Symbiont bleaching in fossil planktonic foraminifera

Size restricted carbon isotopes (δ¹³C) are used to track changes in the ontogenetic life strategies of two species of extinct planktonic foraminifera and demonstrate that the species Morozovelloides crassatus lost their photosymbiotic association prior to their extinction in the latest middle Eocene. M. crassatus exhibit a strong positive correlation between test size and δ¹³C between 39.5 Ma and 38.7 Ma and a Δδ¹³C shift of 1.0‰/100 μm, this is analogous with modern species that possess an association with algal photosymbionts. Turborotalia cerroazulensis is interpreted as an asymbiotic, thermocline dweller and consistently shows no size related δ¹³C trends and greater δ¹⁸O values in comparison to Morozovelloides. We show a long-term (1.5 million year) deterioration of Morozovelloides ecology that culminated in their extinction at 38.021 Ma. The Δδ¹³C /100 μm in M. crassatus is dramatically reduced from 1.0‰ at 39.53 to only 0.2‰ at 38.026 Ma, 5 kyr before their extinction. The decline in ontogenetic δ¹³C suggests diminished photosymbiotic activity (bleaching) and disruption of foraminiferal ecology in the interval preceding their extinction. We conclude that the demise of Morozovelloides was directly related to the deterioration of photosymbiotic partnerships with algae.     

The effect of dispersal on single-species nonautonomous dispersal models with delays

In this paper, single-species nonautonomous dispersal models with delays are considered. An interesting result on the effect of dispersal for persistence and extinction is obtained. That is, if the species is persistent in a patch then it is also persistent in all other patches; if the species is permanent in a patch then it is also permanent in all other patches; if the species is extinct in a patch then it is also extinct in all other patches. Furthermore, some new sufficient conditions for the permanence and extinction of the species in a patch are established. The existence of positive periodic solutions is obtained in the periodic case by employing Teng and Chen's results on the existence of positive periodic solutions for functional differential equations. Received: 26 June 2000 / Revised version: 6 October 2000 / Published online: 10 April 2001     

Chronological and Isotopic data support a revision for the timing of cave bear extinction in Mediterranean Europe

Abstract

The Cave Bear, Ursus spelaeus (sensu lato), was one of many megafaunal species that became extinct during the Late Pleistocene in Europe. With new data we revisit the debate about the extinction and paleoecology of this species by presenting new chronometric, isotopic and taphonomic evidence from two Palaeolithic cave bear sites in northeastern Italy: Paina Cave and Trene Cave. Two direct radiocarbon dates on well-preserved collagen have yielded ages around 24,200–23,500 cal yr BP, which make them the latest known representatives of the species in Europe. The carbon (δ¹³C) and nitrogen (δ¹⁵N) isotopic values of bone collagen exhibit values similar to those of older cave bears from Swabian Jura and France, suggesting that the feedings preferences of cave bears remained unchanged until the disappearance of this species in Europe. Several bear remains preserved traces of human modification such as cut marks, which enables a reconstruction of the main steps of fur recovery and the butchering process. The broad range of plant types available and the favorable location of Berici Hills may have played an important role in the range expansion of cave bears and their interaction with the Paleolithic hunters settled the same area.     

Experimenting with Transmutation: Darwin, the Beagle, and Evolution

Detailed analysis of Darwin’s scientific notes and other writings from the Beagle voyage reveals a focus on endemism and replacement of allied taxa in time and in space that began early in the journey. Though it is impossible to determine exactly when Darwin became a transmutationist, the evidence suggests that he was conversant with the transmutational ideas of Lamarck and others and testing (“experimenting” with) them—before he received a copy of Lyell’s Principles of Geology, vol. 2, in November 1832, in which Lyell describes and disputes Lamarck’s theory. To the two rhea species of Patagonia and the four mockingbird species of the Galapagos, we can now add the living Patagonian cavy (rodent) species, and its extinct putatively related species that Darwin collected at Monte Hermoso (Bahia Blanca) in the Fall of 1832, as a replacement pattern absolutely critical to the development of Darwin’s transmutational thinking. Darwin developed his first transmutational theory by adopting “Brocchi’s analogy” (Rudwick 2008)—i.e. that births and deaths of species are analogous to the births and deaths of individuals. Births and deaths of species, as of individuals, are thus explicable in terms of natural causes. Darwin explored these themes and the replacement of the extinct cavy by the modern species explicitly in his February 1835 essay (Darwin 1835a).

Ancient DNA evidence for the loss of a highly divergent brown bear clade during historical times

The genetic diversity of present-day brown bears (Ursus arctos) has been extensively studied over the years and appears to be geographically structured into five main clades. The question of the past diversity of the species has been recently addressed by ancient DNA studies that concluded to a relative genetic stability over the last 35,000 years. However, the post-last glacial maximum genetic diversity of the species still remains poorly documented, notably in the Old World. Here, we analyse Atlas brown bears, which became extinct during the Holocene period. A divergent brown bear mitochondrial DNA lineage not present in any of the previously studied modern or ancient bear samples was uncovered, suggesting that the diversity of U. arctos was larger in the past than it is now. Specifically, a significant portion (with respect to sequence divergence) of the intraspecific diversity of the brown bear was lost with the extinction of the Atlas brown bear after the Pleistocene/Holocene transition.     

Responses of Metapopulation Dynamics to Two Different Kinds of Habitat Destruction Caused by Human Activities

Habitat destruction can be classified into instantaneous destruction and continuous destruction by the different ways of human destroying habitat. Previous studies, however, always focused on instantaneous destruction. In this study, we develop a universal model, Multi-time scale N-species model, to study and compare the responses of metapopulation dynamics to both kinds of habitat destruction. The model explores that: (1) under instantaneous habitat destruction, species extinction is determined by the proportion of habitat destruction (D) and the structure of metapopulation (q). When D>q, species will go extinct ranked from the best competitor to the worst. When D≤ q, no species will go extinct, but the equilibrium abundances of odd-ranked competitors will decrease, and the equilibrium abundances of even-ranked competitors will increase; (2) under continuous destruction, species extinction is dependent on the speed of habitat destruction and the metapopulation structure. The higher the speed of habitat destruction and the bigger q are, the earlier species go extinct. Usually, there are two possible mechanisms of species extinction: one is that all species go extinct collectively following complete destruction, and the other is that species go extinct in ranked competitive order from best to worst, and the survivals, if they exist, will go extinct collectively following complete destruction. The oscillation amplitudes of inferior competitors are so large as to increase the probability of stochastic extinction under instantaneous destruction. Therefore, it is relatively propitious for the persistence of rare species under slow and continuous destruction, especially when continuous destruction stops.     

A three-dimensional analysis of tooth-root morphology in living bears and implications for feeding behaviour in the extinct cave bear

ABSTRACT

The morphology of both crowns and tooth-roots reflects dietary specialisation in mammalian carnivores. In this article, we analyse the tooth-root morphology of maxillary teeth from CT scans of living bears (Ursus arctos, Ursus americanus, Ursus maritimus, Ursus thibetanus, Melursus ursinus, Helarctos malayanus, Tremarctos ornatus and Ailuropoda melanoleuca) in order to make inferences about the diet and feeding behaviour of the extinct cave bear (Ursus spelaeus sensu lato). Specifically, we investigate two major mitochondrial clades of extinct cave bears recognized by previous authors: Ursus ingressus and Ursus spelaeus (U. spelaeus spelaeus, U. spelaeus ladinicus, U. spelaeus eremus). Our results indicate a close association between tooth-root surface area and feeding behaviour in all living bear species. Tooth-root surface area values of cave bears suggest that they relied more on vegetative matter than living brown bears (Ursus arctos) but subtle differences between these species/subspecies could also indicate different feeding strategies among the members of cave bear complex.     

Evaporation effects as reflected in freshwaters and ostracod calcite from modern environments in Central and Northeast Yakutia (East Siberia,Russia)

Taxonomical and geochemical investigations on freshwater ostracods from 15 waters in Central and Northeast (NE) Yakutia have been undertaken in order to estimate their potential usefulness in palaeoenvironmental reconstructions based on regional fossil records. Higher variability in environmental factors such as pH, electrical conductivity, and ionic content was observed in thermokarst-affected lakes in Central Yakutia than in NE Yakutia lakes. Species diversity of freshwater ostracods reached up to eight taxa per lake, mostly dominated by Candona weltneri Hartwig 1899, in Central Yakutia, whereas in NE Yakutian waters the diversity was lower and Candona muelleri jakutica Pietrzeniuk 1977 or Fabaeformiscandona inaequivalvis (Sars 1898) had highest frequencies. Coupled analyses of stable isotopes (δ¹⁸O, δ¹³C) and element ratios (Sr/Ca, Mg/Ca) were performed on both host waters and ostracod calcite, aiming to estimate the modern relationships. Correlations between host waters and ostracod calcite of single species were found for δ¹⁸O, δ¹³C and Sr/Ca and Mg/Ca ratios. The relationships between δ¹⁸O, Mg/Ca and Sr/Ca ratios and electrical conductivity (salinity) as an expression of solute concentrations in the waters mainly controlled by evaporation are more complicated but evident, and may be useful in future interpretation of geochemical data from fossil Siberian ostracods. Handling editor: K. Martens     

Carbon isotope fractionation between diet and bioapatite in ungulate mammals and implications for ecological and paleoecological studies

 The isotope enrichment ɛ* of ¹³C between tooth enamel of large ruminant mammals and their diet is 14.1 ± 0.5‰. This value was obtained by analyzing both the dental enamel of a variety of wild and captive mammals and the vegetation that comprised their foodstuffs. This isotope enrichment factor applies to a wide variety of ruminant mammals. Non-ruminant ungulates have a similar isotope enrichment, although our data cannot determine if it is significantly different. We also found a ¹³C isotope enrichment ɛ* of 3.1 ± 0.7‰ for horn relative to diet, and 11.1 ± 0.8‰ for enamel relative to horn for ruminant mammals. Tooth enamel is a faithful recorder of diet. Its isotopic composition can be used to track changes in the isotopic composition of the atmosphere, determine the fraction of C₃ or C₄ biomass in diets of modern or fossil mammals, distinguish between mammals using different subpathways of C₄ photosynthesis,and identify those mammals whose diet is derived from closed-canopy habitats. Received: 1 July 1998 / Accepted: 9 February 1999     

Patterns of endemic extinctions among island bird species

The relationship between island biogeography and the vulnerability of island biota to extinction as a result of human activities was examined. In particular, this study analyzed whether island area, maximum elevation of an island, isolation from the nearest continental landmass, or date of human colonization had statistically significant relationships with the proportion of endemic island bird species that have become endangered or extinct. The study examined islands or island groups with endemic bird species, and which have never been connected to a continental landmass. Both modern and fossil bird species were incorporated into the analysis. Islands that were colonized by humans earliest had the lowest proportion of modern species alone, and modern and fossil species combined, that have gone extinct. However, date of human arrival was not correlated with the proportion of modern species that are endangered. Maximum elevation of an island was negatively correlated with the proportion of modern species that are extinct, and was positively correlated with the proportion of modern species that are endangered. Area was negatively correlated with the proportion of modern species that are endangered. Isolation of islands was not significantly correlated with the proportion of modern species extinct or endangered, but was positively correlated with the proportion of modern and fossil species combined that have gone extinct. These results indicate that the initial spasm of island bird extinctions due to human contact may have, in part, passed. They also indicate that bird species on islands colonized earliest by humans may have had more time to adapt to the presence of man and his commensal species, resulting in reduced extinction rates.     

The cave bear’s hibernation: reconstructing the physiology and behaviour of an extinct animal

Abstract

When studying an extinct species such as the cave bear (Ursus spelaeus ROSENMÜLLER 1794), it is possible to apply a variety of molecular biology techniques such as the study of stable isotopes or mitochondrial DNA (mDNA) to infer patterns of behaviour or physiology that would otherwise remain concealed. Throughout Europe and along time, differences in the isotopic values (δ¹³C and δ¹⁵N) of cave bears arise from environmental differences and the Pleistocene climatic evolution. The climate determines the hibernation length, during which the cave bears undergo a particular physiology that can be related to an increase in δ¹⁵N during climate cooling. In order to verify whether hibernation affected the isotopic values, we compared cave bears in different ontogenetic stages. The results show that perinatal values reflect the values for mothers during hibernation, while juveniles show differences in maternal investment. A previous study in the literature based on complete mitochondrial DNA sequences of several individuals collected from closely situated caves showed that each cave housed, almost exclusively, a single lineage of haplotypes. This pattern suggests extreme fidelity to the birth site, or homing behaviour, and that cave bears formed stable maternal social groups, at least for the purpose of hibernation. Studies of this type offer unexpected data on the palaeobiology of this extinct animal.     

<Emphasis Type="Italic">Oncorhynchus kawamurae</Emphasis> “Kunimasu,” a deepwater trout,discovered in Lake Saiko, 70 years after extinction in the original habitat,Lake Tazawa,Japan

Oncorhynchus kawamurae (Osteichthyes: Salmonidae) (common name “Kunimasu”), a species endemic to Lake Tazawa, Akita Prefecture, Japan, was believed to have been extinct since 1940. However, nine specimens were discovered in March and April 2010 in Lake Saiko, Yamanashi Prefecture, one of the lakes to which eyed eggs of the species were introduced in 1935. These were identified as O. kawamurae because of having 47–62 pyloric caeca, 37–43 gill-rakers, a black-colored body, and spawning at 30–40 m depth in early spring, which are unique characteristics within Oncorhynchus. Furthermore, the distinctiveness of Kunimasu from sympatric kokanee (O. nerka) was supported by microsatellite DNA data.     

Aquatic Adaptation and Swimming Mode Inferred from Skeletal Proportions in the Miocene Desmostylian Desmostylus

Desmostylians are enigmatic, extinct, semiaquatic marine mammals that inhabited coastlines of the northern Pacific Rim during the late Oligocene through middle Miocene. Principal components analysis (PCA) of trunk and limb proportions provides a rational multivariate context for separating living semiaquatic mammals on three orthogonal axes: a size axis (PC-I), a degree of aquatic adaptation axis (PC-II), and a forelimb- versus hind-limb-dominated locomotion axis (PC-III). The necessary skeletal measurements are available for Desmostylus hesperus but not for other desmostylians. Among species similar in size to Desmostylus in the study set, the one most similarly proportioned is the polar bear. Projection of Desmostylus on PC-II shows it to have been more aquatic than a polar bear (indicated by its relatively short ilium and femur, combined with relatively long metapodals and phalanges). Projection of Desmostylus on PC-III suggests that its aquatic locomotion was even more forelimb-dominated than that of a bear (indicated by its relatively long metacarpal III and corresponding proximal phalanx, combined with a relatively short metatarsal III and corresponding proximal phalanx). Desmostylians were different from all living semiaquatic mammals, and desmostylians are properly classified in their own extinct order, but their skeletal proportions suggest that bears provide an appropriate baseline for imagining what desmostylians were like in life.     

Particulate organic and dissolved inorganic carbon stable isotopic compositions in Taylor Valley lakes,Antarctica: the effect of legacy

In perennially ice-covered lakes of Taylor Valley, Antarctica, “legacy”, a carryover of past ecosystem events, has primarily been discussed in terms of nutrient and salinity concentrations and its effect on the current ecology of the lakes. In this study, we determine how residual pools of ancient carbon affect the modern carbon abundance and character in the water columns of Lakes Fryxell, Hoare, and Bonney. We measure the stable carbon isotopic compositions and concentrations of particulate organic carbon (POC) and dissolved inorganic carbon (DIC) in the water column of these lakes over four seasons (1999–2002). These data are presented and compared with all the previously published Taylor Valley lacustrine carbon stable isotopic data. Our results show that the carbon concentrations and isotopic compositions of the upper water columns of those lakes are controlled by modern processes, while the lower water columns are controlled to varying degrees by inherited carbon pools. The water column of the west lobe of Lake Bonney is dominated by exceptionally high concentrations of DIC (55,000–75,000 μmol l⁻¹) reflecting the long period of ice-cover on this lake. The east lobe of Lake Bonney has highly enriched δ¹³C_DIC values resulting from paleo-brine evaporation effects in its bottom waters, while its high DIC concentrations provide geochemical evidence that its middle depth waters are derived from West Lake Bonney during a hydrologically connected past. Although ancient carbon is present in both Lake Hoare and Lake Fryxell, the δ¹³C_DIC values in bottom waters suggest dominance by modern primary productivity-related processes. Anaerobic methanogenesis and methanotrophy are also taking place in the lower water column of Lake Fryxell with enough methane, oxidized anaerobically, to contribute to the DIC pool. We also show how stream proximity and high flood years are only a minor influence on the carbon isotopic values of both POC and DIC. The Taylor Valley lake system is remarkably stable in both inter-lake and intra-lake carbon dynamics. Handling editor: K. Martens     

Functional diversity in an Amazonian rainforest of French Guyana: a dual isotope approach (δ15N and δ13C)

Functional aspects of biodiversity were investigated in a lowland tropical rainforest in French Guyana (5°2′N, annual precipitation 2200 mm). We assessed leaf δ¹⁵N as a presumptive indicator of symbiotic N₂ fixation, and leaf and wood cellulose δ¹³C as an indicator of leaf intrinsic water-use efficiency (CO₂ assimilation rate/leaf conductance for water vapour) in dominant trees of 21 species selected for their representativeness in the forest cover, their ecological strategy (pioneers or late successional stage species, shade tolerance) or their potential ability for N₂ fixation. Similar measurements were made in trees of native species growing in a nearby plantation after severe perturbation (clear cutting, mechanical soil disturbance). Bulk soil δ¹⁵N was spatially quite uniform in the forest (range 3–5‰), whereas average leaf δ¹⁵N ranged from −0.3‰ to 3.5‰ in the different species. Three species only, Diplotropis purpurea, Recordoxylon speciosum (Fabaceae), and Sclerolobium melinonii (Caesalpiniaceae), had root bacterial nodules, which was also associated with leaf N concentrations higher than 20 mg g⁻¹. Although nodulated trees displayed significantly lower leaf δ¹⁵N values than non-nodulated trees, leaf δ¹⁵N did not prove a straightforward indicator of symbiotic fixation, since there was a clear overlap of δ¹⁵N values for nodulated and non-nodulated species at the lower end of the δ¹⁵N range. Perturbation did not markedly affect the difference δ¹⁵N_soil−δ¹⁵N_leaf, and thus the isotopic data provide no evidence of an alteration in the different N acquisition patterns. Extremely large interspecific differences in sunlit leaf δ¹³C were observed in the forest (average values from −31.4 to −26.7‰), corresponding to intrinsic water-use efficiencies (ratio CO₂ assimilation rate/leaf conductance for water vapour) varying over a threefold range. Wood cellulose δ¹³C was positively related to total leaf δ¹³C, the former values being 2–3‰ higher than the latter ones. Leaf δ¹³C was not related to leaf δ¹⁵N at either intraspecific or interspecific levels. δ¹³C of sunlit leaves was highest in shade hemitolerant emergent species and was lower in heliophilic, but also in shade-tolerant species. For a given species, leaf δ¹³C did not differ between the pristine forest and the disturbed plantation conditions. Our results are not in accord with the concept of existence of functional types of species characterized by common suites of traits underlying niche differentiation; rather, they support the hypothesis that each trait leads to a separate grouping of species. Received: 18 August 1997 / Accepted: 14 April 1998     

Palaeogenomics

In many ways, palaeogenomics began when the first ancient DNA sequence was reported. This first sequence was derived from a stuffed museum specimen of the quagga, an extinct mammal related to the zebra. Unspecified and unselected DNA was extracted from the quagga specimen, cloned into a bacterial library, and then sequenced. It took another 17 years and the development of PCR before two independent groups successfully sequenced the complete mitochondrial genomes from several extinct moa species. Only 4 years later, using the original approach of cloning nonspecific ancient DNA extract and shotgun sequencing, the first ancient nuclear DNA sequences were determined, this time from the extinct cave bear. Since these early successes, palaeogenomics has rapidly expanded, because of both technological development and increasing interest in ancient DNA research. New methods, developed since the cave bear sequence was reported, have produced nuclear DNA on a megabase scale from two extinct species, the mammoth and the Neanderthal, our closest relative. For both species, low-coverage genome-sequencing projects have been proposed. It is likely that these will be successful, given the rapid technical development in sequencing techniques. This review carefully examines both the promise and the current limitations of palaeogenomic analyses for both mitochondrial and nuclear DNA.     

Minimum Area Required for Local Populations of Japanese Macaques Estimated from the Relationship Between Habitat Area and Population Extinction

I estimated the minimum area required (MAR) for local populations of Japanese macaques (Macaca fuscata) from empirical data on habitat area and population viability. I used logistic regression analysis to examine the relationship between habitat area and survival/extinction among 50 populations over 50 yr. Estimated habitat areas satisfying 95–99% probability of a population persisting for 100–1000 yr range from 525 to 975 km². However, confidence limits of parameters in the logistic regression equation are very large. Moreover, the number of extinct population might be underestimated in the empirical data. Consequently, a much wider habitat area (>1000 km²) should be considered for actual conservation planning for local populations of Japanese macaques. The method involves fewer variables and assumptions than previous methods of MAR estimation, and therefore may be a more useful way to estimate MAR for various species and regions.     

Ecological Predictors of Extinction Risk in the Flora of Lowland England, UK

We used historical and contemporary records to determine the scale of plant extinction in Bedfordshire and Northamptonshire, and to assess whether extinct species share a range of ecological and phytogeographical traits. Since 1700 both counties have lost 94 species (11% of their native floras) with the rate of extinction increasing from 3.8 to 4.8 species per decade in the 19th century to 6–8 species per decade after 1950. The most important predictors of extinction risk were English range size and traits associated with habitat specialisation and competitive ability: poor competitors (i.e. short stress-tolerators) associated with open habitats with very low or high pH and soil moisture (e.g. lowland bogs, dwarf-shrub heath and acid and calcareous grassland) were much more likely to have become extinct in the study region than would have been expected by chance alone. Many of these species have very localised distributions and/or occur at the northern, southern or eastern edges of their range in southern England (i.e. Northern and Oceanic). In contrast, there was no clear or significant relationship between extinction and dispersal ability or reproductive mode. These findings, which parallel national trends, indicate that habitat loss and eutrophication have been the main causes of population extinction in lowland England over the last 300 years. However, more fine-scaled studies are required to assess whether ‘low-level’ stresses, such as habitat fragmentation, climate change and atmospheric pollution, are having additional impacts on populations already severely depleted by habitat loss, as well as to quantify changes in the abundance of more widespread species which are known to have declined over the same period.     

The carbon and nitrogen isotopic values of particulate organic material from the Florida Keys: a temporal and spatial study

The δ¹⁵N and δ¹³C values of particulate organic material (POM) were analyzed from 35 sites in the Florida Keys over the time interval 2000 to 2002. The sites within the study area were delineated into nine transects stretching from Key West to Key Largo. Each transect consisted of three to five sites extending from close to the Keys to the edge of the reef tract. The POM had mean δ¹⁵N and δ¹³C values of +3.6‰ (σ = ±3.2‰) and −19.9‰ (σ = ±0.6‰) respectively. Over the study period there were no statistically significant changes in δ¹⁵N, δ¹³C, or C:N. For the majority of the sampling dates, the δ¹³C values showed a distinct inshore (δ¹³C = −18.3‰, σ = ±1.0‰) to offshore gradient (δ¹³C = −21.4, σ = ±0.9‰). In contrast, the δ¹⁵N values showed no consistent patterns related to the distance from land. The more positive δ¹³C values of the nearshore samples suggest that the source of the carbon and the nitrogen in the POM in the nearshore was mainly derived from the degradation of seagrass detritus and not from the input of anthropogenically derived material from the Florida Keys. In contrast, the POM on the outer reef was dominated by marine plankton. As mineralization and nitrification of the organic nitrogen pool are major contributors to the dissolved inorganic nitrogen in the water column, it is unlikely that variations in the δ¹⁵N of the algae and other benthic organisms reported in the Florida Keys are related to the input of sewage.