Decline of a biome: evolution,contraction, fragmentation,extinction and invasion of the Australian mesic zone biota

Aim The mesic biome, encompassing both rain forest and open sclerophyllous forests, is central to understanding the evolution of Australia’s terrestrial biota and has long been considered the ancestral biome of the continent. Our aims are to review and refine key hypotheses derived from palaeoclimatic data and the fossil record that are critical to understanding the evolution of the Australian mesic biota. We examine predictions arising from these hypotheses using available molecular phylogenetic and phylogeographical data. In doing so, we increase understanding of the mesic biota and highlight data deficiencies and fruitful areas for future research. Location The mesic biome of Australia, along the eastern coast of Australia, and in the south‐east and south‐west, including its rain forest and sclerophyllous, often eucalypt‐dominated, habitats. Methods We derived five hypotheses based on palaeoclimatic and fossil data regarding the evolution of the Australian mesic biota, particularly as it relates to the mesic biome. We evaluated predictions formulated from these hypotheses using suitable molecular phylogenies of terrestrial plants and animals and freshwater invertebrates. Results There was support for the ancestral position of mesic habitat in most clades, with support for rain forest habitat ancestry in some groups, while evidence of ancestry in mesic sclerophyllous habitats was also demonstrated for some plants and herpetofauna. Contraction of mesic habitats has led to extinction of numerous lineages in many clades and this is particularly evident in the rain forest component. Species richness was generally higher in sclerophyllous clades than in rain forest clades, probably due to higher rates of net speciation in the former and extinction in the latter. Although extinction has been prominent in rain forest communities, tropical rain forests appear to have experienced extensive immigration from northern neighbours. Pleistocene climatic oscillations have left genetic signatures at multiple levels of divergence and with complex geographical structuring, even in areas with low topographical relief and few obvious geographical barriers. Main conclusions Our review confirms long‐held views of the ancestral position of the Australian mesic biome but also reveals new insights into the complexity of the processes of contraction, fragmentation, extinction and invasion during the evolution of this biome.     

Phylogeography of sexual Heteronotia binoei (Gekkonidae) in the Australian arid zone: climatic cycling and repetitive hybridization

The biota of much of continental Australia have evolved within the context of gradual aridification of the region over several million years, and more recently of climatic cycling between relatively dry and humid conditions. We performed a phylogeographical study of three sexual chromosome races of the Heteronotia binoei complex of geckos found throughout the Australian arid zone. Two of these three races were involved in two separate hybridization events leading to parthenogenetic lineages (also H. binoei), and the third is widespread and broadly sympatric with the parthenogens. Based on our analyses, the three sexual races diversified approximately 6 million years ago in eastern Australia, during a period of aridification, then each moved west through northern, southern, and central dispersal corridors to occupy their current ranges. In each case, the timing of major phylogeographical inferences corresponds to inferred palaeoclimatic changes in continental Australia. This scenario provides a simple explanation for diversification, secondary contact, and hybridization between the races. However, data presented elsewhere indicate that formation of the parthenogens was considerably more recent than the westward expansion of the hybridizing races, and that multiple hybridization events were geographically and temporally distinct. We suggest that cyclical climate changes may have led to regional range changes that facilitated hybridization between the races, which are not currently known to be in sympatry.     

The evolution of sexual and parthenogenetic Warramaba: a window onto Plio–Pleistocene diversification processes in an arid biome

Environmental changes over the Plio‐Pleistocene have been key drivers of speciation patterns and genetic diversification in high‐latitude and mesic environments, yet comparatively little is known about the evolutionary history of species in arid environments. We applied phylogenetic and phylogeographic analyses to understand the evolutionary history of Warramaba grasshoppers from the Australian arid zone, a group including sexual and parthenogenetic lineages. Sequence data (mitochondrial COI) showed that the four major sexual lineages within Warramaba most likely diverged in the Pliocene, around 2–7 million years ago. All sexual lineages exhibited considerable phylogenetic structure. Detailed analyses of the hybrid parthenogenetic species W. virgo and its sexual progenitors showed a pattern of high phylogenetic diversity and phylogeographic structure in northern lineages, and low diversity and evidence for recent expansion in southern lineages. Northern sexual lineages persisted in localized refugia over the Pleistocene, with sustained barriers promoting divergence over this period. Southern parts of the present range became periodically unsuitable during the Pleistocene, and it is into this region that parthenogenetic lineages have expanded. Our results strongly parallel those for sexual and parthenogenetic lineages of the gecko Heteronotia from the same region, indicating a highly general effect of Plio‐Pleistocene environmental change on diversification processes in arid Australia.     

干旱区绿洲扩张方式对土壤生物优势类群及功能的影响

内陆干旱区人口数量急剧增加驱动了绿洲快速扩张, 扩张方式主要包括: 灌木地、林地和农地扩张, 尚缺乏绿洲扩张方式对土壤生物多样性和生态系统服务功能影响的研究。本文以河西走廊黑河中游张掖绿洲为研究区域, 选择绿洲边缘天然草地及其转变的人工梭梭(Haloxylon ammodendron)灌木地(无灌溉)、人工杨树(Populus gansuensis)林地(灌溉)、玉米(Zea mays)地(灌溉 + 施肥)为研究对象, 测定了4种生境土壤食物网中9种优势功能类群的密度以及反映土壤生态系统功能特征的有机碳储量、氮储量、磷储量与土壤过氧化氢酶、蔗糖酶、脲酶、碱性磷酸酶活性。主要结果如下: (1)灌木地扩张显著降低了甲螨、植食性昆虫密度, 增加了跳虫、捕食性螨密度和真菌的OTUs, 对其余类群无显著影响; 林地扩张增加了捕食性节肢动物、植食性昆虫、捕食性螨、跳虫、甲螨的密度及细菌和真菌OTUs, 对其余类群无显著影响; 农地扩张增加了蚓类、捕食性节肢动物、捕食性螨、跳虫、甲螨的密度及细菌和真菌的OTUs, 对其余类群无显著影响。(2)林地和灌木地扩张显著提高了土壤有机碳储量和氮储量, 而农地扩张显著提高了土壤有机碳储量、氮储量和磷储量。(3) 3种扩张方式显著提高了土壤过氧化氢酶、蔗糖酶、脲酶、碱性磷酸酶活性, 玉米地和杨树林地土壤酶活性的增幅高于灌木地。人工绿洲扩张方式显著和有差异地改变了土壤食物网结构及其生态功能水平, 该结果对建立基于土地利用结构优化调控的人工绿洲生物多样性保护管理新方法具有重要意义, 并为人工绿洲生态系统功能稳定性评价研究提供了基础资料。     

Subterranean archipelago in the Australian arid zone: mitochondrial DNA phylogeography of amphipods from central Western Australia

In 1998, a unique subterranean ecosystem was discovered in numerous isolated calcrete (carbonate) aquifers in the arid Yilgarn region of Western Australia. Previous morphological and genetic analyses of a subterranean water beetle fauna suggest that calcrete aquifers are equivalent to closed island habitats that have been isolated for millions of years. We tested this hypothesis further by phylogeographic analyses of subterranean amphipods (Crangonyctoidea: Paramelitidae and Hyalidae) using mitochondrial DNA sequence data derived from the cytochrome oxidase I gene. Phylogenetic analyses and population genetic analyses (samova) provided strong evidence for the existence of at least 16 crangonyctoid and six hyalid divergent mitochondrial lineages, each restricted in their distribution to a single calcrete aquifer, in support of the 'subterranean island (archipelago) hypothesis' and extending its scope to include entirely water respiring invertebrates. Sequence divergence estimates between proximate calcrete populations suggest that calcretes have been isolated at least since the Pliocene, coinciding with a major aridity phase that led to the intermittent drying of surface water. The distribution of calcretes along palaeodrainage channels and on either side of drainage divides, have had less influence on the overall phylogeographic structure of populations, with evidence that ancestral crangonyctoid and hyalid species moved between catchments multiple times prior to their isolation within calcretes. At least two potential modes of evolution may account for the diversity of subterranean amphipod populations: dispersal/vicariance of stygobitic species or colonization of calcretes by surface species and independent evolution of stygobitic characteristics.     

The role of marine biota in the evolution of terrestrial biota: Gases and genes

There is greater biodiversity (in the senseof genetic distance among higher taxa) ofextant marine than of terrestrialO₂-evolvers. In addition tocontributing the genes from one group ofalgae (Class Charophyceae, DivisionChlorophyta) to produce by evolution thedominant terrestrial plants (Embryophyta),the early marine O₂-evolvers greatlymodified the atmosphere and hence the landsurface when the early terrestrialO₂-evolvers grew. The earliestterrestrial phototrophs (from geochemicalevidence) occurred 1.2 Ga ago, over 0.7 Gabefore the Embryophyta evolved, but wellafter the earliest marine (cyanobacterial)O₂ evolvers (3.45 Ga) and marineeukaryotic O₂ evolvers (2.1 Ga). Evenby the time of evolution of the earliestterrestrial O₂-evolvers the marineO₂-evolvers had modified the atmosphereand land environment in at least thefollowing five ways. Once photosyntheticO₂ paralleling organic C burial hadsatisfied marine (Fe²⁺, S^2-reductants, atmospheric O₂ built (1) upto a considerable fraction of the extantvalue (although some was consumed inoxidising terrestrial exposed Fe²⁺ and(2) provided stratospheric O₃ and thusa UV-screen. (3) CO₂ drawdown to20-30times the extant level is attributableto net production, and burial, of organic Cin the oceans (plus other geologicalprocesses). Furthermore, (4) theirproduction of volatile organic S compoundscould have helped to supply S to inland sitesbut also (5) delivered Cl and Br to thestratosphere thus lowering the O₃ leveland the extent of UV screening.     

Lower fecundity in parthenogenetic geckos than sexual relatives in the Australian arid zone

Theoretical models of the advantage of sexual reproduction typically assume that reproductive output is equal in sexual and parthenogenetic females. We tested this assumption by comparing fecundity between parthenogenetic and sexual races of gekkonid lizards in the Heteronotia binoei complex, collected across a 1200 km latitudinal gradient through the Australian arid zone. Under laboratory conditions, parthenogenetic geckos had approximately 30% lower fecundity when compared with their sexual progenitors, irrespective of body size. Reflecting clutch-size constraints in gekkonids, this fecundity difference was mainly because of fewer clutches over a shorter period. When parthenogens were compared more broadly with all coexisting sexual races across the latitudinal gradient, parthenogens had lower fecundity than sexuals only when corrected for body size. Differences in fecundity between parthenogens and coexisting sexual races depended on which sexual race was considered. There was no significant relationship between fecundity and parasite (mite) load, despite significantly higher mite loads in parthenogens than in sexual races.     

Actin in striated muscle: recent insights into assembly and maintenance

Striated muscle cells are characterised by a para-crystalline arrangement of their contractile proteins actin and myosin in sarcomeres, the basic unit of the myofibrils. A multitude of proteins is required to build and maintain the structure of this regular arrangement as well as to ensure regulation of contraction and to respond to alterations in demand. This review focuses on the actin filaments (also called thin filaments) of the sarcomere and will discuss how they are assembled during myofibrillogenesis and in hypertrophy and how their integrity is maintained in the working myocardium.     

Effects of spines and thorns on Australian arid zone herbivores of different body masses

Summary We investigated the effects of thorns and spines on the feeding of 5 herbivore species in arid Australia. The herbivores were the rabbit (Oryctolagus cuniculus), euro kangaroo (Macropus robustus), red kangaroo (Macropus rufus), sheep (Ovis aries), and cattle (Bos taurus). Five woody plants without spines or thorns and 6 woody plants with thorns were included in the study. The spines and thorns were not found to affect the herbivores' rates of feeding (items ingested/min), but they did reduce the herbivores' rates of biomass ingestion (g-dry/item). The reduction in biomass ingested occurred in two ways: at a given diameter, twigs with spines and thorns had less mass than undefended plants, and the herbivores consumed twigs with smaller diameters on plants with spines and thorns. The relative importance of the two ways that twigs with spines and thorns provided less biomass varied with herbivore body mass. Reduced twig mass was more important for small herbivores, while large herbivores selected smaller diameters. The effectiveness of spines and thorns as anti-herbivore defenses did not vary with the evolutionary history of the herbivores (i.e. native vs. introduced). Spines and thorns mainly affected the herbivores' selection of maximum twig sizes (reducing diameter and mass), but the minimum twig sizes selected were also reduced.     

Relative impacts of cattle grazing and feral animals on an Australian arid zone reptile and small mammal assemblage

The effect of different levels of cattle grazing on an arid Australian small terrestrial mammal and lizard assemblage was assessed in a long‐tem series of cross‐fence comparisons. Cross‐fenced sites were closely matched for edaphic and vegetation characteristics and experienced near identical weather patterns, to ensure that cattle grazing pressure was the principal determinant of any differences in fauna assemblages. In addition, the effects of removal of cattle, cats, foxes and rabbits from three of these long‐term monitoring sites were assessed to determine the relative impacts of cattle grazing and feral animals. Small mammal captures, with the exception of Mus musculus, revealed a significant negative response to cattle grazing pressure but this response was of a considerably lower magnitude than the dramatic increase in rodent captures and species richness within the feral animal‐proof Arid Recovery Reserve. Higher kangaroo numbers in ungrazed controls, compared with treatments grazed by cattle, possibly negated the benefits to small mammals of removing cattle grazing. No reptile species responded significantly to the grazing treatments although reptile richness and captures of geckos and skinks were the lowest and agamid captures were the highest at heavily grazed sites. Nephrurus levis was the only reptile species to increase significantly, while captures of some smaller geckoes declined, within the feral‐proof treatment. Feral predation exerted a more significant effect on most small mammal species than the levels of cattle grazing assessed in this study, yet reptile responses to grazing or feral animals were less apparent and were likely primarily driven by changes in vegetation cover or secondary trophic impacts.     

Fish larvae, growth and biomass relationships in an Australian arid zone river: links between floodplains and waterholes

1. Floodplain inundation provides many benefits to fish assemblages of floodplain river systems, particularly those with a predictable annual flood pulse that drives yearly peaks in fish production. In arid‐zone rivers, hydrological patterns are highly variable and the influence of irregular floods on fish production and floodplain energy subsidies may be less clear‐cut. To investigate the importance of floodplain inundation to a dryland river fish assemblage, we sampled fish life stages on the floodplain of Cooper Creek, an Australian arid‐zone river. Sampling was focused around Windorah during a major flood in January 2004 and in isolated waterholes in March 2004 following flood drawdown. 2. Of the 12 native species known to occur in this region, 11 were present on the floodplain, and all were represented by at least two of three life‐stages – larvae, juveniles or adult fish. Late stage larvae of six fish species were found on the floodplain. There were site‐specific differences in larval species assemblages, individual species abundances and larval distribution patterns among floodplain sites. 3. Significant growth was evident on the floodplain, particularly by larval and juvenile fish, reflecting the combination of high water temperatures and shallow, food rich habitats provided by the relatively flat floodplain. 4. Low variation in biomass, species richness and presence/absence of juvenile and adult fish across four floodplain sites indicates consistently high fish productivity across an extensive area. 5. Similarities and differences in fish biomass between the floodplain and isolated post‐flood waterholes suggest high rates of biomass transfer (involving the most abundant species) into local waterholes and, potentially, biomass transfer by some species to other waterholes in the catchment during floodplain inundation and after floods recede. 6. The high concentration of fish on this shallow floodplain suggests it could be a key area of high fish production that drives a significant proportion of waterhole productivity in the vicinity. The Windorah floodplain provides favourable conditions necessary for the spawning of some species and juvenile recruitment of the majority of species. It is also appears to be a significant conduit for the movements of fish that underpin high genetic similarity, hence population mixing, of many species throughout the Cooper Creek catchment. The high floodplain fish production in turn provides a significant energy subsidy to waterholes after floodwaters recede. 7. The identification of key sites of high fish production, such as the Windorah floodplain, may be important from a conservation perspective. Key management principles should be: maintenance of the natural flooding regime; identification of the most productive floodplain areas; and maintenance of their connectivity to anastomosing river channels and the remnant aquatic habitats that ultimately sustain this fish assemblage through long‐term dry/drought and flood cycles.     

The role of after‐ripening in promoting germination of arid zone seeds: a study on six Australian species

The effects of after‐ripening (storage under warm, dry conditions) on seed germination was examined in six plant species from the arid zone of Western Australia with the aim of improving germination and germination rate for rehabilitation objectives. Study species (Acanthocarpus preissii, Anthocercis littorea, Dioscorea hastifolia, Eremophila oldfieldii, Thryptomene baeckeacea and Zygophyllum fruticulosum) were selected based on diverse plant habits, seed types and requirements for rehabilitation. After‐ripening was investigated by adjusting seed moisture content to 13 and 50 equilibrium relative humidity (eRH) at 23 °C and storing seeds at two temperatures (30 and 45 °C) from 1 to 18 months. Following storage, seeds were incubated in water, gibberellic acid (GA₃) or karrikinolide (KAR₁; the butenolide, 3‐methyl‐2H‐furo[2,3‐c]pyran‐2‐one). All after‐ripening conditions increased germination percentage and rate of A. littorea and D. hastifolia, with A. littorea only germinating when treated with GA₃ or KAR₁. The germination of Z. fruticulosum was dependent on after‐ripening temperature and seed moisture content. After‐ripening had a limited effect on the remaining three species. The restoration implications of the findings are discussed. © 2009 The Linnean Society of London, Botanical Journal of the Linnean Society, 2009, 161 , 411–421.     

Molecular phylogeny of three groups of acacias (Acacia subgenus Phyllodineae) in arid Australia based on the internal and external transcribed spacer regions of nrDNA

The phylogeny of three groups of arid Australian acacias ‐ the Acacia victoriae, A. murrayana and A. pyrifolia groups ‐ was constructed based on parsimony analysis of sequence data from the internal and external transcribed spacers (ITS and ETS) of the nuclear ribosomal DNA. Forty ingroup taxa were sequenced, including multiple accessions for some taxa and two species (A platycarpa and A. longispinea) that had been identified in other analyses as relatives of these acacias. Acacia anthochaera was used as the functional outgroup.

The ITS and ETS regions proved to be sufficiently variable to resolve relationships at both the specific and intra‐specific level. Two main clades were resolved. One clade confirmed the monophyly of the Acacia murrayana group, and relationships of species were strongly supported. All taxa in this clade have a similar pattern of seedling leaf development. In the second clade, the A. pyrifolia group is nested within the A. victoriae group and all taxa have spinose stipules. Acacia platycarpa and A. longispinea are related to this clade. Phyllode nerve number (uninerved or plurinerved) proved to be homoplasious.

Acacia victoriae is a widespread and very variable species. The molecular data identified two major groups: a group of populations occurring across northern Australia and a group of populations from the Western, Central and Eastern deserts. Further analysis of population variation is required to assess the taxonomic status of various forms in this species complex.

The geographic distributions of sister taxa suggest predominantly allopatric speciation. The degree of molecular divergence and position of the clades within subgenus Phyllodineae suggest that the lineages are not of recent origin, but have a history that relates to increased aridity in the Australian Eremean region during the Cenozoic.     

Evolutionary refugia and ecological refuges: key concepts for conserving Australian arid zone freshwater biodiversity under climate change

Refugia have been suggested as priority sites for conservation under climate change because of their ability to facilitate survival of biota under adverse conditions. Here, we review the likely role of refugial habitats in conserving freshwater biota in arid Australian aquatic systems where the major long‐term climatic influence has been aridification. We introduce a conceptual model that characterizes evolutionary refugia and ecological refuges based on our review of the attributes of aquatic habitats and freshwater taxa (fishes and aquatic invertebrates) in arid Australia. We also identify methods of recognizing likely future refugia and approaches to assessing the vulnerability of arid‐adapted freshwater biota to a warming and drying climate. Evolutionary refugia in arid areas are characterized as permanent, groundwater‐dependent habitats (subterranean aquifers and springs) supporting vicariant relicts and short‐range endemics. Ecological refuges can vary across space and time, depending on the dispersal abilities of aquatic taxa and the geographical proximity and hydrological connectivity of aquatic habitats. The most important are the perennial waterbodies (both groundwater and surface water fed) that support obligate aquatic organisms. These species will persist where suitable habitats are available and dispersal pathways are maintained. For very mobile species (invertebrates with an aerial dispersal phase) evolutionary refugia may also act as ecological refuges. Evolutionary refugia are likely future refugia because their water source (groundwater) is decoupled from local precipitation. However, their biota is extremely vulnerable to changes in local conditions because population extinction risks cannot be abated by the dispersal of individuals from other sites. Conservation planning must incorporate a high level of protection for aquifers that support refugial sites. Ecological refuges are vulnerable to changes in regional climate because they have little thermal or hydrological buffering. Accordingly, conservation planning must focus on maintaining meta‐population processes, especially through dynamic connectivity between aquatic habitats at a landscape scale.     

宁夏中部干旱带不同作物根际土壤真菌群落多样性及群落结构

【背景】宁夏中部干旱带常年缺水,植被稀疏,土地沙漠化严重,生态环境十分脆弱。土地沙漠化导致土地生产力下降,制约着该区农业的发展,因此,改善宁夏中部干旱带农田生态环境具有重要意义。【目的】为该区土地资源的合理利用开发及干旱区土壤真菌多样性的深入研究提供基础数据和理论依据。【方法】运用IlluminaMiSeq高通量测序技术对宁夏中部干旱带农田作物土壤真菌种类进行预测,并对其进行真菌多样性和群落结构的分析。【结果】5个处理中真菌种类均较为丰富,丰富度指数无差异;真菌多样性指数分别以‘张杂谷5号’谷子最高,藜麦的多样性最低,且存在极显著差异。不同作物根际土壤中,子囊菌门(Ascomycota)为最优势菌门,相对丰度为73.00%-89.14%,且远远大于次优势菌门——担子菌门(Basidiomycota,3.9%-16.5%),表现出非常明显的优势;支顶孢属(Acremonium)和裂壳菌属(Schizothecium)为共有的优势菌属。土壤速效磷和土壤碱解氮会对土壤真菌群落结构和功能多样性产生影响,土壤微生物群落结构、功能多样性的变化是土壤理化性质与微生物相互作用的结果。【结论】休闲和种植作物的农田土壤养分均可不同程度的提高,土壤pH降低,真菌群落结构和多样性发生变化。说明合理的土地利用有利于丰富农田土壤微生物群落结构和多样性,改良土壤特性,进而促进该区域土壤生态系统的稳定,提高农田土地资源的合理利用。     

A review of the salt sensitivity of the Australian freshwater biota

In Victoria, Australia, both dryland salinity and salinity in irrigation regions are serious agricultural problems. One option to control the latter is to pump groundwater to maintain it below the surface. However, this leaves a saline wastewater for disposal, probably into local streams or wetlands. This review of the salt sensitivity of the biota of Australian streams and wetlands gives information of interest to those responsible for developing controls on these discharges. The review addresses the lethal and sub-lethal effects of salinity on microbes (mainly bacteria), macrophytes and micro-algae, riparian vegetation, invertebrates, fish, amphibians, reptiles, mammals, and birds. Data suggest that direct adverse biological effects are likely to occur in Australian river, stream and wetland ecosystems if salinity is increased to around 1 000 mg L⁻¹. The review highlights a general lack of data on the sensitivity of freshwater plants and animals to salinity increases.     

Pleistocene refugia in an arid landscape: analysis of a widely distributed Australian passerine

While many studies have documented the effect that glacial cycles have had on northern hemisphere species, few have attempted to study the associated effect of aridification at low latitudes in the southern hemisphere. We investigated the past effects that cyclic aridification may have had on the population structure and history of a widespread endemic Australian bird species, the Australian magpie (Gymnorhina tibicen). One thousand one hundred and sixty-six samples from across its native range were analysed for mitochondrial control region sequence variation and variation at six microsatellite loci. Analysis of mitochondrial control region sequence data indicated monophyletic clades that were geographically congruent with an eastern and western region. The contemporary distribution of east and west clades is nonoverlapping but in close proximity. Populations were estimated to have diverged in the Pleistocene around 36,000 years ago. The putative Carpentarian and Nullarbor arid barriers appear to be associated with the divergence between east and west mainland populations. Nested clade analysis indicated a signature of range expansion in the eastern region suggesting movement possibly inland and northward subsequent to the last period of aridity. The island population of Tasmania was of very recent origin, possibly since sea levels rose 16,000 years ago. Given the east-west structure, there was no congruence between morphology and recent history of this species indicating a lack of support for morphological taxa. Overall mitochondrial DNA and microsatellite variation suggest that increasing aridity and Pleistocene refugia played a role in structuring populations of the Australian magpie; however, the dispersal ability and generalist habitat requirements may have facilitated the movement of magpies into an almost contiguous modern distribution across the continent. This study supports the idea that Pleistocene aridification played an important role in structuring intraspecific variation in low latitudinal southern hemisphere avian species.