Evolutionary Distinctiveness Research Articles

Exploring gaps, biases, and research priorities in the evidence for reptile conservation actions

AbstractWith over 21% of reptile species threatened with extinction, there is an urgent need to ensure conservation actions to protect and restore populations are informed by relevant, reliable evidence. We examined the geographic and taxonomic distribution of 707 studies that tested the effects of actions to conserve reptiles synthesized in Conservation Evidence's Reptile Conservation synopsis. More studies were conducted in countries with higher gross domestic product per capita, more reptile species, and higher proportions of threatened reptile species. Studies were clustered in the United States (43%) and Australia (15%), and no studies were conducted in large parts of Southeast Asia, South America, and sub‐Saharan Africa. Taxonomically, 47% of 90 reptile families (mostly Squamata) were not studied at all. Although Squamata and Testudines species featured in approximately 50% of studies, 7 of the 10 most‐studied reptiles (constituting 36% of studies) were turtles or tortoises, and there were significantly more studies per species on Testudines than Squamata. There were also significantly more studies on species: classified as least concern (as opposed to all other International Union for Conservation of Nature categories apart from near threatened); not categorized as endemic or insular; with more Wikipedia page views; and lacking data on venomousness. There was no significant relationship between the number of studies and the evolutionary distinctiveness or body mass of species. Our results highlight pressing evidence needs, particularly for underrepresented regions and threatened and data‐deficient species (e.g., evolutionarily distinct and globally endangered reptiles in South America, sub‐Saharan Africa, and Southeast Asia). To overcome evidence gaps and a lack of basic ecological data, future work should explore how the effects of actions transfer across taxa and regions. We call for greater efforts to coordinate and increase testing and reporting in a strategic manner to inform more effective and efficient conservation actions globally.

Evolutionarily Distinct Species and Their Partners Have Fewer Links in Ecological Networks

ABSTRACTAimEcological networks describe the complex set of interconnections among species and their environment, and network structure can inform the stability, resilience, and functioning of ecosystems. Increasing attention is being paid to the mechanisms that determine species interactions. Phylogeny has informed our understanding of connections within networks, mostly by describing the strength of phylogenetic conservation of interactions. Here, we examine how the phylogenetic position of a species relates to its functional position within a network, testing the relationship between phylogenetic and network topologies.LocationGlobal.Time PeriodEarly 20th century to present.Major Taxa StudiedBirds and plants.MethodsWe used a large dataset of frugivore interactions to calculate the network degree of focal species (degree) and the partners they interact with (partner degree) and bird and plant phylogenies to calculate local evolutionary distinctiveness (ED), a measure of evolutionary distinctiveness calculated on a community‐level phylogeny. We then fit binomial Bayesian models to estimate the effect of species' local ED on their degree and that of their partners. In avian networks, we incorporated bird traits from AVONET in models to determine their contributions to degree and partner degree relative to those of local ED.ResultsThe partners of both high local ED birds and plants tend to have fewer interactions in a network than do partners of low local ED species, and birds with high local ED tend to interact with fewer plant species. In birds, the statistical effect sizes of local ED on degree and partner degree are comparable to or larger than those of measured traits.Main ConclusionsOur analysis illustrates how phylogenetic relationships affect present‐day ecologies and underscores the unique ecological contribution of evolutionary outliers.

DNA metabarcoding improves understanding of the diet and foraging of a critically endangered grassland bird: the Plains-wanderer Pedionomus torquatus

ABSTRACT Effective conservation of threatened cryptic bird species is often inhibited by limited knowledge about their diet and foraging ecology. The critically endangered and taxonomically-unique Plains-wanderer (Pedionomus torquatus) is a small, mostly terrestrial bird that occurs on treeless plains across parts of eastern Australia. The species is highly cryptic and rarely observed foraging. Consequently, most aspects of its diet and foraging habits are poorly understood. Here, we used DNA metabarcoding to analyse faecal samples and identify important food types and seasonal food preferences of Plains-wanderers in native grasslands of the Northern Plains of Victoria, Australia. Here, we also used miniature GPS units to track movements of birds and assess the influence of food availability on habitat selection at patch-scale. We found pronounced seasonal variation in the dietary content of Plains-wanderers, indicating differences in foraging behaviour across seasons. In spring, diet was characterised by plant groups (likely seeds) including Asteraceae, Crassula and Oxalis, and invertebrates from the genus Philobota, comprising concealer moths. In autumn, diet was characterised by material from the plant genus Atriplex (saltbush). Our tracking data suggest that Plains-wanderers displayed selectivity towards native grassland patches with a higher abundance and diversity of invertebrates and seeds. Our findings highlight the flexibility of Plains-wanderer diet, including the ability to exploit native and exotic foods. We discuss the implications of these findings for habitat management and broader conservation efforts for this species, which is of significant global concern because of its high risk of extinction and evolutionary distinctiveness.

Condensates as a Culprit in RAS Activation and Inhibitor Resistance.

Therapy resistance is a significant cause of death in patients treated with targeted cancer therapy in diverse oncogene-driven cancers. A better understanding of resistance mechanisms can lay the foundation for improving existing and developing new therapies. A recent elegant study published in Nature Chemical Biology sheds light on a new resistance mechanism. The authors define a novel role for ARAF, a member of the RAF protein family (ARAF, BRAF, and CRAF), that is distinct from its previously understood role as a RAS effector and MEK protein kinase in the MAPK pathway. They describe how ARAF sequesters active RAS at the plasma membrane in phase-separated condensates to sustain signaling and prevent inactivation by the RAS GTPase-activating protein neurofibromin 1. This study underscores emerging roles for biomolecular condensates in cancer and highlights important implications for disrupting protein condensates to address treatment resistance to RAS (and RAS pathway)-targeted therapies. The study also illuminates evolutionary functional distinction between the RAF proteins and indicates unique biology for ARAF in normal physiology and disease.

What is essential is invisible to the eyes: a conservation approach for poison frogs (Dendrobatidae) based on evolutionary distinctiveness and threat status

What is essential is invisible to the eyes: a conservation approach for poison frogs (Dendrobatidae) based on evolutionary distinctiveness and threat status

Phylogenetic relationships and species delimitation of bunchgrass lizards of the genus Sceloporus from Mexico with the description of a new species.

Molecular data continue to serve as an invaluable tool to assess species limits and patterns of cryptic diversity, particularly in areas harboring high levels of biodiversity. The Sceloporus scalaris group, known as bunchgrass lizards, contains 13 described and one undescribed species distributed throughout high elevation biotas of Mexico. However, recent studies suggest that diversity in the group may be substantially underestimated. We collect new sequence data from four independent loci to determine the evolutionary distinctiveness and phylogenetic relationships of an isolated population of bunchgrass lizard in the Sierra San Juan (SSJ) in the Mexican state of Nayarit. Concatenation and coalescent-based phylogenetic and species delimitation analyses suggest that this population represents a distinct evolutionary lineage allied to the S. scalaris group. We describe the new SSJ population as a new species to better account for its morphological and evolutionary distinctiveness. Divergence within the species occurred during the Neogene and Quaternary, most likely due to range shifts associated with mountain uplift and glacial-interglacial cycles. Our results provide additional evidence that supports the importance of the Mexican highlands as a biodiversity hotspot which maintains cryptic lineages awaiting discovery.

Chromosome-level genome provides novel insights into the starch metabolism regulation and evolutionary history of Tetraselmis helgolandica.

Chromosome-level genome provides novel insights into the starch metabolism regulation and evolutionary history of Tetraselmis helgolandica.

Taxonomic and phylogenetic biases in translocated angiosperm plant species across European countries.

Conservation translocations are a well-known conservation tool used to reverse the effects of local population extinctions and restore ecosystems. Compared with mammals and birds, plants are underrepresented in translocation programs, and little is known about the potential taxonomic and phylogenetic biases of plant translocation efforts. We aimed to assess how translocated plant species may contribute to the conservation of phylogenetic diversity (PD) among European countries. Focusing on angiosperms across 4 European countries with well-documented flora and comprehensive sampling of translocated plant species, we determined whether species translocations were related to species conservation status with binomial generalized linear mixed models with threat status as a binary response variable. Then, we evaluated the taxonomic and phylogenetic biases of translocated plant species relative to national floras based on PD and evolutionary distinctiveness (ED). To evaluate PD and ED, we constructed null models to assess the deviation of observed values from those expected under a scenario in which translocated species were randomly sampled from the species pool of national floras in each country. Although most species lacked conservation status assessment, plant translocations mainly targeted species with high extinction risk at national, European, and global scales. Although plant orders with a higher representativeness of translocated species also tended to have a higher representativeness of native species, the probability of species being translocated varied significantly across plant order, suggesting a significant taxonomic bias. Based on null models and considering all countries, PD and mean ED of translocated plants were higher than expected by chance in most countries. These results suggest that although translocation programs were implemented independently across countries, the diversity of translocated plant species is relevant to conserving PD from national to continental scales and restoring evolutionarily distinct species when these species succeed. We argue that PD indicators should be incorporated into translocation planning to restore target species' evolutionary trajectories and to contribute to conservation of PD.

Differential Expression Pattern of Brassica juncea MIR160 Paralogs and Homeologs and In Silico Analysis of Brassicaceae Promoters Uncover Evolutionary Distinctness of MIR160a

Differential Expression Pattern of Brassica juncea MIR160 Paralogs and Homeologs and In Silico Analysis of Brassicaceae Promoters Uncover Evolutionary Distinctness of MIR160a

Optimizing the NGS-based discrimination of multiple lung cancers from the perspective of evolution

Next-generation sequencing (NGS) offers a promising approach for differentiating multiple primary lung cancers (MPLC) from intrapulmonary metastasis (IPM), though panel selection and clonal interpretation remain challenging. Whole-exome sequencing (WES) data from 80 lung cancer samples were utilized to simulate MPLC and IPM, with various sequenced panels constructed through gene subsampling. Two clonal interpretation approaches primarily applied in clinical practice, MoleA (based on shared mutation comparison) and MoleB (based on probability calculation), were subsequently evaluated. ROC analysis highlighted MoleB’s superior performance, especially with the NCCNplus panel (AUC = 0.950 ± 0.002) and pancancer MoleA (AUC = 0.792 ± 0.004). In two independent cohorts (WES cohort, N = 42 and non-WES cohort, N = 94), NGS-based methodologies effectively stratified disease-free survival, with NCCNplus MoleB further predicting prognosis. Phylogenetic analysis further revealed evolutionary distinctions between MPLC and IPM, establishing an optimized NGS-based framework for differentiating multiple lung cancers.

Unraveling the impact of drought on waterbird community assembly and conservation strategies.

Unraveling the impact of drought on waterbird community assembly and conservation strategies.

Prioritizing future evidence needs for marine and freshwater mammal conservation action

AbstractMarine and freshwater mammals are increasingly threatened due to human activity. To improve conservation practice, decisions should be informed by the available evidence on the effectiveness of conservation actions. Using a systematically collated database of studies that test the effectiveness of actions to conserve marine and freshwater mammals, we investigated the gaps and biases in the available scientific evidence base. While there is a growing evidence base covering actions to address key threats (e.g. fisheries and bycatch) to marine and freshwater mammal populations, we identified large geographic and taxonomic biases. There was no relationship between the number of studies and marine mammal species per ecoregion and we found biases towards coastal areas of the Global North, with many regions and species having little or no evidence available. The number of studies per species did not correlate with (1) the threat level, (2) evolutionary distinctiveness or (3) the public ‘popularity’ of the study species. We also found a mismatch between actions tested and the actions suggested as needed in the International Union for the Conservation of Nature (IUCN) Red List. Several of these gaps and biases likely reflect the feasibility of researching marine mammal populations; many species can be difficult to access, with limited baseline information on populations and threats, and testing actions can require costly long‐term monitoring. Prioritizing the most cost‐effective conservation strategies for marine and freshwater mammal species will require a comprehensive evidence base on the effects of actions. Continuing to build the necessary baseline data, and focusing future research and funding towards the priority gaps identified in this study will be important to deliver this target.

Identification of biodiversity priority conservation areas in China by integrating genetic, species and ecosystem diversity

Identification of biodiversity priority conservation areas in China by integrating genetic, species and ecosystem diversity

Phylogenetic Insights Into Canidae Trait Variation Across Continents

ABSTRACTAimUnderstanding the spatial structuring of ecological communities involves considering the interplay between evolutionary history and environmental factors. This study investigates how the phylogenetic structure of Canidae influences the geographical distribution and trait patterns of lineages globally, and how these patterns relate to Bergmann's and Rapoport's rules.LocationAmericas, Africa, Eurasia.Time Period12 million years ago—present.Major Taxa StudiedCanidae.MethodsUsing distribution data and phylogenetic information for 37 Canidae species, we analysed key ecological, functional and evolutionary variables. We applied phylogenetic fuzzy‐weighting via principal coordinates of phylogenetic structure (PCPS) and variance partitioning analysis (VPA) to assess the contributions of phylogenetic structure and environmental factors to trait variation among species.ResultsOur results revealed distinct global patterns in body size, body weight, range size, habitat use and evolutionary distinctiveness among lineages. We also identified the shared contributions of phylogenetic structure and temperature to trait variation using variance partitioning analysis. The PCPS axes highlighted the influence of phylogenetic relationships on Canidae assemblages, particularly in South America.Main ConclusionsImportantly, the study challenges the applicability of Bergmann's and Rapoport's rules across continents. The unique diversification history of Canidae in South America and Africa and their diverse environmental conditions likely contribute to the observed trait patterns that make both continents so distinguished when compared to North America and Eurasia. Our findings underscore the need to incorporate phylogenetic information in models assessing trait variation across geographic scales for unbiased estimates.

Evolutionary isolation of Canadian terrestrial vertebrate species

Conservation prioritization has become increasingly important as a practical response to ongoing biodiversity loss and limited resources. One tool, evolutionary distinctiveness (ED) is based on a measure of evolutionary isolation and has merit for identifying taxa with few close relatives. Here we present the first ever national-level ED scores for any jurisdiction, applying the measures to all Canadian tetrapods. We updated and pruned global dated phylogenies of all terrestrial vertebrates (amphibians, squamates, turtles, mammals, and birds) down to native Canadian species and calculated Canadian ED scores and rankings for each and compared them to their global ED ranks. Canada’s terrestrial ectotherm vertebrates (amphibians and reptiles) include most of Canada’s most evolutionarily isolated species and many score and rank higher nationally than globally in their ED scores. These taxa are also the most imperilled in Canada and so species with populations assessed as at-risk by the Committee on the Status of Endangered Wildlife in Canada (COSEWIC) represent, on average, more than expected national evolutionary history. Interestingly, several exotic species also have very high national ED scores. To the extent that evolutionary isolation captures aspects of local and national biodiversity worth preserving, our lists may provide useful input to conservation agencies engaging in conservation prioritization exercises.

Global primary predictors of extinction risk in primates.

Identifying the main predictors of species' extinction risk while accounting for the effects of spatial and phylogenetic structures in the data is key to preventing species loss in tropical forests through adequate conservation practices. We recorded 22 705 precise geographical locations of primate occurrence across four major geographic realms (Neotropics, mainland Africa, Madagascar and Asia) to assess predictors of threat status using a novel Bayesian spatio-phylogenetic approach. We estimated the relative contributions of fixed factors (forest amount, body mass, home range, diel activity, locomotion, evolutionary distinctiveness and climatic instability) and random factors (space and phylogeny) to primate extinction risk. Precipitation instability increased the extinction risk in the Neotropics but decreased it in mainland Africa and Madagascar. Forest amount was negatively associated with extinction risk in all realms except Madagascar. Body mass increased the extinction risk in the Neotropics and Madagascar, whereas home range increased the extinction risk in mainland Africa and decreased it in Asia. Evolutionary distinctiveness negatively influenced extinction risk only in mainland Africa. Our findings highlight the importance of climate change mitigation and forest protection strategies. Increasing the protection of large primates and reducing hunting are also essential.

Predicting yolk testosterone allocation using ecological contexts and species-specific traits.

The prenatal transfer of testosterone (T) from mother to offspring is an important source of phenotypic plasticity. In birds, exposure to ecologically relevant stimuli, such as social competition or an attractive mate, can cause females to deposit more T into their egg yolks. Exposure to elevated yolk T can modify the expression of several fitness-related traits in offspring (e.g. growth, immune function, secondary sex traits and behaviour). Despite some of these changes being potentially adaptive, not all studies find that yolk T levels change in response to ecologically relevant stimuli. This heterogeneity is currently unexplained, limiting our ability to predict inter-generational responses to ecological change. Here, we performed a systematic literature search and found 119 observations across 39 wild species that measured inter-female variation in yolk T allocation in response to various stimuli. We used boosted regression trees, a form of machine learning, to examine whether species-specific traits or variation in study-level variables could explain variation in yolk T allocation (i.e. statistically significant vs. non-significant responses). We found that both species-specific traits and study-level variables are important predictors of significant changes in yolk T levels. Geographic range (latitude and longitude), evolutionary distinctiveness, longevity, egg mass relative to female mass, sociality, migration status and time to fledge were among the top 10 most influential predictors of the 48 examined. We also found that studies measuring or manipulating social stimuli (e.g. competition and breeding density) or breeding date were more likely to detect changes in yolk T allocation compared with studies examining other ecological contexts. Overall, these data provide several testable hypotheses concerning yolk T allocation and its adaptive value across species and contexts. Additionally, these findings can help us predict how ecological changes will affect hormonal responses in females that can shape future generations.

Effects of trade and poaching pressure on extinction risk for cacti in the Atacama Desert.

In this era of a global biodiversity crisis, vascular plants are facing unprecedented extinction rates. We conducted an assessment of the extinction risk of 32 species and 7 subspecies of Copiapoa, a genus endemic to Chile's fog-dependent coastal Atacama Desert. We applied the International Union for Conservation of Nature Red List Categories and Criteria enhanced by expert insights and knowledge. Our primary aim was to analyze the impact of trade and poaching on their extinction risk. We employed machine learning models, including multinomial logistic regression (MLR), decision tree (DT), and random forest (RF), to analyze the relationships between conservation status and various factors. These factors encompassed trade and poaching activities, landscape condition, human footprint, monthly cloud frequency, and biological traits such as evolutionary distinctiveness and maximum diameter. Seven taxa had an area of occupancy (AOO) of <10km2, 10 additional taxa had an AOO of <20km2, and 16 taxa had an AOO of ≤100km2. This reassessment exposed a critical level of extinction risk for the genus; 92% of the taxa were classified as threatened, 41% as critically endangered, 41% as endangered, and 10% as vulnerable. MLR, DT, and RF exhibited accuracies of 0.784, 0.730, and 0.598, respectively, and identified trade and poaching pressure and landscape condition as the primary drivers of extinction risk. Our assessment of Copiapoa showed trade, poaching, habitat degradation, and their synergic impacts as the main drivers of the genus' extinction risk. Our results highlight the urgent need for nations to develop and enforce strategies to monitor and control trade and poaching pressure because these factors are crucial for the long-term persistence of desert plants.

Incorporating New Datatypes to Enhance Species Delimitation: A Case Study in Rice Paddy Snakes (Homalopsidae: Hypsiscopus).

Homalopsids (Old World Mud Snakes) include 59 semiaquatic species in Asia and Australasia that display an array of morphological adaptations, behaviors, and microhabitat preferences. These attributes make homalopsids an ideal model system for broader questions in evolutionary biology, but the diversity of this understudied group of snakes is still being described. Recognized species diversity in rice paddy snakes (Hypsiscopus) has recently doubled after nearly 200 years of taxonomic stability. However, the evolutionary distinctiveness of some populations remains in question. In this study, we compare mainland Southeast Asian populations of Hypsiscopus east and west of the Red River Basin in Vietnam, a known biogeographic barrier in Asia, using an iterative approach with molecular phylogenetic reconstruction, machine-learning morphological quantitative statistics, and ecological niche modeling. Our analyses show that populations west of the Red River Basin represent an independent evolutionary lineage that is distinct in genetics, morphospace, and habitat suitability, and so warrants species recognition. The holotype of H. wettsteini, a species originally described in error from Costa Rica, grouped morphometrically with the population at the Red River Basin and eastward, and those west of the Red River Basin are referred to the recently described H. murphyi. The two species may have diversified due to a variety of geological and environmental factors, and their recognition exemplifies the importance of multifaceted approaches in taxonomy for downstream biogeographic studies on speciation scenarios.

Crepuscular and small but not evolutionary unique species are the reptiles less affected by roadkill in Europe

We extensively reviewed scientific literature and extracted a large dataset with roadkill events for reptile species. We examined 300 articles from 33 European countries, gathering 1688 records of reptiles killed by vehicle traffic. A total of 125 taxa were found documented as roadkill (100 native and 25 exotic species). We calculated each species' occurrence frequency within the database (henceforth ‘relative roadkill frequency'). The relative roadkill of species was strongly and significantly correlated when comparing the whole dataset and the subset of systematic studies. We modelled the inter‐specific variation in relative roadkill frequency across the European reptilian phylogeny concerning species traits, evolutionary uniqueness, and distribution range using a phylogenetic generalized least squares (PGLS) model. Overall, reptile casualties are more pronounced for more closely related species. However, the relative roadkill frequency was unrelated to the level of evolutionary distinctiveness of European reptiles. Additionally, relative roadkill frequency was not correlated to the distribution range but was positively correlated with the species' body mass. The reptiles more frequently cited as road casualties were overall relatively large species: Montpellier snake Malpolon monspessulanus, European grass snake Natrix natrix, and Caspian whipsnake Dolichophis caspius. Additionally, more active species during the crepuscular hours were less affected by roadkill. From a conservation point of view, our results suggest that roadkill frequency is not more significant for evolutionary, more unique reptiles than for other species in Europe, while at the same time, widely distributed species are not the main target of roadkill events. Then, the main causes of roadkill in reptiles must be associated with other factors, such as behavioural traits or density of populations, rather than simply the size of their distribution range.Keywords: evolutionary uniqueness, phylogenetic signal, reptile species, roadkill incidence, wildlife conservation