Mutilation of the tree of life via mass extinction of animal genera.

Mass extinctions during the past 500 million y rapidly removed branches from the phylogenetic tree of life and required millions of years for evolution to generate functional replacements for the extinct (EX) organisms. Here we show, by examining 5,400 vertebrate genera (excluding fishes) comprising 34,600 species, that 73 genera became EX since 1500 AD. Beyond any doubt, the human-driven sixth mass extinction is more severe than previously assessed and is rapidly accelerating. The current generic extinction rates are 35 times higher than expected background rates prevailing in the last million years under the absence of human impacts. The genera lost in the last five centuries would have taken some 18,000 y to vanish in the absence of human beings. Current generic extinction rates will likely greatly accelerate in the next few decades due to drivers accompanying the growth and consumption of the human enterprise such as habitat destruction, illegal trade, and climate disruption. If all now-endangered genera were to vanish by 2,100, extinction rates would be 354 (average) or 511 (for mammals) times higher than background rates, meaning that genera lost in three centuries would have taken 106,000 and 153,000 y to become EX in the absence of humans. Such mutilation of the tree of life and the resulting loss of ecosystem services provided by biodiversity to humanity is a serious threat to the stability of civilization. Immediate political, economic, and social efforts of an unprecedented scale are essential if we are to prevent these extinctions and their societal impacts.

Global patterns of raptor distribution and protected areas optimal selection to reduce the extinction crises.

Globally, human-caused environmental impacts, such as habitat loss, have seriously impacted raptor species, with some 50% of species having decreasing populations. We analyzed global patterns of distribution of all 557 raptor species, focusing on richness, endemism, geographic range, conservation status, and population trends. Highest species diversity, endemism, species at risk, or restricted species were concentrated in different regions. Patterns of species distribution greatly differed between nocturnal and diurnal species. To test the efficiency of the global protected areas in conserving raptors, we simulated and compared global reserve systems created with strategies aiming at: 1) constraining the existing system into the final solution; and 2) minimizing the socioeconomic cost of reserve selection. We analyzed three targets of species distribution to be protected (10, 20, 30%). The first strategy was more efficient in meeting targets and less efficient in cost and compactness of reserves. Focusing on actions in the existing protected areas is fundamental to consolidate conservation, and politically and economically more viable than creating new reserves. However, creating new reserves is essential to protect more populations throughout the species' geographic range. Our findings provide a fundamental understanding of reserves to maintain raptor diversity and reduce the global population and species extinction crisis.

Vertebrates on the brink as indicators of biological annihilation and the sixth mass extinction.

The ongoing sixth mass species extinction is the result of the destruction of component populations leading to eventual extirpation of entire species. Populations and species extinctions have severe implications for society through the degradation of ecosystem services. Here we assess the extinction crisis from a different perspective. We examine 29,400 species of terrestrial vertebrates, and determine which are on the brink of extinction because they have fewer than 1,000 individuals. There are 515 species on the brink (1.7% of the evaluated vertebrates). Around 94% of the populations of 77 mammal and bird species on the brink have been lost in the last century. Assuming all species on the brink have similar trends, more than 237,000 populations of those species have vanished since 1900. We conclude the human-caused sixth mass extinction is likely accelerating for several reasons. First, many of the species that have been driven to the brink will likely become extinct soon. Second, the distribution of those species highly coincides with hundreds of other endangered species, surviving in regions with high human impacts, suggesting ongoing regional biodiversity collapses. Third, close ecological interactions of species on the brink tend to move other species toward annihilation when they disappear-extinction breeds extinctions. Finally, human pressures on the biosphere are growing rapidly, and a recent example is the current coronavirus disease 2019 (Covid-19) pandemic, linked to wildlife trade. Our results reemphasize the extreme urgency of taking much-expanded worldwide actions to save wild species and humanity's crucial life-support systems from this existential threat.

Spatial distribution patterns of tick community structure in sympatric jaguars (Panthera onca) and pumas (Puma concolor) from three ecoregions in Mexico.

We examined tick communities on wild felid hosts in three ecoregions of Mexico. We collected 186 ticks of 7 species from 10 pumas (Puma concolor) and 9 jaguars (Panthera onca). Tick community composition varied across the ecoregions, and across host species within each region. Overall, Ixodes affinis, Amblyomma ovale, and Amblyomma tenellum were the most abundant species; however, only the latter two ticks were distributed across all three ecoregions, while I. affinis, along with Ixodes spinipalpis, Amblyomma inornatum, and Amblyomma parvum were restricted to more limited geographical regions. Ixodes affinis occurred strictly in southern tropical rainforest ecoregions and was significantly more abundant in Selva Lacandona compared with the Yucatán Peninsula. Amblyomma ovale was significantly more common in the tropical dry forest in the Pacific coastal ecoregion. Amblyomma tenellum abundance tended to be higher on jaguars, while I. affinis abundance was higher on pumas. Regional distribution patterns of some tick species (e.g., I. affinis and I. spinipalpis) may be determined by off-host environmental conditions rather than host factors. In contrast, at the local scale, occurrence and abundance of some tick species (e.g., A. tenellum, A. ovale and Rhipicephalus microplus) might be driven by ecological-host factors, such as habitat use or predator-prey relationships.

Integrated Metabolomics and Proteomics Analyses in the Local Milieu of Islet Allografts in Rejection versus Tolerance.

An understanding of the immune mechanisms that lead to rejection versus tolerance of allogeneic pancreatic islet grafts is of paramount importance, as it facilitates the development of innovative methods to improve the transplant outcome. Here, we used our established intraocular islet transplant model to gain novel insight into changes in the local metabolome and proteome within the islet allograft's immediate microenvironment in association with immune-mediated rejection or tolerance. We performed integrated metabolomics and proteomics analyses in aqueous humor samples representative of the graft's microenvironment under each transplant outcome. The results showed that several free amino acids, small primary amines, and soluble proteins related to the Warburg effect were upregulated or downregulated in association with either outcome. In general, the observed shifts in the local metabolite and protein profiles in association with rejection were consistent with established pro-inflammatory metabolic pathways and those observed in association with tolerance were immune regulatory. Taken together, the current findings further support the potential of metabolic reprogramming of immune cells towards immune regulation through targeted pharmacological and dietary interventions against specific metabolic pathways that promote the Warburg effect to prevent the rejection of transplanted islets and promote their immune tolerance.

Biological annihilation via the ongoing sixth mass extinction signaled by vertebrate population losses and declines.

The population extinction pulse we describe here shows, from a quantitative viewpoint, that Earth's sixth mass extinction is more severe than perceived when looking exclusively at species extinctions. Therefore, humanity needs to address anthropogenic population extirpation and decimation immediately. That conclusion is based on analyses of the numbers and degrees of range contraction (indicative of population shrinkage and/or population extinctions according to the International Union for Conservation of Nature) using a sample of 27,600 vertebrate species, and on a more detailed analysis documenting the population extinctions between 1900 and 2015 in 177 mammal species. We find that the rate of population loss in terrestrial vertebrates is extremely high-even in "species of low concern." In our sample, comprising nearly half of known vertebrate species, 32% (8,851/27,600) are decreasing; that is, they have decreased in population size and range. In the 177 mammals for which we have detailed data, all have lost 30% or more of their geographic ranges and more than 40% of the species have experienced severe population declines (>80% range shrinkage). Our data indicate that beyond global species extinctions Earth is experiencing a huge episode of population declines and extirpations, which will have negative cascading consequences on ecosystem functioning and services vital to sustaining civilization. We describe this as a "biological annihilation" to highlight the current magnitude of Earth's ongoing sixth major extinction event.

FusionSense: Emotion Classification Using Feature Fusion of Multimodal Data and Deep Learning in a Brain-Inspired Spiking Neural Network.

Using multimodal signals to solve the problem of emotion recognition is one of the emerging trends in affective computing. Several studies have utilized state of the art deep learning methods and combined physiological signals, such as the electrocardiogram (EEG), electroencephalogram (ECG), skin temperature, along with facial expressions, voice, posture to name a few, in order to classify emotions. Spiking neural networks (SNNs) represent the third generation of neural networks and employ biologically plausible models of neurons. SNNs have been shown to handle Spatio-temporal data, which is essentially the nature of the data encountered in emotion recognition problem, in an efficient manner. In this work, for the first time, we propose the application of SNNs in order to solve the emotion recognition problem with the multimodal dataset. Specifically, we use the NeuCube framework, which employs an evolving SNN architecture to classify emotional valence and evaluate the performance of our approach on the MAHNOB-HCI dataset. The multimodal data used in our work consists of facial expressions along with physiological signals such as ECG, skin temperature, skin conductance, respiration signal, mouth length, and pupil size. We perform classification under the Leave-One-Subject-Out (LOSO) cross-validation mode. Our results show that the proposed approach achieves an accuracy of 73.15% for classifying binary valence when applying feature-level fusion, which is comparable to other deep learning methods. We achieve this accuracy even without using EEG, which other deep learning methods have relied on to achieve this level of accuracy. In conclusion, we have demonstrated that the SNN can be successfully used for solving the emotion recognition problem with multimodal data and also provide directions for future research utilizing SNN for Affective computing. In addition to the good accuracy, the SNN recognition system is requires incrementally trainable on new data in an adaptive way. It only one pass training, which makes it suitable for practical and on-line applications. These features are not manifested in other methods for this problem.

Correlation between plasma levels of arginine and citrulline in preterm and full-term neonates: Therapeutical implications.

BACKGROUND: Preterm neonates exhibit several deficiencies that endanger their lives. Understanding those disturbances will provide tools for the management of preterm neonates. The present work focuses on arginine and citrulline which has been flagged among the biochemical landmarks of prematurity. METHODS: We examined blood samples of preterm newborns as compared with mature neonates to determine the levels of arginine and citrulline by capillary zone electrophoresis with laser induced fluorescence detection (CZE-LIFD). RESULTS: Significantly lower levels of arginine and citrulline were found in preterm neonates than in mature neonates (P<.01). Interestingly there was a highly significant correlation between the two amino acids in mature neonates (P<.0001). Such correlation was present in preterm neonates too (P<.01). Pearson coefficient showed that 60% of the citrulline concentration depends on arginine concentration in mature neonates. Only 20% of the citrulline concentration depends on arginine concentration in preterm neonates. Although the ratio arginine/citrulline was lower in preterm neonates than in mature neonates the difference was not statistically significant. CONCLUSIONS: These results suggest that less arginine is converted to citrulline to form nitric oxide in preterm than in full-term neonates. The result is discussed in terms of the immature enzymatic systems in the preterm neonate.

Drivers and hotspots of extinction risk in marine mammals.

The world's oceans are undergoing profound changes as a result of human activities. However, the consequences of escalating human impacts on marine mammal biodiversity remain poorly understood. The International Union for the Conservation of Nature (IUCN) identifies 25% of marine mammals as at risk of extinction, but the conservation status of nearly 40% of marine mammals remains unknown due to insufficient data. Predictive models of extinction risk are crucial to informing present and future conservation needs, yet such models have not been developed for marine mammals. In this paper, we: (i) used powerful machine-learning and spatial-modeling approaches to understand the intrinsic and extrinsic drivers of marine mammal extinction risk; (ii) used this information to predict risk across all marine mammals, including IUCN "Data Deficient" species; and (iii) conducted a spatially explicit assessment of these results to understand how risk is distributed across the world's oceans. Rate of offspring production was the most important predictor of risk. Additional predictors included taxonomic group, small geographic range area, and small social group size. Although the interaction of both intrinsic and extrinsic variables was important in predicting risk, overall, intrinsic traits were more important than extrinsic variables. In addition to the 32 species already on the IUCN Red List, our model identified 15 more species, suggesting that 37% of all marine mammals are at risk of extinction. Most at-risk species occur in coastal areas and in productive regions of the high seas. We identify 13 global hotspots of risk and show how they overlap with human impacts and Marine Protected Areas.

Countryside biogeography of Neotropical reptiles and amphibians.

The future of biodiversity and ecosystem services depends largely on the capacity of human-dominated ecosystems to support them, yet this capacity remains largely unknown. Using the framework of countryside biogeography, and working in the Las Cruces system of Coto Brus, Costa Rica, we assessed reptile and amphibian assemblages within four habitats that typify much of the Neotropics: sun coffee plantations (12 sites), pasture (12 sites), remnant forest elements (12 sites), and a larger, contiguous protected forest (3 sites in one forest). Through analysis of 1678 captures of 67 species, we draw four primary conclusions. First, we found that the majority of reptile (60%) and amphibian (70%) species in this study used an array of habitat types, including coffee plantations and actively grazed pastures. Second, we found that coffee plantations and pastures hosted rich, albeit different and less dense, reptile and amphibian biodiversity relative to the 326-ha Las Cruces Forest Reserve and neighboring forest elements. Third, we found that the small ribbons of "countryside forest elements" weaving through farmland collectively increased the effective size of a 326-ha local forest reserve 16-fold for reptiles and 14-fold for amphibians within our 236-km2 study area. Therefore, countryside forest elements, often too small for most remote sensing techniques to identify, are contributing -95% of the available habitat for forest-dependent reptiles and amphibians in our largely human-dominated study region. Fourth, we found large and pond-reproducing amphibians to prefer human-made habitats, whereas small, stream-reproducing, and directly developing species are more dependent on forest elements. Our investigation demonstrates that tropical farming landscapes can support substantial reptile and amphibian biodiversity. Our approach provides a framework for estimating the conservation value of the complex working landscapes that constitute roughly half of the global land surface, and which are experiencing intensification pressure worldwide.

Global distribution and conservation of marine mammals.

We identified 20 global key conservation sites for all marine (123) and freshwater (6) mammal species based on their geographic ranges. We created geographic range maps for all 129 species and a Geographic Information System database for a 46,184 1° x 1° grid-cells, ∼10,000-km(2). Patterns of species richness, endemism, and risk were variable among all species and species groups. Interestingly, marine mammal species richness was correlated strongly with areas of human impact across the oceans. Key conservation sites in the global geographic grid were determined either by their species richness or by their irreplaceability or uniqueness, because of the presence of endemic species. Nine key conservation sites, comprising the 2.5% of the grid cells with the highest species richness, were found, mostly in temperate latitudes, and hold 84% of marine mammal species. In addition, we identified 11 irreplaceable key conservation sites, six of which were found in freshwater bodies and five in marine regions. These key conservation sites represent critical areas of conservation value at a global level and can serve as a first step for adopting global strategies with explicit geographic conservation targets for Marine Protected Areas.

Correction: Beyond words: From jaguar population trends to conservation and public policy in Mexico.

[This corrects the article DOI: 10.1371/journal.pone.0255555.].

Reservoirs of richness: least disturbed tropical forests are centres of undescribed species diversity.

In the last few decades, there has been a remarkable discovery of new species of plants, invertebrates and vertebrates, in what have been called the new age of discovery. However, owing to anthropogenic impacts such as habitat conversion, many of the still unknown species may go extinct before being scientifically documented (i.e. 'crypto-extinctions'). Here, by applying a mathematical model of species descriptions which accounts for taxonomic effort, we show that even after 250 years of taxonomic classification, about 3050 amphibians and at least 160 land mammal species remain to be discovered and described. These values represent, respectively, 33 and 3 per cent of the current species total for amphibians and land mammals. We found that tropical moist forests of the Neotropics, Afrotropics and Indomalaya probably harbour the greatest numbers of undescribed species. Tropical forests with minimal anthropogenic disturbance are predicted to have larger proportions of undescribed species. However, the protected area coverage is low in many of these key biomes. Moreover, undescribed species are likely to be at a greater risk of extinction compared with known species because of small geographical ranges among other factors. By highlighting the key areas of undescribed species diversity, our study provides a starting template to rapidly document these species and protect them through better habitat management.

Discoveries of new mammal species and their implications for conservation and ecosystem services.

In light of recent discoveries of many new species of poorly-studied organisms, we examine the biodiversity of mammals, a well known "charismatic" group. Many assume that nearly all mammal species are known to scientists. We demonstrate that this assumption is incorrect. Since 1993, 408 new mammalian species have been described, approximately 10% of the previously known fauna. Some 60% of these are "cryptic" species, but 40% are large and distinctive. A substantial number persist only in areas undergoing rapid habitat destruction. Our findings suggest global animal and plant species diversity is badly underestimated even in well studied taxa. This implies even greater threats to ecosystem services and human well-being than previously assumed, and an increased need to explore, understand, and conserve Earth's living resources.

Multiple ecological pathways to extinction in mammals.

As human population and resource demands continue to grow, biodiversity conservation has never been more critical. About one-quarter of all mammals are in danger of extinction, and more than half of all mammal populations are in decline. A major priority for conservation science is to understand the ecological traits that predict extinction risk and the interactions among those predictors that make certain species more vulnerable than others. Here, using a new database of nearly 4,500 mammal species, we use decision-tree models to quantify the multiple interacting factors associated with extinction risk. We show that the correlates of extinction risk vary widely across mammals and that there are unique pathways to extinction for species with different lifestyles and combinations of traits. We find that risk is relative and that all kinds of mammals, across all body sizes, can be at risk depending on their specific ecologies. Our results increase the understanding of extinction processes, generate simple rules of thumb that identify species at greatest risk, and highlight the potential of decision-tree analyses to inform conservation efforts.

Biogeography of terrestrial vertebrates and its conservation implications in a transitional region in western Mexico.

Conservation biogeography, which applies principles, theories, and analyses of biodiversity distribution patterns to address conservation challenges, can provide valuable insight and guidance to policy making for protection of biodiversity at multiple scales. The temperate and tropical ecosystems of the Nearctic-Neotropical transition in the small western state of Colima, Mexico, support a mosaic of remarkably diverse fauna and flora and provide a rare opportunity to determine spatial distribution patterns of terrestrial vertebrate species, assess human-induced threats, and identify potential conservation strategies. We analyzed the spatial distribution patterns and correlated them with the current land cover and extent of the protected areas. Despite its limited geographic extension, 29% (866) of all vertebrates, and almost a quarter of both endemic and threatened species in Mexico, live in Colima. Our analysis identified clear high-richness concentration sites (i.e., "hotspots") coincident for all groups and that elevation and both temperate and tropical ecosystems composition exert significant influence on richness patterns. Furthermore, current species´ distribution also showed significant correlation with natural and disturbed landcover. Significant hotspots for all species groups coincided poorly with the limited protected areas in the state (only 3.8%). The current state of natural land cover (less than 16%) in the state, coupled with its remarkable biological importance, highlights the need for further complementary conservation efforts including expansion and creation of new protected areas, significant restoration efforts and other conservation measures to maintain this uniquely biogeographic and biological diverse region of the country.

Circling the drain: the extinction crisis and the future of humanity.

Humanity has triggered the sixth mass extinction episode since the beginning of the Phanerozoic. The complexity of this extinction crisis is centred on the intersection of two complex adaptive systems: human culture and ecosystem functioning, although the significance of this intersection is not properly appreciated. Human beings are part of biodiversity and elements in a global ecosystem. Civilization, and perhaps even the fate of our species, is utterly dependent on that ecosystem's proper functioning, which society is increasingly degrading. The crisis seems rooted in three factors. First, relatively few people globally are aware of its existence. Second, most people who are, and even many scientists, assume incorrectly that the problem is primarily one of the disappearance of species, when it is the existential threat of myriad population extinctions. Third, while concerned scientists know there are many individual and collective steps that must be taken to slow population extinction rates, some are not willing to advocate the one fundamental, necessary, 'simple' cure, that is, reducing the scale of the human enterprise. We argue that compassionate shrinkage of the human population by further encouraging lower birth rates while reducing both inequity and aggregate wasteful consumption-that is, an end to growthmania-will be required. This article is part of the theme issue 'Ecological complexity and the biosphere: the next 30 years'.

Two new species of Peromyscus (Cricetidae: Neotominae) from the Transverse Volcanic Belt of Mexico.

Specimens of the Peromyscus boylii species group distributed in the western and northeastern montane regions of Michoacán, México, historically have been assigned to P. levipes. Previous studies indicated that these specimens possessed mitochondrial DNA haplotypes that were distinct from both P. levipes and P. kilpatricki, a recently named species in the P. boylii species group from northeastern Michoacán and western Morelos. Herein karyotypic, DNA sequence, and morphological data were analyzed from those populations to evaluate their taxonomic affinity. Karyotypic data indicated that individuals from western Michoacán (Dos Aguas and Aguililla) and from a newly discovered population in northeastern Michoacán (Zinapécuaro) were chromosomally similar to P. carletoni (FN = 68) but distinct from other taxa assigned to the P. boylii species group. Analyses of cranial characteristics indicated that, relative to other species in the P. boylii species group, two morphologically distinct groups were present that corresponded to the Dos Aguas/Aguililla and Zinapécuaro populations, respectively. The latter population, although represented by a small sample size (n = 5 specimens), appeared to exhibit some trenchant morphological distinctions compared with other cryptic species in the P. boylii group. Phylogenetic analyses (parsimony, Bayesian, and likelihood) of DNA sequences obtained from the mitochondrial cytochrome-b gene indicated that although the individuals from Dos Aguas/Aguililla and Zinapécuaro formed a sister group relationship, they formed monophyletic clades that differed genetically (2.54%)-a level approaching that seen between other sister species of Peromyscus. Further, the Dos Aguas/Aguililla and Zinapécuaro clade was more closely aligned with a clade containing representatives of P. carletoni and P. levipes instead of with those from closer geographic proximities (P. kilpatricki) located in eastern Michoacán. Together, these results indicated that these two populations seemingly represent two undescribed species in the P. boylii species group for which we propose the names Peromyscus greenbaumi for populations in western Michoacán (circa Dos Aguas and Aguililla) and Peromyscus ensinki for populations in northeastern Michoacán (circa Zinapécuaro).

Los especímenes del grupo de especies de Peromyscus boylii distribuidos en las regiones montañosas occidentales y el noreste de Michoacán, México, históricamente fueron asignados a P. levipes. Sin embargo, estudios previos han indicado que estos especímenes poseen haplotipos de ADN mitocondrial que son distintos de P. levipes y P. kilpatricki, una especie recientemente nombrada en el grupo de especies P. boylii del noreste de Michoacán y el oeste de Morelos. Los datos cariotípicos indicaron que los individuos del oeste de Michoacán (Dos Aguas y Aguililla) y de una población recién descubierta en el noreste de Michoacán (Zinapécuaro) eran cromosómicamente similares a P. carletoni (FN = 68), pero distintos de otros taxones asignados al grupo de especies P. boylii. Los análisis de las características craneales indicaron que en relación con otras especies del grupo de especies P. boylii, dos grupos morfológicamente distintos estaban presentes, y que correspondían a las poblaciones de Dos Aguas/Aguililla y Zinapécuaro, respectivamente. Aunque representada por un tamaño de muestra pequeño (n = 5 especímenes), esta última población pareció exhibir algunas diferencias morfológicas en comparación con las otras especies crípticas en el grupo P. boylii. Los análisis filogenéticos (parsimonia, inferencia bayesiana y verosimilitud) de secuencias de ADN obtenidas del gen mitocondrial citocromo-b, indicaron que, aunque los individuos de Dos Aguas/Aguililla y Zinapécuaro tienen una relación de grupo hermano, estos forman clados monofiléticos que difieren genéticamente (2.54%), nivel que se acerca al observado entre otras especies hermanas de Peromyscus. Además, el clado de Dos Aguas/Aguililla y Zinapécuaro está más estrechamente alineado con un clado que contenía representantes de P. carletoni y P. levipes en lugar de aquellos de proximidades geográficas más cercanas (P. kilpatricki) ubicados en el este de Michoacán. Estos resultados indicaron que estas dos poblaciones aparentemente representan dos especies no descritas en el grupo de especies P. boylii para las cuales proponemos los nombres Peromyscus greenbaumi para poblaciones en el oeste de Michoacán (hacia Dos Aguas y Aguililla) y Peromyscus ensinki para poblaciones en el noreste de Michoacán (circa Zinapécuaro).

Reference genomes for conservation.

High-quality reference genomes for non-model species can benefit conservation.