Rewriting the history of an extinction—was a population of Steller's sea cows (Hydrodamalis gigas) at St Lawrence Island also driven to extinction?

The Kommandorskiye Islands population of Steller''s sea cow (Hydrodamalis gigas) was extirpated ca 1768 CE. Until now, Steller''s sea cow was thought to be restricted in historic times to Bering and Copper Islands, Russia, with other records in the last millennium from the western Aleutian Islands. However, Steller''s sea cow bone has been obtained by the authors from St Lawrence Island, Alaska, which is significantly further north. Bone identity was verified using analysis of mitochondrial DNA. The nitrogen-15 (δ¹⁵N)/carbon-13 (δ¹³C) values for bone samples from St Lawrence Island were significantly (p ≤ 0.05) different from Bering Island samples, indicating a second population. Bone samples were dated to between 1030 and 1150 BP (approx. 800–920 CE). The samples date from close to the beginning of the mediaeval warm period, which could indicate that the population at St Lawrence Island was driven to extinction by climate change. A warming of the climate in the area may have changed the availability of kelp; alternatively or in addition, the animals may have been driven to extinction by the expansion of the Inuit from the Bering Strait region, possibly due to opening waterways, maybe following bowhead whales (Balaena mysticetus), or searching for iron and copper. This study provides evidence for a previously unknown population of sea cows in the North Pacific within the past 1000 years and a second Steller''s sea cow extirpation event in recent history.     

A new sea cow record from the lower Oligocene of western Germany: new indications on the skeletal morphology of Halitherium schinzii (Mammalia: Sirenia)

Since the discovery of the extinct species Halitherium schinzii in the Mainz Basin, sirenian remains from the German Oligocene are usually assigned to this taxon according to the assumption that this would be the only sea cow species there. The attempts of several authors to determine morphological distinctions on the species level remain unconsidered until today. The new find of a partial sea cow skeleton from the lower Oligocene of Bottrop-Kirchheller Heide (western Germany) stirs up the debate on splitting the species currently referred to as H. schinzii. The Bottrop specimen morphologically corresponds to skullcaps from the Mainz Basin and the Belgian Oligocene, which were the basis for the introduction of new species in the past, but are considered synonymous with H. schinzii today. Despite its fragmentary preservation, the new sirenian record reveals shared morphological features mainly referring to the supraoccipital, such as a distinctly rostrad indenting nuchal crest and a reduced external occipital protuberance. These features are in contrast to the prominent morphology of the specimens generally associated with H. schinzii and support the assumed presence of at least two morphotypes in the Oligocene of Central Europe. Additionally, the sea cow from Bottrop-Kirchheller Heide represents the first occurrence of skeletal elements, which are not preserved in the known specimens from this morphotype so far and may contribute to a better understanding of intra- and/or interspecific differences within Sirenia.     

Chromosome painting in the manatee supports Afrotheria and Paenungulata

Background  

Sirenia (manatees, dugongs and Stellar's sea cow) have no evolutionary relationship with other marine mammals, despite similarities in adaptations and body shape. Recent phylogenomic results place Sirenia in Afrotheria and with elephants and rock hyraxes in Paenungulata. Sirenia and Hyracoidea are the two afrotherian orders as yet unstudied by comparative molecular cytogenetics. Here we report on the chromosome painting of the Florida manatee.     

Hunting the Extinct Steppe Bison (Bison priscus) Mitochondrial Genome in the Trois-Frères Paleolithic Painted Cave

Despite the abundance of fossil remains for the extinct steppe bison (Bison priscus), an animal that was painted and engraved in numerous European Paleolithic caves, a complete mitochondrial genome sequence has never been obtained for this species. In the present study we collected bone samples from a sector of the Trois-Frères Paleolithic cave (Ariège, France) that formerly functioned as a pitfall and was sealed before the end of the Pleistocene. Screening the DNA content of the samples collected from the ground surface revealed their contamination by Bos DNA. However, a 19,000-year-old rib collected on a rock apart the pathway delineated for modern visitors was devoid of such contaminants and reproducibly yielded Bison priscus DNA. High-throughput shotgun sequencing combined with conventional PCR analysis of the rib DNA extract enabled to reconstruct a complete mitochondrial genome sequence of 16,318 bp for the extinct steppe bison with a 10.4-fold coverage. Phylogenetic analyses robustly established the position of the Bison priscus mitochondrial genome as basal to the clade delineated by the genomes of the modern American Bison bison. The extinct steppe bison sequence, which exhibits 93 specific polymorphisms as compared to the published Bison bison mitochondrial genomes, provides an additional resource for the study of Bovinae specimens. Moreover this study of ancient DNA delineates a new research pathway for the analysis of the Magdalenian Trois-Frères cave.     

Paleogenomics in a Temperate Environment: Shotgun Sequencing from an Extinct Mediterranean Caprine

Background

Numerous endemic mammals, including dwarf elephants, goats, hippos and deers, evolved in isolation in the Mediterranean islands during the Pliocene and Pleistocene. Most of them subsequently became extinct during the Holocene. Recently developed high-throughput sequencing technologies could provide a unique tool for retrieving genomic data from these extinct species, making it possible to study their evolutionary history and the genetic bases underlying their particular, sometimes unique, adaptations.

Methodology/Principals Findings

A DNA extraction of a ∼6,000 year-old bone sample from an extinct caprine (Myotragus balearicus) from the Balearic Islands in the Western Mediterranean, has been subjected to shotgun sequencing with the GS FLX 454 platform. Only 0.27% of the resulting sequences, identified from alignments with the cow genome and comprising 15,832 nucleotides, with an average length of 60 nucleotides, proved to be endogenous.

Conclusions

A phylogenetic tree generated with Myotragus sequences and those from other artiodactyls displays an identical topology to that generated from mitochondrial DNA data. Despite being in an unfavourable thermal environment, which explains the low yield of endogenous sequences, our study demonstrates that it is possible to obtain genomic data from extinct species from temperate regions.     

Evidence for Permo-Triassic colonization of the deep sea by isopods

The deep sea is one of the largest ecosystems on Earth and is home to a highly diverse fauna, with polychaetes, molluscs and peracarid crustaceans as dominant groups. A number of studies have proposed that this fauna did not survive the anoxic events that occurred during the Mesozoic Era. Accordingly, the modern fauna is thought to be relatively young, perhaps having colonized the deep sea after the Eocene/Oligocene boundary. To test this hypothesis, we performed phylogenetic analyses of nuclear ribosomal 18S and 28S and mitochondrial cytochrome oxidase I and 16S sequences from isopod crustaceans. Using a molecular clock calibrated with multiple isopod fossils, we estimated the timing of deep-sea colonization events by isopods. Our results show that some groups have an ancient origin in the deep sea, with the earliest estimated dates spanning 232–314 Myr ago. Therefore, anoxic events at the Permian–Triassic boundary and during the Mesozoic did not cause the extinction of all the deep-sea fauna; some species may have gone extinct while others survived and proliferated. The monophyly of the ‘munnopsid radiation’ within the isopods suggests that the ancestors of this group evolved in the deep sea and did not move to shallow-water refugia during anoxic events.     

Mitochondrial genomes reveal the extinct Hippidion as an outgroup to all living equids

Hippidions were equids with very distinctive anatomical features. They lived in South America 2.5 million years ago (Ma) until their extinction approximately 10 000 years ago. The evolutionary origin of the three known Hippidion morphospecies is still disputed. Based on palaeontological data, Hippidion could have diverged from the lineage leading to modern equids before 10 Ma. In contrast, a much later divergence date, with Hippidion nesting within modern equids, was indicated by partial ancient mitochondrial DNA sequences. Here, we characterized eight Hippidion complete mitochondrial genomes at 3.4–386.3-fold coverage using target-enrichment capture and next-generation sequencing. Our dataset reveals that the two morphospecies sequenced (H. saldiasi and H. principale) formed a monophyletic clade, basal to extant and extinct Equus lineages. This contrasts with previous genetic analyses and supports Hippidion as a distinct genus, in agreement with palaeontological models. We date the Hippidion split from Equus at 5.6–6.5 Ma, suggesting an early divergence in North America prior to the colonization of South America, after the formation of the Panamanian Isthmus 3.5 Ma and the Great American Biotic Interchange.     

Complete Mitochondrial Genome and Phylogeny of Pleistocene MammothMammuthus primigenius

Phylogenetic relationships between the extinct woolly mammoth(Mammuthus primigenius), and the Asian(Elephas maximus) and African savanna(Loxodonta africana) elephants remain unresolved. Here, we report the sequence of the complete mitochondrial genome (16,842 base pairs) of a woolly mammoth extracted from permafrost-preserved remains from the Pleistocene epoch—the oldest mitochondrial genome sequence determined to date. We demonstrate that well-preserved mitochondrial genome fragments, as long as ~1,600–1700 base pairs, can be retrieved from pre-Holocene remains of an extinct species. Phylogenetic reconstruction of the Elephantinae clade suggests thatM. primigenius andE. maximus are sister species that diverged soon after their common ancestor split from theL. africana lineage. Low nucleotide diversity found between independently determined mitochondrial genomic sequences of woolly mammoths separated geographically and in time suggests that north-eastern Siberia was occupied by a relatively homogeneous population ofM. primigenius throughout the late Pleistocene.     

Two decades of demography reveals that seed and seedling transitions limit population persistence in a translocated shrub

Background and Aims

Olearia flocktoniae is an endangered shrub that was passively translocated from its natural ecosystem, where it has since gone extinct. This study aimed to determine sensitivities vital to populations persisting in human-created areas.

Methods

Population colonization, longevity and extinction were investigated over 20 years using 133 populations. Seed-bank longevity was determined from germination trials of seeds exhumed from extinct and extant sites via a 10-year glasshouse trial and by in situ sowing experiments. From 27 populations, 98 cohorts were followed and matrix models of transitions from seeds to adults were used to evaluate the intrinsic rate of population growth against disturbance histories. Ten populations (38 cohorts) with different disturbance histories were used to evaluate sensitivities in vital rates.

Key Results

Most populations had few individuals (∼30) and were transient (<5 years above ground). The intrinsic population growth rate was rarely >1 and all but two populations were extinct at year 20. Seeds were short-lived in situ. Although >1000 seeds per plant were produced annually in most populations, sensitivity analysis showed that the transition to the seed bank and the transition from the seed bank to seedlings are key vulnerabilities in the life-cycle.

Conclusions

Seedling establishment is promoted by recent disturbance. Increasing the number of disturbance events in populations, even severe disturbances that almost extirpate populations, significantly increases longer-term population persistence. Only populations that were disturbed annually survived the full 20 years of the study. The results show that translocated populations of O. flocktoniae will fail to persist without active management.     

Caenorhabditis elegans neuron degeneration and mitochondrial suppression caused by selected environmental chemicals

Mitochondrial alterations have been documented for many years in the brains of Parkinson’s disease (PD), a disorder that is characterized by the selective loss of dopamine neurons. Recent studies have demonstrated that Parkinson’s disease-associated proteins are either present in mitochondria or translocated into mitochondria in response to stress, further reinforcing the importance of the mitochondrial function in the pathogenesis of Parkinson’s disease. Exposure to environmental chemicals such as pesticides and heavy metals has been suggested as risk factors in the development of Parkinson’s disease. It has been reported that a number of environmental agents including tobacco smoke and perfluorinated compounds, pesticides, as well as metals (Mn²⁺ and Pb²⁺) modulate mitochondrial function. However the exact mechanism of mitochondrial alteration has not been defined in the context of the development and progression of Parkinson’s disease. The complexity of the mammalian system has made it difficult to dissect the molecular components involved in the pathogenesis of Parkinson’s disease. In the present study we used the nematode Caenorhabditis elegans (C. elegans) model of neuron degeneration and investigated the effect of environmental chemicals on mitochondrial biogenesis and mitochondrial gene regulation. Chronic exposure to low concentration (2 or 4 μM) of pesticide rotenone, resulted in significant loss of dopamine neuron in C. elegans, a classic feature of Parkinson’s disease. We then determined if the rotenone-induced neuron degeneration is accompanied by a change in mitochondria biogenesis. Analysis of mitochondrial genomic replication by quantitative PCR showed a dramatic decrease in mitochondrial DNA (mtDNA) copies of rotenone-treated C. elegans compared to control. This decreased mitochondrial biogenesis occurred prior to the development of loss of dopamine neurons, and was persistent. The inhibition of mtDNA replication was also found in C. elegans exposed to another neuron toxicant Mn²⁺ at the concentration 50 or 100 mM. We further examined the mitochondrial gene expression and found significant lower level of mitochondrial complex IV subunits COI and COII in C. elegans exposed to rotenone. These results demonstrate that environmental chemicals cause persistent suppression of mitochondrial biogenesis and mitochondrial gene expression, and suggest a critical role of modifying mitochondrial biogenesis in toxicants-induced neuron degeneration in C. elegans model.     

Merging ancient and modern DNA: extinct seabird taxon rediscovered in the North Tasman Sea

Ancient DNA has revolutionized the way in which evolutionary biologists research both extinct and extant taxa, from the inference of evolutionary history to the resolution of taxonomy. Here, we present, to our knowledge, the first study to report the rediscovery of an ‘extinct’ avian taxon, the Tasman booby (Sula tasmani), using classical palaeontological data combined with ancient and modern DNA data. Contrary to earlier work, we show an overlap in size between fossil and modern birds in the North Tasman Sea (classified currently as S. tasmani and Sula dactylatra fullagari, respectively). In addition, we show that Holocene fossil birds have mitochondrial control region sequences that are identical to those found in modern birds. These results indicate that the Tasman booby is not an extinct taxon: S. dactylatra fullagari O''Brien & Davies, 1990 is therefore a junior synonym of Sula tasmani van Tets, Meredith, Fullagar & Davidson, 1988 and all North Tasman Sea boobies should be known as S. d. tasmani. In addition to reporting the rediscovery of an extinct avian taxon, our study highlights the need for researchers to be cognizant of multidisciplinary approaches to understanding taxonomy and past biodiversity.     

DJ-1 protects against cell death following acute cardiac ischemia–reperfusion injury

Novel therapeutic targets are required to protect the heart against cell death from acute ischemia–reperfusion injury (IRI). Mutations in the DJ-1 (PARK7) gene in dopaminergic neurons induce mitochondrial dysfunction and a genetic form of Parkinson''s disease. Genetic ablation of DJ-1 renders the brain more susceptible to cell death following ischemia–reperfusion in a model of stroke. Although DJ-1 is present in the heart, its role there is currently unclear. We sought to investigate whether mitochondrial DJ-1 may protect the heart against cell death from acute IRI by preventing mitochondrial dysfunction. Overexpression of DJ-1 in HL-1 cardiac cells conferred the following beneficial effects: reduced cell death following simulated IRI (30.4±4.7% with DJ-1 versus 52.9±4.7% in control; n=5, P<0.05); delayed mitochondrial permeability transition pore (MPTP) opening (a critical mediator of cell death) (260±33 s with DJ-1 versus 121±12 s in control; n=6, P<0.05); and induction of mitochondrial elongation (81.3±2.5% with DJ-1 versus 62.0±2.8% in control; n=6 cells, P<0.05). These beneficial effects of DJ-1 were absent in cells expressing the non-functional DJ-1^L166P and DJ-1^Cys106A mutants. Adult mice devoid of DJ-1 (KO) were found to be more susceptible to cell death from in vivo IRI with larger myocardial infarct sizes (50.9±3.5% DJ-1 KO versus 41.1±2.5% in DJ-1 WT; n≥7, P<0.05) and resistant to cardioprotection by ischemic preconditioning. DJ-1 KO hearts showed increased mitochondrial fragmentation on electron microscopy, although there were no differences in calcium-induced MPTP opening, mitochondrial respiratory function or myocardial ATP levels. We demonstrate that loss of DJ-1 protects the heart from acute IRI cell death by preventing mitochondrial dysfunction. We propose that DJ-1 may represent a novel therapeutic target for cardioprotection.     

Les Cricetidae (Rodentia,Mammalia)de la Milloque (bassin d'Aquitaine): Horizon repère de l'Oligocène supérieur

A screen washed and hand sorted sample of six tons sediments from La Milloque (Lot-et-Garonne) has yielded to the author several thousand micromammal's teeth. Among the Rodents, four extinct species of Cricetids have been recognized: Eucricetodon praecursor (Schaub, 1925); Adelomyarion viretiHugueney, 1969; Pseudocricetodon cf. thaleri (Hugueney, 1969); Melissiodon quercyiSchaub, 1920. The fossil remain's study affords many paleontological informations more particularly for E. praecursor, a previously poorly known species. About the upper Oligocene biochronology the four species' evolution degrees prove the statute of reference locality attributed to La Milloque, «mammalian timemark just below the reference locality of Coderet (Allier). Moreover it's pointed out that the locality of Rickenbach (Switzerland) is slightly older than La Milloque, whereas an intermediate age between La Milloque and Coderet can be suggested for the locality of Dicupentale (Tarn-et-Garonne).     

Mitochondrial Phylogenomics of Modern and Ancient Equids

The genus Equus is richly represented in the fossil record, yet our understanding of taxonomic relationships within this genus remains limited. To estimate the phylogenetic relationships among modern horses, zebras, asses and donkeys, we generated the first data set including complete mitochondrial sequences from all seven extant lineages within the genus Equus. Bayesian and Maximum Likelihood phylogenetic inference confirms that zebras are monophyletic within the genus, and the Plains and Grevy’s zebras form a well-supported monophyletic group. Using ancient DNA techniques, we further characterize the complete mitochondrial genomes of three extinct equid lineages (the New World stilt-legged horses, NWSLH; the subgenus Sussemionus; and the Quagga, Equus quagga quagga). Comparisons with extant taxa confirm the NWSLH as being part of the caballines, and the Quagga and Plains zebras as being conspecific. However, the evolutionary relationships among the non-caballine lineages, including the now-extinct subgenus Sussemionus, remain unresolved, most likely due to extremely rapid radiation within this group. The closest living outgroups (rhinos and tapirs) were found to be too phylogenetically distant to calibrate reliable molecular clocks. Additional mitochondrial genome sequence data, including radiocarbon dated ancient equids, will be required before revisiting the exact timing of the lineage radiation leading up to modern equids, which for now were found to have possibly shared a common ancestor as far as up to 4 Million years ago (Mya).     

Reactive Oxygen Species in Unstimulated Hemocytes of the Pacific Oyster Crassostrea gigas: A Mitochondrial Involvement

The Pacific oyster Crassostrea gigas is a sessile bivalve mollusc whose homeostasis relies, at least partially, upon cells circulating in hemolymph and referred to as hemocytes. Oyster’s hemocytes have been reported to produce reactive oxygen species (ROS), even in absence of stimulation. Although ROS production in bivalve molluscs is mostly studied for its defence involvement, ROS may also be involved in cellular and tissue homeostasis. ROS sources have not yet been described in oyster hemocytes. The objective of the present work was to characterize the ROS sources in unstimulated hemocytes. We studied the effects of chemical inhibitors on the ROS production and the mitochondrial membrane potential (Δψ_m) of hemocytes. First, this work confirmed the specificity of JC-10 probe to measure Δψ_m in oyster hemocytes, without being affected by ΔpH, as reported in mammalian cells. Second, results show that ROS production in unstimulated hemocytes does not originate from cytoplasmic NADPH-oxidase, nitric oxide synthase or myeloperoxidase, but from mitochondria. In contrast to mammalian cells, incubation of hemocytes with rotenone (complex I inhibitor) had no effect on ROS production. Incubation with antimycin A (complex III inhibitor) resulted in a dose-dependent ROS production decrease while an over-production is usually reported in vertebrates. In hemocytes of C. gigas, the production of ROS seems similarly dependent on both Δψ_m and ΔpH. These findings point out differences between mammalian models and bivalve cells, which warrant further investigation about the fine characterization of the electron transfer chain and the respective involvement of mitochondrial complexes in ROS production in hemocytes of bivalve molluscs.     

Extreme convergence in stick insect evolution: phylogenetic placement of the Lord Howe Island tree lobster

The ‘tree lobsters’ are an enigmatic group of robust, ground-dwelling stick insects (order Phasmatodea) from the subfamily Eurycanthinae, distributed in New Guinea, New Caledonia and associated islands. Its most famous member is the Lord Howe Island stick insect Dryococelus australis (Montrouzier), which was believed to have become extinct but was rediscovered in 2001 and is considered to be one of the rarest insects in the world. To resolve the evolutionary position of Dryococelus, we constructed a phylogeny from approximately 2.4 kb of mitochondrial and nuclear sequence data from representatives of all major phasmatodean lineages. Our data placed Dryococelus and the New Caledonian tree lobsters outside the New Guinean Eurycanthinae as members of an unrelated Australasian stick insect clade, the Lanceocercata. These results suggest a convergent origin of the ‘tree lobster’ body form. Our reanalysis of tree lobster characters provides additional support for our hypothesis of convergent evolution. We conclude that the phenotypic traits leading to the traditional classification are convergent adaptations to ground-living behaviour. Our molecular dating analyses indicate an ancient divergence (more than 22 Myr ago) between Dryococelus and its Australian relatives. Hence, Dryococelus represents a long-standing separate evolutionary lineage within the stick insects and must be regarded as a key taxon to protect with respect to phasmatodean diversity.     

Ancient DNA from the extinct Haitian cave-rail (Nesotrochis steganinos) suggests a biogeographic connection between the Caribbean and Old World

Worldwide decline in biodiversity during the Holocene has impeded a comprehensive understanding of pre-human biodiversity and biogeography. This is especially true on islands, because many recently extinct island taxa were morphologically unique, complicating assessment of their evolutionary relationships using morphology alone. The Caribbean remains an avian hotspot but was more diverse before human arrival in the Holocene. Among the recently extinct lineages is the enigmatic genus Nesotrochis, comprising three flightless species. Based on morphology, Nesotrochis has been considered an aberrant rail (Rallidae) or related to flufftails (Sarothruridae). We recovered a nearly complete mitochondrial genome of Nesotrochis steganinos from fossils, discovering that it is not a rallid but instead is sister to Sarothruridae, volant birds now restricted to Africa and New Guinea, and the recently extinct, flightless Aptornithidae of New Zealand. This result suggests a widespread or highly dispersive most recent common ancestor of the group. Prior to human settlement, the Caribbean avifauna had a far more cosmopolitan origin than is evident from extant species.