Trajectories from extinction: where are missing mammals rediscovered?

Aim To determine where mammals that are presumed to be extinct are most likely to be rediscovered, and to test predictions of two hypotheses to explain trajectories of decline in mammals. Range collapse is based on the premise that extinction rates at the edge of species ranges are highest because habitat is suboptimal, so declining species are predicted to survive longer near the centre of their ranges. We predicted that under range collapse, remnant populations are most likely be rediscovered within their former core range. Conversely, if threats usually spread across ranges, declining species will be pushed to the periphery (range eclipse), so rediscoveries are predicted at the edge of the pre‐decline range. If so, species would be more likely to be rediscovered in marginal habitat, and at higher elevations than the sites from which they disappeared. Location World‐wide. Methods Using data on 67 species of mammals which have been rediscovered, I tested whether species were disproportionately rediscovered in the outer 50% of their former range area or at higher elevations than their last recorded locations, and which species characteristics were associated with rediscovery location and habitat change, using both the phylogenetic generalized least squares method to account for phylogenetic non‐independence and linear models of raw species data. Results Species affected by habitat loss were more likely to be rediscovered at the periphery than the centre of their former range, consistent with range eclipse caused by the spread of habitat destruction. High human population pressure predicted which species changed habitat between their previous records and rediscovery. Coastal species experienced higher human population densities, and were more likely to be rediscovered at the periphery of their former ranges, and there was some evidence of an up‐slope shift associated with higher human populations at lower elevations. Main conclusion The locations of rediscoveries of species affected by habitat loss were consistent with range eclipse through a mechanism of spreading habitat loss and human population pressure, rather than with range collapse. Searches for mammals that have declined from habitat loss should include range edges and marginal habitat, especially in areas of high human population density.     

舟山岛自然栖息地的变化及其对兽类物种绝灭影响的初步研究

舟山岛自然栖息地和物种受到人类活动的强烈干扰．占总面积５６．３％的自然栖息地已经消失,自然栖息地已破碎成许多碎片,碎片面积不断变小,碎片数量在增加．自然栖息地的质量发生了很大变化．自然栖息地的易破碎带与其地理特征有关,破碎易发生于被开垦和开发的地带．由于自然栖息地面积损失、破碎、质量下降和过度捕杀,已有５种兽绝灭,３种兽正走向绝灭,绝灭速度高于临近大陆．人口增长是舟山岛自然栖息地损失、破碎、质量下降和物种绝灭的根本原因．本文还讨论了保护自然栖息地和物种多样性的一些措施和原则．     

Rediscovery of Bembidion (Lymnaeum) nigropiceum (Marsham) (= puritanum Hayward) in Massachusetts, with remarks on biology and habitat (Coleoptera, Carabidae, Bembidiini)

Bembidion (Lymnaeum) nigropiceum (Marsham) (=puritanum Hayward), a European species introduced into Massachusetts but presumed not to have become established, has been rediscovered during the Boston Harbor Islands All Taxa Biodiversity Inventory undertaken by the Museum of Comparative Zoology and the National Park Service. A summary is presented of treatment of this species in North America. Data on specimens collected are presented, along with observations on habitat and biology. Some speculations are presented about its highly specialized habitat in the gravel pushed up by high tide, which may act as a food-trapping sieve. A few words are included about future actions needed to resolve questions of distribution and behavior.     

Drivers of extinction risk in African mammals: the interplay of distribution state,human pressure,conservation response and species biology

Although conservation intervention has reversed the decline of some species, our success is outweighed by a much larger number of species moving towards extinction. Extinction risk modelling can identify correlates of risk and species not yet recognized to be threatened. Here, we use machine learning models to identify correlates of extinction risk in African terrestrial mammals using a set of variables belonging to four classes: species distribution state, human pressures, conservation response and species biology. We derived information on distribution state and human pressure from satellite-borne imagery. Variables in all four classes were identified as important predictors of extinction risk, and interactions were observed among variables in different classes (e.g. level of protection, human threats, species distribution ranges). Species biology had a key role in mediating the effect of external variables. The model was 90% accurate in classifying extinction risk status of species, but in a few cases the observed and modelled extinction risk mismatched. Species in this condition might suffer from an incorrect classification of extinction risk (hence require reassessment). An increased availability of satellite imagery combined with improved resolution and classification accuracy of the resulting maps will play a progressively greater role in conservation monitoring.     

Taxon age,origination, and extinction through geologic time

Changes in the taxon ages of fossil marine families that are alive and those that become extinct in each stage of the Phanerozoic reflect changes in the origination rate, differences in the extinction rate of families with different taxon ages, and mass extinction events. Extinct families are generally much younger than the population from which they were drawn. Periods dominated by higher numbers of younger families are more susceptible to larger size extinctions and greater variation in extinction size. As a result the relative size of extinction peaks must be viewed with regard to the taxon age structure of the population. Mass extinctions cause little change in the taxon age of the fauna. However, adaptive radiations cause a large drop in the average age of the families that are alive at any given time. Families must be treated as dynamic entities in macroevolutionary studies because their probabilities of extinction change over time.     

Habitat tracking, stasis and survival in Neogene large mammals

Species response to environmental change may vary from adaptation to the new conditions, to dispersal towards territories with better ecological settings (known as habitat tracking), and to extinction. A phylogenetically explicit analysis of habitat tracking in Caenozoic large mammals shows that species moving over longer distances during their existence survived longer. By partitioning the fossil record into equal time intervals, we showed that the longest distance was preferentially covered just before extinction. This supports the idea that habitat tracking is a key reaction to environmental change, and confirms that tracking causally prolongs species survival. Species covering longer distances also have morphologically less variable cheek teeth. Given the tight relationship between cheek teeth form and habitat selection in large mammals, this supports the well-known, yet little tested, idea that habitat tracking bolsters morphological stasis.     

Movement trajectories and habitat partitioning of small mammals in logged and unlogged rain forests on Borneo

1. Non-volant animals in tropical rain forests differ in their ability to exploit the habitat above the forest floor and also in their response to habitat variability. It is predicted that specific movement trajectories are determined both by intrinsic factors such as ecological specialization, morphology and body size and by structural features of the surrounding habitat such as undergrowth and availability of supportive structures. 2. We applied spool-and-line tracking in order to describe movement trajectories and habitat segregation of eight species of small mammals from an assemblage of Muridae, Tupaiidae and Sciuridae in the rain forest of Borneo where we followed a total of 13,525 m path. We also analysed specific changes in the movement patterns of the small mammals in relation to habitat stratification between logged and unlogged forests. Variables related to climbing activity of the tracked species as well as the supportive structures of the vegetation and undergrowth density were measured along their tracks. 3. Movement patterns of the small mammals differed significantly between species. Most similarities were found in congeneric species that converged strongly in body size and morphology. All species were affected in their movement patterns by the altered forest structure in logged forests with most differences found in Leopoldamys sabanus. However, the large proportions of short step lengths found in all species for both forest types and similar path tortuosity suggest that the main movement strategies of the small mammals were not influenced by logging but comprised generally a response to the heterogeneous habitat as opposed to random movement strategies predicted for homogeneous environments. 4. Overall shifts in microhabitat use showed no coherent trend among species. Multivariate (principal component) analysis revealed contrasting trends for convergent species, in particular for Maxomys rajah and M. surifer as well as for Tupaia longipes and T. tana, suggesting that each species was uniquely affected in its movement trajectories by a multiple set of environmental and intrinsic features.     

Habitat fragmentation and extinction thresholds on fractal landscapes

Habitat fragmentation is a potentially critical factor in determining population persistence. In this paper, we explore the effect of fragmentation when the fragmentation follows a fractal pattern. The habitat is divided into patches, each of which is suitable or unsuitable. Suitable patches are either occupied or unoccupied, and change state depending on rates of colonization and local extinction. We compare the behaviour of two models: a spatially implicit patch-occupancy (PO) model and a spatially explicit cellular automaton (CA) model. The PO model has two fixed points: extinction, and a stable equilibrium with a fixed proportion of occupied patches. Global extinction results when habitat destruction reduces the proportion of suitable patches below a critical threshold. The PO model successfully recreates the extinction patterns found in other models. We translated the PO model into a stochastic cellular automaton. Fractal arrangements of suitable and unsuitable patches were used to simulate habitat fragmentation. We found that: (i) a population on a fractal landscape can tolerate more habitat destruction than predicted by the patch-occupancy model, and (ii) the extinction threshold decreases as the fractal dimension of the landscape decreases. These effects cannot be seen in spatially implicit models. Landscape struc-ture plays a vital role in mediating the effects of habitat fragmentation on persistence.     

Drivers of extinction: the case of Azorean beetles

Oceanic islands host a disproportionately high fraction of endangered or recently extinct endemic species. We report on species extinctions among endemic Azorean beetles following 97% habitat loss since AD 1440. We infer extinctions from historical and contemporary records and examine the influence of three predictors: geographical range, habitat specialization and body size. Of 55 endemic beetle species investigated (out of 63), seven can be considered extinct. Single-island endemics (SIEs) were more prone to extinction than multi-island endemics. Within SIEs restricted to native habitat, larger species were more extinction-prone. We thus show a hierarchical path to extinction in Azorean beetles: species with small geographical range face extinction first, with the larger bodied ones being the most threatened. Our study provides a clear warning of the impact of habitat loss on island endemic biotas.     

Inbreeding and extinction: Effects of rate of inbreeding

Deleterious alleles may be removed (purged) bynatural selection in populations undergoinginbreeding. However, there is controversyregarding the effectiveness of selection inreducing the risk of extinction due toinbreeding, especially in relation to the rateof inbreeding. We evaluated the effect of therate of inbreeding on reducing extinction risk,in populations of Drosophila melanogastermaintained using full-sib mating (160replicates), or at effective population sizes(N _e) of 10 (80) or 20 (80).Extinction rates in the populations maintainedusing full-sib mating occurred at lower levelsof inbreeding than in the larger populations,whereas the two larger populations did notdiffer significantly from each other.Inbreeding coefficients at 50% extinction were0.62, 0.79 and 0.77 for the full-sib (N _e = 2.6), N _e = 10 and N _e = 20 treatments, respectively. Populations of N _e = 20 that remained extant after 60 generations, showed inbreeding depression, with the mean fitness of these populations being only 45% of the outbredcontrols. There was considerable variationamong the 31 inbred populations in fitness, butnone of the N _e = 20 populations hadfitness that was higher than the outbredcontrol. We conclude that purging may slow therate of extinction slightly, but it cannot berelied on to eliminate the deleterious effectsof inbreeding.     

The ghosts of mammals past: biological and geographical patterns of global mammalian extinction across the Holocene

Although the recent historical period is usually treated as a temporal base-line for understanding patterns of mammal extinction, mammalian biodiversity loss has also taken place throughout the Late Quaternary. We explore the spatial, taxonomic and phylogenetic patterns of 241 mammal species extinctions known to have occurred during the Holocene up to the present day. To assess whether our understanding of mammalian threat processes has been affected by excluding these taxa, we incorporate extinct species data into analyses of the impact of body mass on extinction risk. We find that Holocene extinctions have been phylogenetically and spatially concentrated in specific taxa and geographical regions, which are often not congruent with those disproportionately at risk today. Large-bodied mammals have also been more extinction-prone in most geographical regions across the Holocene. Our data support the extinction filter hypothesis, whereby regional faunas from which susceptible species have already become extinct now appear less threatened; they may also suggest that different processes are responsible for driving past and present extinctions. We also find overall incompleteness and inter-regional biases in extinction data from the recent fossil record. Although direct use of fossil data in future projections of extinction risk is therefore not straightforward, insights into extinction processes from the Holocene record are still useful in understanding mammalian threat.     

Generic species richness and body mass in North American mammals: Support for the inverse relationship of body size and speciation rate

Generic species richness, the number of species per genus, is examined as a function of mean generic body mass for extant North American mammals. Species richness decreases as an inverse power function with increased mass, and the Spearman rank correlation coefficient of the logio transformed data is significant (r_s= ‐0.37). When the data are partitioned by trophic level, the relationship is not statistically significant for carnivores but strengthens for herbivores (r_s= ‐0.46). This interesting but incidental effect is due to the negligible number of diminutive and excessively large carnivores, which is in turn determined by foraging strategies. Alternate hypotheses for the “right‐skewed”; size distribution of modern North American mammals, such as disproportionate extinction of large species, differential species longevity, and a geographical scaling function, are rejected in favor of the proposition that elevated levels of speciation are restricted to animals of small body mass, as originally proposed by Gould and Eldredge (1977). This phenomenon is explained as a function of habitat restriction and particularly in herbivores, limited home range size. Aquatic mammals, regardless of body size, speciate rarely. Cope's Rule, the tendency of many animal groups to evolve towards large size, is understood as a probabilistic statement reflecting the phylogenetic tendencies of a disproportionately high number of small species alive at any given point in time.     

On the interpretation and application of mean times to extinction

As a metric of population viability, conservation biologists routinely predict the mean time to extinction (MTE). Interpretation of MTE depends on the underlying distribution of times to extinction (DTE). Despite claims to the contrary, all information regarding extinction risk can be obtained from this single statistic, the MTE, provided the DTE is exponential. We discuss the proper interpretation of MTE and illustrate how to calculate any population viability statistic when only the MTE is known and the DTE is assumed to be exponential. We also discuss the restrictive assumptions underlying the exponential DTE and the conditions under which alternative models for the DTE are preferable to the conventional (exponential) model. Despite superficial similarities between the exponential and alternative DTEs, several key differences can lead to substantially different interpretations of the MTE.     

Transposable elements and the evolution of genome organization in mammals

All mammalian transposable elements characterized to date appear to be nonrandomly distributed in the mammalian genome. While no element has been found to be exclusively restricted in its chromosomal location, LINE elements and some retrovirus-like elements are preferentially accumulated in G-banding regions of the chromosomes, and in some cases in the sex chromosomes, while SINE elements occur preferentially in R-banding regions. Four mechanisms are presented which may explain the nonrandom genomic distribution of mammalian transposons: i) sequence-specific insertion, ii) S-phase insertion, iii) ectopic excision, and iv) recombinational editing. Some of the available data are consistent with each of these four models, but no single model is sufficient to explain all of the existing data.     

Extinction patterns in the avifauna of the Hawaiian islands

Through the continuing accumulation of fossil evidence, it is clear that the avifauna of the Hawaiian Islands underwent a large‐scale extinction event around the time of Polynesian arrival. A second wave of extinctions since European colonization has further altered this unique avifauna. Here I present the first systematic analysis of the factors characterizing the species that went extinct in each time period and those that survived in order to provide a clearer picture of the possible causal mechanisms. These analyses were based on mean body size, dietary and ecological information and phylogenetic lineage of all known indigenous, non‐migratory land and freshwater bird species of the five largest Hawaiian Islands. Extinct species were divided into ‘prehistoric’ and ‘historic’ extinction categories based on the timing of their last occurrence. A model of fossil preservation bias was also incorporated. I used regression trees to predict probability of prehistoric and historic extinction based on ecological variables. Prehistoric extinctions showed a strong bias toward larger body sizes and flightless, ground‐nesting species, even after accounting for preservation bias. Many small, specialized species, mostly granivores and frugivores, also disappeared, implicating a wide suite of human impacts including destruction of dry forest habitat. In contrast, the highest extinction rates in the historic period were in medium‐sized nectarivorous and insectivorous species. These differences result from different causal mechanisms underlying the two waves of extinction.     

Avian life-history determinants of local extinction risk in a hyper-fragmented neotropical forest landscape

The fact that species vary in their vulnerability to extinction is well documented, but the reasons for these differences remain poorly understood. Why should some species/families/guilds decline rapidly with increasing anthropogenic disturbance, while others either tolerate or proliferate in disturbed habitats? We investigated the bird species composition in 31 primary forest patches of varying size in a region of the Amazonian 'Arc of Deforestation' and assessed which species life-history traits predisposed individual species to extinction. Medium-sized non-flocking canopy frugivores/ominvores of low primary forest dependence were least likely to go extinct in small patches, while small-bodied flock-following primary-forest-dependent terrestrial insectivores were most fragmentation sensitive. We found highly idiosyncratic relationships between the minimum size of forest patches occupied by different species and their territory size requirements estimated based on other Amazonian studies. This suggests that avian assemblages in forest fragments primarily comprise species that either have good dispersal abilities or are highly tolerant to the non-forest matrix, rather than those whose minimum spatial requirements can be met by the size of available forest fragments.