De-extinction and the conception of species

Developments in genetic engineering may soon allow biologists to clone organisms from extinct species. The process, dubbed “de-extinction,” has been publicized as a means to bring extinct species back to life. For theorists and philosophers of biology, the process also suggests a thought experiment for the ongoing “species problem”: given a species concept, would a clone be classified in the extinct species? Previous analyses have answered this question in the context of specific de-extinction technologies or particular species concepts. The thought experiment is given more comprehensive treatment here. Given the products of three de-extinction technologies, twenty-two species concepts are “tested” to see which are consistent with the idea that species may be resurrected. The ensuing discussion considers whether or not de-extinction is a conceptually coherent research program and, if so, whether or not its development may contribute to a resolution of the species problem. Ultimately, theorists must face a choice: they may revise their commitments to species concepts (if those concepts are inconsistent with de-extinction) or they may recognize de-extinction as a means to make progress in the species problem.     

A case for resurrecting lost species—review essay of Beth Shapiro’s, “How to Clone a Mammoth: The Science of De-extinction”

The title of Beth Shapiro’s ‘How to Clone a Mammoth’ contains an implicature: it suggests that it is indeed possible to clone a mammoth, to bring extinct species back from the dead. But in fact Shapiro both denies this is possible, and denies there would be good reason to do it even if it were possible. The de-extinct ‘mammoths’ she speaks of are merely ecological proxies for mammoths—elephants re-engineered for cold-tolerance by the addition to their genomes of a few mammoth genes. Shapiro’s denial that genuine species de-extinction is possible is based on her assumption that resurrected organisms would need to be perfectly indistinguishable from the creatures that died out. In this article I use the example of an extinct New Zealand wattlebird, the huia, to argue—contra Shapiro—that there are compelling reasons to resurrect certain species if it can be done. I then argue—again, contra Shapiro—that synthetically created organisms needn’t be perfectly indistinguishable from their genetic forebears in order for species de-extinction to be successful.     

Meet the new mammoth,same as the old? Resurrecting the <Emphasis Type="Italic">Mammuthus primigenius</Emphasis>

Media reporters often announce that we are on the verge of bringing back the woolly mammoth, even while there is growing consensus among scientists that resurrecting the mammoth is unlikely. In fact, current “de-extinction” efforts are not designed to bring back a mammoth, but rather adaptations of the mammoth using close relatives. For example, Harvard scientists are working on creating an Asian elephant with the thick coat of a mammoth by merging mammoth and elephant DNA. But how should such creatures be classified? Are they elephants, mammoths, or both? Answering these questions requires getting clear about the concept of reproduction. What I hope to show is that with an appropriate notion of reproduction—one for which I will argue—resurrecting a member of Mammuthus primigenius is a genuine possibility.     

Alien species as a driver of recent extinctions

We assessed the prevalence of alien species as a driver of recent extinctions in five major taxa (plants, amphibians, reptiles, birds and mammals), using data from the IUCN Red List. Our results show that alien species are the second most common threat associated with species that have gone completely extinct from these taxa since AD 1500. Aliens are the most common threat associated with extinctions in three of the five taxa analysed, and for vertebrate extinctions overall.     

In search of critically endangered species: the current situation of two tiny salamander species in the Neotropical mountains of Mexico

Worldwide, one in every three species of amphibian is endangered, 39 species have gone extinct in the last 500 years and another 130 species are suspected to have gone extinct in recent decades. Of the amphibians, salamanders have the highest portion of their species in one of the risk categories, even higher than the frogs. To date there have been few studies that have used recent field data to examine the status of populations of endangered salamanders. In this study we evaluate the current situation of two tiny salamanders, Parvimolge townsendi and Thorius pennatulus, both of which are distributed at intermediate elevations in the mountains of the northern Neotropics and are considered to be critically endangered; the first has been proposed as possibly extinct. By carrying out exhaustive surveys in both historical and potentially suitable sites for these two species, we evaluated their abundance and the characteristics of their habitats, and we estimated their potential geographic distribution. We visited 22 sites, investing 672 person-hours of sampling effort in the surveys, and found 201 P. townsendi salamanders in 11 sites and only 13 T. pennatulus salamanders in 5 sites. Both species were preferentially found in cloud forest fragments that were well conserved or only moderately transformed, and some of the salamanders were found in shade coffee plantations. The potential distribution area of both species is markedly fragmented and we estimate that it has decreased by more than 48%. The results of this study highlight the importance of carrying out exhaustive, systematic field surveys to obtain accurate information about the current situation of critically endangered species, and help us better understand the crisis that amphibians are facing worldwide.     

Evolutionary suicide

The great majority of species that lived on this earth have gone extinct. These extinctions are often explained by invoking changes in the environment, to which the species has been unable to adapt. Evolutionary suicide is an alternative explanation to such extinctions. It is an evolutionary process in which a viable population adapts in such a way that it can no longer persist. In this paper different models, where evolutionary suicide occurs are discussed, and the theory behind the phenomenon is reviewed.     

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.     

Global Patterns and Drivers of Avian Extinctions at the Species and Subspecies Level

Birds have long fascinated scientists and travellers, so their distribution and abundance through time have been better documented than those of other organisms. Many bird species are known to have gone extinct, but information on subspecies extinctions has never been synthesised comprehensively. We reviewed the timing, spatial patterns, trends and causes of avian extinctions on a global scale, identifying 279 ultrataxa (141 monotypic species and 138 subspecies of polytypic species) that have gone extinct since 1500. Species extinctions peaked in the early 20^th century, then fell until the mid 20^th century, and have subsequently accelerated. However, extinctions of ultrataxa peaked in the second half of the 20^th century. This trend reflects a consistent decline in the rate of extinctions on islands since the beginning of the 20^th century, but an acceleration in the extinction rate on continents. Most losses (78.7% of species and 63.0% of subspecies) occurred on oceanic islands. Geographic foci of extinctions include the Hawaiian Islands (36 taxa), mainland Australia and islands (29 taxa), the Mascarene Islands (27 taxa), New Zealand (22 taxa) and French Polynesia (19 taxa). The major proximate drivers of extinction for both species and subspecies are invasive alien species (58.2% and 50.7% of species and subspecies, respectively), hunting (52.4% and 18.8%) and agriculture, including non-timber crops and livestock farming (14.9% and 31.9%). In general, the distribution and drivers of subspecific extinctions are similar to those for species extinctions. However, our finding that, when subspecies are considered, the extinction rate has accelerated in recent decades is both novel and alarming.     

Kinetics of Photobleaching of β-Carotene in Chloroform and Formation of Transient Carotenoid Species Absorbing in the Near Infrared

Upon laser flash photolysis of β-carotene in chloroform instantaneous bleaching of β-carotene and concomitant formation of near infrared absorbing species are observed. One species, absorbing with maximum at 920 nm, is formed during the laser pulse (10 ns) and is practically gone in one millisecond, the decay showing a bi-exponential behaviour. The second species, absorbing with maximum at 1000 nm, is formed from the species absorbing at 920 nm by first order kinetics with a rate constant of 4.9·10⁴ s^-1 at 20°C. This second species decays by second order kinetics and is gone within a few milliseconds. An additional slow bleaching of β-carotene and formation of the species absorbing at 920 nm is observed. This slow bleaching/formation of transient absorption is probably due to processes involving free radicals generated during the instantaneous bleaching. The species absorbing at 920 nm is suggested to be either (i) a free radical adduct formed from β-carotene and chloroform or (ii) β-carotene after abstraction of a hydrogen atom. The species absorbing at 1000 nm is most likely the radical cation. Formation and decay of the near infrared absorbing species and bleaching of β-carotene are independent of whether oxygen is present or absent in the solutions.     

Chromosome numbers and taxonomy in Cryptocoryne (Araceae). II

Chromosome numbers for 38 species of Cryptocoryne are reported, 16 of which have not been reported earlier. About 90% of the species of Cryptocoryne have now been investigated cytologically. On the basis of chromosome numbers, morphology, and distribution, it is possible to distinguish some 24 groups within the species investigated. The chromosome numbers represent a heteroploid series which is based on the (secondary) base numbers 10, 11, 14, 15, 17, and 18. Evidence is given that 2n = 36 is the more primitive one. Evolution on the chromosome level has most likely gone in the direction of a reduction in numbers. Two new species, Cryptocoryne amicorum De Wit & N. Jacobsen and C. keei N. Jacobsen, are described.     

Species diversity preserved in different numbers of nature reserves of the same total area

The expected number of species occurring in different numbers of reserves of the same total area is examined on different assumptions of the spatial distribution and the probability of extinction. The advantage of one large reserve or several smaller ones of equal total area depends on the spatial distributions of species and the stage after the establishement of reserves. In general, several smaller reserves maintain more species immediately after the establishments unless the spatial distribution are uniform or random, whereas one large reserve excels several smaller ones after some rare species have gone extinct unless the spatial distributions are strongly contagious. Since the extinction of rare species must be facilitated as the size of each reserve reduces, the area of a reserve should be larger than the critical area that ensures the persistence of the species. Hence it is concluded that one or a few large reserves are a better strategy in order to maintain the species diversity.     

我国齿突蟾属(两栖纲：无尾目)资源现状及保护对策

齿突蟾属物种已知19种左右,中国分布有16种。该属大多数物种为珍贵、稀有濒危物种。主要生活在高寒山区及高原地区,卵产于高寒缓流的山溪中。本文梳理了分布于我国齿突蟾物种的资源现状,分析了导致其种群下降的原因。并在此基础上提出了相应的保护对策,以期能对该属物种保护和资源利用起到参考作用。     

Rainforest frogs of the Australian Wet Tropics: guild classification and the ecological similarity of declining species.

Rainforest frogs are classified into nine ecological guilds based on features of reproduction, habitat use, temporal activity, microhabitat and body size. The largest ecological differences are between the microhylid frogs and the rest of the frog species. Within the non-microhylids, there are two primary groups consisting of (i) regionally endemic rainforest specialists, and (ii) a more ecologically diverse group of species that are less specialized in their habitat requirements. Most of the regionally endemic rainforest specialists, which includes species in three ecological guilds, have declined or gone missing in recent years. Multivariate analyses of the ecological characteristics of these species show that it is not a single characteristic that isolates those species that have declined from those which have not. The guilds that have undergone significant population declines in the Wet Tropics are all characterized by the combination of low fecundity, a high degree of habitat specialization and reproduction in flowing streams. These results have important implications for the determination of the causal factors in the unexplained global decline of many amphibian species.     

Arthropod symbiotes of Laonastes aenigmamus (Rodentia:Diatomyidae)

Arthropod symbiotes of the Laotian rock-rat, Laonastes aenigmamus (Rodentia:Diatomyidae), from Laos are examined. This host is a member of Diatomyidae previously thought to have gone extinct >10 million yr ago. Permanent symbiotes are represented by 2 species, a new species of sucking louse, Polyplax sp., near rhizomydis (Phthiraptera:Polyplacidae), and a new species of fur mite, Afrolistrophorus sp., near maculatus (Acariformes:Listrophoridae). The temporary parasites are represented by 18 species, i.e., 1 mesostigmatan species, i.e., a new species of Androlaelaps near casalis (Parasitiformes:Laelapidae); immature stages of 2 tick species, Ixodes granulatus and Haemaphysalis sp. (Parasitiformes:Ixodidae); and a rich fauna of chiggers (Acariformes:Trombiculidae) comprising 8 genera and 15 species. It is hypothesized that this host completely lost its initial fauna of ectosymbiotes and that ancestors of the recorded symbiotes switched to this host from rodents of the superfamily Muroidea.     

Spannungsfeld Forstwirtschaft und Naturschutz

Conflicts between forest management and nature protection This study gives an overview of the change of the German flora over time with special emphasis on species growing in forest habitats. As a consequence of land use plant species numbers have continually increased. Land management has also maintained some endangered plant species. The plant diversity of managed forests is higher than that of unmanaged forests. Not a single obligate forest species has gone extinct over the past 250 years of forest management, the time span of formal records. For organisms with special habitat requirements alternative protection measures other than non‐management are needed to maintain these habitats.     

The fossil record of the sixth extinction

Comparing the magnitude of the current biodiversity crisis with those in the fossil record is difficult without an understanding of differential preservation. Integrating data from palaeontological databases with information on IUCN status, ecology and life history characteristics of contemporary mammals, we demonstrate that only a small and biased fraction of threatened species (< 9%) have a fossil record, compared with 20% of non‐threatened species. We find strong taphonomic biases related to body size and geographic range. Modern species with a fossil record tend to be large and widespread and were described in the 19^th century. The expected magnitude of the current extinction based only on species with a fossil record is about half of that of one based on all modern species; values for genera are similar. The record of ancient extinctions may be similarly biased, with many species having originated and gone extinct without leaving a tangible record.     

Why does the species problem still persist?

Despite many years of discussion, the species problem has still not been adequately resolved. Why is this the case? Here I discuss two recent suggested answers to this question that place the blame on the species problem's empirical aspects or on its philosophical aspects. In contrast, I argue that neither of these two faces of the species problem constitute the principal cause of the species problem's persistence. Rather, they are merely symptoms of the real cause: the species problem has not yet gone away because of a failure to recognize that not one but a number of distinct concepts are at the heart of the problem. To illustrate this point, a recently proposed solution to the problem is examined: the suggestion to understand the concept of species as a family resemblance concept. BioEssays 26:300–305, 2004. © 2004 Wiley Periodicals, Inc.     

Correlates of rediscovery and the detectability of extinction in mammals

Extinction is difficult to detect, even in well-known taxa such as mammals. Species with long gaps in their sighting records, which might be considered possibly extinct, are often rediscovered. We used data on rediscovery rates of missing mammals to test whether extinction from different causes is equally detectable and to find which traits affect the probability of rediscovery. We find that species affected by habitat loss were much more likely to be misclassified as extinct or to remain missing than those affected by introduced predators and diseases, or overkill, unless they had very restricted distributions. We conclude that extinctions owing to habitat loss are most difficult to detect; hence, impacts of habitat loss on extinction have probably been overestimated, especially relative to introduced species. It is most likely that the highest rates of rediscovery will come from searching for species that have gone missing during the 20th century and have relatively large ranges threatened by habitat loss, rather than from additional effort focused on charismatic missing species.     

Goodness of Fit of Probability Distributions for Sightings as Species Approach Extinction

Estimating the probability that a species is extinct and the timing of extinctions is useful in biological fields ranging from paleoecology to conservation biology. Various statistical methods have been introduced to infer the time of extinction and extinction probability from a series of individual sightings. There is little evidence, however, as to which of these models provide adequate fit to actual sighting records. We use L-moment diagrams and probability plot correlation coefficient (PPCC) hypothesis tests to evaluate the goodness of fit of various probabilistic models to sighting data collected for a set of North American and Hawaiian bird populations that have either gone extinct, or are suspected of having gone extinct, during the past 150 years. For our data, the uniform, truncated exponential, and generalized Pareto models performed moderately well, but the Weibull model performed poorly. Of the acceptable models, the uniform distribution performed best based on PPCC goodness of fit comparisons and sequential Bonferroni-type tests. Further analyses using field significance tests suggest that although the uniform distribution is the best of those considered, additional work remains to evaluate the truncated exponential model more fully. The methods we present here provide a framework for evaluating subsequent models.