Are the native giant tortoises from the Seychelles really extinct? A genetic perspective based on mtDNA and microsatellite data

The extinction of the giant tortoises of the Seychelles Archipelago has long been suspected but is not beyond doubt. A recent morphological study of the giant tortoises of the western Indian Ocean concluded that specimens of two native Seychelles species survive in captivity today alongside giant tortoises of Aldabra, which are numerous in zoos as well as in the wild. This claim has been controversial because some of the morphological characters used to identify these species, several measures of carapace morphology, are reputed to be quite sensitive to captive conditions. Nonetheless, the potential survival of giant tortoise species previously thought extinct presents an exciting scenario for conservation. We used mitochondrial DNA sequences and nuclear microsatellites to examine the validity of the rediscovered species of Seychelles giant tortoises. Our results indicate that the morphotypes suspected to represent Seychelles species do not show levels of variation and genetic structuring consistent with long periods of reproductive isolation. We found no variation in the mitochondrial control region among 55 individuals examined and no genetic structuring in eight microsatellite loci, pointing to the survival of just a single lineage of Indian Ocean tortoises.     

马边大风顶自然保护区大熊猫种群生存力模拟分析

采用漩涡模型Vortex mondel 713 , 模拟了马边大风顶自然保护区大熊猫种群在未来100年内的变动趋势。结果显示: 在无交配限制、无密度制约、无近亲交配衰退等条件下, 马边大风顶自然保护区大熊猫种群数量呈下降趋势; 在考虑近交衰退的影响后, 遗传多样性水平降低, 灭绝率提高; 竹子开花虽能加速大熊猫种群的绝灭, 但由于保护区分布有多个竹种,因此并不会对大熊猫种群产生灾难性影响; 但是人为捕杀可迅速减少大熊猫种群数量, 加速其灭绝过程。因此, 对该保护区大熊猫进行保护的最重要措施就是严格控制人为捕杀, 并保护栖息地及走廊带。     

Evolutionary dynamics of giant viruses and their virophages

Giant viruses contain large genomes, encode many proteins atypical for viruses, replicate in large viral factories, and tend to infect protists. The giant virus replication factories can in turn be infected by so called virophages, which are smaller viruses that negatively impact giant virus replication. An example is Mimiviruses that infect the protist Acanthamoeba and that are themselves infected by the virophage Sputnik. This study examines the evolutionary dynamics of this system, using mathematical models. While the models suggest that the virophage population will evolve to increasing degrees of giant virus inhibition, it further suggests that this renders the virophage population prone to extinction due to dynamic instabilities over wide parameter ranges. Implications and conditions required to avoid extinction are discussed. Another interesting result is that virophage presence can fundamentally alter the evolutionary course of the giant virus. While the giant virus is predicted to evolve toward increasing its basic reproductive ratio in the absence of the virophage, the opposite is true in its presence. Therefore, virophages can not only benefit the host population directly by inhibiting the giant viruses but also indirectly by causing giant viruses to evolve toward weaker phenotypes. Experimental tests for this model are suggested.     

Intricate trophic links between threatened vertebrates confined to a small island in the Atlantic Ocean

Trophic networks in small isolated islands are in a fragile balance, and their disturbance can easily contribute toward the extinction vortex of species. Here, we show, in a small Atlantic island (Raso) in the Cabo Verde Archipelago, using DNA metabarcoding, the extent of trophic dependence of the Endangered giant wall gecko Tarentola gigas on endemic populations of vertebrates, including one of the rarest bird species of the world, the Critically Endangered Raso lark Alauda razae. We found that the Raso lark (27%), Iago sparrow Passer iagoensis (12%), Bulwer's petrel Bulweria bulwerii (15%), and the Cabo Verde shearwater Calonectris edwardsii (10%) are the most frequent vertebrate signatures found in the feces of the giant wall gecko. This work provides the first integrative assessment of their trophic links, an important issue to be considered for the long‐term conservation of these small and isolated island ecosystems.     

圈养繁殖在大熊猫保护生物学中的作用

栖息地的日益恶化、片段化和种群孤岛化已成为保护大熊猫的严重障碍。尽管就地保护濒危物种是最有希望的措施,但对于大熊猫而言,研究表明圈养繁殖也是保护这一极危物和中的有效手段之一,对保护遗传多样性起以了重要作用,是延缓绝灭速率的保证。本文阐述了大圈养繁殖的必要性及其在保护生物学中的作用。     

Extinction and quasi-stationarity in the Verhulst logistic model.

We formulate and analyse a stochastic version of the Verhulst deterministic model for density-dependent growth of a single population. Three parameter regions with qualitatively different behaviours are identified. Explicit approximations of the quasi-stationary distribution and of the expected time to extinction are presented in each of these regions. The quasi-stationary distribution is approximately normal, and the time to extinction is long, in one of these regions. Another region has a short time to extinction and a quasi-stationary distribution that is approximately truncated geometric. A third region is a transition region between these two. Here the time to extinction is moderately long and the quasi-stationary distribution has a more complicated behaviour. Numerical illustrations are given.     

Modelling the extinction of Steller's sea cow

Steller's sea cow, a giant sirenian discovered in 1741 and extinct by 1768, is one of the few megafaunal mammal species to have died out during the historical period. The species is traditionally considered to have been exterminated by 'blitzkrieg'-style direct overharvesting for food, but it has also been proposed that its extinction resulted from a sea urchin population explosion triggered by extirpation of local sea otter populations that eliminated the shallow-water kelps on which sea cows fed. Hunting records from eighteenth century Russian expeditions to the Commander Islands, in conjunction with life-history data extrapolated from dugongs, permit modelling of sea cow extinction dynamics. Sea cows were massively and wastefully overexploited, being hunted at over seven times the sustainable limit, and suggesting that the initial Bering Island sea cow population must have been higher than suggested by previous researchers to allow the species to survive even until 1768. Environmental changes caused by sea otter declines are unlikely to have contributed to this extinction event. This indicates that megafaunal extinctions can be effected by small bands of hunters using pre-industrial technologies, and highlights the catastrophic impact of wastefulness when overexploiting resources mistakenly perceived as 'infinite'.     

Genetic evidence of recent population contraction in the southernmost population of giant pandas

Anthropogenic habitat loss and fragmentation have been implicated in the endangerment and extinction of many species. Here we assess genetic variation and demographic history in the southernmost population of giant pandas (Ailuropoda melanoleuca) that continues to be threatened by habitat degradation and fragmentation, using noninvasive genetic sampling, mitochondrial control region sequence and 12 microsatellite loci. Compared to other giant panda populations, this population has medium-level genetic diversity based on the measure of both mitochondrial and nuclear markers. Mitochondrial DNA-based demographic analyses revealed that no historical population expansion or contraction has occurred, indicating a relatively stable population size. However, a Bayesian-coalescent method based on the observed allele distribution and allele frequencies of microsatellite clearly did detect, quantify and date a recent decrease in population size. Overall, the results indicate that a population contraction in the order of 95-96% has taken place over the last 910-999 years and is most likely due to anthropogenic habitat loss. These findings highlight the need for a greater focus on habitat protection and restoration for the long-term survival of this giant panda population.     

Markov chain models predict the consequences of experimental extinctions

Predicting the effects of species extinction is challenging because of ecosystem complexity. Using novel long‐term experimental deletions of two mussel species, I found that a multi‐species Markov chain model, which was parameterized under non‐experimental conditions, accurately predicted the effects of local extinction in an intertidal community. Systematically deleting species from the model predicted declining ecosystem biomass with reduced biodiversity, but relatively constant ecosystem resilience following disturbance. The effects of reduced biodiversity on these variables ranged widely, illustrating the need for species‐specific predictions of extinction effects. The results show that Markov chain models can be useful tools for predicting consequences of local species extinction without extensive experimentation.     

Identification of Release Habitat of Captive-bred Mammals Demonstrated for Giant Panda in Sichuan Province,China

Biology Bulletin - Two thirds of the giant panda population in the Sichuan Province of China is at risk of extinction due to habitat fragmentation. Connectivity constraints prevent spontaneous...     

Was the Late Ordovician mass extinction truly exceptional?

The Late Ordovician mass extinction event is the oldest of the five great extinction events in the fossil record. It has long been regarded as an outlier among mass extinctions, primarily due to its association with a cooling climate. However, recent temporally better resolved fossil biodiversity estimates complicate this view, providing growing evidence for a prolonged but punctuated biodiversity decline modulated by changes in atmospheric composition, ocean chemistry, and viable habitat area. This evolving view invokes extinction drivers similar to those that occurred during other major extinctions; some are even factors in the current human-induced biodiversity crisis. Even this very ancient and, at first glance, exceptional event conveys important lessons about the intensifying ‘sixth mass extinction’.     

四川江油渔洞子下三叠统飞仙关组巨鲕灰岩中疑似蓝细菌及早三叠世疑似蓝细菌的双幕式爆发

二叠纪末海洋生态环境的恶化导致海洋底栖生物的大灭绝及早三叠世蓝细菌的爆发,有关这一时期我国华南蓝细菌化石的报道主要来自早三叠世早期的微生物岩。四川江油渔洞子剖面下三叠统飞仙关组下部巨鲕灰岩中首次发现有丰富的疑似蓝细菌,在种类和结构上与以往所报道的蓝细菌有着明显区别。疑似蓝细菌在巨鲕内和围岩中的富集,表明巨鲕灰岩的成因与疑似蓝细菌的活动有关,与飞仙关组底部微生物岩在成因上有着密切联系,显示早三叠世早期在这一地区发生了疑似蓝细菌的双幕式爆发,同时,暗示着这一地区二叠纪-三叠纪之交至少发生了两次海洋环境恶化及动物灭绝事件。疑似蓝细菌的爆发性生长,对于海洋生态环境的修复和海洋含氧条件的改善,进而为早三叠世末、中三叠世的生物全面复苏、辐射有着重要意义。     

Important population viability analysis parameters for giant pandas (Aliuropoda melanoleuca)

Population viability analysis(PVA) is a tool to evaluate the risk of extinction for endangered species and aid conservation decision-making.The quality of PVA output is dependent on parameters related to population dynamics and life-history;however,it has been difficult to collect this information for the giant panda(Aliuropoda melanoleuca),a rare and endangered mammal native to China,confined to some 30 fragmented habitat patches.Since giant pandas are long-lived,mature late,have lower reproductive rates,and show little sexual dimorphism,obtaining data to perform adequate PVA has been difficult.Here,we develop a parameter sensitivity index by modeling the dynamics of six giant panda populations in the Minshan Mountains,in order to determine the parameters most influential to giant panda populations.Our data shows that the giant panda populations are most sensitive to changes in four female parameters:initial breeding age,reproductive rate,mortality rate between age 0 and 1,and mortality rate of adults.The parameter sensitivity index strongly correlated with initial population size,as smaller populations were more sensitive to changes in these four variables.This model suggests that demographic parameters of females have more influence on the results of PVA,indicating that females may play a more important role in giant panda population dynamics than males.Consequently,reintroduction of female individuals to a small giant panda population should be a high priority for conservation efforts.Our findings form a technical basis for the coming program of giant panda reintroduction,and inform which parameters are crucial to successfully and feasibly monitoring wild giant panda populations.     

The Use of Extant Non-Indigenous Tortoises as a Restoration Tool to Replace Extinct Ecosystem Engineers

We argue that the introduction of non-native extant tortoises as ecological replacements for extinct giant tortoises is a realistic restoration management scheme, which is easy to implement. We discuss how the recent extinctions of endemic giant Cylindraspis tortoises on the Mascarene Islands have left a legacy of ecosystem dysfunction threatening the remnants of native biota, focusing on the island of Mauritius because this is where most has been inferred about plant–tortoise interactions. There is a pressing need to restore and preserve several Mauritian habitats and plant communities that suffer from ecosystem dysfunction. We discuss ongoing restoration efforts on the Mauritian offshore Round Island, which provide a case study highlighting how tortoise substitutes are being used in an experimental and hypothesis-driven conservation and restoration project. The immediate conservation concern was to prevent the extinction and further degradation of Round Island's threatened flora and fauna. In the long term, the introduction of tortoises to Round Island will lead to valuable management and restoration insights for subsequent larger-scale mainland restoration projects. This case study further highlights the feasibility, versatility and low-risk nature of using tortoises in restoration programs, with particular reference to their introduction to island ecosystems. Overall, the use of extant tortoises as replacements for extinct ones is a good example of how conservation and restoration biology concepts applied at a smaller scale can be microcosms for more grandiose schemes and addresses more immediate conservation priorities than large-scale ecosystem rewilding projects.     

野生大熊猫现状、面临的挑战及展望

截至2003年底,我国野生大熊猫种群数量达1596只,分布在陕西、四川和甘肃3省的45个县境内,总栖息地面积达2304991hm^2。与第2次大熊猫调查相比,野生大熊猫生存状况已得到改善,分布范围扩大、栖息地面积增加、种群数量进一步增长。本文在第3次大熊猫调查的基础上,就野生大熊猫种群及栖息地现状进行了分析,指出未来保护大熊猫所面临的3个方面的挑战,即来自物种自身生物学特性的挑战、栖息地破碎化及隔离小种群未来命运的挑战以及大熊猫保护与社区经济发展需求相冲突的挑战。作者还就我国大熊猫保护前景进行了展望,即自然保护区数量将进一步增加,栖息地状况将进一步改善;种群数量在总体保持稳定的基础上将逐步增长,但局部小种群灭绝风险将加剧;圈养种群将形成能自我维持的种群,圈养个体通过培训将逐步放归到隔离野生小种群中以改变其命运。     

Using functional traits and phylogeny to understand local extinction risk in dragonflies and damselflies (Odonata)

Understanding the risk of local extinction of a species is vital in conservation biology, especially now when anthropogenic disturbances and global warming are severely changing natural habitats. Local extinction risk depends on species traits, such as its geographical range size, fresh body mass, dispersal ability, length of flying period, life history variation, and how specialized it is regarding its breeding habitat. We used a phylogenetic approach because closely related species are not independent observations in the statistical tests. Our field data contained the local extinction risk of 31 odonate (dragonflies and damselflies) species from Central Finland. Species relatedness (i.e., phylogenetic signal) did not affect local extinction risk, length of flying period, nor the geographical range size of a species. However, we found that closely related species were similar in hind wing length, length of larval period, and habitat of larvae. Both phylogenetically corrected (PGLS) and uncorrected (GLM) analysis indicated that the geographical range size of species was negatively related to local extinction risk. Contrary to expectations, habitat specialist species did not have higher local extinction rates than habitat generalist species nor was it affected by the relatedness of species. As predicted, species’ long larval period increased, and long wings decreased the local extinction risk when evolutionary relatedness was controlled. Our results suggest that a relatively narrow geographical range size is an accurate estimate for a local extinction risk of an odonate species, but the species with long life history and large habitat niche width of adults increased local extinction risk. Because the results were so similar between PGLS and GLM methods, it seems that using a phylogenetic approach does not improve predicting local extinctions.     

SHORT COMMUNICATION: A phantom extinction? New insights into extinction dynamics of the Don‐hare Lepus tanaiticus

The Pleistocene to Holocene transition was accompanied by a worldwide extinction event affecting numerous mammalian species. Several species such as the woolly mammoth and the giant deer survived this extinction wave, only to go extinct a few thousand years later during the Holocene. Another example for such a Holocene extinction is the Don‐hare, Lepus tanaiticus, which inhabited the Russian plains during the late glacial. After being slowly replaced by the extant mountain hare (Lepus timidus), it eventually went extinct during the middle Holocene. Here, we report the phylogenetic relationship of L. tanaiticus and L. timidus based on a 339‐basepair (bp) fragment of the mitochondrial D‐loop. Phylogenetic tree‐ and network reconstructions do not support L. tanaiticus and L. timidus being different species. Rather, we suggest that the two taxa represent different morphotypes of a single species and the extinction of ‘L. tanaiticus’ represents the disappearance of a local morphotype rather than the extinction of a species.     

Environmental stochasticity and extinction risk in a population of a small songbird, the great tit

Using a long-term demographic data set, we estimated the separate effects of demographic and environmental stochasticity in the growth rate of the great tit population in Wytham Wood, United Kingdom. Assuming logistic density regulation, both the demographic (sigma2d = 0.569) and environmental (sigma2e = 0.0793) variance, with interactions included, were significantly greater than zero. The estimates of the demographic variance seemed to be relatively insensitive to the length of the study period, whereas reliable estimates of the environmental variance required long time series (at least 15 yr of data). The demographic variance decreased significantly with increasing population density. These estimates are used in a quantitative analysis of the demographic factors affecting the risk of extinction of this population. The very long expected time to extinction of this population (approximately 10(19) yr) was related to a relatively large population size (>/=120 pairs during the study period). However, for a given population size, the expected time to extinction was sensitive to both variation in population growth rate and environmental stochasticity. Furthermore, the form of the density regulation strongly affected the expected time to extinction. Time to extinction decreased when the maximum density regulation approached K. This suggests that estimates of viability of small populations should be given both with and without inclusion of density dependence.     

Neural function in an alpine grylloblattid: a comparison with the house cricket, Acheta domesticus

ABSTRACT. The effect of temperature on evoked activity in giant interneurons was compared in Grylloblatta sp. (an alpine insect with a temperature preference close to 0°C) and Acheta domesticus. The response to sound and air-puff stimulation of the abdominal cerci was monitored with extracellular electrodes placed under the ventral nerve cord. Responses to air puffs were elicited in Grylloblatta while the animal was supercooled to -6°C. The supercooling point was reached and freezing occurred in the range -5.5 to 8.5°C. The upper extinction temperature could not be determined due to massive spontaneous giant fibre activity in the 12–15°C range masking responses to air puffs. Lethal heat coma occurred at 15–20°C, although most animals did not recover from the spontaneous CNS activity which preceded it. The extinction ranges for Acheta giant neurons were 3.5-4.0°C and 42–44°C. Spike number peaked at 33–36 C and amplitude levels diminished as heat or cold coma was approached; -7.5 C was the mean supercooling point. Both species recovered from cold coma if supercooling was avoided; in Acheta , heat coma was also reversible. Giant fibre latencies in Acheta displayed a Q₁₀ of 1.2 above 11–14°C, below which a break occurred in the curve and delays increased sharply. Latencies for the grylloblattid exhibited a Q₁₀ of 2 but no break in the curve was observed until 0° C was approached. Spike number and amplitude increased with temperature until spontaneous CNS activity obliterated responses to air puffs. The potential role of unsaturated fatty acids in low temperature adaptation in Grylloblatta is discussed.     

Good‐bye to tropical alpine plant giants under warmer climates? Loss of range and genetic diversity in Lobelia rhynchopetalum

The main aim of this paper is to address consequences of climate warming on loss of habitat and genetic diversity in the enigmatic tropical alpine giant rosette plants using the Ethiopian endemic Lobelia rhynchopetalum as a model. We modeled the habitat suitability of L. rhynchopetalum and assessed how its range is affected under two climate models and four emission scenarios. We used three statistical algorithms calibrated to represent two different complexity levels of the response. We analyzed genetic diversity using amplified fragment length polymorphisms and assessed the impact of the projected range loss. Under all model and scenario combinations and consistent across algorithms and complexity levels, this afro‐alpine flagship species faces massive range reduction. Only 3.4% of its habitat seems to remain suitable on average by 2,080, resulting in loss of 82% (CI 75%–87%) of its genetic diversity. The remaining suitable habitat is projected to be fragmented among and reduced to four mountain peaks, further deteriorating the probability of long‐term sustainability of viable populations. Because of the similar morphological and physiological traits developed through convergent evolution by tropical alpine giant rosette plants in response to diurnal freeze‐thaw cycles, they most likely respond to climate change in a similar way as our study species. We conclude that specialized high‐alpine giant rosette plants, such as L. rhynchopetalum, are likely to face very high risk of extinction following climate warming.