High variability in patterns of population decline: the importance of local processes in species extinctions

A fundamental goal of conservation science is to improve conservation practice. Understanding species extinction patterns has been a central approach towards this objective. However, uncertainty remains about the extent to which species-level patterns reliably indicate population phenomena at the scale of local sites, where conservation ultimately takes place. Here, we explore the importance of both species- and site-specific components of variation in local population declines following habitat disturbance, and test a suite of hypotheses about their intrinsic and extrinsic drivers. To achieve these goals, we analyse an unusually detailed global dataset for species responses to habitat disturbance, namely primates in timber extraction systems, using cross-classified generalized linear mixed models. We show that while there are consistent differences in the severity of local population decline between species, an equal amount of variation also occurs between sites. The tests of our hypotheses further indicate that a combination of biological traits at the species level, and environmental factors at the site level, can help to explain these patterns. Specifically, primate populations show a more marked decline when the species is characterized by slow reproduction, high ecological requirements, low ecological flexibility and small body size; and when the local environment has had less time for recovery following disturbance. Our results demonstrate that individual species show a highly heterogeneous, yet explicable, pattern of decline. The increased recognition and elucidation of local-scale processes in species declines will improve our ability to conserve biodiversity in the future.     

Non-linearities, synergisms and plant extinctions in South African fynbos and Australian kwongan

This paper explores the determinants of extinction of endemic plant taxa in mediterranean-climate regions in South Africa and southwestern Australia. Major threats to biodiversity in these areas include agriculture, deforestation, fragmentation, invasive alien organisms and urbanization. Case studies from the two regions show that synergisms between factors can lead to discontinuous, or non-linear, responses that have increased extinction rates (or threaten to) beyond predictions based on simple deterministic processes.     

Uncertainty in identifying local extinctions: the distribution of missing data and its effects on biodiversity measures

Identifying local extinctions is integral to estimating species richness and geographic range changes and informing extinction risk assessments. However, the species occurrence records underpinning these estimates are frequently compromised by a lack of recorded species absences making it impossible to distinguish between local extinction and lack of survey effort—for a rigorously compiled database of European and Asian Galliformes, approximately 40% of half-degree cells contain records from before but not after 1980. We investigate the distribution of these cells, finding differences between the Palaearctic (forests, low mean human influence index (HII), outside protected areas (PAs)) and Indo-Malaya (grassland, high mean HII, outside PAs). Such cells also occur more in less peaceful countries. We show that different interpretations of these cells can lead to large over/under-estimations of species richness and extent of occurrences, potentially misleading prioritization and extinction risk assessment schemes. To avoid mistakes, local extinctions inferred from sightings records need to account for the history of survey effort in a locality.     

Tea: Biological control of insect and mite pests in China

Tea is one of the most economically important crops in China. To secure its production and quality, biological control measures within the context of integrated pest management (IPM) has been widely popularized in China. IMP programs also provide better control of arthropod pests on tea with less chemical insecticide usage and minimal impact on the environment. More than 1100 species of natural enemies including about 80 species of viruses, 40 species of fungi, 240 species of parasitoids and 600 species of predators, as well as several species of bacteria have been recorded in tea ecosystems in China. Biological and ecological characteristics of some dominant natural enemies have been well documented. Several viral, bacterial, and fungal insecticides have been commercially utilized at large scale in China. Progress in biological control methods in conjunction with other pest control approaches for tea insect pest management is reviewed in this article. Knowledge gaps and future directions for tea pest management are also discussed.     

Endemism, diversity, and the threat of tropical moist forest extinctions

Extinction rates have risen to perhaps 10⁴ the background rate. Much of this increase is due to projected influences of habitat loss on regions of the world with tropical moist forest. This ecosystem, home to a disproportionate amount of global biodiversity and a major regulator of regional and global climate, also faces disproportionately severe threats. In this study, we collect diversity and endemism data for tropical forested countries of the world, along with areal and socioeconomic data. While a correlation between overall numbers of species and endemic species per country is expected, we demonstrate that endemism patterns among birds and mammals remain very strongly convergent even after statistically rendering all countries equal in size and overall species richness and after adjusting for spatial autocorrelation. On a per country basis, mammals are generally more threatened than birds in these tropical moist forested countries. Human population growth rates and rising debt among these nations should be viewed as priorities for amelioration by the developed countries. Reserve network extent is not related to numbers of endemic mammals or birds at this large spatial scale.     

Predation of potential insect pests in oil palm plantations,rubber tree plantations,and fruit orchards

In human‐modified landscapes, important ecological functions such as predation are negatively affected by anthropogenic activities, including the use of pesticides and habitat degradation. Predation of insect pests is an indicator of healthy ecosystem functioning, which provides important ecosystem services, especially for agricultural systems. In this study, we compare predation attempts from arthropods, mammals, and birds on artificial caterpillars in the understory, between three tropical agricultural land‐use types: oil palm plantations, rubber tree plantations, and fruit orchards. We collected a range of local and landscape‐scale data including undergrowth vegetation structure; elevation; proximity to forest; and canopy cover in order to understand how environmental variables can affect predation. In all three land‐use types, our results showed that arthropods and mammals were important predators of artificial caterpillars and there was little predation by birds. We did not find any effect of the environmental variables on predation. There was an interactive effect between land‐use type and predator type. Predation by mammals was considerably higher in fruit orchards and rubber tree than in oil palm plantations, likely due to their ability to support higher abundances of insectivorous mammals. In order to maintain or enhance natural pest control in these common tropical agricultural land‐use types, management practices that benefit insectivorous animals should be introduced, such as the reduction of pesticides, improvement of understory vegetation, and local and landscape heterogeneity.     

Factors determining the host plant range of the phytophagous mite, Tetranychus urticae (Acari: Tetranychidae): a method for quantifying host plant acceptance

The host plant acceptance of the phytophagous mite Tetranychus urticae was experimentally quantified. Host plant acceptance is described as the proportion of adult females settling on the test plant on which they have been placed. On the other hand, the host plant suitability of T. urticae on different plant species is expressed as the mean number of eggs produced by the females within 5 days (hereafter 'fecundity'). An inbred T. urticae line was tested with regard to host plant acceptance and fecundity on 11 potential host plants. These two variables were positively correlated across host plants; host plant species on which the fecundity was low were also those on which females settled less readily compared to host plants with high fecundity. The characteristics of host plant acceptance of the T. urticae are discussed in light of their potential food resource under natural conditions.     

The Pseudoplagioporinae,a new subfamily in the Opecoelidae Ozaki, 1925 (Trematoda) for a small clade parasitizing mainly lethrinid fishes,with three new species

The Pseudoplagioporinae n. subf. (Opecoelidae) is proposed for species of Pseudoplagioporus Yamaguti, 1938, Fairfaxia Cribb, 1989, and Shimazuia Cribb, 2005, a small group of relatively distinctive, Indo-West Pacific taxa reliably known almost entirely from emperor fishes (Perciformes: Lethrinidae). These taxa were previously recognized in the Plagioporinae Manter, 1947, but that subfamily has recently been restricted to a clade of Holarctic, freshwater taxa, whereas analyses of new genetic data find the pseudoplagioporines to form a distinct clade among a larger assemblage of marine taxa. New material was sourced from fishes collected mainly in Queensland waters, Australia, but with some specimens from off Western Australia, the Northern Territory, and Japan. Orthodena tropica Durio & Manter, 1968 is transferred to Pseudoplagioporus as P. tropicus (Durio & Manter, 1968) n. comb., and Orthodena Durio & Manter, 1968 thus becomes a synonym of that genus. Three new species of Pseudoplagioporus are proposed. One, P. mediocris n. sp., like other species of Pseudoplagioporus, occurs in several species of Lethrinus. The other two new species, P. labiatus n. sp. and P. roseovulatus n. sp., apparently do not infect species of Lethrinus and were instead found only in the Bigeye emperor Monotaxis grandoculis (Forsskål) and the Redfin emperor M. heterodon (Bleeker), respectively. New host-locality combinations and the first genetic data, for the ribosomal ITS2 DNA region, and the 28S rRNA, 18S rRNA, and cox1 mtDNA genes, are reported for Pseudoplagioporus lethrini Yamaguti, 1938, P. interruptus Durio & Manter, 1968, P. tropicus, Fairfaxia lethrini Cribb, 1989, Fairfaxia cribbi Hassanine & Gibson, 2005, and Shimazuia lethrini (Yamaguti, 1938) Cribb, 2005.     

Speciation,phenotypic plasticity,or ontogeny,the case of the genus Galkinius (Pyrgomatidae,Cirripedia, Crustacea)

Barnacles of the genus Galkinius occupy a large spectrum of host corals, making it one of the least host‐specific genera within the Pyrgomatidae. Molecular analyses show that within the genus Galkinius there are highly supported clades, suggesting that the genus Galkinius is a complex of evolutionarily significant units (ESUs). The morphology of the opercular valves has been used as the basis for the separation of species of Galkinius. In this study, morphological variability was found both between specimens within ESUs extracted from different host species and between specimens extracted from the same colony. Identifications based on the opercular valves cannot therefore be assigned to different species despite being genetically distinguishable. It is proposed that in many cases the differences between valve morphology of different species of Galkinius are the outcome of ontogeny. Allometric growth of the valves has resulted in differences in the proportions of the parts of the valve. © 2015 The Linnean Society of London     

Paleoecological patterns in molluscan extinctions and recoveries: comparison of the Cretaceous-Paleogene and Eocene-Oligocene extinctions in North America

Exposures across the Cretaceous-Tertiary (K-T) and Eocene-Oligocene (E-O) boundaries, in Texas and Mississippi, respectively, probably represent the most complete and best-preserved fossil molluscan sequences across these boundary intervals in the world. Outcrops from both boundaries contain pristine aragonitic and calcitic molluscan shells, which were deposited in fine-grained sediments from open marine environments. The K-T and the E-O extinctions exhibit very different recovery patterns, probably reflecting very different causes as well as magnitudes of extinction.The K-T sequence contains a molluscan fossil record that is consistent with an abrupt extinction event at the K-T boundary and a prolonged initial recovery in hostile oceanographic conditions. The uppermost 10 m of Upper Cretaceous sediments contain a diverse (approximately 40 species) molluscan fauna dominated by suspension feeders. The earliest Paleocene sediments immediately above the tsunami bed contain an impoverished fauna dominated by deposit feeders. The Paleocene fauna slowly climbs in diversity but remains relatively impoverished and dominated by deposit feeders for several hundred thousand years after the extinction in conjunction with anomalous δ¹³C values that suggest prolonged suppression of marine primary productivity. Diverse suspension-feeder dominated molluscan assemblages reappear with the resumption of normal conditions of primary production. In the long term, early to middle Paleocene gamma diversity includes evolutionary “bloom taxa,” families that exhibit unusual speciation bursts that subside in the Eocene. Total diversity for the Gulf Coast does not approach Cretaceous levels until the Late Eocene representing a total recovery interval of nearly 25 million years.While the E-O event also reflects a molluscan extinction rate of over 90% in the Gulf of Mexico, there are no signs of hostile environmental conditions in the recovery fauna. Early Oligocene molluscan assemblages are diverse and dominated by suspension feeders characteristic of normal marine conditions. The hiatus at the E-O boundary, however, could have obscured a short-term recovery fauna. There is also no sign of long-term perturbation by the E-O extinction. There are no bloom taxa and gamma diversity approaches pre-extinction levels within a few million years. The overall pattern of the E-O extinction is consistent with extinction (and/or migration) associated with long-term cooling.     

Impacts and management of feral cats Felis catus in Australia

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Insect, not plant, determines gall morphology in the Apiomorpha pharetrata species-group (Hemiptera: Coccoidea)

Abstract  Scale insects of the genus Apiomorpha Rübsaamen (Hemiptera: Coccoidea: Eriococcidae) induce sexually dimorphic galls on Eucalyptus, but the Apiomorpha pharetrata species-group is unusual in that nymphal males aggregate on the surface of the maternal gall where they induce a compound structure. Although originally described as distinct species on the basis of differences in gall morphology, A. pharetrata (Schrader) and A. thorntoni (Froggatt) were subsequently synonymised, primarily because the adult females of the two are morphologically indistinguishable. The two gall types of A. pharetrata sensu lato are allopatric and found on different host eucalypt species. To test the hypothesis that gall morphology may be determined by the host species on which the female feeds, we reared crawlers of field-collected females from both gall types on eucalypts in a glasshouse. Both gall types were induced on the same eucalypt species, with the gall type matching that of the maternal gall from which the crawlers had emerged. This indicates that it is the insect, not the host, that determines the gall morphology in these taxa. In addition, insects from the two gall types were different chromosomally and could be distinguished by one fixed allozyme difference. Thus, Brachyscelis (=  Apiomorpha ) thorntoni (Froggatt) revised status is removed from synonymy with Brachyscelis (=  Apiomorpha ) pharetrata (Schrader), and recognised as a distinct biological species. However, the extent of chromosomal variation among the populations of both A. pharetrata and A. thorntoni suggests that there may be further cryptic species present.     

Redescription of the western Balkan species Xerocampylaea waldemari and its phylogenetic relationships to other Urticicolini (Gastropoda: Hygromiidae)

The proper identification of species has significant implications for conservation and general knowledge of ecosystem variety. It is especially important for biodiversity hotspots and former Pleistocene refugia, such as the Balkans. In this paper, we evaluate the taxonomic status of the endemic Balkan species Fruticicola waldemari A. J. Wagner, 1912, using both recently collected material and museum specimens. Phylogenetic analyses based on two mitochondrial markers, 16S rRNA and cytochrome c oxidase subunit I, show that this species is closely related to the representatives of Xerocampylaea, including a conchologically similar and partly sympatric species, X. erjaveci. Analyses of shell and genital morphology as well as mitochondrial DNA sequences indicate that X. waldemari and X. erjaveci are separate but closely related species. These species differ in shell morphology (size, umbilicus diameter, microsculpture) as well as genital morphology. Nevertheless, a further study with more comprehensive sampling of both taxa is required to fully understand the complex pattern of genetic and morphological variation observed.     

Assessing the vulnerability of an assemblage of subtropical rainforest vertebrate species to climate change in south‐east Queensland

Global climate change is a threat to ecosystems that are rich in biodiversity and endemism, such as the World Heritage‐listed subtropical rainforests of central eastern Australia. Possible effects of climate change on the biota of tropical rainforests have been studied, but subtropical rainforests have received less attention. We analysed published data for an assemblage of 38 subtropical rainforest vertebrate species in four taxonomic groups to evaluate their relative vulnerability to climate change. Focusing on endemic and/or threatened species, we considered two aspects of vulnerability: (i) resistance, defined by indicators of rarity (geographical range, habitat specificity and local abundance); and (ii) resilience, defined by indicators of a species potential to recover (reproductive output, dispersal potential and climatic niche). Our analysis indicated that frogs are most vulnerable to climate change, followed by reptiles, birds, then mammals. Many species in our assemblage are regionally endemic montane rainforest specialists with high vulnerability. Monitoring of taxa in regenerating rainforest showed that many species with high resilience traits also persisted in disturbed habitat, suggesting that they have capacity to recolonize habitats after disturbance, that is climate change‐induced events. These results will allow us to prioritize adaptation strategies for species most at risk. We conclude that to safeguard the most vulnerable amphibian, reptile and bird species against climate change, climatically stable habitats (cool refugia) that are currently without protection status need to be identified, restored and incorporated in the current reserve system. Our study provides evidence that montane subtropical rainforest deserves highest protection status as habitat for vulnerable taxa.     

Fossil evidence for key innovations in the evolution of insect diversity

Explaining the taxonomic richness of the insects, comprising over half of all described species, is a major challenge in evolutionary biology. Previously, several evolutionary novelties (key innovations) have been posited to contribute to that richness, including the insect bauplan, wings, wing folding and complete metamorphosis, but evidence over their relative importance and modes of action is sparse and equivocal. Here, a new dataset on the first and last occurrences of fossil hexapod (insects and close relatives) families is used to show that basal families of winged insects (Palaeoptera, e.g. dragonflies) show higher origination and extinction rates in the fossil record than basal wingless groups (Apterygota, e.g. silverfish). Origination and extinction rates were maintained at levels similar to Palaeoptera in the more derived Polyneoptera (e.g. cockroaches) and Paraneoptera (e.g. true bugs), but extinction rates subsequently reduced in the very rich group of insects with complete metamorphosis (Holometabola, e.g. beetles). Holometabola show evidence of a recent slow-down in their high net diversification rate, whereas other winged taxa continue to diversify at constant but low rates. These data suggest that wings and complete metamorphosis have had the most effect on family-level insect macroevolution, and point to specific mechanisms by which they have influenced insect diversity through time.     

Duplication of genes encoding non-clathrin coat protein gamma-COP in vertebrate, insect and plant evolution

Coatomer is a major component of COPI vesicles and consists of seven subunits. The gamma-COP subunit of the coatomer is believed to mediate the binding to the cytoplasmic dilysine motifs of membrane proteins. We characterized cDNAs for Copg genes encoding gamma-COP from mouse, zebrafish, Drosophila melanogaster and Bombyx mori. Two copies of Copg genes are present in vertebrates and in B. mori. Phylogenetic analysis revealed that two paralogous genes had been derived from a single ancestral gene by duplication independently in vertebrates and in B. mori. Mouse Copg1 showed ubiquitous expression with the highest level in testis. Zebrafish copg2 was biallelically expressed in hybrid larvae in contrast to its mammalian ortholog expressed in a parent-of-origin-specific manner. A phylogenetic analysis with partial plant cDNA sequences suggested that copg gene was also duplicated in the grass family (Poaceae).     

Spatial patterns of plant diversity and communities in Alpine ecosystems of the Hengduan Mountains,Northwest Yunnan,China

Aims Conduct a quantitative, but rapid, regional-level assessment of the alpine flora across northwest Yunnan (NWY) to provide a broad-based understanding of local and regional patterns of the composition, diversity and health of alpine ecosystems across NWY.Methods A stratified random sampling design was employed to select sites across the different mountain ranges of NWY. Vegetation was sampled by stratifying each site by the three major alpine vegetation community types: meadow, dwarf shrub and scree. Two 50-m transects were randomly located within each community type at each sampling site with 10 1-m 2 subplots systematically placed along each transect. Environmental variables were recorded at each transect. Multivariate analyses were used to classify the major plant community assemblages and link community patterns to environmental and habitat variables.Important findings Forb species richness varied from 19 to 105 species per site (21 sites total) with an average of 59 species per site (60 m 2 sampled per site). Most species were patchily distributed with narrow distributions and/or small population sizes; over half the species occurred at only one or two sites. Distinct species assemblages were identified in the meadow vegetation that was strongly aggregated by geographic location suggesting the presence of distinct phytogeographic zones of the meadow alpine flora. Elevation and geographic location were the dominant environmental gradients underlying the variations in species composition. Jaccard's coefficient of similarity averaged only 10% among sites indicating there was little similarity in the alpine flora across the region. The alpine vegetation is highly heterogeneous across the complex landscape of the Hengduan Mountains of NWY. Conservation strategies need to take into account the large geographic differences in the flora to maximize protection of biodiversity.