Application of a Gondwanan perspective to restore ecological integrity in the south‐western Australian global biodiversity hotspot

Bounded by ocean and desert, the isolated, predominately Mediterranean‐climate region of south‐western Australia (SWA) includes nine bioregions (circa 44 million hectares). The ecological integrity of the landscapes in this global biodiversity hotspot has been compromised by deforestation, fragmentation, exploitation, and introduced biota. Nature and degree of transformation varies between four interconnected landscapes (Swan Coastal Plain; South‐west Forests; Wandoo Woodlands; and Great Western Woodlands). A Gondwanan perspective emphasizes a venerable biota and a cultural component to deep time. The particular importance of remnants and protected areas is recognized in restoring ecological integrity to Gondwanan landscapes. The nature and magnitude of the restoration task in these ancient, and neighboring, landscapes require higher levels of investment and more time than do recent landscapes. The protection, conservation, restoration, and rehabilitation of ecological integrity require multiple approaches in each landscape as well as consideration of the whole. Active conservation of biota and minimizing the impact of industrial‐ and agricultural‐use are priorities. Integrating a climate focus and rethinking fire are critical restoration considerations to future trajectories under anthropogenic climate change. A legislative mandate to coordinate industrial‐scale restoration and active conservation to build from protected areas must become a societal priority to restore ecological integrity.     

Climatic fluctuations shape the phylogeography of a mesic direct‐developing frog from the south‐western Australian biodiversity hotspot

Aim To assess phylogeographic pattern throughout the range of Metacrinia nichollsi in order to develop specific biogeographical hypotheses for the wet forests of south‐western Australia. This was carried out by contrasting a direct‐developing frog species, M. nichollsi, that breeds independently of free surface water with conventional, aquatic breeders and highly specialized direct developers. Location Wet forests of the south‐western Australian biodiversity hotspot – an area of high species richness and endemism for myobatrachid frogs and many other faunal groups. Methods We compiled an extensive phylogeographic data set from field‐collected samples based on mitochondrial ND2 sequences. Phylogenetic analyses combined with estimates of divergence times were used to build a model of major biogeographical events affecting the species. Phylogeographic analyses were used to provide insights into smaller‐scale processes acting within each major lineage. Results Phylogenetic analysis recovered three major lineages, with divergence dates coincident with late Miocene–early Pliocene arid cycles. One lineage was confined to geographically isolated populations in the Stirling Ranges (Stirling Ranges Lineage, SRL). The continuous range of M. nichollsi was split into two: the Main Range Lineage (MRL) and the Southern Coastal Lineage (SCL). The SCL displays a strong drainage‐based population structure, whereas the MRL displays a strong signature of recent expansion, suggesting that these two lineages have had very different biogeographical histories. Main conclusions Late Miocene–Pliocene aridity appears to have isolated populations in the Stirling Ranges and resulted in the formation of two additional lineages on a north–south gradient that are independent of southward‐flowing drainage systems. Our results demonstrate that climatic fluctuations are likely to have generated fine‐scale phylogeographic structure within M. nichollsi and that catchment regions are important refugia during arid cycles.     

Diversity, endemism and species turnover of millipedes within the south-western Australian global biodiversity hotspot

Aim To examine how current and historical environmental gradients affect patterns of millipede (Diplopoda) endemism and species turnover in a global hotspot of floristic diversity, and to identify regions of high endemism and taxonomic distinctness for conservation management. Location South‐western Australia. Methods Museum database records of millipedes (subclasses Pentazonia and Helminthomorpha), supplemented with extensive fieldwork, were used to map species richness, species turnover (β‐diversity), weighted endemism, average taxonomic distinctness and variation in taxonomic distinctness in half‐degree grid squares (c. 2500 km²). Generalized linear models were used to examine relationships between these parameters with rainfall (present day and historical), topography and human disturbance (clearing for agriculture and urbanization). Results Millipede species richness, particularly within the order Spirostreptida, and millipede endemism were positively associated with large within‐cell differences in elevation (mountainous regions). Large variation in taxonomic distinctness (unevenness in the taxonomic tree) in higher‐rainfall areas was mainly due to speciation within the Spirostreptida genus Atelomastix. Hotspots of millipede endemism and taxonomic distinctness were identified within three categories of importance: primary (Stirling Range East, Cape Le Grand, Cape Arid, Walpole, Porongurups), secondary (Mount Manypeaks, Bremer Bay, Stirling Range West, Duke of Orleans Bay, Ravensthorpe, Albany, Busselton) and tertiary (Nornalup). A species turnover boundary was positively associated with rainfall, broadly located in the transition zone of 300–600 mm year^?1. Main conclusions The current lack of knowledge on the endemism of invertebrates hampers their incorporation into conservation planning. With this knowledge we can identify global biodiversity hotspots and, at a smaller scale, significant conservation areas within a region. Here we have shown that weighted endemism and taxonomic distinctness are useful tools in identifying centres of high endemism and speciation for millipedes within the south‐west Australian hotspot. Moreover, it is unlikely that either vertebrates or vascular plants will be useful surrogates for identifying significant areas for invertebrate conservation. While other workers have shown that vascular plants, mammals and frogs have different centres of endemism within south‐west Australia, our results show that centres of endemism for millipedes encompass all of these plus other areas.     

Vouchering DNA‐barcoded specimens: test of a nondestructive extraction protocol for terrestrial arthropods

Morphology‐based keys support accurate identification of many taxa. However, identification can be difficult for taxa that are either not well studied, very small, members of cryptic species complexes, or represented by immature stages. For such cases, DNA barcodes may provide diagnostic characters. Ecologists and evolutionary biologists deposit museum vouchers to document the species studied in their research. If DNA barcodes are to be used for identification, then both the DNA and the specimen from which it was extracted should be vouchered. We describe a protocol for the nondestructive extraction of DNA from terrestrial arthropods, using as examples members of the orders Acarina, Araneae, Coleoptera, Diptera, and Hymenoptera chosen to represent the ranges in size, overall sclerotization, and delicacy of key morphological characters in the group. We successfully extracted sequenceable DNA from all species after 1–4 h of immersion in extraction buffer. The extracted carcasses, processed and imaged using protocols standard for the taxon, were distinguishable from closely related species, and adequate as morphological vouchers. We provide links from the carcasses and DNA vouchers to image (MorphBank) and sequence (GenBank) databases.     

The invertebrate fauna of the sandstone caves of the Cape Peninsula (South Africa): patterns of endemism and conservation priorities

The temperate sandstone caves of the Cape Peninsula, South Africa, support 85 cavernicolous invertebrate species across six phyla. Six of these, including two blind and depigmented species of insects (Dermaptera) and spiders (Araneae: Hahniidae) were previously unknown. Twenty-one species are endemic to the Peninsula. Thirteen of these are presumed troglobitic Gondwanan relicts, including highly specialized, phylogenetically unique, rare species with restricted distributions and specialized habitat requirements. According to the criteria listed in the IUCN Red List Categories (1994), the onychophoran Peripatopsis alba and crustacean Spelaeogriphus lepidops should be considered Critically Endangered, their extents of occurrence being less than 100km². Furthermore, Data Deficient species, such as the freshwater shrimps Protojanira leleupi and Paramelita barnardi, the spider Hahnia sp.nov., the earwig Dermaptera sp.nov. and the centipede Cryptops stupendus, are likely to be additional Critically Endangered species on account of their exceptional rarity or restricted distributions. The remaining endemic cavernicoles are considered Endangered on account of their limited distributions (extent of occurrence <5000km²). Therefore, conservation considerations are clearly an urgent priority and appropriate recommendations are provided. Management-orientated research, long-term population monitoring and the conservation of pseudokarst areas, are urgent requirements for the conservation of these rare and threatened evolutionary relicts in their isolated island-like habitats.     

Anomalies in grasstree fire history reconstructions for south‐western Australian vegetation

Abstract A new fire history for south‐western Australian sclerophyll forests was proposed recently based on grasstree (Xanthorrhoea preissii ) records that were interpreted to show a high frequency (3–5 years) ‘pre‐European burning regime’. Such a fire regime appears incompatible with the long‐term survival of many fire‐killed woody taxa. We investigated the local fire history in a small area of the northern sand‐plain shrub‐lands of south‐western Australia using 15 grasstrees, examining individual grasstree records in detail and comparing this with the decadal or averaged approach used in the original research, and with fire histories reconstructed from satellite images for the period since 1975. Results lead us to question the utility of the proposed grasstree fire history record as a tool for understanding past fire regimes for two reasons: First, inconsistencies in fire histories among individual grasstrees were considerable – some individuals were not burnt by known fires, while some apparently were burned many times during periods when others were not burned at all. Second, the grasstree record indicates a possible increase in patchiness of fires since 1930, while contemporary evidence and interpretations of the nature of Aboriginal (pre‐European) fire regimes would suggest the opposite. We believe that further research is needed to identify to what extent the grasstree method for reconstruction of fire histories can be used to re‐interpret how fire operated in many highly diverse ecosystems prior to European settlement of Australia.     

Hogfish Lachnolaimus maximus (Labridae) confirmed in the south‐western Atlantic Ocean

Based on material deposited in collections, photographic records and other reports from fishermen and divers, the occurrence of the hogfish Lachnolaimus maximus (Labridae) is confirmed in the south‐western Atlantic Ocean, near the Brazilian coast as far south as southern Brazil. The recognized range of this species should therefore be extended c. 3000 km further south.     

Orchid biogeography and factors associated with rarity in a biodiversity hotspot,the Southwest Australian Floristic Region

Aim The causes of orchid diversification and intrinsic rarity are poorly resolved. The Orchidaceae of the Southwest Australian Floristic Region use a diversity of pollination strategies and sites of mycorrhizal infection, and occupy a diversity of habitats. We combined a biogeographic analysis with analysis of factors associated with rarity to establish: (1) the landscape features correlated with taxon turnover and speciation, and (2) the possible role in taxon rarity of geographic region, pollination strategy, edaphic habitat and site of mycorrhizal infection. Location Southwest Australian Floristic Region. Methods The distributions of 407 orchid taxa (species and subspecies) were mapped at the quarter‐degree scale using 13,267 collections in the Western Australian Herbarium. This database was used to map taxon richness, for a biogeographic analysis and to quantify rarity of taxa. Using herbarium records, rarity was expressed as mean abundance, mean distribution and incidence of rarity based on abundance and distribution for each genus. We tested for differences in rarity of species between pollination strategies, edaphic habitats and sites of mycorrhizal infection. Results Taxon richness was highest in the High Rainfall Province. Biogeographic provincial boundaries for orchids were aligned with rainfall, while district boundaries tended to follow geological formations. When rarity was defined as either low abundance or small distribution, the greatest number of rare taxa occurred in areas of high taxon richness and naturally fragmented edaphic environments. For both abundance and distributional extent, sexual deception had a significantly higher incidence of rarity than food‐rewarding taxa. There was no significant difference in rarity with site of mycorrhizal infection. Main conclusions While large‐scale edaphic and climatic variation are correlated with orchid taxon turnover and speciation in a similar fashion to the flora in general, the processes responsible for patterns of diversity may differ. Fragmented edaphic environments appear to be associated with a higher incidence of rare species due to limited dispersal/colonization opportunities or radiations of taxa in allopatry. The high incidence of rarity in sexually deceptive taxa could be due to either low fruit set or the risk of specializing on a single pollinator species.     

The role of bracket fungi in creating alpha diversity of invertebrates in the Białowieża National Park,Poland

Bracket fungi are seen mainly as the cause of economic losses in forestry, and their role as creators of biodiversity is relatively poorly understood. The aim of the study was defining the manner in which the degree of decay (DD) of the fruiting bodies determines the character of the invertebrate assemblages colonising them. The effect of this group of fungi on the modification of biodiversity of invertebrates (Aranae, Opiliones, Pseudoscorpionida, two groups of mites—Mesostigmata and Oribatida, and Collembola and Insecta) was investigated by analyzing 100 fruiting bodies of 10 species of bracket fungi divided into four DD classes. The material was collected at Białowieża National Park, which is considered to be the largest area of natural forests in the North European Plain. 16 068 invertebrate individuals classified into 224 species were obtained. Oribatid mites (12 543 individuals) constituted the largest group of individuals, which were classified into 115 species with the most numerous Carabodes femoralis (8,811 individuals). Representatives of this group of mites have been reported previously in the publications on bracket fungi; however, the contributions of Oribatida and other groups of invertebrates were not broadly compared. Moreover, the species such as Hoploseius mariae and H. oblongus, which were predominantly found in fruiting bodies of bracket fungi, have also been discerned. The invertebrate fauna differs depending on DD of the samples: In the more decayed samples, a higher number of both individuals and species were recorded compared to the samples with lower DDs; however, this trend proved to be nonlinear. The DCA and cluster analysis revealed a similarity of the invertebrate assemblages from the 2 DD and 4 DD samples. They also indicated that the group 3 DD differed the most from all the other samples. The indicator species analysis identified species characteristic to individual DDs: For group 1 DD, it was, for example, Hoploseius oblongus; for 2 DD—Orchesella bifasciata; and for 3 DD—Chernes cimicoides, while for 4 DD—Dinychus perforatus.     

Land use legacy effects on woody vegetation in agricultural landscapes of south‐western Ethiopia

Aim

Past land use legacy effects—extinction debts and immigration credits—might be particularly pronounced in regions characterized by complex and dynamic landscape change. The aim of this study was to evaluate how current woody plant species distribution, composition and richness related to historical and present land uses.

Location

A smallholder farming landscape in south‐western Ethiopia.

Methods

We surveyed woody plants in 72 randomly selected 1‐ha sites in farmland and grouped them into forest specialist, generalist and pioneer species. First, we investigated woody plant composition and distribution using non‐metric multidimensional scaling. Second, we modelled species richness in response to historical and current distance from the forest edge. Third, we examined diameter class distributions of trees in recently converted vs. permanent farmland.

Results

Historical distance was a primary driver of woody plant composition and distribution. Generalist and pioneer species richness increased with historical distance. Forest specialists, however, did not respond to historical distance. Only few old individuals of forest specialist species remained in both recently converted and permanent farmlands.

Main conclusions

Our findings suggest that any possible extinction debt for forest specialist species in farmland at the landscape scale was rapidly paid off, possibly because farmers cleared large remnant trees. In contrast, we found substantial evidence of immigration credits in farmland for generalist and pioneer species. This suggests that long‐established farmland may have unrecognized conservation values, although apparently not for forest specialist species. We suggest that conservation policies in south‐western Ethiopia should recognize not only forests, but also the complementary value of the agricultural mosaic—similar to the case of European cultural landscapes. A possible future priority could be to better reintegrate forest species in the farmland mosaic.

     

Genetic connectivity and phenotypic plasticity in the cyprinodont Aphanius farsicus from the Maharlu Basin,south‐western Iran

Meristic and morphometric characteristics, including otolith data, of the Farsi tooth‐carp Aphanius farsicus, which is endemic to the endorheic Maharlu Basin in south‐western Iran, were analysed for a sample of 92 individuals from four spring‐streams; DNA sequence data (cytochrome b gene) are presented for 29 specimens. Some phenotypic variation was detected but the genetic data clearly indicate connectivity between the populations. Possible links between phenotypic variation and environmental variables such as water temperature, habitat size and absence or presence of predators and competitors are discussed. Based on a literature survey and the new data, it is concluded that population connectivity is maintained during times of droughts via large aquifers that formed during the late Pliocene to early Pleistocene, when the extant endorheic Maharlu Basin was created. Based on new data presented here and previous work, it is apparent that plastic and constant characteristics are present in Aphanius species, and that, if a population becomes isolated, a given trend of evolution may give rise to a taxonomically useful characteristic.     

Biodiversity responses to land‐use and restoration in a global biodiversity hotspot: Ant communities in Brazilian Cerrado

Given that land‐use change is the main cause of global biodiversity decline, there is widespread interest in adopting land‐use practices that maintain high levels of biodiversity, and in restoring degraded land that previously had high biodiversity value. In this study, we use ant taxonomic and functional diversity to examine the effects of different land uses (agriculture, pastoralism, silviculture and conservation) and restoration practices on Cerrado (Brazilian savanna) biodiversity. We also examine the extent to which ant diversity and composition can be explained by vegetation attributes that apply across the full land management spectrum. We surveyed vegetation attributes and ant communities in five replicate plots of each of 13 land‐use and restoration treatments, including two types of native vegetation as reference sites: cerrado sensu stricto and cerradão. Several land‐use and restoration treatments had comparable plot richness to that of the native reference habitats. Ant species and functional composition varied systematically among land‐use treatments following a gradient from open habitats such as agricultural fields to forested sites. Tree basal area and grass cover were the strongest predictors of ant species richness. Losses in ant diversity were higher in land‐use systems that transform vegetation structure. Among productive systems, therefore, uncleared pastures and old pine plantations had similar species composition to that occurring in cerrado sensu stricto. Restoration techniques currently applied to sites that were previously Cerrado have focused on returning tree cover, and have failed to restore ant communities typical of savanna. To improve restoration outcomes for Cerrado biodiversity, greater attention needs to be paid to the re‐establishment and maintenance of the grass layer, which requires frequent fire. At the broader scale, conservation planning in agricultural landscapes, should recognize the value of land‐use mosaics and the risks of homogenization.     

Continental‐scale syntheses of Australian pyromes – misclassification of south‐western eucalypt woodlands misinforms management

Global and continental‐scale analysis of ecological phenomena can offer important insights through the identification of patterns and associations not detectable at smaller scales. However, using proxies for ecological phenomena, such as vegetation mapping for spatially projecting fire regime niches and post‐fire plant responses, require critical examination of predictions to determine utility. Using local studies in south‐western Australia, we demonstrate that while this approach has been largely successful in mallee woodland and shrubland, it has failed in eucalypt woodland, with the consequence that values for a range of fire‐related parameters from the continent‐wide approaches, if adopted in informing management, would result in undesirable conservation outcomes for the world's largest extant temperate woodland.     

Population structure and cryptic speciation in bonnethead sharks Sphyrna tiburo in the south‐eastern U.S.A. and Caribbean

Population structure and lineage diversification within a small, non‐dispersive hammerhead shark species, the bonnethead shark Sphyrna tiburo, was assessed. Sphyrna tiburo is currently described as one continuously distributed species along the Atlantic continental margins of North, Central and South America, but recent genetic analysis of an insular population (Trinidad) suggests the possibility of cryptic speciation. To address this issue S. tiburo were sampled at six sites along c. 6200 km of continuous, continental coastline and from one island location (Grand Bahama) across a discontinuity in their distribution (the Straits of Florida), in order to test if they constitute a single lineage over this distribution. A total of 1030 bp of the mitochondrial control region (CR) was obtained for 239 S. tiburo, revealing 73 distinct haplotypes, high nucleotide diversity (0·01089) and a pair of highly divergent lineages estimated to have separated 3·61–5·62 million years ago. Mitochondrial cytochrome oxidase I and nuclear internal transcribed spacer loci show the same pattern. Divergence is similar within S. tiburo to that observed between established elasmobranch sister species, providing further evidence of cryptic speciation. A global AMOVA based on CR confirms that genetic diversity is primarily partitioned among populations (Φ_ST = 0·828, P < 0·001) because the divergent lineages are almost perfectly segregated between Belize and North America–The Bahamas. An AMOVA consisting solely of the North American and Bahamian samples is also significantly different from zero (Φ_ST = 0·088, P < 0·001) and pairwise F_ST is significantly different between all sites. These findings suggest that S. tiburo comprises a species complex and supports previous research indicating fine population structure, which has implications for fisheries management and biodiversity conservation.     

Recent rapid speciation and ecomorph divergence in Indo‐Australian sea snakes

The viviparous sea snakes (Hydrophiinae) are a young radiation of at least 62 species that display spectacular morphological diversity and high levels of local sympatry. To shed light on the mechanisms underlying sea snake diversification, we investigated recent speciation and eco‐morphological differentiation in a clade of four nominal species with overlapping ranges in Southeast Asia and Australia. Analyses of morphology and stomach contents identified the presence of two distinct ecomorphs: a ‘macrocephalic’ ecomorph that reaches >2 m in length, has a large head and feeds on crevice‐dwelling eels and gobies; and a ‘microcephalic’ ecomorph that rarely exceeds 1 m in length, has a small head and narrow fore‐body and hunts snake eels in burrows. Mitochondrial sequences show a lack of reciprocal monophyly between ecomorphs and among putative species. However, individual assignment based on newly developed microsatellites separated co‐distributed specimens into four significantly differentiated clusters corresponding to morphological species designations, indicating limited recent gene flow and progress towards speciation. A coalescent species tree (based on mitochondrial and nuclear sequences) and isolation‐migration model (mitochondrial and microsatellite markers) suggest between one and three transitions between ecomorphs within the last approximately 1.2 million to approximately 840 000 years. In particular, the macrocephalic ‘eastern’ population of Hydrophis cyanocinctus and microcephalic H. melanocephalus appear to have diverged very recently and rapidly, resulting in major phenotypic differences and restriction of gene flow in sympatry. These results highlight the viviparous sea snakes as a promising system for speciation studies in the marine environment.