinction.

Cryptic diversity patterns of subterranean estuaries

Subterranean estuaries are coastal ecosystems characterized by vertically stratified groundwater. The biota within these ecosystems is relatively understudied due to the inherent difficulty of accessing such extreme environments. The fauna inhabiting these ecosystems is considered vulnerable to extinction, and the presence of cryptic species has major implications for research and conservation efforts. Most species lack molecular data; however, the evaluation of genetic data for some taxa has revealed that undocumented species are common. This study employs molecular species delimitation methods and DNA barcoding through the analysis of publicly and newly generated sequences, including individuals from type localities and non-crustacean phyla; the latter are typically overlooked in biodiversity assessments of subterranean estuaries. We analysed 376 cytochrome c oxidase subunit I (COI) gene sequences and 154 16S rRNA gene sequences. The COI sequences represented 32% of previously described species and 50% of stygobiont species from the Yucatan Peninsula and Cozumel Island, while sequences of the 16S rRNA represented 14% of described species and 22% of stygobionts. Our results revealed cryptic genetic lineages and taxonomic misidentification of species. As several species from these ecosystems are recognized as endangered, the use of molecular approaches will improve biodiversity estimates and highlight overlooked cryptic lineages in need of evaluation of conservation status.

The Amphibian Genomics Consortium: advancing genomic and genetic resources for amphibian research and conservation

Amphibians represent a diverse group of tetrapods, marked by deep divergence times between their three systematic orders and families. Studying amphibian biology through the genomics lens increases our understanding of the features of this animal class and that of other terrestrial vertebrates. The need for amphibian genomic resources is more urgent than ever due to the increasing threats to this group. Amphibians are one of the most imperiled taxonomic groups, with approximately 41% of species threatened with extinction due to habitat loss, changes in land use patterns, disease, climate change, and their synergistic effects. Amphibian genomic resources have provided a better understanding of ontogenetic diversity, tissue regeneration, diverse life history and reproductive modes, anti-predator strategies, and resilience and adaptive responses. They also serve as essential models for studying broad genomic traits, such as evolutionary genome expansions and contractions, as they exhibit the widest range of genome sizes among all animal taxa and possess multiple mechanisms of genetic sex determination. Despite these features, genome sequencing of amphibians has significantly lagged behind that of other vertebrates, primarily due to the challenges of assembling their large, repeat-rich genomes and the relative lack of societal support. The emergence of long-read sequencing technologies, combined with advanced molecular and computational techniques that improve scaffolding and reduce computational workloads, is now making it possible to address some of these challenges. To promote and accelerate the production and use of amphibian genomics research through international coordination and collaboration, we launched the Amphibian Genomics Consortium (AGC, https://mvs.unimelb.edu.au/amphibian-genomics-consortium ) in early 2023. This burgeoning community already has more than 282 members from 41 countries. The AGC aims to leverage the diverse capabilities of its members to advance genomic resources for amphibians and bridge the implementation gap between biologists, bioinformaticians, and conservation practitioners. Here we evaluate the state of the field of amphibian genomics, highlight previous studies, present challenges to overcome, and call on the research and conservation communities to unite as part of the AGC to enable amphibian genomics research to "leap" to the next level.

The Amphibian Genomics Consortium: advancing genomic and genetic resources for amphibian research and conservation

Amphibians represent a diverse group of tetrapods, marked by deep divergence times between their three systematic orders and families. Studying amphibian biology through the genomics lens increases our understanding of the features of this animal class and that of other terrestrial vertebrates. The need for amphibian genomic resources is more urgent than ever due to the increasing threats to this group. Amphibians are one of the most imperiled taxonomic groups, with approximately 41% of species threatened with extinction due to habitat loss, changes in land use patterns, disease, climate change, and their synergistic effects. Amphibian genomic resources have provided a better understanding of ontogenetic diversity, tissue regeneration, diverse life history and reproductive modes, antipredator strategies, and resilience and adaptive responses. They also serve as essential models for studying broad genomic traits, such as evolutionary genome expansions and contractions, as they exhibit the widest range of genome sizes among all animal taxa and possess multiple mechanisms of genetic sex determination. Despite these features, genome sequencing of amphibians has significantly lagged behind that of other vertebrates, primarily due to the challenges of assembling their large, repeat-rich genomes and the relative lack of societal support. The emergence of long-read sequencing technologies, combined with advanced molecular and computational techniques that improve scaffolding and reduce computational workloads, is now making it possible to address some of these challenges. To promote and accelerate the production and use of amphibian genomics research through international coordination and collaboration, we launched the Amphibian Genomics Consortium (AGC, https://mvs.unimelb.edu.au/amphibian-genomics-consortium) in early 2023. This burgeoning community already has more than 282 members from 41 countries. The AGC aims to leverage the diverse capabilities of its members to advance genomic resources for amphibians and bridge the implementation gap between biologists, bioinformaticians, and conservation practitioners. Here we evaluate the state of the field of amphibian genomics, highlight previous studies, present challenges to overcome, and call on the research and conservation communities to unite as part of the AGC to enable amphibian genomics research to "leap" to the next level.

Progress or burden? Formal description of every apparently new species available in collections is neither necessary nor useful

A new species of the Sub-Saharan spider genus Quamtana Huber, 2003 is described that has been collected in garden centers in Poland and the UK. Its closest known relative is probably Q.lotzi Huber, 2003, known from Free State Province in South Africa. Working on the premise that placing species in time and space is the fundamental task of taxonomy, and acknowledging that we cannot provide biologically meaningful spatial information for this species, we prefer open nomenclature to make this species known to science without formally describing it, using the unique provisional name Quamtana sp. ZFMK Ar 24490 aff.lotzi. We argue that the judicious use of open nomenclature can serve to improve the quality of species lists, reducing the noise in large-scale analyses of biodiversity data. We expand this argument to 'fragmentary' species descriptions in general, such as single-sex descriptions in large genera with many male-only and female-only descriptions. Not every taxonomic act allowed by the Code is necessarily beneficial. Under certain conditions, the informal description of a putatively new species may serve science better than a formal description based on inadequate material or data.

Using DNA barcoding to identify high-priority taxa (Hymenoptera: Ichneumonidae) from Great Smoky Mountains National Park

The All Taxa Biodiversity Inventory (ATBI) in Great Smoky Mountains National Park (GSMNP) seeks to document every species of living thing in the park. The ATBI is decades in progress, yet some taxa remain virtually untouched by taxonomists. Such "high priority" taxa include the hyper-diverse parasitoid wasp family Ichneumonidae. Despite the positive and multifaceted effects ichneumonids have on their environment, only a small percentage of those collected in the park have been identified as species, mostly to their complex morphology and overwhelming diversity. Recently, DNA barcoding has transformed biodiversity inventories, streamlining the process to be more rapid and efficient. To test the effectiveness of barcoding 20 + year-old specimens of Ichneumonidae and catalog new records for GSMNP, COI was amplified from 95 ichneumonid morphospecies collected from Andrew's Bald, NC. Species identifications were confirmed morphologically. Eighty-one ichneumonids generated sequence data, representing 16 subfamilies and 44 genera. The subfamily Oxytorinae is newly recorded from GSMNP, along with 10 newly recorded genera and 23 newly recorded species across Ichneumonidae. These results contribute significantly to the ATBI by adding new park records for a high-priority taxon and demonstrate the effectiveness of applying DNA barcoding to samples in long-term storage or those lacking immediate taxonomic expertise.

Mapping Asia Plants: Plant Diversity and a Checklist of Vascular Plants in Indonesia

Indonesia, located in Southeast Asia, is the world's largest tropical island country. It is globally recognized as a unique center of biodiversity in the Asian-Australian transitional zone. To date, however, no national plant checklist of Indonesia has been published. Here, we collected botanical information on the flora of Indonesia and presented for the first time a checklist of known native species of vascular plants in the country. Our checklist included 30,466 species belonging to 2968 genera and 317 families, representing 8.7% of the 351,180 vascular plant species worldwide. Among the seven regions, Sumatra had the highest number of species at 10,902, followed by Indonesian New Guinea (9935), Java (9289), Kalimantan (9191), Sulawesi (7048), Maluku (5294), and Lesser Sunda Islands (4514). In contrast, Indonesian New Guinea had a much higher proportion of locally endemic species than other regions (59%). The seven regions were divided into three phytogeographical areas: the Sunda Shelf, the Sahul Shelf, and the Wallacea, based on similarities in floristic composition. Our checklist for Indonesia provides basic information for biodiversity conservation and associated research.

Global mismatches between threat mapping research effort and the potential of threat abatement actions to reduce extinction risk

Threat mapping is a necessary tool for identifying and abating direct threats to species in the ongoing extinction crisis. There are known gaps in the threat mapping literature for particular threats and geographic locations, and it remains unclear if the distribution of research effort is appropriately targeted relative to conservation need. We aimed to determine the drivers of threat mapping research effort and to quantify gaps that, if filled, could inform actions with the highest potential to reduce species' extinction risk. We used a negative binomial generalized linear model to analyze research effort as a function of threat abatement potential (quantified as the potential reduction in species extinction risk from abating threats), species richness, land area, and human pressure. The model showed that threat mapping research effort increased by 1.1 to 1.2 times per standardized unit change in threat abatement potential. However, species richness and land area were stronger predictors of research effort overall. The greatest areas of mismatch between research effort and threat abatement potential, receiving disproportionately low research effort, were related to the threats to species of agriculture, aquaculture, and biological resource use across the tropical regions of the Americas, Asia, and Madagascar. Conversely, the threat of linear infrastructure (e.g., roads and rails) across regions, the threat of biological resource use (e.g., hunting or collection) in sub-Saharan Africa, and overall threats in North America and Europe all received disproportionately high research effort. We discuss the range of methodological and sociopolitical factors that may be behind the overall trends and specific areas of mismatch we found. We urge a stronger emphasis on targeting research effort toward those threats and geographic locations where threat abatement activities could make the greatest contribution to reducing global species extinction risk.

Integrative systematic revision of the Montseny brook newt (Calotriton arnoldi), with the description of a new subspecies

The Montseny brook newt (Calotriton arnoldi), a glacial relict endemic to a small, isolated massif in northeast Spain, is considered the only Critically Endangered urodele in Europe. Its restricted range is divided by a deep valley that acts as an impassable barrier to dispersal, separating two isolated metapopulations (Western and Eastern) that correspond to independent lineages with different evolutionary trajectories, based on genetic and genomic data. Here, we address the ecological differentiation between lineages and discuss its potential effect on the phenotypic distinctness of each lineage. Based on multiple lines of evidence, we formally describe the Western Montseny brook newt as a new subspecies: Calotriton arnoldi laietanus ssp. nov. Finally, our study underscores the importance of considering taxonomic progress in the conservation policies of endangered species, ensuring appropriate management and protection of the newly described taxa.

Hidden hotspots of amphibian biodiversity in China

Identifying and protecting hotspots of endemism and species richness is crucial for mitigating the global biodiversity crisis. However, our understanding of spatial diversity patterns is far from complete, which severely limits our ability to conserve biodiversity hotspots. Here, we report a comprehensive analysis of amphibian species diversity in China, one of the most species-rich countries on Earth. Our study combines 20 y of field surveys with new molecular analyses of 521 described species and also identifies 100 potential cryptic species. We identify 10 hotspots of amphibian diversity in China, each with exceptional species richness and endemism and with exceptional phylogenetic diversity and phylogenetic endemism (based on a new time-calibrated, species-level phylogeny for Chinese amphibians). These 10 hotspots encompass 59.6% of China's described amphibian species, 49.0% of cryptic species, and 55.6% of species endemic to China. Only four of these 10 hotspots correspond to previously recognized biodiversity hotspots. The six new hotspots include the Nanling Mountains and other mountain ranges in South China. Among the 186 species in the six new hotspots, only 9.7% are well covered by protected areas and most (88.2%) are exposed to high human impacts. Five of the six new hotspots are under very high human pressure and are in urgent need of protection. We also find that patterns of richness in cryptic species are significantly related to those in described species but are not identical.

Conservation units alone are insufficient to protect Brazilian Amazonian chelonians

The creation of protected areas (PAs) is not always based on science; consequently, some aquatic species may not receive the same level of protection as terrestrial ones. The objective of this study was to identify priority areas for the conservation of chelonians in the Brazilian Amazon basin and assess the contribution of PAs, distinguishing between Full Protection Areas, Sustainable Use Areas, and Indigenous Lands for group protection. The entire species modeling procedure was carried out using Species Distribution Models. Location records were obtained from platforms such as SpeciesLink, GBIF, the Hydroatlas database, and WorldClim for bioclimatic variables adjusted with algorithms like Maximum Entropy, Random Forest, Support Vector Machine, and Gaussian-Bayesian. Indigenous lands cover more than 50% of the distribution areas of chelonian species in the Brazilian Amazon. Protected areas with higher conservation importance (Full Protection Areas and Sustainable Use Areas) hold less than 15% of the combined species distribution. Researchers face significant challenges when making decisions with models, especially in conservation efforts involving diverse taxa that differ significantly from one another within a group of individuals.

Twenty years of big plant genera

In 2004, David Frodin published a landmark review of the history and concepts of big plant genera. Two decades of taxonomic activity have taken place since, coinciding with a revolution in phylogenetics and taxonomic bioinformatics. Here we use data from the World Flora Online (WFO) to provide an updated list of big (more than 500 species) and megadiverse (more than 1000 species) flowering plant genera and highlight changes since 2004. The number of big genera has increased from 57 to 86; today one of every four plant species is classified as a member of a big genus, with 14% in just 28 megadiverse genera. Most (71%) of the growth in big genera since 2000 is the result of new species description, not generic re-circumscription. More than 15% of all currently accepted flowering plant species described in the last two decades are in big genera, suggesting that groups previously considered intractable are now being actively studied taxonomically. Despite this rapid growth in big genera, they remain a significant yet understudied proportion of plant diversity. They represent a significant proportion of global plant diversity and should remain a priority not only for taxonomy but for understanding global diversity patterns and plant evolution in general.

Integration of genomic and ecological methods inform management of an undescribed, yet highly exploited, sardine species

Assessing genetic diversity within species is key for conservation strategies in the context of human-induced biotic changes. This is important in marine systems, where many species remain undescribed while being overfished, and conflicts between resource-users and conservation agencies are common. Combining niche modelling with population genomics can contribute to resolving those conflicts by identifying management units and understanding how past climatic cycles resulted in current patterns of genetic diversity. We addressed these issues on an undescribed but already overexploited species of sardine of the genus Harengula. We find that the species distribution is determined by salinity and depth, with a continuous distribution along the Brazilian mainland and two disconnected oceanic archipelagos. Genomic data indicate that such biogeographic barriers are associated with two divergent intraspecific lineages. Changes in habitat availability during the last glacial cycle led to different demographic histories among stocks. One coastal population experienced a 3.6-fold expansion, whereas an island-associated population contracted 3-fold, relative to the size of the ancestral population. Our results indicate that the island population should be managed separately from the coastal population, and that a Marine Protected Area covering part of the island population distribution can support the viability of this lineage.

Shall we promote natural history collection today?-Answered by reviewing Ernest Henry Wilson's plant collection process in China

Plant diversity exploration needs to be accelerated because many species will go extinct before their discovery and description, and many species-rich regions remain poorly studied. However, most contemporary plant collections prefer to focus on a specific group, which hinders the exploration and conservation of plant diversity. Therefore, we need an alternative approach to the dilemma at hand. The comprehensive Natural History Collection (NHC), which existed throughout the pinnacle of biodiversity exploration in the 20th century could be considered. We explore Ernest Henry Wilson's (one of the most successful naturalists in the 20th) plant collections in China as a case to illustrate the advantages of NHC and discuss whether NHC deserves to be promoted again today. From multiple sources, we gathered 19,218 available specimen records of 11,884 collecting numbers assigned and analyzed the collected species, the collection's nature, and restored four routes of his explorations. Results reveal that Wilson's specimens were collected from 28 prefecture-level cities and 38 county-level regions of 7 provinces or municipalities, they belong to 200 families, 1046 genera, 3794 species, and 342 infraspecific taxa, approximately 41 %, 22 %, 10 %, 5 % of Chinese plant families, genera, species, and infraspecific taxa respectively. The Wilson case study shows that NHC is particularly effective in emphasizing species discovery and conservation, recording ecological information, understanding a region's flora, and developing landscape applications. Therefore, we strongly advocate for the expansion of natural history collections in species-rich regions. Furthermore, we recommend the employment of specialized collectors, the enlistment of international cooperation, and the standardization of guidelines for future NHCs.

Conservation gaps and priorities of range-restricted birds in the Northern Andes

The ongoing destruction of habitats in the tropics accelerates the current rate of species extinction. Range-restricted species are exceptionally vulnerable, yet we have insufficient knowledge about their protection. Species' current distributions, range sizes, and protection gaps are crucial to determining conservation priorities. Here, we identified priority range-restricted bird species and their conservation hotspots in the Northern Andes. We employed maps of the Area of Habitat (AOH), that better reflect their current distributions than existing maps. AOH provides unprecedented resolution and maps a species in the detail essential for practical conservation actions. We estimated protection within each species' AOH and for the cumulative distribution of all 335 forest-dependent range-restricted birds across the Northern Andes. For the latter, we also calculated protection across the elevational gradient. We estimated how much additional protection community lands (Indigenous and Afro-Latin American lands) would contribute if they were conservation-focused. AOHs ranged from 8 to 141,000 km2. We identified four conservation priorities based on cumulative species richness: the number of AOHs stacked per unit area. These priorities are high-resolution mapped representations of Endemic Bird Areas for the Tropical Andes that we consider critically important. Protected areas cover only 31% of the cumulative AOH, but community lands could add 19% more protection. Sixty-two per cent of the 335 species have ranges smaller than their published estimates, yet IUCN designates only 23% of these as Threatened. We identified 50 species as top conservation priorities. Most of these concentrate in areas of low protection near community lands and at middle elevations where, on average, only 34% of the land is protected. We highlight the importance of collaborative efforts among stakeholders: governments should support private and community-based conservation practices to protect the region with the most range-restricted birds worldwide.

Extinction risk of the world's freshwater mammals

The continued loss of freshwater habitats poses a significant threat to global biodiversity. We reviewed the extinction risk of 166 freshwater aquatic and semiaquatic mammals-a group rarely documented as a collective. We used the International Union for the Conservation of Nature Red List of Threatened Species categories as of December 2021 to determine extinction risk. Extinction risk was then compared among taxonomic groups, geographic areas, and biological traits. Thirty percent of all freshwater mammals were listed as threatened. Decreasing population trends were common (44.0%), including a greater rate of decline (3.6% in 20 years) than for mammals or freshwater species as a whole. Aquatic freshwater mammals were at a greater risk of extinction than semiaquatic freshwater mammals (95% CI -7.20 to -1.11). Twenty-nine species were data deficient or not evaluated. Large species (95% CI 0.01 to 0.03) with large dispersal distances (95% CI 0.03 to 0.15) had a higher risk of extinction than small species with small dispersal distances. The number of threatening processes associated with a species compounded their risk of extinction (95% CI 0.28 to 0.77). Hunting, land clearing for logging and agriculture, pollution, residential development, and habitat modification or destruction from dams and water management posed the greatest threats to these species. The basic life-history traits of many species were poorly known, highlighting the need for more research. Conservation of freshwater mammals requires a host of management actions centered around increased protection of riparian areas and more conscientious water management to aid the recovery of threatened species.

An in situ digital synthesis strategy for the discovery and description of ocean life

Revolutionary advancements in underwater imaging, robotics, and genomic sequencing have reshaped marine exploration. We present and demonstrate an interdisciplinary approach that uses emerging quantitative imaging technologies, an innovative robotic encapsulation system with in situ RNA preservation and next-generation genomic sequencing to gain comprehensive biological, biophysical, and genomic data from deep-sea organisms. The synthesis of these data provides rich morphological and genetic information for species description, surpassing traditional passive observation methods and preserved specimens, particularly for gelatinous zooplankton. Our approach enhances our ability to study delicate mid-water animals, improving research in the world's oceans.

How many species will Earth lose to climate change?

Climate change may be an important threat to global biodiversity, potentially leading to the extinction of numerous species. But how many? There have been various attempts to answer this question, sometimes yielding strikingly different estimates. Here, we review these estimates, assess their disagreements and methodology, and explore how we might reach better estimates. Large-scale studies have estimated the extinction of ~1% of sampled species up to ~70%, even when using the same approach (species distribution models; SDMs). Nevertheless, worst-case estimates often converge near 20%-30% species loss, and many differences shrink when using similar assumptions. We perform a new review of recent SDM studies, which show ~17% loss of species to climate change under worst-case scenarios. However, this review shows that many SDM studies are biased by excluding the most vulnerable species (those known from few localities), which may lead to underestimating global species loss. Conversely, our analyses of recent climate change responses show that a fundamental assumption of SDM studies, that species' climatic niches do not change over time, may be frequently violated. For example, we find mean rates of positive thermal niche change across species of ~0.02°C/year. Yet, these rates may still be slower than projected climate change by ~3-4 fold. Finally, we explore how global extinction levels can be estimated by combining group-specific estimates of species loss with recent group-specific projections of global species richness (including cryptic insect species). These preliminary estimates tentatively forecast climate-related extinction of 14%-32% of macroscopic species in the next ~50 years, potentially including 3-6 million (or more) animal and plant species, even under intermediate climate change scenarios.

Naming the menagerie: creativity, culture and consequences in the formation of scientific names

The coining of scientific names for newly described species is one of the most creative acts in science. We briefly review the history of species naming, with an emphasis on constraints and freedoms in the choice of new names and how they came to be. We then consider patterns in etymologies and linguistic origins of scientific names across clades and through time. Use of 'non-classical' languages (those other than Latin and Greek) in naming species has increased, as has the use of eponymous names (despite recent controversy around the practice). Finally, we consider ways in which creativity in naming has consequences for the conduct and outcome of scientific work. For example, sale of naming rights has funded research and conservation, while naming species after celebrities has increased media attention to the science of species discovery. Other consequences of naming are more surprising, including a strong effect of species-name etymology on the kinds of scientific studies conducted for plant-feeding arthropods. Scientific naming is a clear example of how science and scientists are socially situated, and how culturally influenced decisions such as what to name a new species can affect both public perception of science and the conduct of science itself.

Three in four undescribed plant species are threatened with extinction

This article is part of the Special Collection ‘Global plant diversity and distribution’. See https://www.newphytologist.org/global-plant-diversity for more details.

Updated list of the mammals of Costa Rica, with notes on recent taxonomic changes

Although Costa Rica occupies a mere 0.03% of the Earths land area, it nevertheless has recorded within its borders approximately 5% of the global diversity of mammals, thus making it one of the worlds megadiverse countries. Over the past ten years, 22 species have been added to the countrys inventory, bringing the total number known as here documented to 271; Chiroptera account for ten of these, having grown to 124 from 114; rodents have increased by eight species, from 47 to 55, with the caveat that we include three invasive species of Muridae that have gone feral. In contrast, the number of orders has decreased by one, by Artiodactyla incorporating the former Cetacea. Notes are provided for all taxonomic novelties since the last update. Since the first taxonomic compendium of the mammals of Costa Rica in 1869, the number of known species has grown by approximately 1.22 species year-1 (R2 = 0.96). Since 1983 however, this growth rate has been 1.64 species year-1 (R2 = 0.98). Despite this strong growth, an asymptote in the number of known species has not been reached. Conservation remains a primary need: over 60% of the countrys mammal species show population trends that are decreasing (13%), unknown (37%), or not assessed (11%), based on IUCN criteria. These analyses suggest that much remains to be known regarding the number of mammal species living in Costa Rica, but also that much more remains to be done to safeguard Costa Ricas exceptional biodiversity heritage.

Monitoring Endangered and Rare Wildlife in the Field: A Foundation Deep Learning Model Integrating Human Knowledge for Incremental Recognition with Few Data and Low Cost

Intelligent monitoring of endangered and rare wildlife is important for biodiversity conservation. In practical monitoring, few animal data are available to train recognition algorithms. The system must, therefore, achieve high accuracy with limited resources. Simultaneously, zoologists expect the system to be able to discover unknown species to make significant discoveries. To date, none of the current algorithms have these abilities. Therefore, this paper proposed a KI-CLIP method. Firstly, by first introducing CLIP, a foundation deep learning model that has not yet been applied in animal fields, the powerful recognition capability with few training resources is exploited with an additional shallow network. Secondly, inspired by the single-image recognition abilities of zoologists, we incorporate easily accessible expert description texts to improve performance with few samples. Finally, a simple incremental learning module is designed to detect unknown species. We conducted extensive comparative experiments, ablation experiments, and case studies on 12 datasets containing real data. The results validate the effectiveness of KI-CLIP, which can be trained on multiple real scenarios in seconds, achieving in our study over 90% recognition accuracy with only 8 training samples, and over 97% with 16 training samples. In conclusion, KI-CLIP is suitable for practical animal monitoring.

Acknowledging more biodiversity without more species

Delimiting and naming biodiversity is a vital step toward wildlife conservation and research. However, species delimitation must be consistent across biota so that the limited resources available for nature protection can be spent effectively and objectively. To date, newly discovered lineages typically are either left undescribed and thus remain unprotected or are being erroneously proposed as new species despite mixed evidence for completed speciation, in turn contributing to the emerging problem of taxonomic inflation. Inspired by recent conceptual and methodological progress, we propose a standardized workflow for species delimitation that combines phylogenetic and hybrid zone analyses of genomic datasets ("genomic taxonomy"), in which phylogeographic lineages that do not freely admix are ranked as species, while those that have remained fully genetically compatible are ranked as subspecies. In both cases, we encourage their formal taxonomic naming, diagnosis, and description to promote social awareness toward biodiversity. The use of loci throughout the genome overcomes the unreliability of widely used barcoding genes when phylogeographic patterns are complex, while the evaluation of divergence and reproductive isolation unifies the long-opposed concepts of lineage species and biological species. We suggest that a shift in conservation assessments from a single level (species) toward a two-level hierarchy (species and subspecies) will lead to a more balanced perception of biodiversity in which both intraspecific and interspecific diversity are valued and more adequately protected.

Progress in the discovery of isopods (Crustacea: Peracarida)-is the description rate slowing down?

Taxonomic species are the best standardised metric of biodiversity. Therefore, there is broad scientific and public interest in how many species have already been named and how many more may exist. Crustaceans comprise about 6% of all named animal species and isopods about 15% of all crustaceans. Here, we review progress in the naming of isopods in relation to the number of people describing new species and estimate how many more species may yet be named by 2050 and 2100, respectively. In over two and a half centuries of discovery, 10,687 isopod species in 1,557 genera and 141 families have been described by 755 first authors. The number of authors has increased over time, especially since the 1950s, indicating increasing effort in the description of new species. Despite that the average number of species described per first author has declined since the 1910s, and the description rate has slowed down over the recent decades. Authors' publication lifetimes did not change considerably over time, and there was a distinct shift towards multi-authored publications in recent decades. Estimates from a non-homogeneous renewal process model predict that an additional 660 isopod species will be described by 2100, assuming that the rate of description continues at its current pace.

Insights into cryptic speciation of quillworts in China

Cryptic species are commonly misidentified because of high morphological similarities to other species. One group of plants that may harbor large numbers of cryptic species is the quillworts (Isoëtes spp.), an ancient aquatic plant lineage. Although over 350 species of Isoëtes have been reported globally, only ten species have been recorded in China. The aim of this study is to better understand Isoëtes species diversity in China. For this purpose, we systematically explored the phylogeny and evolution of Isoëtes using complete chloroplast genome (plastome) data, spore morphology, chromosome number, genetic structure, and haplotypes of almost all Chinese Isoëtes populations. We identified three ploidy levels of Isoëtes in China-diploid (2n = 22), tetraploid (2n = 44), and hexaploid (2n = 66). We also found four megaspore and microspore ornamentation types in diploids, six in tetraploids, and three in hexaploids. Phylogenetic analyses confirmed that I. hypsophila as the ancestral group of the genus and revealed that Isoëtes diploids, tetraploids, and hexaploids do not form monophyletic clades. Most individual species possess a single genetic structure; however, several samples have conflicting positions on the phylogenetic tree based on SNPs and the tree based on plastome data. All 36 samples shared 22 haplotypes. Divergence time analysis showed that I. hypsophila diverged in the early Eocene (∼48.05 Ma), and most other Isoëtes species diverged 3-20 Ma. Additionally, different species of Isoëtes were found to inhabit different water systems and environments along the Yangtze River. These findings provide new insights into the relationships among Isoëtes species in China, where highly similar morphologic populations may harbor many cryptic species.

A new Bolitoglossa (Amphibia, Caudata, Plethodontidae) from the Cordillera Oriental of Colombia

A new salamander species of the genus Bolitoglossa is here described from the cloud forests of the western slopes of the Cordillera Oriental of Colombia, in the Cundinamarca department. The most salient characters of this new species are its numerous maxillary and vomerine teeth, its moderate webbing on hands and feet, its short and robust tail, and its chromatic variation. Based on molecular analyses this new species is assigned to the adspersa species group and its status established as the sister species of B.adspersa, with which it was previously confused. Lastly, the distribution, natural history, and conservation status of the new species are discussed.

Regional environmental and climatic concerns on preserving native gene pools of a least concern species: Brown trout lineages in Mediterranean streams

The European brown trout, Salmo trutta, is a cold-adapted fish reported as a Least Concern species in the IUCN Red List. This species colonized new territories from southern refuges during the last glacial melting, but during the 20th century suffered from anthropic impacts on its habitats. The long-time survival of the species relies on the genetic diversity within and among populations. Brown trout is among the genetically most diverse vertebrate species; however, native populations in Mediterranean rivers have dramatically suffered of introgressive hybridization from extensive releases of evolutionary distant non-native Atlantic stocks. In addition, in Mediterranean rivers climate change will result in unsuitable conditions for the species during the 21st century. Using brown trout populations at the headstreams of a Pyrenean river as a model, this paper revised how hatchery releases have affected the native gene pools and how environmental and climatic variables controlled the amount of local introgression at intra-basin level. Introgressive hybridization was detected in all studied sites. Ten times larger divergence was observed among populations at tributaries than among populations along the main stem. A highly impacted population distributed in a long transect in the main stem suggested that hatchery fish move towards the main stem wherever released. From already highly impacted populations and despite the cessation of hatchery releases, warmer temperatures and lower precipitation expected from climate change will extend the introgressive hybridization along the basin, contributing to the extinction of the native gene pools. Based on available morphological distinction of native, hatchery and hybrid brown trout, we advocate the involvement of regional social groups (e.g. riverside dwellers, anglers, conservationists, hikers) in citizen science programs to detect the spread of non-native phenotypes along the rivers. These are cheap and fast methods to collaborate with fishery managers in the preservation and recovery of the regional native populations.

Investigating an Unknown Biodiversity: Evidence of Distinct Lineages of the Endemic Chola Guitarfish Pseudobatos percellens Walbaum, 1792 in the Western Atlantic Ocean

Anthropogenic actions have affected marine species for a long time, through overexploitation of natural stocks and habitat degradation, influencing the life strategies of several taxa, especially rays and sharks, which have suffered significant population declines in recent years. Therefore, conservation actions and stock management have become paramount. In this regard, chola guitarfish, Pseudobatos percellens, distributed throughout the Brazilian coast, is often commercially fished by local artisanal fleets or as by-catch in shrimp trawl fisheries. Therefore, this study aimed to understand the genetic diversity of P. percellens throughout the Brazilian coast, using single nucleotide polymorphisms (SNPs). Genetic analyses employing 3329 SNPs revealed a hidden biodiversity within P. percellens, with at least one lineage occurring in the Northern and Northeastern regions and another distributed in the Southeastern/Southern Brazilian coast, with high genetic differentiation between them. However, the Discriminant Analysis of Principal Components (DAPC) indicated the presence of in fact three lineages distributed in these regions that must still be better investigated. Therefore, to ensure adequate conservation of chola guitarfish biodiversity, populations must be managed separately along the Brazilian coast. Furthermore, the need for a taxonomic review for this group is noted.

Who will name new plant species? Temporal change in the origins of taxonomists in China

Discovery rates of new plant species need to be accelerated because many species will be extinct before they are formally described. Current studies have focused on where new species may occur and their characteristics. However, who will actually discover and describe these new species has received limited attention. Here, we used 31 576 vascular plant species distributed and described in China as a case study to explore the temporal patterns of the nationalities of the taxonomists. We found that most recently described species are endemic species, and there has been an increasing proportion of species descriptions by resident Chinese taxonomists over time. The proportion of species described by resident taxonomists reached an average of 80.8% between 1977 and 2018. By contrast, species discoveries by non-resident experts, often non-endemic species, showed signs of levelling off. Our study underscores an urgent need for training of, support for and collaboration with resident taxonomists in megadiverse countries with a high potential of discovering undescribed plant species.

Madagascar’s extraordinary biodiversity: Threats and opportunities

Madagascar’s unique biota is heavily affected by human activity and is under intense threat. Here, we review the current state of knowledge on the conservation status of Madagascar’s terrestrial and freshwater biodiversity by presenting data and analyses on documented and predicted species-level conservation statuses, the most prevalent and relevant threats, ex situ collections and programs, and the coverage and comprehensiveness of protected areas. The existing terrestrial protected area network in Madagascar covers 10.4% of its land area and includes at least part of the range of the majority of described native species of vertebrates with known distributions (97.1% of freshwater fishes, amphibians, reptiles, birds, and mammals combined) and plants (67.7%). The overall figures are higher for threatened species (97.7% of threatened vertebrates and 79.6% of threatened plants occurring within at least one protected area). International Union for Conservation of Nature (IUCN) Red List assessments and Bayesian neural network analyses for plants identify overexploitation of biological resources and unsustainable agriculture as the most prominent threats to biodiversity. We highlight five opportunities for action at multiple levels to ensure that conservation and ecological restoration objectives, programs, and activities take account of complex underlying and interacting factors and produce tangible benefits for the biodiversity and people of Madagascar.

Lepocranus and Valalyllum gen. nov. (Orthoptera, Tetrigidae, Cladonotinae), endangered Malagasy dead-leaf-like grasshoppers

Only two leaf-like pygmy grasshopper species and specimens are known from Madagascar: the Leatherback Pygmy Grasshopper (Lepocranusfuscus Devriese, 1991) -which has a relatively low median carina of the pronotum; and the Malagasy Litterhopper (Valalyllumfolium gen. et. sp. nov.), herein described - which has a high median carina. Lepocranusfuscus is known from the rainforests around Tampolo, Manakambahiny, and Mahavelona (Foulpointe). The new taxon, Valalyllumfolium gen. et. sp. nov. is known only from the Belanono forest. Both species inhabit northeastern Madagascar. The new species could be rare or not-easy-to-spot in the rainforest leaf litter, where it most probably lives. A new tribe, Valalyllinitrib. nov., is described for the two mentioned genera because its members are different from the Caribbean leaf-like Choriphyllini Cadena-Castañeda & Silva, 2019, from the African leaf-like Xerophyllini Günther, 1979, and from the Asian leaf-like Cladonotini Bolívar, 1887. A tabular key to the tribes of Cladonotinae with leaf-like representatives is provided, together with photographs of type specimens of both species belonging to the newly described tribe. The holotype of the new species belongs to the Muséum national d'Histoire naturelle Orthoptera collection, Paris.

Red Junglefowl Resource Management Guide: Bioresource Reintroduction for Sustainable Food Security in Thailand

The domestication of wild animals represents a major milestone for human civilization. Chicken is the largest domesticated livestock species and used for both eggs and meat. Chicken originate from the red junglefowl (Gallus gallus). Its adaptability to diverse environments and ease of selective breeding provides a unique genetic resource to address the challenges of food security in a world impacted by climatic change and human population growth. Habitat loss has caused population declines of red junglefowl in Thailand. However, genetic diversity is likely to remain in captive stocks. We determine the genetic diversity using microsatellite genotyping and the mitochondrial D-loop sequencing of wild red junglefowl. We identified potential distribution areas in Thailand using maximum entropy models. Protected areas in the central and upper southern regions of Thailand are highly suitable habitats. The Bayesian clustering analysis of the microsatellite markers revealed high genetic diversity in red junglefowl populations in Thailand. Our model predicted that forest ranges are a highly suitable habitat that has enabled the persistence of a large gene pool with a nationwide natural distribution. Understanding the red junglefowl allows us to implement improved resource management, species reintroduction, and sustainable development to support food security objectives for local people.