Statistical method for testing the neutral mutation hypothesis by DNA polymorphism.

Motivation: Analogous to biological sequence comparison, comparing cellular networks is an important problem that could provide insight into biological understanding and therapeutics. For technical reasons, comparing large networks is computationally infeasible, and thus heuristics, such as the degree distribution, clustering coefficient, diameter, and relative graphlet frequency distribution have been sought. It is easy to demonstrate that two networks are different by simply showing a short list of properties in which they differ. It is much harder to show that two networks are similar, as it requires demonstrating their similarity in all of their exponentially many properties. Clearly, it is computationally prohibitive to analyze all network properties, but the larger the number of constraints we impose in determining network similarity, the more likely it is that the networks will truly be similar.

Results: We introduce a new systematic measure of a network's local structure that imposes a large number of similarity constraints on networks being compared. In particular, we generalize the degree distribution, which measures the number of nodes 'touching' k edges, into distributions measuring the number of nodes 'touching' k graphlets, where graphlets are small connected non-isomorphic subgraphs of a large network. Our new measure of network local structure consists of 73 graphlet degree distributions of graphlets with 2--5 nodes, but it is easily extendible to a greater number of constraints (i.e. graphlets), if necessary, and the extensions are limited only by the available CPU. Furthermore, we show a way to combine the 73 graphlet degree distributions into a network 'agreement' measure which is a number between 0 and 1, where 1 means that networks have identical distributions and 0 means that they are far apart. Based on this new network agreement measure, we show that almost all of the 14 eukaryotic PPI networks, including human, resulting from various high-throughput experimental techniques, as well as from curated databases, are better modeled by geometric random graphs than by Erdos--Reny, random scale-free, or Barabasi--Albert scale-free networks.

Availability: Software executables are available upon request.

Contact: natasha@ics.uci.edu

pdf/biological-network-comparison-using-graphlet-degree-101en0jrqn.pdf

Biological network comparison using graphlet degree distribution

The estimation of phylogenetic divergence times from sequence data is an important component of many molecular evolutionary studies. There is now a general appreciation that the procedure of divergence dating is considerably more complex than that initially described in the 1960s by Zuckerkandl and Pauling (1962, 1965). In particular, there has been much critical attention toward the assumption of a global molecular clock, resulting in the development of increasingly sophisticated techniques for inferring divergence times from sequence data. In response to the documentation of widespread departures from clocklike behavior, a variety of local- and relaxed-clock methods have been proposed and implemented. Local-clock methods permit different molecular clocks in different parts of the phylogenetic tree, thereby retaining the advantages of the classical molecular clock while casting off the restrictive assumption of a single, global rate of substitution (Rambaut and Bromham 1998; Yoder and Yang 2000).

Accounting for calibration uncertainty in phylogenetic estimation of evolutionary divergence times

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.

A review of the salt sensitivity of the Australian freshwater biota

Many of the world's saline lakes have been shrinking due to consumptive water use. The Great Salt Lake, USA, provides an example for how the health of and ecosystem services provided by saline lakes can be sustained. Many of the world's saline lakes are shrinking at alarming rates, reducing waterbird habitat and economic benefits while threatening human health. Saline lakes are long-term basin-wide integrators of climatic conditions that shrink and grow with natural climatic variation. In contrast, water withdrawals for human use exert a sustained reduction in lake inflows and levels. Quantifying the relative contributions of natural variability and human impacts to lake inflows is needed to preserve these lakes. With a credible water balance, causes of lake decline from water diversions or climate variability can be identified and the inflow needed to maintain lake health can be defined. Without a water balance, natural variability can be an excuse for inaction. Here we describe the decline of several of the world's large saline lakes and use a water balance for Great Salt Lake (USA) to demonstrate that consumptive water use rather than long-term climate change has greatly reduced its size. The inflow needed to maintain bird habitat, support lake-related industries and prevent dust storms that threaten human health and agriculture can be identified and provides the information to evaluate the difficult tradeoffs between direct benefits of consumptive water use and ecosystem services provided by saline lakes.

https://www.fs.fed.us/rm/pubs_journals/2017/rmrs_2017_wurtsbaugh_w001.pdf

Decline of the world's saline lakes

The Australian Cladocera are revised on the basis of numerous samples, collections in the Australian Museum and a critical consideration of the literature. Six families are represented in inland waters of Australia: Sididae, Chydoridae, Macrothricidae, Moinidae, Bosminidae, and Daphniidae. Altogether 125 species in 40 genera were found, 15 species being new: Pseudosida australiensis n.sp., Archepleuroxus baylyi n. gen., n.sp., Rak obtusus n. gen., n.sp., Rak labrosus n. gen., n.sp., Australochydorus aporus n. gen., n.sp., Rhynchochydorus australiensis n. gen., n.sp., Alona macracantha n.sp., Alona investis n.sp., Alona setuloides n.sp., Biapertura rusticoides n.sp., Monospilus diporus n.sp., Monospi/us elongatus n.sp., Echinisca williamsi n.sp., Echiniscaflagellata n.sp., and Simocephalus victoriensis n.sp. One new subspecies is recognized: Alona davidi vermiculata n.subsp. Some 49 species (including the new species) are recorded in Australia for the first time. In addition, the presence of a further 6 species of marine Cladocera in the families Podonidae and Sididae is noted. The cladoceran fauna of Australia, besides including many cosmopolitan and pantropical forms, also has some species widely distributed in the Holarctic, some Gondwanaland species, and a large number (46) of endemics. Keys to all families and genera of Cladocera are given as well as keys for Australian species. Ecology, community structure, faunal composition and zoogeography are considered. The revision provides a basis for the identification of Australian Cladocera and for further taxonomic studies. SMIRNOV. N.N., & B.V. TIMMS. 1983. A Revision of the Australian Cladocera (Crustacea). Records of the Australian Museum. Supplement 1. 132 pp.

A revision of the Australian Cladocera (Crustacea)

Recent collections from the remote Kimberley in Western Australia, have added three species to the known fauna of gnammas, Limnadopsis multilineata Timms, 2009 and two new species described herein, Eulimnadia kimberleyensis sp. nov. and Ozestheria pellucida sp. nov.. A further gnamma icon, Paralimnadia laharum sp. nov. is added from the Grampians in western Victoria. The numerous records of clam shrimps from Australian gnammas are examined.

Three new species of spinicaudatan clam shrimps from Australia, all from gnammas (rock pools)

Australia is a land of salt lakes and despite low human population density, many lakes are adversely impacted by a range of factors. Secondary salinisation is the most pernicious force degrading lakes, especially in south-west Western Australia where up to 30% of the landscape is predicted to be affected. Mining also impinges on many salt lakes in this state, mainly through the dewatering of saline groundwater. Exploitation of groundwater for irrigation caused some lakes in Victoria, Australia, to dry, especially the significant Red Rock Complex. Global climate change will result in new water balances in endorheic lakes, with most having less water, particularly the seasonal lakes of southern Australia. This has already happened in Lake Corangamite, Victoria, but the prime reason is diversion of inflowing floodwater. Consequently, the lake has retreated and become salinised compromising its status as a Ramsar site. Various other lakes suffer from enhanced sedimentation, have introduced biota or their catchments are being disturbed to their detriment. Enlightened management should be able to maintain some important lakes in an acceptable condition, but, for most others, the future is bleak.

Salt lakes in Australia : present problems and prognosis for the future

Paralimnadia was recently re-erected to accommodate Australian limnadiids formally placed in Limnadia. They are characterised by the lack of a spine on the posterior ventral corner of the telson, a cercopod divided by a spine midlength into a cylindrical seta bearing basal section and a narrowing denticle bearing distal section, males amplex females on the posterior body margin keeping the body in line, and gonochoristic reproduction, so typically sex ratios are broadly 1:1. These characters separate Paralimnadia from the closely related Eulimandia. Paralimnadia is endemic to and diverse in Australia, and includes the transferred P. stanleyana (King), P. sordida (King), P. badia (Wolf), P. cygnorum (Dakin) and P. urukhai (Webb & Bell) as well as 10 new species. All are variable morphologically, the most conservative characters being the morphology of their eggs and the cercopod setae. Although found across Australia, there are hot spots of diversity in the coast and montane areas of New South Wales and southwest of areas of Western Australia and few in the vast inland arid zone. As in Eulimnadia, a few occur in rock pools. However those in sandy coastal pools subject to urbanisation or mining are becoming rare.

A review of the Australian endemic clam shrimp, Paralimnadia Sars 1896 (Crustacea: Branchiopoda: Spinicaudata)

The original type species of Australimnadia is made a junior synonym of A. grobbeni , originally described as Limnadia grobbeni Daday, 1925. A second species of Australimnadia is described from Onslow, Western Australia; it differs in having unique egg morphology and is distinct in many morphological characters, including those of the telson and cercopod, but also of the thoracopods. Its validity is confirmed by molecular differences between the two species in COI and EF1α. A third species from southwestern Western Australia is separated morphologically by unique spination of the telson and setation of the cercopod, and by its egg morphology.

A revision of the clam shrimp Australimnadia Timms and Schwentner, 2012 (Crustacea: Spinicaudata: Limnadiidae) with two new species from Western Australia

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