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opencc-by-4.0Apr 2020View details →

Galactic extinction within 400pc in cartesian coordinates

Galactic 3D extinction of Leike et al 2020 using data of Anders et al 2019. See readme.txt or the information within the h5 files for more details.

opencc-zeroAug 2020View details →

External anatomy of the extinct giant shark Otodus megalodon

Inferring the size and shape of extinct animals is fraught with danger, especially when they were much larger than their modern relatives. Such extrapolations are particularly risky when allometry is present. The extinct giant shark Otodus megalodonis known almost exclusively from fossilised teeth, and estimates have been made from these of its total length and body mass using the great white shark (Carcharodon carcharias) as the modern analogue. This is problematic as the two species likely belong to different families within Lamniformes, and the position of theOtoduslineage is unclear. Here, we infer the body dimensions of the giant O. megalodon based on anatomical measurements of five ecologically and physiologically similar lamniform sharks.We first assessed for allometry in all species using linear regressions and geometric morphometric analyses. Because no evidence of allometry was found, we made morphological extrapolations to infer body dimensions of O. megalodonat different sizes. Our results suggest that a 16 m O. megalodonlikely had a head ~4.65 m long, a dorsal fin ~1.62 m tall and a tail ~3.85 m high. Our morphometric analyses further reveal dorsal and caudal fins adaptedfor fast predatory swimming, but slower, more sustained long-distance swimming.

opencc-zeroAug 2020View details →

Functional traits of avian frugivores have shifted following species extinction and introduction in the Hawaiian Islands

The extinction and introduction of species can alter ecological processes owing to the loss or gain of species roles. In vertebrate-dependent seed dispersal, mutualisms between frugivores and fruiting plants depend, in part, on matching of functional traits. High species turnover of frugivores has occurred on the Hawaiian Islands, owing to both the loss of native frugivores and the introduction of a new suite of frugivores. How this turnover has altered the functional traits of frugivores and the potential impacts on seed dispersal remain unclear. We investigated how avian frugivore traits differed between historic and modern assemblages of the Hawaiian Islands. We also tested how traits shifted within foraging guilds (ground versus arboreal) to distinguish potential impacts on plants within low versus high forest strata. Compared to historic frugivores, the modern assemblage is smaller in gape width and body mass in both ground and arboreal guilds. Wing shape did not significantly change between assemblages. From results, we postulate that changes in the frugivore community have likely altered seed dispersal processes by reducing (1) the size of seeds consumed, (2) frugivory rates per animal, and (3) seed dispersal distances. Owing to seed size placing strong constraints on consumption, we reviewed recent studies on frugivory by modern birds in the Hawaiian Islands and compared the size of seeds consumed versus seeds available. We found that larger-seeded plants (>8.1mm seed width) were not consumed by modern birds and were more likely to be of conservation risk compared to smaller-seeded plants. Consequently, dispersal limitation may threaten Hawaiian plant communities, with larger-seeded plants at greatest risk of extinction. Broadly, we show that extensive turnover within assemblages may lead to significant changes in functional traits, with potential knock-on effects for mutualistic interactions and communities.

opencc-zeroSep 2020View details →

Size variations in foraminifers from the Early Permian to the Late Triassic: implications for the Guadalupian-Lopingian and the Permian-Triassic mass extinctions

The final 10 Myr of the Paleozoic saw two of the biggest biologic crises in Earth history: the Middle Permian extinction (often termed the Guadalupian-Lopingian extinction, GLE) that was followed 7–8 Myr later by Earth's most catastrophic loss of diversity, the Permian-Triassic mass extinction (PTME). These crises are not only manifest as sharp decreases in biodiversity and - particularly for the PTME - total ecosystem collapse, but they also drove major changes in biological morphological characteristics such as the Lilliput effect. The evolution of test size among different clades of foraminifera during these two extinction events has been less studied. We analyzed a global database of foraminiferal test size (volume) including 20226 specimens in 464 genera, 98 families, and 9 suborders from 632 publications. Our analyses reveal significant reductions in foraminiferal mean test size across the Guadalupian-Lopingian boundary (GLB) and the Permian-Triassic boundary (PTB), from 8.89 to 7.60 log10 μm3 (lg μm3), and from 7.25 to 5.82 lg μm3, respectively. The decline in test size across the GLB is a function of preferential extinction of genera exhibiting gigantism such as fusulinoidean fusulinids. Other clades show little change in size across the GLB. In contrast, all Lopingian suborders in our analysis (Fusulinina, Lagenina, Miliolina, and Textulariina) experienced a significant decrease in test size across the PTB mainly due to size-biased extinction and within-lineage change. The PTME was clearly a major catastrophe that affected many groups simultaneously, and the GLE was more selective, perhaps hinting at a subtler, less extreme driver than the later PTME.

opencc-by-4.0Sep 2020View details →

How a Homo goes extinct. Climatic change and the demise of our ancestors - Supplemental Data Tables

Supplemental Data Tables (Table S1-S4) for results related to manuscript "How a Homo goes extinct. Climatic change and the demise of our ancestors"

opencc-zeroOct 2020View details →

Empirical and methodological challenges to the model-based inference of diversification rates in extinct clades

Changes in speciation and extinction rates are key to the dynamics of clade diversification, but attempts to infer them from phylogenies of extant species face challenges. Methods capable of synthesizing information from extant and fossil species have yielded novel insights into diversification rate variation through time, but little is known about their behavior when analyzing entirely extinct clades. Here, we use empirical and simulated data to assess how two popular methods, PyRate and Fossil BAMM, perform in this setting. We inferred the first tip-dated trees for ornithischian dinosaurs, and combined them with fossil occurrence data to test whether the clade underwent an end-Cretaceous decline. We then simulated phylogenies and fossil records under empirical constraints to determine whether macroevolutionary and preservation rates can be teased apart under paleobiologically realistic conditions. We obtained discordant inferences about ornithischian macroevolution including a long-term speciation rate decline (BAMM), mostly flat rates with (PyRate) or without (BAMM) a steep diversification drop, and episodes of implausibly accelerated speciation and extinction (PyRate). Simulations revealed little to no conflation between speciation and preservation, but yielded spuriously correlated speciation and extinction estimates while time-smearing tree-wide shifts (BAMM) or overestimating their number (PyRate). Our results indicate that the small phylogenetic datasets available to vertebrate paleontologists and the assumptions made by current model-based methods combine to hinder inferences about the diversification of extinct clades. We provide guidelines for interpreting the results of the existing approaches in light of their limitations, and suggest how the latter may be mitigated.

opencc-zeroOct 2020View details →

Dental molds from: Three-dimensional dental topography and feeding ecology in the extinct cave bear

The cave bear (Ursus spelaeus s.l.) is an iconic extinct bear that inhabited the Pleistocene of Eurasia whose extinction causes are controversial. To identify the actual causes of the cave bear extinction, it is crucial to understand their feeding preferences. Here, we quantify shape descriptor metrics (DNE, RFI and OPCR) in three dimensional (3D) models of cave bear upper teeth (P4-M2) to make inferences on its controversial feeding behaviour. We use a comparative sample including representatives of all living bear species with known diets as a template. Our topographic analyses evidence that the complexity of upper tooth rows in living bears is more associated with the mechanical properties of the items consumed than with the type of food. Cave bears exhibit intermediate values on topographic metrics between those exhibited by the bamboo-feeder giant panda (Ailuropoda melanoleuca) and those taken by specialists in hard-mast consumption (Ursus arctos and Ursus thibetanus). The crown topography of cave bear upper teeth suggests a high efficiency to chew on tough vegetal resources of lower-quality, and no living bear is currently exploiting it. Our results align with a climatic-driven hypothesis to explain demise in cave bear populations during the late Pleistocene.

opencc-zeroNov 2020View details →

Data from: Anthropogenic extinctions conceal widespread evolution of flightlessness in birds

Human-driven extinctions can affect our understanding of evolution, through the nonrandom loss of certain types of species. Here, we explore how knowledge of a major evolutionary transition—the evolution of flightlessness in birds—is biased by anthropogenic extinctions. Adding data on 581 known anthropogenic extinctions to the extant avifauna increases the number of species by 5%, but quadruples the number of flightless species. The evolution of flightlessness in birds is a widespread phenomenon, occurring in more than half of bird orders and evolving independently at least 150 times. Thus, we estimate that this major evolutionary transition occurred at a rate four times higher than it would appear based solely on extant species. Our analysis of preanthropogenic avian diversity shows how anthropogenic effects can conceal the frequency of major evolutionary transitions in life forms and highlights that macroevolutionary studies with only small amounts of missing data can still be highly biased.

opencc-zeroNov 2020View details →

Supplementary data from: Decoupling of morphological disparity and taxonomic diversity during the end-Permian mass extinction

An increasing number of unexpectedly diverse benthic communities are being reported from microbially-precipitated carbonate facies in shallow-marine platform settings after the end-Permian mass extinction. Ostracoda, which was one of the most diverse and abundant metazoan groups during this interval, recorded their greatest diversity and abundance associated with these facies. Previous studies, however, focused mainly on their taxonomic diversity and, therefore, left room for discussion of paleoecological significance. Here, we apply a morphometric method (semi-landmarks) to investigate morphological variance through time to better understand the ecological consequences of the end-Permian mass extinction, and to examine the hypothesis that microbial mats played a key role in ostracod survival. Our results show that taxonomic diversity and morphological disparity were decoupled during the end-Permian extinction, and that morphological disparity declined rapidly at the onset of the end-Permian extinction, even though the high diversity of ostracods initially survived in some places. The decoupled changes in taxonomic diversity and morphological disparity suggest that the latter is a more robust proxy for understanding the ecological impact of the extinction event, and the low morphological disparity of ostracod faunas is a consequence of sustained environmental stress or a delayed post-Permian radiation. Furthermore, the similar morphological disparity of ostracods between microbialite and non-microbialite facies indicates that microbial mats most likely represent a taphonomic window rather than a biological refuge during the end-Permian extinction interval.

opencc-zeroDec 2020View details →

Impacts of speciation and extinction measured by an evolutionary decay clock

The hypothesis that destructive mass extinctions enable creative evolutionary radiations (creative destruction) is central to classic concepts of macroevolution[1,2]. However, the relative impacts of extinction and radiation on the co-occurrence of species have not been directly quantitatively compared across the Phanerozoic eon. Here we apply machine learning to generate a spatial embedding (multidimensional ordination) of the temporal co-occurrence structure of the Phanerozoic fossil record, covering 1,273,254 occurrences in the Paleobiology Database for 171,231 embedded species. This facilitates simultaneous comparison of macroevolutionary disruptions, using measures independent of secular diversity trends. Among the 5% most significant periods of disruption, we identify the 'big five' mass extinction events[2], seven additional mass extinctions, two combined mass extinction–radiation events and 15 mass radiations. In contrast to narratives that emphasize post-extinction radiations[1,3], we find that the proportionally most comparable mass radiations and extinctions (such as the Cambrian explosion and the end-Permian mass extinction) are typically decoupled in time, refuting any direct causal relationship between them. Moreover, in addition to extinctions[4], evolutionary radiations themselves cause evolutionary decay (modelled co-occurrence probability and shared fraction of species between times approaching zero), a concept that we describe as destructive creation. A direct test of the time to over-threshold macroevolutionary decay[4] (shared fraction of species between two times ≤ 0.1), counted by the decay clock, reveals saw-toothed fluctuations around a Phanerozoic mean of 18.6 million years. As the Quaternary period began at a below-average decay-clock time of 11 million years, modern extinctions further increase life's decay-clock debt.

opencc-zeroDec 2020View details →

Data for manuscript: Extinction pulse at Eocene–Oligocene boundary drives diversification dynamics of the two Australian temperate floras

The diversification dynamics of the Australian temperate flora remains poorly understood. Here, we investigate whether differences in plant richness in the southwest Australian biodiversity hotspot (SWA) and southeast (SEA) regions of the Australian continent can be attributed to higher net diversification, more time for species accumulation, or both. We assembled dated molecular phylogenies for the 21 most species-rich flowering plant families found across mesic temperate Australia, encompassing both SWA and SEA regions, and applied a series of diversification models to investigate responses across different groups and time scales. We show that the high richness in SWA can be attributed to a higher net rate of lineage diversification and more time for species accumulation. Different pulses of diversification were retrieved in each region. A decrease in diversification rate across major flowering plant lineages at the Eocene–Oligocene boundary (c. 34 Ma) was witnessed in SEA but not in SW A.

FIGURE 3 in A new and likely extinct species of Antilissus Sharp, 1879 (Coleoptera: Zopheridae Colydiinae) from Makauwahi Cave, Kauai, Hawaiian Islands

FIGURE 3. Head of non-type specimen of Antilissus makauwahi sp. nov. from BAC-NW 2009 GG74 'Sump' 4.0–4.5 metres. Scale bar = 0.25 mm.

FIGURE 2 in A new and likely extinct species of Antilissus Sharp, 1879 (Coleoptera: Zopheridae Colydiinae) from Makauwahi Cave, Kauai, Hawaiian Islands

FIGURE 2. Type series prothoraces of Antilissus makauwahi from Makauwahi Cave. All paratypes other than the holotype. A-D, F. BAW-NW Pit, 2009 square GG74, 'Sump' 4.0–4.5 metres depth. E. Holotype of A. makauwahi. Scale bar = 0.5 mm.

FIGURE 1 in A new and likely extinct species of Antilissus Sharp, 1879 (Coleoptera: Zopheridae Colydiinae) from Makauwahi Cave, Kauai, Hawaiian Islands

FIGURE 1. Holotype Antilissus makauwahi articulated prothorax and head, dorsal (left) and ventral (right) - (Hawaiian Islands, Kauai, Makauwahi Cave, BAW-NW Pit, Bucket auger sample, 3.3–3.6 metres depth). Scale bar = 0.5 mm.

FIGURE 4 in A new and likely extinct species of Antilissus Sharp, 1879 (Coleoptera: Zopheridae Colydiinae) from Makauwahi Cave, Kauai, Hawaiian Islands

FIGURE 4. Antilissus aper, Sharp, 1879: A. Historical specimen of A. aper from Oahu (Labels: Kaumuahona, 6.17.17, Oahu; J.C. Bridwell, collector; Bobea; Antilissus aper, Sharp, 1879 det.?; BPBM ENT, 2004012430); B. Subfossil specimen of A. aper from Makauwahi Cave sequence (Sample: BAC-NW 2009 PHD).

Reconstructing cranial evolution in an extinct hominin

Homo erectus occupies a central position in human evolution as a likely ancestor of the modern human (Homo sapiens) and Neanderthal / Denisovan lineages and the first hominin species with a truly cosmopolitan distribution. Understanding the evolutionary population dynamics of Homo erectus has larger implications for the emergence of later Homo lineages in the Middle Pleistocene. Quantitative genetics models provide a means of interrogating aspects of longstanding Homo erectus population history narratives. For the current study, cranial fossils were sorted into six major paleodemes from sites across Africa and Asia spanning 1.8 to 0.1 Ma. Three-dimensional shape data from the occipital and frontal bones were used to test population genetic hypotheses. Results indicate that Homo erectus had higher individual and group variation than Homo sapiens, likely reflecting different levels of genetic diversity and population history in these spatially disperse species. This study also revealed distinct evolutionary histories for frontal and occipital bone shape in Homo erectus,with a larger role for natural selection in the former. One scenario consistent with these findings is climate-driven facial adaptation in Homo erectus, which is reflected in the frontal bone through integration with the orbits.

Data from: Postcranial anatomy of the extinct terrestrial sloth Simomylodon uccasamamensis (Xenarthra: Mylodontidae) from the Pliocene of the Bolivian Altiplano and its evolutionary implications

Extinct terrestrial sloths are common elements of the late Cenozoic South American fossil record. Among them, Mylodontinae species were particularly abundant in the Americas throughout the Pleistocene epoch, and their anatomy is relatively well known. In contrast, less information is available from the Neogene record and particularly from localities at low latitudes, with an additional and considerable bias in favor of craniodental rather than postcranial remains. In this contribution, we provide comparative descriptions of several postcranial bony elements ascribed to Simomylodon uccasamamensis, a moderate-sized extinct mylodontine from the Andean Altiplano. This species was particularly abundant during latest Miocene–late Pliocene times in the high altitudes of the Andean Cordillera, and so far represents the best known mylodontine from the Neogene of South America. Its anatomy is compared with that of several extinct terrestrial sloths, with the aim of using the observed morphologies to elucidate taxonomy, phylogeny, and locomotion. From a morphofunctional perspective, the postcranium of S. uccasamamensis is consistent with that of a terrestrial graviportal quadruped, with moderate climbing and digging capabilities.

Data from: The history of foot-and-mouth disease virus serotype C: the first known extinct serotype?

Foot-and-mouth disease (FMD) is a highly contagious animal disease caused by an RNA virus subdivided into seven serotypes that are unevenly distributed in Asia, Africa and South America. Despite the challenges of controlling FMD, since 1996 there have been only two outbreaks attributed to serotype C, in Brazil and in Kenya, in 2004. This review describes the historical distribution and origins of serotype C and its disappearance. The serotype was first described in Europe in the 1920s, where it mainly affected pigs and cattle but as a less common cause of outbreaks than serotypes O and A. No serotype C outbreaks have been reported in Europe since vaccination stopped in 1990. FMD virus is presumed to have been introduced into South America from Europe in the 19th century, although whether serotype C evolved there or in Europe is not known. As in Europe, this serotype was less widely distributed and caused fewer outbreaks than serotypes O and A. Since 1994, serotype C had not been reported from South America until four small outbreaks were detected in the Amazon region in 2004. Elsewhere, serotype C was introduced to Asia, in the 1950s to the 1970s, persisting and evolving for several decades in the Indian subcontinent and for eighteen years in the Philippines. Serotype C virus also circulated in East Africa between 1957 and 2004. Many serotype C viruses from European and Kenyan outbreaks were closely related to vaccine strains, including the most recently recovered Kenyan isolate from 2004. International surveillance has not confirmed any serotype C cases, worldwide, for over 15 years, despite more than 2000 clinical submissions per year to reference laboratories. Serology provides limited evidence for absence of this serotype, as unequivocal interpretation is hampered by incomplete intra-serotype specificity of immunoassays and the continued use of this serotype in vaccines. It is recommended to continue strengthening surveillance in regions of FMD endemicity, to stop vaccination against serotype C and to reduce working with the virus in laboratories, since inadvertent escape of virus during such activities is now the biggest risk for its reappearance in the field.

Microsatellite Dataset for: Weaving et al. Conservation genetics of regionally extinct peregrine falcons (Falco peregrinus) and unassisted recovery without genetic bottleneck in southern England

The peregrine falcon (Falco peregrinus) has been affected by persecution, pollution, trade, and habitat degradation, but it is considered a flagship conservation success story because of successful reintroductions and population recoveries across broad ranges. However, in the UK there were never formal reintroduction programmes for peregrine falcons, and it appears that UK populations—and specifically the Sussex peregrines of the English south coast—recently recovered from a population crash unassisted. To study this, we obtained samples from contemporary populations in southern England, Ireland, continental Europe, domestic-bred peregrine falcons, and from England pre-population crash. Using microsatellite and mtDNA control region data, the genetic diversity and structure, signatures of genetic bottlenecks, and potential origin of the Sussex peregrines was investigated. We found low levels of genetic diversity across all peregrine falcon groups, low but significant genetic differentiation, and a few private alleles, indicating some level of genetic structure among European peregrines. Although we could not pinpoint the origin of the Sussex peregrines, the data suggests that it is not likely to have originated from escaped domestic birds or from adjacent European populations. The results obtained here parallel other studies on peregrines elsewhere showing low genetic diversity but genetic structure. We conclude that not enough time elapsed for genetic erosion to occur due to the population bottleneck, and that at least for the Sussex peregrines there is no need for genetic conservation by wild-take and subsequent captive breeding programmes as long as current protection measures remain in place.

Characterizing the spatio-temporal threats, conservation hotspots and conservation gaps for the most extinction-prone bird family (Aves: Rallidae)

Here we worked on the rails (bird family Rallidae), looking at whether the current threats are consistent with those that led to recent extinctions, and ultimately, what conservation actions might be necessary to mitigate further losses. We undertook a global synthesis of the temporal and spatial threat patterns for Rallidae and determined conservation priorities and gaps.