Error-induced extinction in a multi-type critical birth-death process.

Extreme mutation rates in microbes and cancer cells can result in error-induced extinction (EEX), where every descendant cell eventually acquires a lethal mutation. In this work, we investigate critical birth-death processes with n distinct types as a birth-death model of EEX in a growing population. Each type-i cell divides independently ( i ) → ( i ) + ( i ) or mutates ( i ) → ( i + 1 ) at the same rate. The total number of cells grows exponentially as a Yule process until a cell of type-n appears, which cell type can only divide or die at rate one. This makes the whole process critical and hence after the exponentially growing phase eventually all cells die with probability one. We present large-time asymptotic results for the general n-type critical birth-death process. We find that the mass function of the number of cells of type-k has algebraic and stationary tail ( size ) - 1 - χ k , with χ k = 2 1 - k , for k = 2 , ⋯ , n , in sharp contrast to the exponential tail of the first type. The same exponents describe the tail of the asymptotic survival probability ( time ) - ξ k . We present applications of the results for studying extinction due to intolerable mutation rates in biological populations.

Imbalanced speciation pulses sustain the radiation of mammals.

The evolutionary histories of major clades, including mammals, often comprise changes in their diversification dynamics, but how these changes occur remains debated. We combined comprehensive phylogenetic and fossil information in a new "birth-death diffusion" model that provides a detailed characterization of variation in diversification rates in mammals. We found an early rising and sustained diversification scenario, wherein speciation rates increased before and during the Cretaceous-Paleogene (K-Pg) boundary. The K-Pg mass extinction event filtered out more slowly speciating lineages and was followed by a subsequent slowing in speciation rates rather than rebounds. These dynamics arose from an imbalanced speciation process, with separate lineages giving rise to many, less speciation-prone descendants. Diversity seems to have been brought about by these isolated, fast-speciating lineages, rather than by a few punctuated innovations.

Fishing for oil and meat drives irreversible defaunation of deepwater sharks and rays.

The deep ocean is the last natural biodiversity refuge from the reach of human activities. Deepwater sharks and rays are among the most sensitive marine vertebrates to overexploitation. One-third of threatened deepwater sharks are targeted, and half the species targeted for the international liver-oil trade are threatened with extinction. Steep population declines cannot be easily reversed owing to long generation lengths, low recovery potentials, and the near absence of management. Depth and spatial limits to fishing activity could improve conservation when implemented alongside catch regulations, bycatch mitigation, and international trade regulation. Deepwater sharks and rays require immediate trade and fishing regulations to prevent irreversible defaunation and promote recovery of this threatened megafauna group.

Response to Comment on "Dying in the Sun: Direct evidence for elevated UV-B radiation at the end-Permian mass extinction".

Seddon and Zimmermann have raised questions about the evidence for increased UV-B flux across the end-Permian mass extinction (EPME) that was presented in our recent study, specifically regarding the measurement of UV-B-absorbing compound (UAC) levels in fossil pollen. We respond to these points, arguing that the comparison of FTIR spectra of >250 million-year-old Permian fossil pollen with ~700-year-old subfossil pollen is not valid and that negligible nonrandom interference derived from water vapor fluctuations during data generation cannot coincidentally produce a substantial UAC peak during the EPME. Furthermore, we refute the suggestion that the measured aromatic peak at 1600 cm-1 could have been influenced by diagenetic products from other organic constituents of pollen. The most productive route forward will be to generate sporomorph geochemical data from additional Permian-Triassic boundary sections to test the results put forward in our study.

Inference of Ancient Polyploidy from Genomic Data.

Whole-genome sequence data have revealed that numerous eukaryotic organisms derive from distant polyploid ancestors, even when these same organisms are genetically and karyotypically diploid. Such ancient whole-genome duplications (WGDs) have been important for long-term genome evolution and are often speculatively associated with important evolutionary events such as key innovations, adaptive radiations, or survival after mass extinctions. Clearly, reliable methods for unveiling ancient WGDs are key toward furthering understanding of the long-term evolutionary significance of polyploidy. In this chapter, we describe a set of basic established comparative genomics approaches for the inference of ancient WGDs from genomic data based on empirical age distributions and collinearity analyses, explain the principles on which they are based, and illustrate a basic workflow using the software "wgd," geared toward a typical exploratory analysis of a newly obtained genome sequence.

Constraining Whole-Genome Duplication Events in Geological Time.

The timing of whole-genome duplication (WGD) events is crucial to understanding their role in evolution and underpins many hypotheses linking WGD to increased diversity and complexity. As such, means of estimating the timing of the WGD events relative to their macroevolutionary outcomes are of considerable importance. Molecular clock methods facilitate direct estimation of the absolute timing of WGD events, integrating information on the rate of sequence evolution between species while accommodating the uncertainty inherent to the fossil record. We present an explanation of the best practice for constructing fossil calibrations and estimating the age of WGD events via molecular clock methods in the program MCMCtree, with an example dataset based on a well-characterized WGD event within the flowering dogwoods (Cornus). The approach presented herein allows for the estimation of the age of WGD events and subsequent speciation events, allowing the relationship between WGD and the macroevolutionary outcomes to be explored. In our example, we show that in the case of flowering dogwoods, the WGD event long predates the end-Cretaceous mass extinction and that the two events may be independent.

Genomes From Historic DNA Unveil Massive Hidden Extinction and Terminal Endangerment in a Tropical Asian Songbird Radiation.

Quantifying the magnitude of the global extinction crisis is important but remains challenging, as many extinction events pass unnoticed owing to our limited taxonomic knowledge of the world's organisms. The increasing rarity of many taxa renders comprehensive sampling difficult, further compounding the problem. Vertebrate lineages such as birds, which are thought to be taxonomically well understood, are therefore used as indicator groups for mapping and quantifying global extinction. To test whether extinction patterns are adequately gauged in well-studied groups, we implemented ancient-DNA protocols and retrieved whole genomes from the historic DNA of museum specimens in a widely known songbird radiation of shamas (genus Copsychus) that is assumed to be of least conservation concern. We uncovered cryptic diversity and an unexpected degree of hidden extinction and terminal endangerment. Our analyses reveal that >40% of the phylogenetic diversity of this radiation is already either extinct in the wild or nearly so, including the two genomically most distinct members of this group (omissus and nigricauda), which have so far flown under the conservation radar as they have previously been considered subspecies. Comparing the genomes of modern samples with those from roughly a century ago, we also found a significant decrease in genetic diversity and a concomitant increase in homozygosity affecting various taxa, including small-island endemics that are extinct in the wild as well as subspecies that remain widespread across the continental scale. Our application of modern genomic approaches demonstrates elevated levels of allelic and taxonomic diversity loss in a songbird clade that has not been listed as globally threatened, highlighting the importance of ongoing reassessments of extinction incidence even across well-studied animal groups. Key words: extinction, introgression, white-rumped shama, conservation.

Erasing the extinct: the hunt for Caribbean monk seals and museum collection practices / O desaparecimento do que está extinto: a caça às focas-monge-do-caribe e as práticas de acervos museológicos

Abstract The Caribbean monk seal (Monachus tropicalis), the only seal species native to Central America, was declared extinct in 2008, with the last confirmed sighting in 1952. This species historically had a broad range throughout the gulf of Mexico. This article discusses the history of Western science on the monk seal, from its first recorded sighting by a Western colonizer in 1492 to scientific collection in the 1800s and 1900s, as a history of the erasure of this species. Museum practices of collecting and displaying Caribbean monk seals have directly contributed to this erasure, and ways of writing a new history by giving the Caribbean monk seal the capacity to refuse erasure are suggested.

Resumo A foca-monge-do-caribe (Monachus tropicalis), a única espécie de focas nativa da América Central, foi declarada extinta em 2008, tendo o último registro de avistamento confirmado em 1952. Historicamente, essa espécie ocupou vastas áreas do golfo do México. Este artigo discute a história da ciência ocidental sobre a foca-monge, desde o primeiro registro de seu avistamento por um colonizador ocidental, em 1492, até a coleção científica nos anos 1800 e 1900, como uma história de desaparecimento da espécie. As práticas museológicas de coleta e exposição de focas-monge-do-caribe contribuíram diretamente para tal desaparecimento, e aqui são sugeridas maneiras de escrever uma nova história concedendo à foca-monge-do-caribe a possibilidade de recusa ao desaparecimento.

Computed tomography reveals hip dysplasia in the extinct Pleistocene saber-tooth cat Smilodon.

Reconstructing the behavior of extinct species is challenging, particularly for those with no living analogues. However, damage preserved as paleopathologies on bone can record how an animal moved in life, potentially reflecting behavioral patterns. Here, we assess hypothesized etiologies of pathology in a pelvis and associated right femur of a Smilodon fatalis saber-toothed cat, one of the best-studied species from the Pleistocene-age Rancho La Brea asphalt seeps, California, USA, using visualization by computed tomography (CT). The pelvis exhibits massive destruction of the right hip socket that was interpreted, for nearly a century, to have developed from trauma and infection. CT imaging reveals instead that the pathological distortions characterize chronic remodeling that began at birth and led to degeneration of the joint over the animal's life. These results suggest that this individual suffered from hip dysplasia, a congenital condition common in domestic dogs and cats. This individual reached adulthood but could not have hunted properly nor defended territory on its own, likely relying on a social group for feeding and protection. While extant social felids are rare, these fossils and others with similar pathologies are consistent with a spectrum of social strategies in Smilodon supported by a predominance of previous studies.

La administración de nicotina aguda retarda la extinción en automoldeamiento pavloviano: un estudio preliminar / Acute nicotine administration retards extinction from pavlovian autoshaping: A preliminary study

Resumen Introducción y objetivo: Los procesos de aprendizaje y motivación han sido centrales para la comprensión de los mecanismos que subyacen al tabaquismo. En particular, existe evidencia creciente sobre la importancia de valores motivacionales de incentivo para entender el inicio y mantenimiento del tabaquismo. El objetivo general de este experimento fue evaluar el papel de la nicotina aguda sobre el valor de incentivo de una recompensa natural, (comida) asociada con un estímulo ambiental, (palanca experimental). Método: Se utilizaron ratas Wistar. Se administró nicotina (0.4 mg/kg) de manera aguda en momentos específicos del entrenamiento, utilizando un procedimiento de diez sesiones de adquisición y cuatro sesiones extinción en una tarea pavloviana de automoldeamiento. El diseño experimental incluyó tres grupos, el grupo control de solución salina y grupos de nicotina durante la adquisición y la extinción. Resultados: Se encontró que la administración aguda de nicotina, de manera específica y en comparación con los otros dos grupos experimentales, resultó en un efecto de retardo durante la fase de extinción, y que una administración similar de nicotina no resultó en efectos observables durante el desempeño comportamental en adquisición. Conclusiones: Estos resultados apoyan el papel de la nicotina como fortalecedora del valor de incentivo de las claves ambientales durante la extinción para una tarea de automoldeamiento.

Abstract Introduction and goal: Learning and motivational processes have been central for a modern understanding of tobacco addiction. There is evidence that supports the importance of incentive motivational processes for the maintenance of tobacco addiction. The main goal of the present experiment was to evaluate the effects of acute nicotine on the incentive value of a natural reward, (food) paired with an environmental cue (pressing lever). Method: Wistar rats were used. Accute nicotine (0.4 mg/kg) was administered on key sessions, using a pavlovian autoshaping procedure involving ten acquisition and four extinction sessions. The experimental design included three groups, a saline administration control group and groups with specific nicotine administration during either acquisition or extinction. Results: We found that acute administration of nicotine, in contrast with saline only or previous nicotine administration during acquisition, had an enhancing effect on responding for the environmental cue during autoshaping extinction, but we did not find evidence that acute nicotine affected acquisition performance. Conclusion: Our results are consistent with a role of nicotine enhancing the incentive value of stimuli during extinction from a pavlovian autoshaping task.

Mammaliaform extinctions as a driver of the morphological radiation of Cenozoic mammals.

Adaptive radiations are hypothesized as a generating mechanism for much of the morphological diversity of extant species.1-7 The Cenozoic radiation of placental mammals, the foundational example of this concept,8,9 gave rise to much of the morphological disparity of extant mammals, and is generally attributed to relaxed evolutionary constraints following the extinction of non-avian dinosaurs.10-13 However, study of this and other radiations has focused on variation in evolutionary rates,4,5,7,14 leaving the extent to which relaxation of constraints enabled the origin of novel phenotypes less well characterized.15-17 We evaluate constraints on morphological evolution among mammaliaforms (mammals and their closest relatives) using a new method that quantifies the capacity of evolutionary change to generate phenotypic novelty. We find that Mesozoic crown-group therians, which include the ancestors of placental mammals, were significantly more constrained than other mammaliaforms. Relaxation of these constraints occurred in the mid-Paleocene, post-dating the extinction of non-avian dinosaurs at the K/Pg boundary, instead coinciding with important environmental shifts and with declining ecomorphological diversity in non-theriimorph mammaliaforms. This relaxation occurred even in small-bodied Cenozoic mammals weighing <100 g, which are unlikely to have competed with dinosaurs. Instead, our findings support a more complex model whereby Mesozoic crown therian evolution was in part constrained by co-occurrence with disparate mammaliaforms, as well as by the presence of dinosaurs, within-lineage incumbency effects, and environmental factors. Our results demonstrate that variation in evolutionary constraints can occur independently of variation in evolutionary rate, and that both make important contributions to the understanding of adaptive radiations.

The Origin of the Legumes is a Complex Paleopolyploid Phylogenomic Tangle Closely Associated with the Cretaceous-Paleogene (K-Pg) Mass Extinction Event.

The consequences of the Cretaceous-Paleogene (K-Pg) boundary (KPB) mass extinction for the evolution of plant diversity remain poorly understood, even though evolutionary turnover of plant lineages at the KPB is central to understanding assembly of the Cenozoic biota. The apparent concentration of whole genome duplication (WGD) events around the KPB may have played a role in survival and subsequent diversification of plant lineages. To gain new insights into the origins of Cenozoic biodiversity, we examine the origin and early evolution of the globally diverse legume family (Leguminosae or Fabaceae). Legumes are ecologically (co-)dominant across many vegetation types, and the fossil record suggests that they rose to such prominence after the KPB in parallel with several well-studied animal clades including Placentalia and Neoaves. Furthermore, multiple WGD events are hypothesized to have occurred early in legume evolution. Using a recently inferred phylogenomic framework, we investigate the placement of WGDs during early legume evolution using gene tree reconciliation methods, gene count data and phylogenetic supernetwork reconstruction. Using 20 fossil calibrations we estimate a revised timeline of legume evolution based on 36 nuclear genes selected as informative and evolving in an approximately clock-like fashion. To establish the timing of WGDs we also date duplication nodes in gene trees. Results suggest either a pan-legume WGD event on the stem lineage of the family, or an allopolyploid event involving (some of) the earliest lineages within the crown group, with additional nested WGDs subtending subfamilies Papilionoideae and Detarioideae. Gene tree reconciliation methods that do not account for allopolyploidy may be misleading in inferring an earlier WGD event at the time of divergence of the two parental lineages of the polyploid, suggesting that the allopolyploid scenario is more likely. We show that the crown age of the legumes dates to the Maastrichtian or early Paleocene and that, apart from the Detarioideae WGD, paleopolyploidy occurred close to the KPB. We conclude that the early evolution of the legumes followed a complex history, in which multiple auto- and/or allopolyploidy events coincided with rapid diversification and in association with the mass extinction event at the KPB, ultimately underpinning the evolutionary success of the Leguminosae in the Cenozoic. [Allopolyploidy; Cretaceous-Paleogene (K-Pg) boundary; Fabaceae, Leguminosae; paleopolyploidy; phylogenomics; whole genome duplication events].

In vitro Propagation to Conserve the Local Endemic and Endangered Medicinal Plant Helianthemum germanicopolitanum Bornm

Abstract In this study, in vitro propagation and acclimatization of Helianthemum germanicopolitanum Bornm. plant, a local endemic in Çankırı Province (Turkey) with arid and semi-arid lands, and an endangered species taking part among medicinal and aromatic plants were accomplished, which is under-researched. In this study, three basal media [a) Murashige and Skoog b) Gamborg's B5, and c) Nitsch & Nitsch], two gelling agents (agar 7 g/L, and gelrite 2.1 g/L), eight cytokinins and eight auxin doses of plant growth regulators [a) 6-benzyladenin, b) Kinetin-(0, 0.5, 1, and 2 mg/L), c) Indole-3-butyric acid, d) α-napthaleneacetic acid-(0, 0.25, 0.5, and 1 mg/L)] prepared in 64 different combinations with 30 g/L sucrose was added to the basal media and adjusted to pH 5.7 for in vitro propagation of H. germanicopolitanum. During in vitro propagation of the plant, external and internal infections were frequently encountered and this was solved by the developed protocol. The best shoot growth (1.141 cm) and shoot length (0.572 cm) were obtained in the Gamborg's B5 medium in combination with Kinetin (0.5 mg/L)+Indole-3-butyric acid (0.5 mg/L)+gelrite. The maximum number of shoots (19.50) and the best multiplication rate (94%) were obtained in the media containing benzyladenin (1 mg/L)+Indole-3-butyric acid (0.5 mg/L) plant growth regulator in Murashige and Skoog medium solidified with agar. At the rooting stage, the maximum number of roots (30) was reached in the Murashige and Skoog medium containing gelrite and the best rooting rate (92%) with agar. A hundred plants representing the best shoot and root growth were taken to acclimatization stage, and 32 of these plants adapted to external conditions.

A transmissible cancer shifts from emergence to endemism in Tasmanian devils.

Emerging infectious diseases pose one of the greatest threats to human health and biodiversity. Phylodynamics is often used to infer epidemiological parameters essential for guiding intervention strategies for human viruses such as severe acute respiratory syndrome coronavirus 2 (SARS-Cov-2). Here, we applied phylodynamics to elucidate the epidemiological dynamics of Tasmanian devil facial tumor disease (DFTD), a fatal, transmissible cancer with a genome thousands of times larger than that of any virus. Despite prior predictions of devil extinction, transmission rates have declined precipitously from ~3.5 secondary infections per infected individual to ~1 at present. Thus, DFTD appears to be transitioning from emergence to endemism, lending hope for the continued survival of the endangered Tasmanian devil. More generally, our study demonstrates a new phylodynamic analytical framework that can be applied to virtually any pathogen.

A comparative genomics multitool for scientific discovery and conservation.

The Zoonomia Project is investigating the genomics of shared and specialized traits in eutherian mammals. Here we provide genome assemblies for 131 species, of which all but 9 are previously uncharacterized, and describe a whole-genome alignment of 240 species of considerable phylogenetic diversity, comprising representatives from more than 80% of mammalian families. We find that regions of reduced genetic diversity are more abundant in species at a high risk of extinction, discern signals of evolutionary selection at high resolution and provide insights from individual reference genomes. By prioritizing phylogenetic diversity and making data available quickly and without restriction, the Zoonomia Project aims to support biological discovery, medical research and the conservation of biodiversity.

Division of the genus Chryseobacterium: Observation of discontinuities in amino acid identity values, a possible consequence of major extinction events, guides transfer of nine species to the genus Epilithonimonas, eleven species to the genus Kaistella, and three species to the genus Halpernia gen. nov., with description of Kaistella daneshvariae sp. nov. and Epilithonimonas vandammei sp. nov. derived from clinical specimens.

The genus Chryseobacterium in the family Weeksellaceae is known to be polyphyletic. Amino acid identity (AAI) values were calculated from whole-genome sequences of species of the genus Chryseobacterium, and their distribution was found to be multi-modal. These naturally-occurring non-continuities were leveraged to standardise genus assignment of these species. We speculate that this multi-modal distribution is a consequence of loss of biodiversity during major extinction events, leading to the concept that a bacterial genus corresponds to a set of species that diversified since the Permian extinction. Transfer of nine species (Chryseobacterium arachidiradicis, Chryseobacterium bovis, Chryseobacterium caeni, Chryseobacterium hispanicum, Chryseobacterium hominis, Chryseobacterium hungaricum,, Chryseobacterium pallidum and Chryseobacterium zeae) to the genus Epilithonimonas and eleven (Chryseobacterium anthropi, Chryseobacterium antarcticum, Chryseobacterium carnis, Chryseobacterium chaponense, Chryseobacterium haifense, Chryseobacterium jeonii, Chryseobacterium montanum, Chryseobacterium palustre, Chryseobacterium solincola, Chryseobacterium treverense and Chryseobacterium yonginense) to the genus Kaistella is proposed. Two novel species are described: Kaistella daneshvariae sp. nov. and Epilithonimonas vandammei sp. nov. Evidence is presented to support the assignment of Planobacterium taklimakanense to a genus apart from Chryseobacterium, to which Planobacterium salipaludis comb nov. also belongs. The novel genus Halpernia is proposed, to contain the type species Halpernia frigidisoli comb. nov., along with Halpernia humi comb. nov., and Halpernia marina comb. nov.

Repeated evolution of durophagy during ichthyosaur radiation after mass extinction indicated by hidden dentition.

Marine tetrapods quickly diversified and were established as marine top predators after the end-Permian Mass extinction (EPME). Ichthyosaurs were the forerunner of this rapid radiation but the main drivers of the diversification are poorly understood. Cartorhynchus lenticarpus is a basal ichthyosauriform with the least degree of aquatic adaptation, holding a key to identifying such a driver. The unique specimen appeared edentulous based on what was exposed but a CT scanning revealed that the species indeed had rounded teeth that are nearly perpendicular to the jaw rami, and thus completely concealed in lateral view. There are three dental rows per jaw ramus, and the root lacks infoldings of the dentine typical of ichthyopterygians. The well-developed and worn molariform dentition with three tooth rows supports the previous inference that the specimen is not of a juvenile. The premaxilla and the corresponding part of the dentary are edentulous. Molariform dentition evolved three to five times independently within Ichthyosauriformes in the Early and Middle Triassic. Convergent exploitation of hard-shelled invertebrates by different subclades of ichthyosauriforms likely fueled the rapid taxonomic diversification of the group after EPME.

The apparent exponential radiation of Phanerozoic land vertebrates is an artefact of spatial sampling biases.

There is no consensus about how terrestrial biodiversity was assembled through deep time, and in particular whether it has risen exponentially over the Phanerozoic. Using a database of 60 859 fossil occurrences, we show that the spatial extent of the worldwide terrestrial tetrapod fossil record itself expands exponentially through the Phanerozoic. Changes in spatial sampling explain up to 67% of the change in known fossil species counts, and these changes are decoupled from variation in habitable land area that existed through time. Spatial sampling therefore represents a real and profound sampling bias that cannot be explained as redundancy. To address this bias, we estimate terrestrial tetrapod diversity for palaeogeographical regions of approximately equal size. We find that regional-scale diversity was constrained over timespans of tens to hundreds of millions of years, and similar patterns are recovered for major subgroups, such as dinosaurs, mammals and squamates. Although the Cretaceous/Palaeogene mass extinction catalysed an abrupt two- to three-fold increase in regional diversity 66 million years ago, no further increases occurred, and recent levels of regional diversity do not exceed those of the Palaeogene. These results parallel those recovered in analyses of local community-level richness. Taken together, our findings strongly contradict past studies that suggested unbounded diversity increases at local and regional scales over the last 100 million years.