Population-structure and genetic diversity in a haplochromine cichlid fish [corrected] of a satellite lake of Lake Victoria

The approximately 500 species of the cichlid fish species flock of Lake Victoria, East Africa, have evolved in a record-setting 100,000 years and represent one of the largest adaptive radiations. We examined the population structure of the endangered cichlid species Xystichromis phytophagus from Lake Kanyaboli, a satellite lake to Lake Victoria in the Kenyan Yala wetlands. Two sets of molecular markers were analysed--sequences of the mitochondrial control region as well as six microsatellite loci--and revealed surprisingly high levels of genetic variability in this species. Mitochondrial DNA sequences failed to detect population structuring among the three sample populations. A model-based population assignment test based on microsatellite data revealed that the three populations most probably aggregate into a larger panmictic population. However, values of population pairwise FST indicated moderate levels of genetic differentiation for one population. Eleven distinct mitochondrial haplotypes were found among 205 specimens of X. phytophagus, a relatively high number compared to the total number of 54 haplotypes that were recovered from hundreds of specimens of the entire cichlid species flock of Lake Victoria. Most of the X. phytophagus mitochondrial DNA haplotypes were absent from the main Lake Victoria, corroborating the putative importance of satellite lakes as refugia for haplochromine cichlids that went extinct from the main lake in the last decades and possibly during the Late Pleistocene desiccation of Lake Victoria.     

Genetic variation in the marbled lungfish Protopterus aethiopicus in Lake Victoria and introduction to Lake Baringo, Kenya

Marbled lungfish Protopterus aethiopicus in Lake Victoria and two nearby smaller lakes were found to have high levels of DNA sequence variation in their mitochondrial control regions (35 haplotypes in 61 fish) but no population genetic structure (Φ_ST= 0·00). In contrast, marbled lungfish in Lake Baringo, Kenya, appeared to be fixed for a single control region haplotype, which occurred at low frequency in the other lakes. Using FLUCTUATE software, the female effective population size in Lake Victoria during the late Pleistocene was estimated to be c. 500 000, similar to the value estimated for the present-day population. These observations suggest that, during the late Pleistocene dry period, a large marbled lungfish population survived either in wet refugial areas within the lake basin or in surrounding areas. Marbled lungfish were reported to have been introduced into Lake Baringo 30 years ago with a founding population of only three individuals. The lack of control region variation in the Lake Baringo population is consistent with that situation.     

Genetic affinities of an introduced predator: Nile perch in Lake Victoria, East Africa

Although the introduction of Nile perch, Lates niloticus , to Lake Victoria has received intense global attention, especially in relation to its impact on endemic cichlid species and on fishery yields, fundamental information on its taxonomy and population genetics is lacking. Most importantly, the introduced fish originated from two lakes (Lakes Albert and Turkana) containing three Lates species, and it has never been entirely clear which of these became established in Lake Victoria, or indeed whether the Lake Victoria population is derived from hybridization between Lates species. In addition, genetic drift caused by the relatively small founder population (≈ 400), the initially slow population increase followed by a period of explosive population growth, and selection pressures in the new environment may have resulted in substantial genetic changes. Allozyme data indicated that the introduced Nile perch of Lake Victoria were mainly L. niloticus from Lake Albert, although maximum likelihood estimates of stock contributions (GSI) suggested the presence of L. macrophthalmus. In contrast, introduced Nile perch in adjacent smaller lakes (Lakes Kyoga and Nabugabo) appeared to be entirely L. niloticus . The effect of the introductions on allozyme diversity varied among lakes and appeared to be uncorrelated to the number of fish introduced.     

Particle-attached and free-living bacterial communities in a contrasting marine environment: Victoria Harbor, Hong Kong

Diversity of particle-attached and free-living marine bacteria in Victoria Harbor, Hong Kong, and its adjacent coastal and estuarial environments was investigated using DNA fingerprinting and clone library analysis. Denaturing gradient gel electrophoresis (DGGE) analysis of 16S rRNA genes showed that bacterial communities in three stations of Victoria Harbor were similar, but differed from those in adjacent coastal and estuarine stations. Particle-attached and free-living bacterial community composition differed in the Victoria Harbor area. DNA sequencing of 28 bands from DGGE gel showed Alphaproteobacteria was the most abundant group, followed by the Bacteroidetes, and other Proteobacteria. Bacterial species richness (number of DGGE bands) differed among stations and populations (particle-attached and free-living; bottom and surface). BIOENV analysis indicated that the concentrations of suspended solids were the major contributing parameter for the spatial variation of total bacterial community structure. Samples from representative stations were selected for clone library (548 clones) construction and their phylogenetic distributions were similar to those of sequences from DGGE. Approximately 80% of clones were affiliated to Proteobacteria, Bacteroidetes and Cyanobacteria. The possible influences of dynamic pollution and hydrological conditions in the Victoria Harbor area on the particle-attached and free-living bacterial community structures were discussed.     

Phylogenetic Relationships Among East African Haplochromine Fish as Revealed by Short Interspersed Elements (SINEs)

Genomic DNA libraries were prepared from two endemic species of Lake Victoria haplochromine (cichlid) fish and used to isolate and characterize a set of short interspersed elements (SINEs). The distribution and sequences of the SINEs were used to infer phylogenetic relationships among East African haplochromines. The SINE-based classification divides the fish into four groups, which, in order of their divergence from a stem lineage, are the endemic Lake Tanganyika flock (group 1); fish of the nonendemic, monotypic, widely distributed genus Astatoreochromis (group 2); the endemic Lake Malawi flock (group 3); and group 4, which contains fish from widely dispersed East African localities including Lakes Victoria, Edward, George, Albert, and Rukwa, as well as many rivers. The group 4 haplochromines are characterized by a subset of polymorphic SINEs, each of which is present in some individuals and absent in others of the same population at a given locality, the same morphologically defined species, and the same mtDNA-defined haplogroup. SINE-defined group 4 contains six of the seven previously described mtDNA haplogroups. One of the polymorphic SINEs appears to be fixed in the endemic Lake Victoria flock; four others display the presence-or-absence polymorphism within the species of this flock. These findings have implications for the origin of Lake Victoria cichlids and for their founding population sizes.     

Contrasting phylogeographical patterns for springtails reflect different evolutionary histories between the Antarctic Peninsula and continental Antarctica

Aim  We examined the genetic structure among populations and regions for the springtails Cryptopygus antarcticus antarcticus and Gomphiocephalus hodgsoni (Collembola) to identify potential historical refugia and subsequent colonization routes, and to examine population growth/expansion and relative ages of population divergence.
Location  Antarctic Peninsula for C. a. antarcticus ; Antarctic continent (southern Victoria Land) for G. hodgsoni .
Methods  Samples were collected from 24 and 28 locations across the Antarctic Peninsula and southern Victoria Land regions for C. a. antarcticus and G. hodgsoni , respectively. We used population genetic, demographic and nested clade analyses based on mitochondrial DNA (cytochrome c oxidase subunit I and subunit II).
Results  Both species were found to have population structures compatible with the presence of historical glacial refugia on Pleistocene (2 Ma–present) time-scales, followed by post-glacial expansion generating contemporary geographically isolated populations. However, G. hodgsoni populations were characterized by a fragmented pattern with several 'phylogroups' (likely ancestral haplotypes present in high frequency) retaining strong ancestral linkages among present-day populations. Conversely, C. a. antarcticus had an excess of rare haplotypes with a much reduced volume of ancestral lineages, possibly indicating historical founder/bottleneck events and widespread expansion.
Main conclusions  We infer that these differences reflect distinct evolutionary histories in each locality despite the resident species having similar life-history characteristics. We suggest that this has predominantly been influenced by variation in the success of colonization events as a result of intrinsic historical glaciological differences between the Antarctic Peninsula and continental Antarctic environments.     

Animal Hoarding in Victoria,Australia: An Exploratory Study

Animal hoarding not only presents significant welfare issues for the animals involved, but also for the hoarders and people in the surrounding community. Existing studies on the issue have primarily been undertaken in the USA and little is known about animal hoarding in other countries, including Australia. It has been estimated that the per-capita prevalence of animal hoarding in Victoria, Australia, is similar to that in the USA, but in order to design effective intervention strategies, the extent of the issue and its characteristics need to be identified. This study analyzes data from 22 recent cases of animal hoarding from a number of agencies in Victoria. The demographics and living conditions of animal hoarders in Victoria and the USA were found to be similar. In contrast, the animals involved in hoarding cases in Victoria were in a better condition than the animals in the USA, with behavioral issues being the leading animal welfare concern in Australia. Behavioral problems resulted in euthanasia of the animals in 45% of the cases studied. All of the agencies included in this study call for a greater involvement or support from human mental health services to fully address the root of the problem. The information from this study can be used to help identify groups at risk to develop effective and appropriate means of prevention of, and intervention in, animal hoarding cases.     

A comparison of some populations of Eucalyptus viminalis Labill. growing on calcareous and acid soils in Victoria,Australia

A study of populations of Eucalyptus viminalis found on both acid and alkaline soils showed that seedlings differ in their tolerance of calcareous soils and their susceptibility to lime chlorosis. Seedlings from an open-forest population on calcareous dunes in the Otway Ranges, Victoria, averaged a significantly greater yield than seedlings of three other populations found on acid soils when all were grown on calcareous soil of pH 6.8. A tall ribbon gum form of E. viminalis, from Paradise gully in the Otways, was the least tolerant of alkaline conditions and showed severe signs of chlorosis and reddening of leaf margins. The latter appeared to be related to high uptake of phosphorus. This population showed rapid growth on a fertile acid loam. The data presented also emphasize the need to consider the variation in soils which can occur at any one site. Population differences were most marked when seedlings were grown on soils of pH near 7.0. Yield was reduced in the Otways calcareous population when seedlings were grown on the more leached soil from swales (pH 6.5) between dunes and on the highly calcareous soil from the dune crests (pH 7.8–8.0). The failure of any of the populations of E. viminalis studied to grow well on soils of high pH suggest that this species is not tolerant of highly calcareous soils. This may in part explain the absence of this species from the drier calcareous areas on the Mornington Peninsula and the Yanakie Isthmus, Victoria. Since seedlings had reduced root development on the soil collected from the Peninsula, E. viminalis may be restricted, in effect because of drought stress, to non-calcareous sites in the eastern part of Victoria.     

Differences in egg parasitism of Chrysophtharta agricola (Chapuis) (Coleoptera: Chrysomelidae) by Enoggera nassaui Girault (Hymenoptera: Pteromalidae) in relation to host and parasitoid origin

Abstract The first instances of egg parasitism of Chrysophtharta agricola , a pest of eucalypt plantations, are recorded. Enoggera nassaui was found parasitising C. agricola egg batches in Tasmania, the Australian Capital Territory (ACT), New South Wales and Victoria: this is the first record of this parasitoid species from Victoria. One instance of Neopolycystus sp. parasitising C. agricola eggs in Victoria was also recorded. Parasitism of egg batches by E. nassaui ranged from 0 to 55% between five geographical populations collected in mainland Australia ( n  = 45), and from 0 to 2% between two populations collected in Tasmania ( n  = 300). For mainland sites at which parasitism was recorded, parasitism rates within sites differed significantly from either population in Tasmania. Reciprocal exposure experiments using one Tasmanian (Florentine Valley) and one parasitised mainland (Picadilly Circus, ACT) population were conducted in the laboratory to examine whether these different parasitism rates were attributable to egg or parasitoid origin. Parasitoids from the ACT parasitised C. agricola eggs of both origins more successfully than parasitoids from Tasmania, with up to 65% wasp emergence compared with 33% from Tasmania. Parasitoid origin significantly affected the number of wasps that emerged from exposed batches, but not the total loss from parasitism.     

Genetic structure and gene flow in an endangered native tilapia fish (Oreochromis esculentus) compared to invasive Nile tilapia (Oreochromis niloticus) in Yala swamp, East Africa

The introduction of invasive Nile tilapia (Oreochromis niloticus), and the rapacious predator Nile perch (Lates niloticus), into Lake Victoria resulted in a decline in population sizes, genetic diversity and even extirpation of native species which were previously the mainstay of local fisheries. However, remnant populations of native fish species, including tilapia, still persist in satellite lakes around Lake Victoria where they may coexist with O. niloticus. In this study we assessed population genetic structure, diversity, and integrity of the native critically endangered Singidia tilapia (O. esculentus) in its refugial populations in the Yala swamp, Kenya, and contrasted this diversity with populations of the invasive tilapia O. niloticus in satellite lakes (Kanyaboli, Namboyo and Sare) and Lake Victoria. Based on mtDNA control region sequences and eight nuclear microsatellite loci, we did not detect any mtDNA introgression between the native and the invasive species in Lakes Kanyaboli and Namboyo, but did find low levels of nuclear admixture, primarily from O. niloticus to O. esculentus. Some genetic signal of O. esculentus in O. niloticus was found in Lake Sare, where O. esculentus is not found, suggesting it has recently been extirpated by the O. niloticus invasion. In both species, populations in the satellite lakes are significantly genetically isolated from each other, with private mtDNA haplotypes and microsatellite alleles. For O. niloticus, genetic diversity in satellite lakes was similar to that found in Lake Victoria. Our data imply a low frequency of immigration exchange between the two populations of O. esculentus and we suggest that the populations of this endangered species and important fisheries resource should be conserved separately in Lakes Kanyaboli and Namboyo and with high priority.     

Divergence in aerobic scope and thermal tolerance is related to local thermal regime in two populations of introduced Nile perch (Lates niloticus)

We tested whether thermal tolerance and aerobic performance differed between two populations of Nile perch (Lates niloticus) originating from the same source population six decades after their introduction into two lakes in the Lake Victoria basin in East Africa. We used short-term acclimation of juvenile fish to a range of temperatures from ambient to +6°C, and performed critical thermal maximum (CT_max) and respirometry tests to measure upper thermal tolerance, resting and maximum metabolic rates, and aerobic scope (AS). Across acclimation temperatures, Nile perch from the cooler lake (Lake Nabugabo, Uganda) tended to have lower thermal tolerance (i.e., CT_max) and lower aerobic performance (i.e., AS) than Nile perch from the warmer waters of Lake Victoria (Bugonga region, Uganda). Effects of temperature acclimation were more pronounced in the Lake Victoria population, with the Lake Nabugabo fish showing less thermal plasticity in most metabolic traits. Our results suggest phenotypic divergence in thermal tolerance between these two introduced populations in a direction consistent with an adaptive response to local thermal regimes.     

Genetic variation in Antarctic populations of the moss Sarconeurum glaciale

Sixty-six isolates of the moss Sarconeurum glaciale were collected from sites in continental Antarctica at Ross Island, southern Victoria Land and the Vestfold Hills. Genetic variation within and among the populations was estimated using isozymes and random amplified polymorphic DNA (RAPD) technology. Isozyme results only reproducibly showed variation between the populations with one enzyme; RAPDs indicated significantly higher levels of genetic variability within and among the Vestfold Hills samples than in the Ross Sea region samples. A dendrogram produced from the RAPD bands suggested that the Ross Island and southern Victoria Land samples form one population, and those from the Vestfold Hills form a separate and more variable population, possibly resulting from separate colonisation events on the continent. Received: 15 March 1996 / Accepted: 1 May 1997     

Variation and distribution of total mercury in water, sediment and soil from northern Lake Victoria, East Africa

Lake Victoria, the world's largest tropical freshwater lake, is an important resource, ecologically and economically. THg distribution in the northern parts of the lake are not well known, so to answer this gap, patterns in total mercury (THg) in water, soil and two dated sediment cores from northern Lake Victoria were determined. Water THg concentrations ranged from 0.7 to 5.8 ng/L, and there were no apparent differences observed between Napoleon and Winam Gulfs. Two precipitation samples had Hg concentrations of 7 and 31 ng/L. Surface soil samples collected from various agricultural sites around Jinja, Napoleon Gulf, have THg concentrations between 12.7 and 48.4 ng/g dry weight; they were correlated with organic carbon, total phosphorus and % clay. A near-shore core taken in Itome Bay in Napoleon Gulf, and an offshore core collected from the deepest part of the lake had similar THg concentrations and profiles (78 to 458 ng/g dry weight). The increase in THg concentration in the profiles of both cores began around 1960 and peaked around 1980. The similar sedimentary THg profiles and fluxes in the cores suggest that the THg sources to L. Victoria are primarily atmospheric, with some erosion inputs, and that equatorial African ecosystems are not exempt from the global increase in baseline THg concentrations.     

Benthic algal mats of some lakes of Inexpressible Island (northern Victoria Land,Antarctica)

 Benthic algal mats from four lakes located on Inexpressible Island (northern Victoria Land, Antarctica) were studied, analysing their structure and floristic composition. Thirty taxa of algae were identified: 11 Cyanophyta, 15 Bacillariophyta and 4 Chlorophyta. The lake mats contained from 15 (lake C) to 26 species (lake D). The number of diatom frustules in the mats varied from 771×10³ (lake C) to 9428×10³ frustules g^-1 (lake B). In terms of floristic composition and macromorphology, these mats were observed to be very similar to moat mats described from Lake Gondwana (northern Victoria Land) and the Dry Valleys lakes of southern Victoria Land. Received: 9 July 1995/Accepted: 12 February 1996     

Genetic diversity and population structure of the endangered ripon barbel,Barbus altianalis (Boulenger, 1900) in Lake Victoria catchment,Kenya based on mitochondrial DNA sequences

Approximately 850 bp of the mitochondrial control region was used to assess the genetic diversity, population structure and demographic expansion of the endangered cyprinid Barbus altianalis, a species known to be potamodramous in the Lake Victoria drainage system. The 196 samples taken from the four main rivers draining the Lake Victoria catchment (Nzoia, Yala, Nyando and Sondu–Miriu) yielded 49 mitochondrial DNA haplotypes; 83.7% thereof were private haplotypes restricted to particular rivers. The overall mean haplotype diversity was high (0.93663 ± 0.008) and ranged between 0.566 (Sondu – Miriu) and 0.944 (Nzoia). The overall mean nucleotide diversity was low (0.01322 ± 0.00141), ranging from 0.0342 (Sondu – Miriu) to 0.0267 (Nzoia). Population differentiation tests revealed strong and highly significant (P ≤ 0.001) segregation of populations in the four river basins. F_ST values among the four river‐based populations ranged from 0.05202 to 0.44352. The samples formed two main haplotype networks based on a 95% parsimony criterion, each exhibiting a strong signature of past population expansion. The smaller network was restricted to the River Nzoia, whereas the larger network contained representatives from all four rivers; within this the central haplotypes were found in more than one river, whereas the peripheral haplotypes tended to be river‐specific. The degree of population differentiation and the number of river‐specific haplotypes are too high to be explained by recent anthropogenic impacts alone and suggest that the species has probably existed in the Lake Victoria catchment as two populations: the now ‘extinct’ migratory population and the extant river restricted non‐migratory populations.     

Genomic Signatures for Species-Specific Adaptation in Lake Victoria Cichlids Derived from Large-Scale Standing Genetic Variation

The cichlids of Lake Victoria are a textbook example of adaptive radiation, as >500 endemic species arose in just 14,600 years. The degree of genetic differentiation among species is very low due to the short period of time after the radiation, which allows us to ascertain highly differentiated genes that are strong candidates for driving speciation and adaptation. Previous studies have revealed the critical contribution of vision to speciation by showing the existence of highly differentiated alleles in the visual opsin gene among species with different habitat depths. In contrast, the processes of species-specific adaptation to different ecological backgrounds remain to be investigated. Here, we used genome-wide comparative analyses of three species of Lake Victoria cichlids that inhabit different environments—Haplochromis chilotes, H. sauvagei, and Lithochromis rufus—to elucidate the processes of adaptation by estimating population history and by searching for candidate genes that contribute to adaptation. The patterns of changes in population size were quite distinct among the species according to their habitats. We identified many novel adaptive candidate genes, some of which had surprisingly long divergent haplotypes between species, thus showing the footprint of selective sweep events. Molecular phylogenetic analyses revealed that a large fraction of the allelic diversity among Lake Victoria cichlids was derived from standing genetic variation that originated before the adaptive radiation. Our analyses uncovered the processes of species-specific adaptation of Lake Victoria cichlids and the complexity of the genomic substrate that facilitated this adaptation.     

Genetic structure and diversity of the koala population in South Gippsland,Victoria: a remnant population of high conservation significance

In the Australian state of Victoria, the history of koalas and their management has resulted in the homogenisation and reduction of genetic diversity in many contemporary populations. Decreased genetic diversity may reduce a species’ ability to adapt to future environmental pressures such as climate change or disease. The South Gippsland koala population is considered to be unique in Victoria, as it is believed to be a remnant population, not originating from managed populations that have low genetic variation. This study investigated genetic structure and diversity of koalas in South Gippsland, with comparison to other populations in Victoria (French Island/Cape Otway, FI and Raymond Island, RI), New South Wales and south east Queensland. Population analyses were undertaken using both microsatellite genotype and mitochondrial DNA sequence data. Non-invasive sampling of koala scats was used to source koala DNA, allowing 222 South Gippsland koalas to be genotyped. Using nuclear data the South Gippsland koala population was found to be significantly differentiated (D_jost 95% CI SG–RI?=?0.03–0.06 and SG–FI?=?0.08–012) and more diverse (A_R 95% CI SG?=?4.7–5.6, RI?=?3.1–3.3, FI?=?3.0–3.3; p?=?0.001) than other Victorian koala populations, supporting the premise that koalas in the South Gippsland region are part of a remnant population, not derived from translocated island stock. These results were also supported by mitochondrial data where eight haplotypes (Pc4, Pc17, Pc26, Pc27, and Pc56–Pc59) were identified in South Gippsland while a single haplotype (Pc27) was found in all island koalas tested. Compared to other Victorian koala populations, greater genetic diversity found in South Gippsland koalas, may provide this population with a greater chance of survival in the face of future environmental pressures. The South Gippsland koala population is, therefore, of high conservation significance, warranting the implementation of strategies to conserve this population and its diversity into the future.     

An apparent population decrease,or change in distribution,of Weddell seals along the Victoria Land coast

Ground counts during 1959–1968 compared with counts using high resolution (0.6 m²) satellite imagery during 2008–2012 indicated many fewer Weddell seals (Leptonychotes weddellii) at two major molting areas in the western Ross Sea: Edisto Inlet‐Moubray Bay, northern Victoria Land, and McMurdo Sound, southern Victoria Land. Breeding seals have largely disappeared from Edisto‐Moubray, though the breeding population in McMurdo Sound appears to have recovered from harvest in the 1960s. The timing of decline, or perhaps spreading (lower numbers of seals in more places), is unknown but appears unrelated to changes in sea ice conditions. We analyzed both historic and satellite‐derived ice data confirming a large expansion of pack ice mostly offshore of the Ross Sea, and not over the continental shelf (main Weddell seal habitat), and a thinning of fast ice along Victoria Land (conceivably beneficial to seals). Timing of fast ice presence and extent in coves and bays along Victoria Land, remains the same. The reduction in numbers is consistent with an altered food web, the reasons for which are complex. In the context of a recent industrial fishery targeting a seal prey species, a large‐scale seal monitoring program is required to increase understanding of seal population changes.     

THE OCCURRENCE OF PHYTOSEIULUS PERSIMILIS ATHIAS-HENRIOT (ACARINA:PHYTOSEIIDAE) IN AN ORCHARD IN VICTORIA

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High numbers of the predatory mite, Phytoseiulus persimilis , were found on apple and nectarine trees in a commercial orchard at Werribee, Victoria in February 1981. In the following season, again it was not detected on trees or broad-leaved weeds in the orchard until late summer. Slide-dip tests on the Werribee population of P. persimilis and a population originating from strawberries in Sydney, New South Wales, showed that azinphos-methyl was equally toxic to the 2 strains and DDT was considerably less toxic to both.