Journal articles
Brask JB, Croft D, Edenbrow M, James R, Bleakley BH, Ramnarine IW, Heathcote R, Tyler C, Hamilton P, Dabelsteen T, et al (In Press). Evolution of non-kin cooperation: social assortment by cooperative phenotype in guppies. Royal Society Open Science
Hamilton P (In Press). Feminizing effects of ethinylestradiol in roach (Rutilus rutilus) populations with different estrogenic pollution exposure histories. Aquatic Toxicology
Hamilton PB, Baynes A, Nicol E, Harris G, Uren Webster TM, Beresford N, Straszkiewicz M, Jobling S, Tyler CR (2022). Feminizing effects of ethinylestradiol in roach (Rutilus rutilus) populations with different estrogenic pollution exposure histories. Aquatic Toxicology, 249, 106229-106229.
Wright PGR, Bellamy C, Hamilton PB, Schofield H, Finch D, Mathews F (2021). Characterising the relationship between suitable habitat and gene flow for Myotis bechsteinii and Eptesicus serotinus in Britain.
LANDSCAPE ECOLOGY,
36(12), 3419-3428.
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Wood E, Pablo C-L, Cram D, Walker L, York J, Anke L, Hamilton P, Tyler C, Young A (2021). Social dominance and rainfall predict telomere dynamics in a cooperative arid-zone bird. Molecular Ecology
Hamilton PB, Lockyer AE, Uren Webster TM, Studholme DJ, Paris JR, Baynes A, Nicol E, Dawson DA, Moore K, Farbos A, et al (2020). Investigation into Adaptation in Genes Associated with Response to Estrogenic Pollution in Populations of Roach (Rutilus rutilus) Living in English Rivers.
Environ Sci Technol,
54(24), 15935-15945.
Abstract:
Investigation into Adaptation in Genes Associated with Response to Estrogenic Pollution in Populations of Roach (Rutilus rutilus) Living in English Rivers.
Exposure of male fish to estrogenic substances from wastewater treatment works (WwTWs) results in feminization and reduced reproductive fitness. Nevertheless, self-sustaining populations of roach (Rutilus rutilus) inhabit river stretches polluted with estrogenic WwTW effluents. In this study, we examine whether such roach populations have evolved adaptations to tolerate estrogenic pollution by comparing frequency differences in single-nucleotide polymorphisms (SNPs) between populations sampled from rivers receiving either high- or low-level WwTW discharges. SNPs within 36 "candidate" genes, selected for their involvement in estrogenic responses, and 120 SNPs in reference genes were genotyped in 465 roaches. There was no evidence for selection in highly estrogen-dependent candidate genes, including those for the estrogen receptors, aromatases, and vitellogenins. The androgen receptor (ar) and cytochrome P450 1A genes were associated with large shifts in allele frequencies between catchments and in individual populations, but there is no clear link to estrogen pollution. Selection at ar in the effluent-dominated River Lee may have resulted from historical contamination with endocrine-disrupting pesticides. Critically, although our results suggest population-specific selection including at genes related to endocrine disruption, there was no strong evidence that the selection resulted from exposure to estrogen pollution.
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Wright PGR, Mathews F, Schofield H, Morris C, Burrage J, Smith A, Dempster EL, Hamilton PB (2018). Application of a novel molecular method to age free-living wild Bechstein's bats.
Mol Ecol Resour,
18(6), 1374-1380.
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Application of a novel molecular method to age free-living wild Bechstein's bats.
The age profile of populations fundamentally affects their conservation status. Yet, age is frequently difficult to assess in wild animals. Here, we assessed the use of DNA methylation of homologous genes to establish the age structure of a rare and elusive wild mammal: the Bechstein's bat (Myotis bechsteinii). We collected 62 wing punches from individuals whose ages were known as a result of a long-term banding study. DNA methylation was measured at seven CpG sites from three genes, which have previously shown age-associated changes in humans and laboratory mice. All CpG sites from the tested genes showed a significant relationship between DNA methylation and age, both individually and in combination (multiple linear regression R2 = 0.58, p
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Wright PGR, Hamilton PB, Schofield H, Glover A, Damant C, Davidson-Watts I, Mathews F (2018). Genetic structure and diversity of a rare woodland bat, Myotis bechsteinii: comparison of continental Europe and Britain.
Conservation Genetics,
19(4), 777-787.
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Genetic structure and diversity of a rare woodland bat, Myotis bechsteinii: comparison of continental Europe and Britain
The Bechstein’s bat (Myotis bechsteinii) is a rare sedentary bat considered to be highly reliant on the presence of ancient woodland. Understanding the genetic connectivity and population structure of such elusive mammals is important for assessing their conservation status. In this study, we report the genetic diversity and structure of M. bechsteinii across Britain and Europe. Assessments were made using 14 microsatellite markers and a 747 bp region of the mitochondrial cytochrome b gene. Nuclear DNA (microsatellites) showed high levels of genetic diversity and little inbreeding across the species range, though genetic diversity was slightly lower in Britain than in mainland Europe. Bayesian and spatial PCA analysis showed a clear separation between the British and European sites. Within Europe, the Italian population south of the Alps was isolated from the other sites. In Britain, there was genetic structuring between the northern and southern part of the geographical range. Despite there being little genetic divergence in mitochondrial DNA (mtDNA) sequences throughout most of Europe, the mtDNA patterns in Britain confirmed this separation of northern and southern populations. Such genetic structuring within Britain—in the absence of any obvious physical barriers—suggests that other factors such as land-use may limit gene-flow.
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Garcia HA, Rodrigues CMF, Rodrigues AC, Pereira DL, Pereira CL, Camargo EP, Hamilton PB, Teixeira MMG (2018). Remarkable richness of trypanosomes in tsetse flies (Glossina morsitans morsitans and Glossina pallidipes) from the Gorongosa National Park and Niassa National Reserve of Mozambique revealed by fluorescent fragment length barcoding (FFLB).
Infect Genet Evol,
63, 370-379.
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Remarkable richness of trypanosomes in tsetse flies (Glossina morsitans morsitans and Glossina pallidipes) from the Gorongosa National Park and Niassa National Reserve of Mozambique revealed by fluorescent fragment length barcoding (FFLB).
Trypanosomes of African wild ungulates transmitted by tsetse flies can cause human and livestock diseases. However, trypanosome diversity in wild tsetse flies remains greatly underestimated. We employed FFLB (fluorescent fragment length barcoding) for surveys of trypanosomes in tsetse flies (3086) from the Gorongosa National Park (GNP) and Niassa National Reserve (NNR) in Mozambique (MZ), identified as Glossina morsitans morsitans (GNP/NNR=77.6%/90.5%) and Glossina pallidipes (22.4%/9.5%). Trypanosomes were microscopically detected in 8.3% of tsetse guts. FFLB of gut samples revealed (GNP/NNR): Trypanosoma congolense of Savannah (27%/63%), Kilifi (16.7%/29.7%) and Forest (1.0%/0.3%) genetic groups; T. simiae Tsavo (36.5%/6.1%); T. simiae (22.2%/17.7%); T. godfreyi (18.2%/7.0%); subgenus Trypanozoon (20.2%/25.7%); T. vivax/T. vivax-like (1.5%/5.2%); T. suis/T. suis-like (9.4%/11.9%). Tsetse proboscises exhibited similar species composition, but most prevalent species were (GNP/NNR): T. simiae (21.9%/28%), T. b. brucei (19.2%/31.7%), and T. vivax/T. vivax-like (19.2%/28.6%). Flies harboring mixtures of trypanosomes were common (~ 64%), and combinations of more than four trypanosomes were especially abundant in the pristine NNR. The non-pathogenic T. theileri was found in 2.5% while FFLB profiles of unknown species were detected in 19% of flies examined. This is the first report on molecular diversity of tsetse flies and their trypanosomes in MZ; all trypanosomes pathogenic for ungulates were detected, but no human pathogens were detected. Overall, two species of tsetse flies harbor 12 species/genotypes of trypanosomes. This notable species richness was likely uncovered because flies were captured in wildlife reserves and surveyed using the method of FFLB able to identify, with high sensitivity and accuracy, known and novel trypanosomes. Our findings importantly improve the knowledge on trypanosome diversity in tsetse flies, revealed the greatest species richness so far reported in tsetse fly of any African country, and indicate the existence of a hidden trypanosome diversity to be discovered in African wildlife protected areas.
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Espinosa-Álvarez O, Ortiz PA, Lima L, Costa-Martins AG, Serrano MG, Herder S, Buck GA, Camargo EP, Hamilton PB, Stevens JR, et al (2018). Trypanosoma rangeli is phylogenetically closer to Old World trypanosomes than to Trypanosoma cruzi.
Int J Parasitol,
48(7), 569-584.
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Trypanosoma rangeli is phylogenetically closer to Old World trypanosomes than to Trypanosoma cruzi.
Trypanosoma rangeli and Trypanosoma cruzi are generalist trypanosomes sharing a wide range of mammalian hosts; they are transmitted by triatomine bugs, and are the only trypanosomes infecting humans in the Neotropics. Their origins, phylogenetic relationships, and emergence as human parasites have long been subjects of interest. In the present study, taxon-rich analyses (20 trypanosome species from bats and terrestrial mammals) using ssrRNA, glycosomal glyceraldehyde-3-phosphate dehydrogenase (gGAPDH), heat shock protein-70 (HSP70) and Spliced Leader RNA sequences, and multilocus phylogenetic analyses using 11 single copy genes from 15 selected trypanosomes, provide increased resolution of relationships between species and clades, strongly supporting two main sister lineages: lineage Schizotrypanum, comprising T. cruzi and bat-restricted trypanosomes, and Tra[Tve-Tco] formed by T. rangeli, Trypanosoma vespertilionis and Trypanosoma conorhini clades. Tve comprises European T. vespertilionis and African T. vespertilionis-like of bats and bat cimicids characterised in the present study and Trypanosoma sp. Hoch reported in monkeys and herein detected in bats. Tco included the triatomine-transmitted tropicopolitan T. conorhini from rats and the African NanDoum1 trypanosome of civet (carnivore). Consistent with their very close relationships, Tra[Tve-Tco] species shared highly similar Spliced Leader RNA structures that were highly divergent from those of Schizotrypanum. In a plausible evolutionary scenario, a bat trypanosome transmitted by cimicids gave origin to the deeply rooted Tra[Tve-Tco] and Schizotrypanum lineages, and bat trypanosomes of diverse genetic backgrounds jumped to new hosts. A long and independent evolutionary history of T. rangeli more related to Old World trypanosomes from bats, rats, monkeys and civets than to Schizotrypanum spp. and the adaptation of these distantly related trypanosomes to different niches of shared mammals and vectors, is consistent with the marked differences in transmission routes, life-cycles and host-parasite interactions, resulting in T. cruzi (but not T. rangeli) being pathogenic to humans.
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Hamilton PB, Rolshausen G, Uren Webster TM, Tyler CR (2017). Adaptive capabilities and fitness consequences associated with pollution exposure in fish.
Philos Trans R Soc Lond B Biol Sci,
372(1712).
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Adaptive capabilities and fitness consequences associated with pollution exposure in fish.
Many fish populations are exposed to harmful levels of chemical pollution and selection pressures associated with these exposures have led to the evolution of tolerance. Our understanding of the physiological basis for these adaptations is limited, but they are likely to include processes involved with the absorption, distribution, metabolism and/or excretion of the target chemical. Other potential adaptive mechanisms include enhancements in antioxidant responses, an increased capacity for DNA and/or tissue repair and alterations to the life cycle of fish that enable earlier reproduction. Analysis of single-nucleotide polymorphism frequencies has shown that tolerance to hydrocarbon pollutants in both marine and estuarine fish species involves alteration in the expression of the xenobiotic metabolism enzyme CYP1A. In this review, we present novel data showing also that variants of the CYP1A gene have been under selection in guppies living in Trinidadian rivers heavily polluted with crude oil. Potential costs associated with these adaptations could reduce fitness in unpolluted water conditions. Integrating knowledge of local adaptation to pollution is an important future consideration in conservation practices such as for successful restocking, and improving connectivity within river systems.This article is part of the themed issue 'Human influences on evolution, and the ecological and societal consequences'.
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Rodrigues CM, Garcia HA, Rodrigues AC, Costa-Martins AG, Pereira CL, Pereira DL, Bengaly Z, Neves L, Camargo EP, Hamilton PB, et al (2017). New insights from Gorongosa National Park and Niassa National Reserve of Mozambique increasing the genetic diversity of Trypanosoma vivax and Trypanosoma vivax-like in tsetse flies, wild ungulates and livestock from East Africa.
Parasit Vectors,
10(1).
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New insights from Gorongosa National Park and Niassa National Reserve of Mozambique increasing the genetic diversity of Trypanosoma vivax and Trypanosoma vivax-like in tsetse flies, wild ungulates and livestock from East Africa.
BACKGROUND: Trypanosoma (Duttonella) vivax is a major pathogen of livestock in Africa and South America (SA), and genetic studies limited to small sampling suggest greater diversity in East Africa (EA) compared to both West Africa (WA) and SA. METHODS: Multidimensional scaling and phylogenetic analyses of 112 sequences of the glycosomal glyceraldehyde phosphate dehydrogenase (gGAPDH) gene and 263 sequences of the internal transcribed spacer of rDNA (ITS rDNA) were performed to compare trypanosomes from tsetse flies from Gorongosa National Park and Niassa National Reserve of Mozambique (MZ), wild ungulates and livestock from EA, and livestock isolates from WA and SA. RESULTS: Multidimensional scaling (MDS) supported Tvv (T. vivax) and TvL (T. vivax-like) evolutionary lineages: 1) Tvv comprises two main groups, TvvA/B (all SA and WA isolates plus some isolates from EA) and TvvC/D (exclusively from EA). The network revealed five ITS-genotypes within Tvv: Tvv1 (WA/EA isolates), Tvv2 (SA) and Tvv3-5 (EA). EA genotypes of Tvv ranged from highly related to largely different from WA/SA genotypes. 2) TvL comprises two gGAPDH-groups formed exclusively by EA sequences, TvLA (Tanzania/Kenya) and TvLB-D (MZ). This lineage contains more than 11 ITS-genotypes, seven forming the lineage TvL-Gorongosa that diverged from T. vivax Y486 enough to be identified as another species of the subgenus Duttonella. While gGAPDH sequences were fundamental for classification at the subgenus, major evolutionary lineages and species levels, ITS rDNA sequences permitted identification of known and novel genotypes. CONCLUSIONS: Our results corroborate a remarkable diversity of Duttonella trypanosomes in EA, especially in wildlife conservation areas, compared to the moderate diversity in WA. Surveys in wilderness areas in WA may reveal greater diversity. Biogeographical and phylogenetic data point to EA as the place of origin, diversification and spread of Duttonella trypanosomes across Africa, providing relevant insights towards the understanding of T. vivax evolutionary history.
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Hamilton PB, Cowx IG, Oleksiak MF, Griffiths AM, Grahn M, Stevens JR, Carvalho GR, Nicol E, Tyler CR (2016). Population-level consequences for wild fish exposed to sublethal concentrations of chemicals – a critical review.
Fish and Fisheries,
17(3), 545-566.
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Population-level consequences for wild fish exposed to sublethal concentrations of chemicals – a critical review
Concentrated chemical spills have been shown to impact adversely on fish populations and even cause localized population extinctions. Evaluating population-level impacts of sublethal exposure concentrations is, however, complex and confounded by other environmental pressures. Applying effect measures derived from laboratory-based chemical exposures to impacts in wild fish populations is constrained by uncertainty on how biochemical response measures (biomarkers) translate into health outcomes, lack of available data for chronic exposures and the many uncertainties in available fish population models. Furthermore, wild fish show phenotypic plasticity and local adaptations can occur that adds geographic and temporal variance on responses. Such population-level factors are rarely considered in the chemical risk assessment process and can probably be derived only from studies on wild fish. Molecular technologies, including microsatellite and SNP genotyping, and RNASeq for gene expression studies, are advancing our understanding of mechanisms of eco-toxicological response, tolerance, adaptation and selection in wild populations. We examine critically the application of such approaches with examples including using microsatellites that has identified roach (Rutilus rutilus) populations living in rivers contaminated with sewage effluents that are self-sustaining, and studies of stickleback (Gasterosteus aculeatus) and killifish (Fundulus heteroclitus) that have identified genomic regions under selection putatively related to pollution tolerance. Integrating data on biological effects between laboratory-based studies and wild populations, and building understanding on adaptive responses to sublethal exposure are some of the priority research areas for more effective evaluation of population risks and resilience to contaminant exposure.
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Jürgens MD, Crosse J, Hamilton PB, Johnson AC, Jones KC (2016). The long shadow of our chemical past - High DDT concentrations in fish near a former agrochemicals factory in England.
Chemosphere,
162, 333-344.
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The long shadow of our chemical past - High DDT concentrations in fish near a former agrochemicals factory in England.
A total of 81 roach (Rutilus rutilus) collected from 13 southern English river sites between 2007 and 2012, were analysed for organochlorine pesticides, PCBs, PBDEs and some metals. Unexpectedly high concentrations of the banned insecticide DDT and its degradation products DDE and DDD (∑DDTs) were found in the 10 fish from the river Lee (or Lea) which averaged 88 ± 70 (standard deviation) μg/kg ww, almost 20 times higher than the average for the remaining sites (4.8 ± 3.1 μg/kg). All fish from that site exceeded the Canadian Tissue Residue Guideline (environmental quality standard) of 14 μg/kg ∑DDTs. Concentrations of the insecticides chlordane and lindane as well as copper, which is often used as a fungicide, were also elevated in fish from the Lee, though not as much as those of DDTs. A likely explanation for these observations was found in a nearby former pesticide factory, which had stopped production about three decades earlier. An extensive review of recent literature data on DDT in wild European fish found that, while levels are now generally low, there were several other hotspots with ∑DDTs levels that may still be of concern.
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Hamilton PB, Uren Webster TM, Basiewicz M, Kennedy EV, De-Bastos ESR, Mathews F (2015). A rapid PCR-based test for identification of fifteen British bat species.
Conservation Genetics Resources,
7(3), 651-657.
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A rapid PCR-based test for identification of fifteen British bat species
The development of a rapid method for identification of the fifteen common species of British bat is described: Barbastella barbastellus, Eptesicus serotinus, Myotis bechsteinii, Myotis daubentonii, Myotis mystacinus, Myotis nattereri, Nyctalus leisleri, Nyctalus noctula, Plecotus auritus, Plecotus austriacus, Pipistrellus nathusii, Pipistrellus pipistrellus, Pipistrellus pygmaeus,Rhinolophus ferrumequinum and Rhinolophus hipposideros. A single multiplex PCR containing five fluorescently-tagged primers and fifteen species-specific primers targeting the mitochondrial control region and genes for cytb and ND1 produces clear peaks that are unique to each species when visualised on a DNA sequencer. The multiplex also includes primers to test for PCR-amplifiable bat DNA. This method will facilitate high throughput species identification of British bats, particularly in cases where phenotypic identification is difficult.
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Rolshausen G, Phillip DAT, Beckles DM, Akbari A, Ghoshal S, Hamilton PB, Tyler CR, Scarlett AG, Ramnarine I, Bentzen P, et al (2015). Do stressful conditions make adaptation difficult? Guppies in the oil-polluted environments of southern Trinidad.
Evol Appl,
8(9), 854-870.
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Do stressful conditions make adaptation difficult? Guppies in the oil-polluted environments of southern Trinidad.
The ability of populations to rapidly adapt to new environments will determine their future in an increasingly human-modified world. Although meta-analyses do frequently uncover signatures of local adaptation, they also reveal many exceptions. We suggest that particular constraints on local adaptation might arise when organisms are exposed to novel stressors, such as anthropogenic pollution. To inform this possibility, we studied the extent to which guppies (Poecilia reticulata) show local adaptation to oil pollution in southern Trinidad. Neutral genetic markers revealed that paired populations in oil-polluted versus not-polluted habitats diverged independently in two different watersheds. Morphometrics revealed some divergence (particularly in head shape) between these environments, some of which was parallel between rivers. Reciprocal transplant experiments in nature, however, found little evidence of local adaptation based on survival and growth. Moreover, subsequent laboratory experiments showed that the two populations from oil-polluted sites showed only weak local adaptation even when compared to guppies from oil-free northern Trinidad. We conclude that guppies show little local adaptation to oil pollution, which might result from the challenges associated with adaptation to particularly stressful environments. It might also reflect genetic drift owing to small population sizes and/or high gene flow between environments.
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Hamilton PB, Lange A, Nicol E, Bickley LK, De-Bastos ESR, Jobling S, Tyler CR (2015). Effects of Exposure to WwTW Effluents over Two Generations on Sexual Development and Breeding in Roach Rutilus rutilus.
Environ Sci Technol,
49(21), 12994-13002.
Abstract:
Effects of Exposure to WwTW Effluents over Two Generations on Sexual Development and Breeding in Roach Rutilus rutilus.
Exposure to environmental estrogens in wastewater treatment works (WwTW) effluents induces feminized responses in male fish, including the development of eggs in male testes. However, the impacts on the offspring of exposed fish are not well understood. In this study, we examined whether roach (Rutilus rutilus) from mothers that had been exposed to an undiluted WwTW effluent from early life to sexual maturity had altered susceptibility to gonadal feminization and an impaired capacity to reproduce. For males from both WwTW effluent exposed mothers and dilution water exposed mothers, effluent exposure for up to 3 years and 9 months induced feminized male gonads, although the intersex condition was relatively mild. There was no difference in the severity of gonadal feminization in roach derived from either WwTW effluent exposed or dilution water exposed mothers. Furthermore, a breeding study revealed that roach with effluent-exposed mothers reproduced with an equal success as roach with mothers exposed to clean water. Roach exposed to the effluent for 3 years in this study were able to reproduce successfully. Our findings provide no evidence for impacts of WwTW effluent exposure on reproduction or gonadal disruption in roach down the female germ line and add to existing evidence that male roach with a mild intersex condition are able to breed competitively.
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Lima L, Espinosa-Álvarez O, Pinto CM, Cavazzana M, Pavan AC, Carranza JC, Lim BK, Campaner M, Takata CSA, Camargo EP, et al (2015). New insights into the evolution of the Trypanosoma cruzi clade provided by a new trypanosome species tightly linked to Neotropical Pteronotus bats and related to an Australian lineage of trypanosomes.
Parasit Vectors,
8Abstract:
New insights into the evolution of the Trypanosoma cruzi clade provided by a new trypanosome species tightly linked to Neotropical Pteronotus bats and related to an Australian lineage of trypanosomes.
BACKGROUND: Bat trypanosomes are implicated in the evolution of the T. cruzi clade, which harbours most African, European and American trypanosomes from bats and other trypanosomes from African, Australian and American terrestrial mammals, including T. cruzi and T. rangeli, the agents of the American human trypanosomiasis. The diversity of bat trypanosomes globally is still poorly understood, and the common ancestor, geographical origin, and evolution of species within the T. cruzi clade remain largely unresolved. METHODS: Trypanosome sequences were obtained from cultured parasites and from museum archived liver/blood samples of bats captured from Guatemala (Central America) to the Brazilian Atlantic Coast. Phylogenies were inferred using Small Subunit (SSU) rRNA, glycosomal glyceraldehyde phosphate dehydrogenase (gGAPDH), and Spliced Leader (SL) RNA genes. RESULTS: Here, we described Trypanosoma wauwau n. sp. from Pteronotus bats (Mormoopidae) placed in the T. cruzi clade, then supporting the bat-seeding hypothesis whereby the common ancestor of this clade likely was a bat trypanosome. T. wauwau was sister to the clade T. spp-Neobats from phyllostomid bats forming an assemblage of trypanosome species exclusively of Noctilionoidea Neotropical bats, which was sister to an Australian clade of trypanosomes from indigenous marsupials and rodents, which possibly evolved from a bat trypanosome. T. wauwau was found in 26.5% of the Pteronotus bats examined, and phylogeographical analysis evidenced the wide geographical range of this species. To date, this species was not detected in other bats, including those that were sympatric or shared shelters with Pteronotus. T. wauwau did not develop within mammalian cells, and was not infective to Balb/c mice or to triatomine vectors of T. cruzi and T. rangeli. CONCLUSIONS: Trypanosoma wauwau n. sp. was linked to Pteronotus bats. The positioning of the clade T. wauwau/T.spp-Neobats as the most basal Neotropical bat trypanosomes and closely related to an Australian lineage of trypanosomes provides additional evidence that the T. cruzi clade trypanosomes likely evolved from bats, and were dispersed in bats within and between continents from ancient to unexpectedly recent times.
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Garcia HA, Rodrigues AC, Rodrigues CMF, Bengaly Z, Minervino AHH, Riet-Correa F, Machado RZ, Paiva F, Batista JS, Neves L, et al (2014). Microsatellite analysis supports clonal propagation and reduced divergence of Trypanosoma vivax from asymptomatic to fatally infected livestock in South America compared to West Africa.
Parasites and Vectors,
7(1).
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Microsatellite analysis supports clonal propagation and reduced divergence of Trypanosoma vivax from asymptomatic to fatally infected livestock in South America compared to West Africa
Background: Mechanical transmission of the major livestock pathogen Trypanosoma vivax by other biting flies than tsetse allows its spread from Africa to the New World. Genetic studies are restricted to a small number of isolates and based on molecular markers that evolve too slowly to resolve the relationships between American and West African populations and, thus, unable us to uncover the recent history of T. vivax in the New World. Methods. T. vivax genetic diversity, population structure and the source of outbreaks was investigated through the microsatellite multiloci (7 loci) genotype (MLGs) analysis in South America (47isolates from Brazil, Venezuela and French Guiana) and West Africa (12 isolates from the Gambia, Burkina Faso, Ghana, Benin and Nigeria). Relationships among MLGs were explored using phylogenetic, principal component and STRUCTURE analyses. Results: Although closely phylogenetically related, for the first time, genetic differences were detected between T. vivax isolates from South America (11 genotypes/47 isolates) and West Africa (12 genotypes/12 isolates) with no MLGs in common. Diversity was far greater across West Africa than in South America, where genotypes from Brazil (MLG1-6), Venezuela (MLG7-10) and French Guiana (MLG11) shared similar but not identical allele composition. No MLG was exclusive to asymptomatic (endemic areas) or sick (outbreaks in non-endemic areas) animals, but only MLGs1, 2 and 3 were responsible for severe haematological and neurological disorders. Conclusions: Our results revealed closely related genotypes of T. vivax in Brazil and Venezuela, regardless of endemicity and clinical conditions of the infected livestock. The MLGs analysis from T. vivax across SA and WA support clonal propagation, and is consistent with the hypothesis that the SA populations examined here derived from common ancestors recently introduced from West Africa. The molecular markers defined here are valuable to assess the genetic diversity, to track the source and dispersion of outbreaks, and to explore the epidemiological and pathological significance of T. vivax genotypes. © 2014 Garcia et al.; licensee BioMed Central Ltd.
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Hamilton PB, Nicol E, De-Bastos ESR, Williams RJ, Sumpter JP, Jobling S, Stevens JR, Tyler CR (2014). Populations of a cyprinid fish are self-sustaining despite widespread feminization of males.
BMC Biol,
12Abstract:
Populations of a cyprinid fish are self-sustaining despite widespread feminization of males.
BACKGROUND: Treated effluents from wastewater treatment works can comprise a large proportion of the flow of rivers in the developed world. Exposure to these effluents, or the steroidal estrogens they contain, feminizes wild male fish and can reduce their reproductive fitness. Long-term experimental exposures have resulted in skewed sex ratios, reproductive failures in breeding colonies, and population collapse. This suggests that environmental estrogens could threaten the sustainability of wild fish populations. RESULTS: Here we tested this hypothesis by examining population genetic structures and effective population sizes (N(e)) of wild roach (Rutilus rutilus L.) living in English rivers contaminated with estrogenic effluents. N(e) was estimated from DNA microsatellite genotypes using approximate Bayesian computation and sibling assignment methods. We found no significant negative correlation between N(e) and the predicted estrogen exposure at 28 sample sites. Furthermore, examination of the population genetic structure of roach in the region showed that some populations have been confined to stretches of river with a high proportion of estrogenic effluent for multiple generations and have survived, apparently without reliance on immigration of fish from less polluted sites. CONCLUSIONS: These results demonstrate that roach populations living in some effluent-contaminated river stretches, where feminization is widespread, are self-sustaining. Although we found no evidence to suggest that exposure to estrogenic effluents is a significant driving factor in determining the size of roach breeding populations, a reduction in N(e) of up to 65% is still possible for the most contaminated sites because of the wide confidence intervals associated with the statistical model.
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Bickley LK, Brown AR, Hosken DJ, Hamilton PB, Le Page G, Paull GC, Owen SF, Tyler CR (2013). Interactive effects of inbreeding and endocrine disruption on reproduction in a model laboratory fish.
Evolutionary Applications,
6(2), 279-289.
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Interactive effects of inbreeding and endocrine disruption on reproduction in a model laboratory fish
Inbreeding depression is expected to be more severe in stressful environments. However, the extent to which inbreeding affects the vulnerability of populations to environmental stressors, such as chemical exposure, remains unresolved. Here we report on the combined impacts of inbreeding and exposure to an endocrine disrupting chemical (the fungicide clotrimazole) on zebrafish (Danio rerio). We show that whilst inbreeding can negatively affect reproductive traits, not all traits are affected equally. Inbreeding depression frequently only became apparent when fish were additionally stressed by chemical exposure. Embryo viability was significantly reduced in inbred exposed fish and there was a tendency for inbred males to sire fewer offspring when in direct competition with outbred individuals. Levels of plasma 11-ketotestosterone, a key male sex hormone, showed substantial inbreeding depression that was unaffected by addition of the fungicide. In contrast, there was no effect of inbreeding or clotrimazole exposure on egg production. Overall, our data provide evidence that stress may amplify the effects of inbreeding on key reproductive traits, particularly those associated with male fitness. This may have important implications when considering the consequences of exposure to chemical pollutants on the fitness of wild populations. Journal compilation © 2013 Blackwell Publishing Ltd62 February 2013 10.1111/j.1752-4571.2012.00288.x Original Article Original Articles © 2012 Blackwell Publishing Ltd. This is an open access article under the terms of the Creative Commons Attribution Non Commercial License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited and is not used for commercial purposes.
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Santos EM, Hamilton PB, Coe TS, Ball JS, Cook AC, Katsiadaki I, Tyler CR (2013). Population bottlenecks, genetic diversity and breeding ability of the three-spined stickleback (Gasterosteus aculeatus) from three polluted English Rivers.
Aquatic Toxicology,
142-143, 264-271.
Abstract:
Population bottlenecks, genetic diversity and breeding ability of the three-spined stickleback (Gasterosteus aculeatus) from three polluted English Rivers
Pollution is a significant environmental pressure on fish populations in both freshwater and marine environments. Populations subjected to chronic exposure to pollutants can experience impacts ranging from altered reproductive capacity to changes in population genetic structure. Few studies, however, have examined the reproductive vigor of individuals within populations inhabiting environments characterized by chronic pollution. In this study we undertook an analysis of populations of three-spined sticklebacks (Gasterosteus aculeatus) from polluted sites, to determine levels of genetic diversity, assess for evidence of historic population genetic bottlenecks and determine the reproductive competitiveness of males from these locations. The sites chosen included locations in the River Aire, the River Tees and the River Birket, English rivers that have been impacted by pollution from industrial and/or domestic effluents for over 100 years. Male reproductive competitiveness was determined via competitive breeding experiments with males and females derived from a clean water site, employing DNA microsatellites to determine parentage outcome. Populations of stickleback collected from the three historically polluted sites showed evidence of recent population bottlenecks, although only the River Aire population showed low genetic diversity. In contrast, fish collected from two relatively unpolluted sites within the River Gowy and Houghton Springs showed weak, or no evidence of such bottlenecks. Nevertheless, males derived from polluted sites were able to reproduce successfully in competition with males derived from clean water exposures, indicating that these bottlenecks have not resulted in any substantial loss of reproductive fitness in males. © 2013 Elsevier B.V.
Abstract.
Fermino BR, Viola LB, Paiva F, Garcia HA, De Paula CD, Botero-Arias R, Takata CSA, Campaner M, Hamilton PB, Camargo EP, et al (2013). The phylogeography of trypanosomes from South American alligatorids and African crocodilids is consistent with the geological history of South American river basins and the transoceanic dispersal of Crocodylus at the Miocene.
Parasites and Vectors,
6(1).
Abstract:
The phylogeography of trypanosomes from South American alligatorids and African crocodilids is consistent with the geological history of South American river basins and the transoceanic dispersal of Crocodylus at the Miocene
Background: Little is known about the diversity, phylogenetic relationships, and biogeography of trypanosomes infecting non-mammalian hosts. In this study, we investigated the influence of host species and biogeography on shaping the genetic diversity, phylogenetic relationship, and distribution of trypanosomes from South American alligatorids and African crocodilids. Methods. Small Subunit rRNA (SSU rRNA) and glycosomal Glyceraldehyde Phosphate Dehydrogenase (gGAPDH) genes were employed for phylogenetic inferences. Trypanosomes from crocodilians were obtained by haemoculturing. Growth behaviour, morphology, and ultrastructural features complement the molecular description of two new species strongly supported by phylogenetic analyses. Results: the inferred phylogenies disclosed a strongly supported crocodilian-restricted clade comprising three subclades. The subclade T. grayi comprised the African Trypanosoma grayi from Crocodylus niloticus and tsetse flies. The subclade T. ralphi comprised alligatorid trypanosomes represented by Trypanosoma ralphi n. sp. from Melanosuchus niger, Caiman crocodilus and Caiman yacare from Brazilian river basins. T. grayi and T. ralphi were sister subclades. The basal subclade T. terena comprised alligatorid trypanosomes represented by Trypanosoma terena n. sp. from Ca. yacare sharing hosts and basins with the distantly genetic related T. ralphi. This subclade also included the trypanosome from Ca. crocodilus from the Orinoco basin in Venezuela and, unexpectedly, a trypanosome from the African crocodilian Osteolaemus tetraspis. Conclusion: the close relationship between South American and African trypanosomes is consistent with paleontological evidence of recent transoceanic dispersal of Crocodylus at the Miocene/Pliocene boundaries (4-5 mya), and host-switching of trypanosomes throughout the geological configuration of South American hydrographical basins shaping the evolutionary histories of the crocodilians and their trypanosomes. © 2013 Fermino et al.; licensee BioMed Central Ltd.
Abstract.
Fermino BR, Viola LB, Paiva F, Garcia HA, de Paula CD, Botero-Arias R, Takata CSA, Campaner M, Hamilton PB, Camargo EP, et al (2013). The phylogeography of trypanosomes from South American alligatorids and African crocodilids is consistent with the geological history of South American river basins and the transoceanic dispersal of Crocodylus at the Miocene.
PARASITES & VECTORS,
6 Author URL.
Lima L, Espinosa-Álvarez O, Hamilton PB, Neves L, Takata CS, Campaner M, Attias M, De Souza W, Camargo EP, Teixeira MM, et al (2013). Trypanosoma livingstonei: a new species from African bats supports the bat seeding hypothesis for the Trypanosoma cruzi clade.
Parasites and Vectors,
6(1).
Abstract:
Trypanosoma livingstonei: a new species from African bats supports the bat seeding hypothesis for the Trypanosoma cruzi clade
Background: Bat trypanosomes have been implicated in the evolutionary history of the T. cruzi clade, which comprises species from a wide geographic and host range in South America, Africa and Europe, including bat-restricted species and the generalist agents of human American trypanosomosis T. cruzi and T. rangeli. Methods. Trypanosomes from bats (Rhinolophus landeri and Hipposideros caffer) captured in Mozambique, southeast Africa, were isolated by hemoculture. Barcoding was carried out through the V7V8 region of Small Subunit (SSU) rRNA and Fluorescent Fragment Length barcoding (FFLB). Phylogenetic inferences were based on SSU rRNA, glyceraldehyde phosphate dehydrogenase (gGAPDH) and Spliced Leader (SL) genes. Morphological characterization included light, scanning and transmission electron microscopy. Results: New trypanosomes from bats clustered together forming a clade basal to a larger assemblage called the T. cruzi clade. Barcoding, phylogenetic analyses and genetic distances based on SSU rRNA and gGAPDH supported these trypanosomes as a new species, which we named Trypanosoma livingstonei n. sp. The large and highly polymorphic SL gene repeats of this species showed a copy of the 5S ribosomal RNA into the intergenic region. Unique morphological (large and broad blood trypomastigotes compatible to species of the subgenus Megatrypanum and cultures showing highly pleomorphic epimastigotes and long and slender trypomastigotes) and ultrastructural (cytostome and reservosomes) features and growth behaviour (when co-cultivated with HeLa cells at 37°C differentiated into trypomastigotes resembling the blood forms and do not invaded the cells) complemented the description of this species. Conclusion: Phylogenetic inferences supported the hypothesis that Trypanosoma livingstonei n. sp. diverged from a common ancestral bat trypanosome that evolved exclusively in Chiroptera or switched at independent opportunities to mammals of several orders forming the clade T. cruzi, hence, providing further support for the bat seeding hypothesis to explain the origin of T. cruzi and T. rangeli. © 2013 Lima et al.; licensee BioMed Central Ltd.
Abstract.
Brown AR, Bickley LK, Ryan TA, Paull GC, Hamilton PB, Owen SF, Sharpe AD, Tyler CR (2012). Differences in sexual development in inbred and outbred zebrafish (Danio rerio) and implications for chemical testing.
Aquat Toxicol,
112-113, 27-38.
Abstract:
Differences in sexual development in inbred and outbred zebrafish (Danio rerio) and implications for chemical testing.
Outbred laboratory animal strains used in ecotoxicology are intended to represent wild populations. However, breeding history may vary considerably between strains, driving differences in genetic variation and phenotypes used for assessing effects of chemical exposure. We compared a range of phenotypic endpoints in zebrafish from four different "breeding treatments" comprising a Wild Indian Karyotype (WIK) zebrafish strain and a WIK/Wild strain with three levels of inbreeding (F(IT)=n, n+0.25, n+0.375) in a new Fish Sexual Development Test (FSDT). There were no differences between treatments in terms of egg viability, hatch success or fry survival. However, compared with WIKs, WIK/Wild hybrids were significantly larger in size, with more advanced gonadal (germ cell) development at the end of the test (63 days post fertilisation). Increasing the levels of inbreeding in the related WIK/Wild lines did not affect body size, but there was a significant male-bias (72%) in the most inbred line (F(IT)=n+0.375). Conversely, in the reference WIK strain there was a significant female-bias in the population (80% females). Overall, our results support the use of outbred zebrafish strains in the FSDT, where one of the core endpoints is sex ratio. Despite increased variance (and reduced statistical power) for some endpoints, WIK/Wild outbreds (F(IT)=n) met all acceptance criteria for controls in this test, whereas WIKs failed to comply with tolerance limits for sex ratio (30-70% females). Sexual development was also more advanced in WIK/Wild outbreds (cf. WIKs), providing greater scope for detection of developmental reproductive toxicity following chemical exposure.
Abstract.
Author URL.
Lima L, Silva FMD, Neves L, Attias M, Takata CSA, Campaner M, de Souza W, Hamilton PB, Teixeira MMG (2012). Evolutionary Insights from Bat Trypanosomes: Morphological, Developmental and Phylogenetic Evidence of a New Species, Trypanosoma (Schizotrypanum) erneyi sp. nov. in African Bats Closely Related to Trypanosoma (Schizotrypanum) cruzi and Allied Species.
Protist,
163(6), 856-872.
Abstract:
Evolutionary Insights from Bat Trypanosomes: Morphological, Developmental and Phylogenetic Evidence of a New Species, Trypanosoma (Schizotrypanum) erneyi sp. nov. in African Bats Closely Related to Trypanosoma (Schizotrypanum) cruzi and Allied Species
Parasites of the genus Trypanosoma are common in bats and those of the subgenus Schizotrypanum are restricted to bats throughout the world, with the exception of Trypanosoma (Schizotrypanum) cruzi that also infects other mammals and is restricted to the American Continent. We have characterized trypanosome isolates from Molossidae bats captured in Mozambique, Africa. Morphology and behaviour in culture, supported by phylogenetic inferences using SSU (small subunit) rRNA, gGAPDH (glycosomal glyceraldehyde 3-phosphate dehydrogenase) and Cyt b (cytochrome b) genes, allowed to classify the isolates as a new Schizotrypanum species named Trypanosoma (Schizotrypanum) erneyi sp. nov. This is the first report of a Schizotrypanum species from African bats cultured, characterized morphologically and biologically, and positioned in phylogenetic trees. The unprecedented finding of a new species of the subgenus Schizotrypanum from Africa that is closest related to the America-restricted Trypanosoma (Schizotrypanum) cruzi marinkellei and T. cruzi provides new insights into the origin and evolutionary history of T. cruzi and closely related bat trypanosomes. Altogether, data from our study support the hypothesis of an ancestor trypanosome parasite of bats evolving to infect other mammals, even humans, and adapted to transmission by triatomine bugs in the evolutionary history of T. cruzi in the New World. © 2012 Elsevier GmbH.
Abstract.
Hamilton PB (2012). Is Trypanosoma vivax genetically diverse?. Trends in Parasitology, 28(5).
Hamilton PB (2012). Is Trypanosoma vivax genetically diverse?.
Trends Parasitol,
28(5).
Author URL.
Hamilton PB, Cruickshank C, Stevens JR, Teixeira MMG, Mathews F (2012). Parasites reveal movement of bats between the New and Old Worlds.
Mol Phylogenet Evol,
63(2), 521-526.
Abstract:
Parasites reveal movement of bats between the New and Old Worlds.
The global distribution of bat taxa indicates that the Atlantic and Pacific Oceans are effective barriers to movement between the Old and New Worlds. For instance, one of the major suborders, Yinpterochiroptera, has an exclusively Old World distribution, and within the other, Yangochiroptera, no species and only five genera are common to both. However, as bats are sometimes blown out to sea, and have colonised isolated islands, occasional natural movement between the New and Old Worlds does appear to be possible. Here we identify new genotypes of a blood parasite, Trypanosoma dionisii, in Old World bats that are closely related to South American strains. Using highly conservative calibration points, divergence of Old and New World strains is estimated to have occurred 3.2-5.0 million years ago (MYA), depending on the method used (upper 95% CL for maximum time 11.4MYA). The true date of divergence is likely to be considerably more recent. These results demonstrate that taxon-specific parasites can indicate historical movements of their hosts, even where their hosts may have left no lasting phylogenetic footprint.
Abstract.
Author URL.
Hamilton PB, Teixeira MMG, Stevens JR (2012). The evolution of Trypanosoma cruzi: the 'bat seeding' hypothesis.
Trends in Parasitology,
28(4), 136-141.
Abstract:
The evolution of Trypanosoma cruzi: the 'bat seeding' hypothesis
Recent discussions on the evolution of. Trypanosoma cruzi have been dominated by the southern super-continent hypothesis, whereby. T. cruzi and related parasites evolved in isolation in the mammals of South America, Antarctica and Australia. Here, we consider recent molecular evidence suggesting that. T. cruzi evolved from within a broader clade of bat trypanosomes, and that bat trypanosomes have successfully made the switch into other mammalian hosts in both the New and Old Worlds. Accordingly, we propose an alternative hypothesis - the bat seeding hypothesis - whereby lineages of bat trypanosomes have switched into terrestrial mammals, thereby seeding the terrestrial lineages within the clade. One key implication of this finding is that. T. cruzi may have evolved considerably more recently than previously envisaged. © 2012 Elsevier Ltd.
Abstract.
Croft DP, Hamilton PB, Darden SK, Jacoby DMP, James R, Bettaney EM, Tyler CR (2012). The role of relatedness in structuring the social network of a wild guppy population. Oecologia, 1-9.
Brown AR, Bickley LK, Le Page G, Hosken DJ, Paull GC, Hamilton PB, Owen SF, Robinson J, Sharpe AD, Tyler CR, et al (2011). Are toxicological responses in laboratory (inbred) zebrafish representative of those in outbred (wild) populations? - a case study with an endocrine disrupting chemical.
Environ Sci Technol,
45(9), 4166-4172.
Abstract:
Are toxicological responses in laboratory (inbred) zebrafish representative of those in outbred (wild) populations? - a case study with an endocrine disrupting chemical.
Laboratory animals tend to be more inbred and less genetically diverse than wild populations, and thus may differ in their susceptibility to chemical stressors. We tested this hypothesis by comparing the responses of related inbred (theoretical inbreeding F(IT) = n + 0.25) and outbred (F(IT) = n) zebrafish (Danio rerio) WIK/Wild family lines to an endocrine disrupting chemical, clotrimazole. Exposure of inbred and outbred zebrafish to 2.9 μg clotrimazole/L had no effect on survival, growth, or gonadal development. Exposure of both lines to 43.7 μg clotrimazole/L led to male-biased sex ratios compared with controls (87% versus 55% and 92% vs 64%, for inbred and outbred males, respectively), advanced germ cell development, and reduced plasma 11-ketotestosterone concentrations in males. However, outbred males (but not inbred males) developed testis that were more than twice the weight of controls, which corresponded with a proliferation of Leydig cells and maintenance of the expression (rather than down-regulation occurring in inbreds) of gonadal aromatase (cyp19a1a) and insulin-like growth factor (igf1). Our results illustrate that the effects of an endocrine disrupting chemical (clotrimazole) on some end points (here testis development) can differ between inbred and outbred zebrafish. This highlights the need for reporting pedigree/genetic information and consistency in the responses of laboratory animals (e.g. by using model compounds as positive controls).
Abstract.
Author URL.
Hamilton PB, Lewis MD, Cruickshank C, Gaunt MW, Yeo M, Llewellyn MS, Valente SA, Maia da Silva F, Stevens JR, Miles MA, et al (2011). Identification and lineage genotyping of South American trypanosomes using fluorescent fragment length barcoding.
Infect Genet Evol,
11(1), 44-51.
Abstract:
Identification and lineage genotyping of South American trypanosomes using fluorescent fragment length barcoding.
Trypanosoma cruzi and Trypanosoma rangeli are human-infective blood parasites, largely restricted to Central and South America. They also infect a wide range of wild and domestic mammals and are transmitted by a numerous species of triatomine bugs. There are significant overlaps in the host and geographical ranges of both species. The two species consist of a number of distinct phylogenetic lineages. A range of PCR-based techniques have been developed to differentiate between these species and to assign their isolates into lineages. However, the existence of at least six and five lineages within T. cruzi and T. rangeli, respectively, makes identification of the full range of isolates difficult and time consuming. Here we have applied fluorescent fragment length barcoding (FFLB) to the problem of identifying and genotyping T. cruzi, T. rangeli and other South American trypanosomes. This technique discriminates species on the basis of length polymorphism of regions of the rDNA locus. FFLB was able to differentiate many trypanosome species known from South American mammals: T. cruzi cruzi, T. cruzi marinkellei, T. dionisii-like, T. evansi, T. lewisi, T. rangeli, T. theileri and T. vivax. Furthermore, all five T. rangeli lineages and many T. cruzi lineages could be identified, except the hybrid lineages TcV and TcVI that could not be distinguished from lineages III and II respectively. This method also allowed identification of mixed infections of T. cruzi and T. rangeli lineages in naturally infected triatomine bugs. The ability of FFLB to genotype multiple lineages of T. cruzi and T. rangeli together with other trypanosome species, using the same primer sets is an advantage over other currently available techniques. Overall, these results demonstrate that FFLB is a useful method for species diagnosis, genotyping and understanding the epidemiology of American trypanosomes.
Abstract.
Author URL.
Lange A, Paull GC, Hamilton PB, Iguchi T, Tyler CR (2011). Implications of persistent exposure to treated wastewater effluent for breeding in wild roach (Rutilus rutilus) populations.
Environ Sci Technol,
45(4), 1673-1679.
Abstract:
Implications of persistent exposure to treated wastewater effluent for breeding in wild roach (Rutilus rutilus) populations.
Feminized responses are widespread in wild populations of roach, Rutilus rutilus, living in UK rivers, and some of these responses have been shown to arise as a consequence of exposure to wastewater treatment works (WwTW) effluent discharges and the endocrine disrupting chemicals (EDCs) they contain. The causation of the ovotestis condition in wild roach, however, has yet to be established. Furthermore, the impact of long-term exposure to WwTW effluents on the reproductive fitness of wild fish populations is not known, and this information is crucial for population level effect assessments. We undertook a chronic exposure of roach to a treated estrogenic wastewater effluent for up to 3.5 years to assess principally for effects on subsequent reproductive fitness, as determined through parentage analysis on offspring from a competitive breeding study. In generating the fish for the breeding study we found that exposure to full strength WwTW effluent until sexual maturity resulted in sex reversal in almost all males in the population; 98% of the exposed fish were phenotypic females, containing ovaries. Furthermore, fish exposed to a 50% dilution of WwTW effluent contained ovotestis (21% of the male roach) that was absent from the control population. In competitive breeding studies, and applying DNA microsatellites to assess parentage, we show that presumptive females exposed to sexual maturity to WwTW effluent bred normally, albeit in the absence of nonexposed females, but putative sex-reversed males breeding as females contributed poorly, if at all, in a breeding population, depending on the competition. These novel findings on sex reversal add a new dimension for impact assessments of exposure to WwTW effluents on fish populations.
Abstract.
Author URL.
Garcia HA, Rodrigues AC, Martinkovic F, Minervino AHH, Campaner M, Nunes VLB, Paiva F, Hamilton PB, Teixeira MMG (2011). Multilocus phylogeographical analysis of Trypanosoma (Megatrypanum) genotypes from sympatric cattle and water buffalo populations supports evolutionary host constraint and close phylogenetic relationships with genotypes found in other ruminants.
International Journal for Parasitology,
41(13-14), 1385-1396.
Abstract:
Multilocus phylogeographical analysis of Trypanosoma (Megatrypanum) genotypes from sympatric cattle and water buffalo populations supports evolutionary host constraint and close phylogenetic relationships with genotypes found in other ruminants
Species of the subgenus Trypanosoma (Megatrypanum) have been reported in cattle and other domestic and wild ruminants worldwide. A previous study in Brazil found at least four genotypes infecting cattle (Bos taurus), but only one in water buffalo (Bubalus bubalis). However, the small number of isolates examined from buffalo, all inhabiting nearby areas, has precluded evaluation of their diversity, host associations and geographical structure. To address these questions, we evaluated the genetic diversity and phylogeographical patterns of 25 isolates from water buffalo and 28 from cattle from four separate locations in Brazil and Venezuela. Multigene phylogenetic analyses of ssrRNA, internal transcribed spacer of rDNA (ITSrDNA), 5SrRNA, glycosomal glyceraldehyde 3-phosphate dehydrogenase (gGAPDH), mitochondrial cytochrome b (Cyt b), spliced leader (SL) and cathepsin L-like (CATL) sequences positioned all isolates from sympatric and allopatric buffalo populations into the highly homogeneous genotype TthIA, while the cattle isolates were assigned to three different genotypes, all distinct from TthIA. Polymorphisms in all of these sequences separated the trypanosomes infecting water buffalo, cattle, sheep, antelope and deer, and suggested that they correspond to separate species. Congruent phylogenies inferred with all genes indicated a predominant clonal structure of the genotypes. The multilocus analysis revealed one monophyletic assemblage formed exclusively by trypanosomes of ruminants, which corresponds to the subgenus T. (Megatrypanum). The high degree of host specificity, evidenced by genotypes exclusive to each ruminant species and lack of genotype shared by different host species, suggested that the evolutionary history of trypanosomes of this subgenus was strongly constrained by their ruminant hosts. However, incongruence between ruminant and trypanosome phylogenies did not support host-parasite co-evolution, indicating that host switches have occurred across ruminants followed by divergences, giving rise to new trypanosome genotypes adapted exclusively to one host species. © 2011 Australian Society for Parasitology Inc.
Abstract.
Hamilton PB, Stevens JR (2011). Resolving relationships between Australian trypanosomes using DNA barcoding data.
Trends Parasitol,
27(3).
Author URL.
Harris CA, Hamilton PB, Runnalls TJ, Vinciotti V, Henshaw A, Hodgson D, Coe TS, Jobling S, Tyler CR, Sumpter JP, et al (2011). The consequences of feminization in breeding groups of wild fish.
Environ Health Perspect,
119(3), 306-311.
Abstract:
The consequences of feminization in breeding groups of wild fish.
BACKGROUND: the feminization of nature by endocrine-disrupting chemicals (EDCs) is a key environmental issue affecting both terrestrial and aquatic wildlife. A crucial and as yet unanswered question is whether EDCs have adverse impacts on the sustainability of wildlife populations. There is widespread concern that intersex fish are reproductively compromised, with potential population-level consequences. However, to date, only in vitro sperm quality data are available in support of this hypothesis. OBJECTIVE: the aim of this study was to examine whether wild endocrine-disrupted fish can compete successfully in a realistic breeding scenario. METHODS: in two competitive breeding experiments using wild roach (Rutilus rutilus), we used DNA microsatellites to assign parentage and thus determine reproductive success of the adults. RESULTS: in both studies, the majority of intersex fish were able to breed, albeit with varying degrees of success. In the first study, where most intersex fish were only mildly feminized, body length was the only factor correlated with reproductive success. In the second study, which included a higher number of more severely intersex fish, reproductive performance was negatively correlated with severity of intersex. The intersex condition reduced reproductive performance by up to 76% for the most feminized individuals in this study, demonstrating a significant adverse effect of intersex on reproductive performance. CONCLUSION: Feminization of male fish is likely to be an important determinant of reproductive performance in rivers where there is a high prevalence of moderately to severely feminized males.
Abstract.
Author URL.
Adams ER, Hamilton PB, Gibson WC (2010). African trypanosomes: Celebrating diversity.
Trends in Parasitology,
26(7), 324-328.
Abstract:
African trypanosomes: Celebrating diversity
Recent advances in molecular identification techniques and phylogenetic analysis have revealed the presence of previously unidentified tsetse-transmitted trypanosomes in Africa. This is surprising in a comparatively well-known group of pathogens that includes the causative agents of human and animal trypanosomiasis. Despite levels of genetic divergence that warrant taxonomic recognition, only one of these new trypanosomes has been named as a new species; the increased diversity is largely ignored or regarded as an inconvenient complication. Yet, some of these trypanosomes have demonstrated pathogenicity, whereas others are closely related to known pathogens, and might share this trait. We should first acknowledge that these novel trypanosomes exist and then take steps to investigate their host range, pathogenicity to livestock and response to chemotherapy. © 2010 Elsevier Ltd.
Abstract.
Paull GC, Filby AL, Giddins HG, Coe TS, Hamilton PB, Tyler CR (2010). Dominance hierarchies in zebrafish (Danio rerio) and their relationship with reproductive success.
Zebrafish,
7(1), 109-117.
Abstract:
Dominance hierarchies in zebrafish (Danio rerio) and their relationship with reproductive success.
The zebrafish has considerable potential for use as a model in the study of behavior in social systems, particularly dominance hierarchies, which are widespread in nature and can affect the lifelong success of individuals. There is, however, a paucity of information relating to the characterization of social groups and significance of dominance hierarchies in the zebrafish model. This study set out to bridge this knowledge gap and better characterize dominance and its implications for reproductive success in both male and female zebrafish in colonies comprising of two males and two females. Analyses of four aggressive behaviors (chase, bite, repel, spar) were conducted twice daily over a 5-day period, and fertilized eggs were collected for parentage analyses using DNA microsatellite markers. Dominant-subordinate relationships occurred both between males and between females, and in both sexes, dominance was associated with a greater body size and higher levels of aggression. During the spawning period, dominant females were, however, less aggressive toward their subordinates than dominant males to their subordinates. Aggressive behaviors employed for maintaining dominance did not differ between the sexes, but in females, in contrast with males, the level of aggression directed toward the subordinate fish increased over the study period. Overall, dominance resulted in a greater total reproductive success in males but not in females; however, dominant females sired more offspring with the dominant male. The findings illustrate that energy invested in dominance behavior appears beneficial for both sexes in zebrafish.
Abstract.
Author URL.
Adams ER, Hamilton PB, Rodrigues AC, Malele II, Delespaux V, Teixeira MMG, Gibson W (2010). New Trypanosoma (Duttonella) vivax genotypes from tsetse flies in East Africa.
Parasitology,
137(4), 641-650.
Abstract:
New Trypanosoma (Duttonella) vivax genotypes from tsetse flies in East Africa
Salivarian trypanosomes pose a substantial threat to livestock, but their full diversity is not known. To survey trypanosomes carried by tsetse in Tanzania, DNA samples from infected proboscides of Glossina pallidipes and G. swynnertoni were identified using fluorescent fragment length barcoding (FFLB), which discriminates species by size polymorphisms in multiple regions of the ribosomal RNA locus. FFLB identified the trypanosomes in 65 of 105 (619%) infected proboscides, revealing 9 mixed infections. of 7 different FFLB profiles, 2 were similar but not identical to reference West African Trypanosoma vivax; 5 other profiles belonged to known species also identified in fly midguts. Phylogenetic analysis of the glycosomal glyceraldehyde phosphate dehydrogenase gene revealed that the Tanzanian T. vivax samples fell into 2 distinct groups, both outside the main clade of African and South American T. vivax. These new T. vivax genotypes were common and widespread in tsetse in Tanzania. The T. brucei-like trypanosome previously described from tsetse midguts was also found in 2 proboscides, demonstrating a salivarian transmission route. Investigation of mammalian host range and pathogenicity will reveal the importance of these new trypanosomes for the epidemiology and control of animal trypanosomiasis in East Africa. © 2009 Cambridge University Press.
Abstract.
Coe TS, Hamilton PB, Griffiths AM, Hodgson DJ, Wahab MA, Tyler CR (2009). Genetic variation in strains of zebrafish (Danio rerio) and the implications for ecotoxicology studies.
Ecotoxicology,
18(1), 144-150.
Abstract:
Genetic variation in strains of zebrafish (Danio rerio) and the implications for ecotoxicology studies.
There is substantial evidence that genetic variation, at both the level of the individual and population, has a significant effect on behaviour, fitness and response to toxicants. Using DNA microsatellites, we examined the genetic variation in samples of several commonly used laboratory strains of zebrafish, Danio rerio, a model species in toxicological studies. We compared the genetic variation to that found in a sample of wild fish from Bangladesh. Our findings show that the wild fish were significantly more variable than the laboratory strains for several measures of genetic variability, including allelic richness and expected heterozygosity. This lack of variation should be given due consideration for any study which attempts to extrapolate the results of ecotoxicological laboratory tests to wild populations.
Abstract.
Author URL.
Coe TS, Hamilton PB, Hodgson D, Paull GC, Tyler CR (2009). Parentage outcomes in response to estrogen exposure are modified by social grouping in zebrafish.
Environ Sci Technol,
43(21), 8400-8405.
Abstract:
Parentage outcomes in response to estrogen exposure are modified by social grouping in zebrafish.
Evidence has recently emerged that endocrine-disrupting chemicals (EDCs) can affect various behaviors, including dominance and aggression in social groups, including fish. This study investigated the effect of short-term exposure of male adult zebrafish to 17alpha-ethinylestradiol (EE(2)) on subsequent reproductive output and parentage in colonies with differing numbers of competing males. It was predicted that impacts of EDCs might differ in social groups of fish of differing size because of the greater costs of maintaining dominance hierarchies in large groups. Adult male zebrafish were exposed for 14 days to clean water, 2 ng/L EE(2) or 10 ng/L via the water, prior to placement into colonies in clean water with unexposed females. Exposure to EE(2) at the concentrations adopted prior to the breeding trials did not significantly affect subsequent colony reproductive output. The reproductive success of the most reproductively successful (MRS) male within colonies containing two males (relative to controls) was also unaffected. There was, however, a significant impact of previous EE(2) exposure in tanks containing four males, resulting in a reduction in paternity for the most successful male. Hence, nonlethal behavioral impacts of even short-term exposure to EDCs can have significant impacts on social dominance hierarchies and population genetic diversity.
Abstract.
Author URL.
Hamilton PB, Adams ER, Njiokou F, Gibson WC, Cuny G, Herder S (2009). Phylogenetic analysis reveals the presence of the Trypanosoma cruzi clade in African terrestrial mammals.
Infect Genet Evol,
9(1), 81-86.
Abstract:
Phylogenetic analysis reveals the presence of the Trypanosoma cruzi clade in African terrestrial mammals.
Despite the impact of some trypanosome species on human and livestock health, the full diversity of trypanosomes in Africa is poorly understood. A recent study examined the prevalence of trypanosomes among a wide variety of wild vertebrates in Cameroon using species-specific PCR tests, but six trypanosome isolates remained unidentified. Here they have been re-examined using fluorescent fragment length barcoding (FFLB) and phylogenetic analysis of glycosomal glyceraldehyde phosphate dehydrogenase gGAPDH and 18S ribosomal RNA (rDNA) genes. Isolates from a monkey (Cercopithecus nictitans) and a palm civet (Nandinia binotata) belonged to the Trypanosoma cruzi clade, known previously only from New World and Australian terrestrial mammals, and bats from Africa, Europe and South America. of the four other isolates, three from antelope were identified as Trypanosoma theileri, and one from a crocodile as T. grayi. This is the first report of trypanosomes of the T. cruzi clade in African terrestrial mammals and expands the clade's known global distribution in terrestrial mammals. Previously it has been hypothesized that African and New World trypanosomes diverged after continental separation, dating the divergence to around 100 million years ago. The new evidence instead suggests that intercontinental transfer occurred well after this, possibly via bats or rodents, allowing these trypanosomes to establish and evolve in African terrestrial mammals, and questioning the validity of calibrating trypanosome molecular trees using continental separation.
Abstract.
Author URL.
Hamilton PB, Adams ER, Malele II, Gibson WC (2008). A novel, high-throughput technique for species identification reveals a new species of tsetse-transmitted trypanosome related to the Trypanosoma brucei subgenus, Trypanozoon.
Infect Genet Evol,
8(1), 26-33.
Abstract:
A novel, high-throughput technique for species identification reveals a new species of tsetse-transmitted trypanosome related to the Trypanosoma brucei subgenus, Trypanozoon.
We describe a novel method of species identification, fluorescent fragment length barcoding, based on length variation in regions of the 18S and 28Salpha ribosomal DNA. Fluorescently tagged primers, designed in conserved regions of the 18S and 28Salpha ribosomal DNA, were used to amplify fragments with inter-species size variation, and sizes determined accurately using an automated DNA sequencer. By using multiple regions and different fluorochromes, a barcode unique to each species was generated. The technique was developed for the identification of African tsetse-transmitted trypanosomes and validated using DNA from laboratory isolates representing known species, subspecies and subgroups. To test the methodology, we examined 91 trypanosome samples from infected tsetse fly midguts from Tanzania, most of which had already been identified by species-specific and generic PCR tests. Identifications were mainly in agreement, but the presence of an unknown trypanosome in several samples was revealed by its unique barcode. Phylogenetic analyses based on 18S rDNA and glycosomal glyceraldehyde phosphate dehydrogenase gene sequences confirmed that this trypanosome is a new species and it is within the Trypanosoma brucei clade, as a sister group of subgenus Trypanozoon. The overall identification rate of trypanosome-infected midgut samples increased from 78 to 96% using FFLB instead of currently available PCR tests. This was due to the high sensitivity of FFLB as well as its capacity to identify previously unrecognised species. FFLB also allowed the identification of multiple species in mixed infections. The method enabled high-throughput and accurate species identification and should be applicable to any group of organisms where there is length variation in regions of rDNA.
Abstract.
Author URL.
Coe TS, Hamilton PB, Hodgson D, Paull GC, Stevens JR, Sumner K, Tyler CR (2008). An environmental estrogen alters reproductive hierarchies, disrupting sexual selection in group-spawning fish.
Environ Sci Technol,
42(13), 5020-5025.
Abstract:
An environmental estrogen alters reproductive hierarchies, disrupting sexual selection in group-spawning fish.
There is global concern regarding the potential impacts of endocrine-disrupting chemicals (EDCs) on the health of wildlife and humans. Exposure to some estrogens, at concentrations found in the environment impairs reproductive function and behavior. However, nearly all work on endocrine disruption has investigated the effects of exposure on individuals and there is an urgent need to understand impacts on populations. Many fish have mating systems with complex social structures and it is not known whether EDCs will exaggerate or buffer the reproductive skews caused by the dominance hierarchies that normally occur for these species. This study investigated the impact of exposure to the pharmaceutical estrogen ethinylestradiol (EE2) on reproductive hierarchies and sexual selection in group-spawning fish. Breeding zebrafish were exposed to environmentally relevant concentrations of EE2, and effects were determined on reproductive output, plasma androgen concentrations (in males), and reproductive success through microsatellite analyses of the offspring. Reproductive hierarchies in breeding colonies of zebrafish were disrupted by exposure to EE2 at a concentration that did not affect the number of eggs produced. The effect was a reduction in the skew in male paternity and increased skew in female maternity. This disruption in the reproductive hierarchy in group spawning fish, if it occurs in the wild, has potentially major implications for population genetic diversity. Reproductive success in male zebrafish was associated with elevated plasma concentrations of the male sex hormone 11-ketotestosterone and this hormone was suppressed in EE2-exposed males.
Abstract.
Author URL.
Adams ER, Hamilton PB (2008). New molecular tools for the indentification of trypanosome species.
Future Microbiology,
3(2), 167-176.
Abstract:
New molecular tools for the indentification of trypanosome species
Trypanosomes are the causative agents of many diseases of medical and veterinary importance, including sleeping sickness and nagana in Africa, and Chagas disease in South America. Accurate identification of trypanosome species is essential, as some species are morphologically indistinguishable, yet differ greatly in their pathogenicity. A range of molecular tools has been developed for identification of species and strains of trypanosomes. PCR, using primer sets designed to amplify a specific DNA fragment from each trypanosome species, is frequently used. More recently, generic systems have been developed that can potentially recognize all trypanosome species, such as amplification of the internal transcribed spacer and fluorescent fragment length barcoding, both of which use interspecies size variation in PCR fragments amplified from the ribosomal RNA locus. Loop-mediated isothermal amplification is a promising technique and is able to detect trypanosomes in blood, serum and cerebrospinal fluid. The advantages of these techniques for high-throughput and sensitive molecular identification will be discussed. © 2008 Future Medicine Ltd.
Abstract.
Tyler, C.R. (2007). Identification of microsatellite loci for parentage analysis in roach Rutilus rutilus and 8 other cyprinids by cross-species amplification, and a novel test for detecting hybrids between roach and other cyprinids. Molecular Ecology Notes
Hamilton PB, Gibson WC, Stevens JR (2007). Patterns of co-evolution between trypanosomes and their hosts deduced from ribosomal RNA and protein-coding gene phylogenies.
Mol Phylogenet Evol,
44(1), 15-25.
Abstract:
Patterns of co-evolution between trypanosomes and their hosts deduced from ribosomal RNA and protein-coding gene phylogenies.
Trypanosomes (genus Trypanosoma) are widespread blood parasites of vertebrates, usually transmitted by arthropod or leech vectors. Most trypanosomes have lifecycles that alternate between a vertebrate host, where they exist in the bloodstream, and an invertebrate host, where they develop in the alimentary tract. This raises the question of whether one type of host has had greater influence on the evolution of the genus. Working from the generally accepted view that trypanosomes are monophyletic, here we examine relationships between trypanosomes using phylogenies based on the genes for the small subunit ribosomal RNA (SSU rRNA) and the glycosomal glyceraldehyde phosphate dehydrogenase (gGAPDH). New analysis of a combined dataset of both these genes provides strong support for many known clades of trypanosomes. It also resolves the deepest split within the genus between the Aquatic clade, which mainly contains trypanosomes of aquatic and amphibious vertebrates, and a clade of trypanosomes from terrestrial vertebrates. There is also strengthened support for two deep clades, one comprising a wide selection of mammalian trypanosomes and a tsetse fly-transmitted reptilian trypanosome, and the other combining two bird trypanosome subclades. Considering the vertebrate and invertebrate hosts of each clade, it is apparent that co-speciation played little role in trypanosome evolution. However most clades are associated with a type of vertebrate or invertebrate host, or both, indicating that 'host fitting' has been the principal mechanism for evolution of trypanosomes.
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Hamilton PB, Stevens, J.R. Gidley, P. Holz, P. Gibson WC (2005). A new lineage of trypanosomes from Australian vertebrates and terrestrial bloodsucking leeches (Haemadipsidae). International Journal for Parasitology, 35, 431-443.
Hamilton PB, Stevens, J.R. Holz, P. Boag, B. Gibson WC (2005). The accidental introduction of the trypanosome of the introduced European rabbit (Oryctolagus cuniculus) to Australia and its potential for biocontrol. Molecular Ecology, 35, 431-443.
Hamilton PB, Stevens JR, Holz P, Boag B, Cooke B, Gibson WC (2005). The inadvertent introduction into Australia of Trypanosoma nabiasi, the trypanosome of the European rabbit (Oryctolagus cuniculus), and its potential for biocontrol.
Mol Ecol,
14(10), 3167-3175.
Abstract:
The inadvertent introduction into Australia of Trypanosoma nabiasi, the trypanosome of the European rabbit (Oryctolagus cuniculus), and its potential for biocontrol.
Wild rabbits (Oryctolagus cuniculus) in Australia are the descendents of 24 animals from England released in 1859. We surveyed rabbits and rabbit fleas (Spilopsyllus cuniculi) in Australia for the presence of trypanosomes using parasitological and PCR-based methods. Trypanosomes were detected in blood from the European rabbits by microscopy, and PCR using trypanosome-specific small subunit ribosomal RNA (SSU rRNA) gene primers and those in rabbit fleas by PCR. This is the first record of trypanosomes from rabbits in Australia. We identified these Australian rabbit trypanosomes as Trypanosoma nabiasi, the trypanosome of the European rabbit, by comparison of morphology and SSU rRNA gene sequences of Australian and European rabbit trypanosomes. Phylogenetic analysis places T. nabiasi in a clade with rodent trypanosomes in the subgenus Herpetosoma and their common link appears to be transmission by fleas. Despite the strict host specificity of trypanosomes in this clade, phylogenies presented here suggest that they have not strictly cospeciated with their vertebrate hosts. We suggest that T. nabiasi was inadvertently introduced into Australia in the 1960s in its flea vector Spilopsyllus cuniculi, which was deliberately introduced as a potential vector of the myxoma virus. In view of the environmental and economic damage caused by rabbits in Australia and other islands, the development of a virulent or genetically modified T. nabiasi should be considered to control rabbits.
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Author URL.
GIBSON WC, LOM J, PECKOVÁ H, FERRIS VR, HAMILTON PB (2004). Phylogenetic analysis of freshwater fish trypanosomes from Europe using ssu rRNA gene sequences and random amplification of polymorphic DNA. Parasitology, 130(4), 405-412.
Hamilton PB, Stevens, J.R. Gaunt, M.W. Gidley, J. Gibson WC (2004). Trypanosomes are monophyletic: evidence from genes for glyceraldehyde phosphate dehydrogenase and small subunit ribosomal RNA. International Journal for Parasitology, 34, 1393-1404.
Malele I, Craske L, Knight C, Ferris V, Njiru Z, Hamilton P, Lehane S, Lehane M, Gibson W (2003). The use of specific and generic primers to identify trypanosome infections of wild tsetse flies in Tanzania by PCR. Infection Genetics and Evolution, 3(4), 271-279.
