Papers by Juan C García-R
Biological Conservation, 2020
New Zealand is well known as the “land of birds” with 168 extant native breeding species within a... more New Zealand is well known as the “land of birds” with 168 extant native breeding species within an area of 270,000 km2. About 40 endemic avian species have gone extinct since human arrival 700 years ago, and a high proportion of the remaining ones are currently threatened with extinction. Here, we compile a retrospective assessment of the extinction risk of New Zealand's endemic birds from the 1980s to the present date using global and national information. We projected trends in extinction risk of species during the last four decades as well as trends for species with different life-history characteristics using the Red List Index (RLI). Overall, the RLI of New Zealand endemic birds has decreased from 0.83 in the 1980s to 0.68 in the 2010s, indicating a higher risk of extinction today than 40 years ago. The conservation status of 23 species (64%) deteriorated throughout the study period. We found that flightless and large species are more likely to have a decline in conservation status compared to volant and small species. Ground-nesting birds and those with long incubation times also face higher extinction risk compared to species nesting above 1 m height and short incubation periods. Species classified as habitat specialists and inhabiting water systems showed a more rapid increase in extinction risk than non-specialist species or those inhabiting forests. Our retrospective assessment can help conservationists to identify the characteristics that make endemic birds more likely to face a higher risk of extinction. Integrating historical conservation assessments and species' traits with extinction risk will improve our ability to manage and protect endangered species.
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Parasitology Research, 2020
Cryptosporidium is one of the most common causes of diarrhoea around the world. Successful manage... more Cryptosporidium is one of the most common causes of diarrhoea around the world. Successful management and prevention of this infectious disease requires knowledge of the diversity of species and subtypes causing human disease. We use sequence data from 2598 human faecal samples collected during an 11-year period (2009–2019) to better understand the impact of different species and subtypes on public health and to gain insights into the variation of human cryptosporidiosis in New Zealand. Human cryptosporidiosis in New Zealand is caused by a high diversity of species and subtypes. Six species cause human disease in New Zealand: C. hominis, C. parvum, C. cuniculus, C. erinacei, C. meleagridis and C. tyzzeri. Sequence analysis of the gp60 gene identified 16 subtype families and 101 subtypes. Cryptosporidium hominis IbA10G2 and C. parvum IIaA18G3R1 were the most frequent causes of human cryptosporidiosis with 27% and 29% of infections, respectively. Cryptosporidium hominis presented a peak of notified human cases during autumn (March–May) whereas most cases of human cryptosporidiosis caused by C. parvum are found during the calving and lambing season in spring (September–November). We also reported some subtypes that have been rarely detected in other countries such as IbA20G2 and IIoA13G1 and a low prevalence of the hypertransmissible and virulent IIaA15G2R1. This study provides insight into the variability of cryptosporidiosis in New Zealand essential for disease management and surveillance to prevent the introduction or spread of new species and subtypes in the country.
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Parasitology, 2020
Parasites sometimes expand their host range and cause new disease aetiologies. Genetic changes ca... more Parasites sometimes expand their host range and cause new disease aetiologies. Genetic changes can then occur due to host-specific adaptive alterations, particularly when parasites cross between evolutionarily distant hosts. Characterizing genetic variation in
Cryptosporidium from humans and other animals may have important implications for understanding disease dynamics and transmission. We analyse sequences from four loci (gp60, HSP-70, COWP and actin) representing multiple Cryptosporidium species reported in humans. We predicted low genetic diversity in species that present unusual human infections due to founder events and bottlenecks. High genetic diversity was observed in isolates from humans of C. meleagridis, C. cuniculus, C. hominis and C. parvum. A deviation of expected values of neutrality using Tajima’s D was observed in C. cuniculus and C. meleagridis. The
high genetic diversity in C. meleagridis and C. cuniculus did not match our expectations but deviations from neutrality indicate a recent decrease in genetic variability through a population bottleneck after an expansion event. Cryptosporidium hominis was also found with a significant Tajima’s D positive value likely caused by recent population expansion of unusual genotypes in humans. These insights indicate that changes in genetic diversity can help us to understand host-parasite adaptation and evolution.
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Deep Sea Research Part I: Oceanographic Research Papers, 2020
Intraspecific genetic differentiation reflects processes that underpin biodiversity in deep-sea h... more Intraspecific genetic differentiation reflects processes that underpin biodiversity in deep-sea habitats. We examined the spatial genetic structure of epibenthic amphipod taxa from upper bathyal depths (200–1200 m) along New Zealand's continental margins. Genetic variability in amphipods was assessed using cytochrome c oxidase I (COI) to characterise inter-regional diversity and phylogeographic patterns in the Chatham Rise and Challenger Plateau to the east and west of New Zealand, respectively. Automatic barcode gap discovery methods identified 263 MOTUs, of which 14 were detected in both regions. Population genetic analyses found contrasting patterns of diversity among different MOTUs within and between regions. Overall, a pattern of increasing genetic differentiation (K2P distances) with decreasing depth was observed between regions. Genetic differentiation was highest among MOTUs found at shallow depths, while taxa from deeper waters showed little evidence of divergence. Our results suggest that intraspecific genetic diversity is correlated with amphipod family traits, particularly dispersal abilities inferred from habitat preferences (infaunal, epibenthic or pelagic) and may also be linked to regional geological history. Such insights have important implications for regional-scale patterns of diversity associated with local processes in promoting differentiation among populations of bathyal amphipods on New Zealand's continental margins.
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Journal of Applied Microbiology, 2020
Aim
The aim of our study was to assess the presence and risk of waterborne pathogens in the drink... more Aim
The aim of our study was to assess the presence and risk of waterborne pathogens in the drinking water of outdoor facilities in New Zealand and track potential sources of microbial contamination in water sources.
Methods and results
A serial cross‐sectional study with a risk‐based sample collection strategy was conducted at 15 public campgrounds over two summer seasons (2011–2012 and 2012–2013). Drinking water supplied to these campgrounds was not compliant with national standards, based on Escherichia coli as an indicator organism, in more than half of the sampling occasions. Campylobacter contamination of drinking water at the campgrounds was likely to be of wild bird origin. Faecal samples from rails (pukeko and weka) were 35 times more likely to return a Campylobacter‐positive result compared to passerines. Water treatment using ultraviolet (UV) irradiation or a combination of filtration and UV irradiation or chemicals was more likely to result in water that was compliant with the national standards than water from a tap without any treatment. The use of filters alone was not associated with the likelihood of compliance.
Conclusions
Providing microbiologically safe drinking water at outdoor recreational facilities is imperative to avoid gastroenteritis outbreaks. This requires an in‐depth understanding of potential sources of contamination in drinking water sources and the installation of adequate water treatment facilities.
Significance and Impact of the Study
Our study provides evidence that drinking water without treatment or filter‐only treatment in public campgrounds is unlikely to comply with national standards for human consumption and extra water treatment measures such as UV irradiation or chemical treatment are needed.
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Diversity, 2020
The integration of state-of-the-art molecular techniques and analyses, together with a broad taxo... more The integration of state-of-the-art molecular techniques and analyses, together with a broad taxonomic sampling, can provide new insights into bird interrelationships and divergence. Despite their evolutionary significance, the relationships among several rail lineages remain unresolved as does the general timescale of rail evolution. Here, we disentangle the deep phylogenetic structure of rails using anchored phylogenomics. We analysed a set of 393 loci from 63 species, representing approximately 40% of the extant familial diversity. Our phylogenomic analyses reconstruct the phylogeny of rails and robustly infer several previously contentious relationships. Concatenated maximum likelihood and coalescent species-tree approaches recover identical topologies with strong node support. The results are concordant with previous phylogenetic studies using small DNA datasets, but they also supply an additional resolution. Our dating analysis provides contrasting divergence times using fossils and Bayesian and non-Bayesian approaches. Our study refines the evolutionary history of rails, offering a foundation for future evolutionary studies of birds.
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Current Biology, 2019
Islands are at the frontline of the anthropogenic extinction crisis [1]. A vast number of island ... more Islands are at the frontline of the anthropogenic extinction crisis [1]. A vast number of island birds have gone extinct since human colonization [2], and an important proportion is currently threatened with extinction [3]. While the number of lost or threatened avian species has often been quantified [4], the macroevolutionary consequences of human impact on island biodiversity have rarely been measured [5]. Here, we estimate the amount of evolutionary time that has been lost or is under threat due to anthropogenic activity in a classic example, New Zealand. Half of its bird taxa have gone extinct since humans arrived [6, 7] and many are threatened [8], including lineages forming highly distinct branches in the avian tree of life [9, 10, 11]. Using paleontological and ancient DNA information, we compiled a dated phylogenetic dataset for New Zealand’s terrestrial avifauna. We extend the method DAISIE developed for island biogeography [12] to allow for the fact that many of New Zealand’s birds are evolutionarily isolated and use it to estimate natural rates of speciation, extinction, and colonization. Simulating under a range of human-induced extinction scenarios, we find that it would take approximately 50 million years (Ma) to recover the number of species lost since human colonization of New Zealand and up to 10 Ma to return to today’s species numbers if currently threatened species go extinct. This study puts into macroevolutionary perspective the impact of humans in an isolated fauna and reveals how conservation decisions we take today will have repercussions for millions of years.
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Ecography, 2019
Geospatial patterns in the distribution of regional biodiversity reflect the composite processes ... more Geospatial patterns in the distribution of regional biodiversity reflect the composite processes that underpin evolution: speciation, dispersal and extinction. The spatial distribution and phylogeny of a globally widespread and species rich bird family (Rallidae) were used to help assess the role of large‐scale biogeographical processes in diversity and diversification. Here, we examine how different geostatistical diversity metrics enhance our understanding of species distribution by linking occurrence records of rail species to corresponding species level phylogeny. Tropical regions and temperate zones contained a large proportion of rail species richness and phylogenetic diversity whilst small islands in Australian, Oceanian and Oriental regions held the highest weighted and phylogenetic endemism. Our results suggest that habitat connectivity and dispersal were important ecological features in rail evolution and distribution. Spatial isolation was a significant driver of diversification where islands in Oceania were centres of neo‐endemism with recent multiple and independent speciation events and could be considered as nurseries of biodiversity. Palaeo‐endemism was mostly associated with older stable regions, so despite extensive long distance range shifting these areas retain their own ancient and distinct character. Madagascar was the major area of palaeo‐endemism associated with the oldest rail lineages and could be considered a museum of rail diversity. This implies a mixture of processes determine the current distribution and diversity of rail clades with some areas dominated by recent ‘in situ’ speciation while others harbour old diversity with ecological traits that have stood the test of time.
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Journal of Building Engineering, 2018
Health problems and respiratory diseases are associated with indoor air particulate matter (PM) m... more Health problems and respiratory diseases are associated with indoor air particulate matter (PM) mass. This is specially a concern in schools as children spend most of their time indoors. Understanding factors that affect PM mass such as occupant activities, ventilation and the infiltrating outdoor environment are important to safeguard occupant health. We investigated the air quality inside and outside two low decile primary school classrooms (children ages 7–9) over a three-week period during the southern hemisphere winter season in Palmerston North, New Zealand. Both classrooms were heated with wall mounted inverter heat pumps and in addition one classroom roof was fitted with a solar air heated ventilation unit (treatment). Particulate matter was continuously sampled and monitored to identify particles less than 10 µm in aerodynamic diameter (PM10) both outside and inside both classrooms to compare their indoor air quality. Significantly higher PM10 concentrations occurred within both classrooms during school hours (0845–1500), but the ventilated treatment classroom had PM10 concentrations on average 66% lower than those measured in the unventilated control classroom. Elemental composition and source apportionment of hourly samples showed that outdoor sources of PM10 infiltrated indoors, with similar contributions in both classrooms to those measured outdoors. However, the increased PM10 in the classrooms was predominantly from crustal sources, thought to be soil tracked in from outside on children's footwear and re-suspended during activities within the classrooms. Our results indicate that ventilation plays an important role in the quality of indoor air of classrooms and will contribute to the wellbeing of the students. In addition, there is a need to improve dust exposure mitigation strategies (carpet cleaning regime, dust reducing carpet) in classrooms fitted with carpets.
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New Zealand veterinary journal, 2018
AIM: To describe the Chlamydia psittaci genotypes in samples from native and introduced birds fro... more AIM: To describe the Chlamydia psittaci genotypes in samples from native and introduced birds from New Zealand by analysis of the sequence variation of the ompA gene.
METHODS: DNA was extracted from samples collected from a non-random sample of birds; either swabs from live asymptomatic birds or birds with clinical signs, or formalin-fixed, paraffin-embedded (FFPE) samples from historical post-mortem cases. The presence of C. psittaci in all samples had been confirmed using a quantitative PCR assay. The C. psittaci ompA gene was amplified and sequenced from samples from 26 native and introduced infected birds comprising 12 different species. These sequences were compared to published available C. psittaci genotypes.
RESULTS: Genotypes A and C of C. psittaci were identified in the samples. Genotype A was identified in samples from nine birds, including various native and introduced species. Genotype C was identified in samples from 16 different waterfowl species, and a mixed infection of both genotypes was found in a kaka (Nestor meridionalis). In native birds, C. psittaci infection was confirmed in seven new host species.
CONCLUSIONS AND CLINICAL RELEVANCE: Two genotypes (A and C) of C. psittaci were found in samples from a wider range of both native and introduced species of birds in New Zealand than previously reported. Both genotypes have been globally associated with significant disease in birds and humans. These initial results suggest the host range of C. psittaci in New Zealand birds is under-reported. However, the prevalence of C. psittaci infection in New Zealand, and the associated impact on avian and public health, remains to be determined. There are biosecurity implications associated with the importation of birds to New Zealand if there is a limited diversity of C. psittaci genotypes present.
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Cryptosporidiosis and giardiasis are recognized as significant enteric diseases due to their long... more Cryptosporidiosis and giardiasis are recognized as significant enteric diseases due to their long-term health effects in humans and their economic impact in agriculture and medical care. Molecular analysis is essential to identify species and genotypes causing these infectious diseases and provides a potential tool for monitoring. This study uses information on species and genetic variants to gain insights into the geographical distribution and spatial patterns of Cryptosporidium and Giardia parasites. Here, we describe the population hetero-geneity of genotypic groups within Cryptosporidium and Giardia present in New Zealand using gp60 and gdh markers to compare the observed variation with other countries around the globe. Four species of Cryptosporidium (C. hominis, C. parvum, C. cuniculus and C. eri-nacei) and one species of Giardia (G. intestinalis) were identified. These species have been reported worldwide and there are not unique Cryptosporidium gp60 subtype families and Giardia gdh assemblages in New Zealand, most likely due to high gene flow of historical and current human activity (travel and trade) and persistence of large host population sizes. The global analysis revealed that genetic variants of these pathogens are widely distributed. However, genetic variation is underestimated by data biases (e.g. neglected submission of sequences to genetic databases) and low sampling. New genotypes are likely to be discovered as sampling efforts increase according to accumulation prediction analyses, especially for C. parvum. Our study highlights the need for greater sampling and archiving of genotypes globally to allow comparative analyses that help understand the population dynamics of these protozoan parasites. Overall our study represents a comprehensive overview for exploring local and global protozoan genotype diversity and advances our understanding of the importance for surveillance and potential risk associated with these infectious diseases.
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Studies of fragmented habitat, such as island archipelagos, provide insights into the microevolut... more Studies of fragmented habitat, such as island archipelagos, provide insights into the microevolutionary processes that drive early stages of diversification. Here, we examined genetic variation and gene flow among populations of the widespread buff-banded rail Gallirallus philippensis in Oceania to understand the factors that promote speciation associated within this bird lineage. We analysed mtDNA Control Region sequences and six microsatellite loci from a total of 152 individuals of buff-banded rail on islands and continental areas. We used a phylogeographic model-testing approach and a structured spatial design ranging from within to among archipelagoes in the south Pacific. Buff-banded rail populations in the Philippines archipelago and nearby Palau and Wallacea had high genetic diversity while those in geographically distant Australia showed lower variation. Other archipelagos sampled were found to have less genetic diversity and included haplotypes closely related to Wallacea (Bismarck, Vanuatu, New Caledonia) or Australia (New Zealand, Samoa, Fiji, Cocos Islands). Nucleotide diversity and allele frequency declined with degree of geographic isolation but haplotype diversity remained more even. However, both nucleotide and haplotype diversities were positively correlated with land area. Microsatellite data for a subset of locations showed moderate to high genetic differentiation and significant pairwise F ST despite a relatively high migration rate. Our results are mostly consistent with a model of abrupt genetic changes due to founder events with multiple dispersals into Australia from Wallacea and Bismarck. Australia has probably been the source of birds for islands in the Pacific. This is shown by decreasing genetic diversity and growing genetic differentiation when distances separating populations increased from Australia. A history of range expansion and divergent natural selection may help explain the existence of numerous sympatric Gallirallus island endemics.
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Cryptosporidiosis is one of the most common human infectious diseases globally. The gp60 gene has... more Cryptosporidiosis is one of the most common human infectious diseases globally. The gp60 gene has been adopted as a key marker for molecular epidemiological investigations into this protozoan disease because of the capability to characterize genotypes and detect variants within Cryptosporidium species infecting humans. However, we know relatively little about the potential spatial and temporal variation in population demography that can be inferred from this gene beyond that it is recognized to be under selective pressure. Here, we analyzed the genetic variation in time and space within two putative populations of Cryptosporidium in New Zealand to infer the processes behind the patterns of sequence polymorphism. Analyses using Tajima's D, Fu, and Li's D* and F* tests show significant departures from neutrality in some populations and indicate the selective maintenance of alleles within some populations. Demographic analyses showed distortions in the pattern of the genetic variability caused by high recombination rates and population expansion, which was observed in case notification data. Our results showed that processes acting on populations that have similar effects can be distinguished from one another and multiple processes can be detected acting at the same time. These results are significant for prediction of the parasite dynamics and potential mechanisms of long-term changes in the risk of cryptosporidiosis in humans.
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Rabies virus kills tens of thousands of people globally each year, especially in resource-limited... more Rabies virus kills tens of thousands of people globally each year, especially in resource-limited countries. Yet, there are genetically-and antigenically-related lyssaviruses, all capable of causing the disease rabies, circulating globally among bats without causing conspicuous disease outbreaks. The species richness and greater genetic diversity of African lyssa-viruses, along with the lack of antibody cross-reactivity among them, has led to the hypothesis that Africa is the origin of lyssaviruses. This hypothesis was tested using a probabilistic phylogeographical approach. The nucleoprotein gene sequences from 153 representatives of 16 lyssavirus species, collected between 1956 and 2015, were used to develop a phylo-genetic tree which incorporated relevant geographic and temporal data relating to the viruses. In addition, complete genome sequences from all 16 (putative) species were analysed. The most probable ancestral distribution for the internal nodes was inferred using three different approaches and was confirmed by analysis of complete genomes. These results support a Palearctic origin for lyssaviruses (posterior probability = 0.85), challenging the 'out of Africa' hypothesis, and suggest three independent transmission events to the Afrotropical region, representing the three phylogroups that form the three major lyssavirus clades. Rabies virus kills tens of thousands of people globally each year and causes indescribable misery and family disturbance, especially in developing countries. Yet in much of the world there are related viruses, called lyssaviruses, which circulate among bats without causing conspicuous outbreaks. The greater diversity of African lyssaviruses has led to the hypothesis that Africa is the origin of these viruses. To test this hypothesis, the genetic data from 153 representative viruses from 16 available lyssavirus species from across the world dated between 1956 and 2015 were analysed. Statistical models were used to reconstruct the historical processes that lead to the contemporary distribution of these viruses.
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Molecular phylogenetic analysis has demonstrated that the genus Gallinula is not mono-phyletic an... more Molecular phylogenetic analysis has demonstrated that the genus Gallinula is not mono-phyletic and comprises four major lineages. a review of the nomenclature of Gallinula shows that generic names are available for three lineages but that a fourth is as yet unnamed. a new monotypic genus, Paragallinula gen. nov., is described for Lesser Moorhen (Gallinula angulata Sundevall, 1850).
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Journal of Avian Biology, 2015
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The geology of the northern Andean region has driven the evolutionary history of Neotropical faun... more The geology of the northern Andean region has driven the evolutionary history of Neotropical fauna
through the creation of barriers and connections that have resulted in speciation and dispersal events,
respectively. One of the most conspicuous groups of anuran fauna in the Andes and surrounding areas
is the direct-developing species of the genus Pristimantis. We investigated the molecular phylogenetic
placement of 12 species from the montane Andes of Colombia in a broader geographical context with
a new genus-level phylogeny in order to identify the role of Andean orogeny over the last 40 million years
and the effect of elevational differences in diversification of Pristimantis. We examined the biogeographic
history of the genus using ancestral range reconstruction by biogeographic regions and elevational
ranges. We recognized the middle elevational band (between 1000 and 3000 m) in the Northwestern
Andes region of Colombia and Ecuador as a focal point for the origin and radiation of Pristimantis species.
Additionally, we found several Andean migrations toward new habitats in Central Andes and Merida
Andes for some species groups. We suggest that the paleogeological changes in the Northwestern Andes
were the main promoter of speciation in Pristimantis, and may have served as a corridor for the dispersion
of lowland species.
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Dispersal, when accompanied by reduced gene flow and natural selection, influences speciation rat... more Dispersal, when accompanied by reduced gene flow and natural selection, influences speciation rates among groups
of organisms. We used molecular phylogenetics, divergence time estimates, and population genetics to reconstruct
the mode, pattern, and tempo of diversification within the wide-ranging purple swamphens (genus Porphyrio), with
emphasis on the ‘‘supertramp’’ P. porphyrio. Our results suggest that the Porphyrio clade arose during the Middle
Miocene in Africa, with a single colonization in the Americas and several other colonizations in Southeast Asia and the
Indo-Pacific around 10 mya. We found that the widespread P. porphyrio is not monophyletic. Indeed, several
subspecies and subspecies groups may represent species-level lineages. The P. p. melanotus lineage probably reached
Australasia during the Pleistocene (600 kya), although some islands were colonized only in the past few hundred years.
New Zealand, and some other islands, had previously been colonized (~2.5 mya) by flying Porphyrio that evolved into
flightless endemic species. Early and recent lineages are now sympatric. Widespread occupation of oceanic islands
implies high dispersal and colonization rates, but gene flow probably occurs episodically and follows varying routes at
different times. This pattern of colonization enables populations to differentiate and, ultimately, speciate.
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Papers by Juan C García-R
Cryptosporidium from humans and other animals may have important implications for understanding disease dynamics and transmission. We analyse sequences from four loci (gp60, HSP-70, COWP and actin) representing multiple Cryptosporidium species reported in humans. We predicted low genetic diversity in species that present unusual human infections due to founder events and bottlenecks. High genetic diversity was observed in isolates from humans of C. meleagridis, C. cuniculus, C. hominis and C. parvum. A deviation of expected values of neutrality using Tajima’s D was observed in C. cuniculus and C. meleagridis. The
high genetic diversity in C. meleagridis and C. cuniculus did not match our expectations but deviations from neutrality indicate a recent decrease in genetic variability through a population bottleneck after an expansion event. Cryptosporidium hominis was also found with a significant Tajima’s D positive value likely caused by recent population expansion of unusual genotypes in humans. These insights indicate that changes in genetic diversity can help us to understand host-parasite adaptation and evolution.
The aim of our study was to assess the presence and risk of waterborne pathogens in the drinking water of outdoor facilities in New Zealand and track potential sources of microbial contamination in water sources.
Methods and results
A serial cross‐sectional study with a risk‐based sample collection strategy was conducted at 15 public campgrounds over two summer seasons (2011–2012 and 2012–2013). Drinking water supplied to these campgrounds was not compliant with national standards, based on Escherichia coli as an indicator organism, in more than half of the sampling occasions. Campylobacter contamination of drinking water at the campgrounds was likely to be of wild bird origin. Faecal samples from rails (pukeko and weka) were 35 times more likely to return a Campylobacter‐positive result compared to passerines. Water treatment using ultraviolet (UV) irradiation or a combination of filtration and UV irradiation or chemicals was more likely to result in water that was compliant with the national standards than water from a tap without any treatment. The use of filters alone was not associated with the likelihood of compliance.
Conclusions
Providing microbiologically safe drinking water at outdoor recreational facilities is imperative to avoid gastroenteritis outbreaks. This requires an in‐depth understanding of potential sources of contamination in drinking water sources and the installation of adequate water treatment facilities.
Significance and Impact of the Study
Our study provides evidence that drinking water without treatment or filter‐only treatment in public campgrounds is unlikely to comply with national standards for human consumption and extra water treatment measures such as UV irradiation or chemical treatment are needed.
METHODS: DNA was extracted from samples collected from a non-random sample of birds; either swabs from live asymptomatic birds or birds with clinical signs, or formalin-fixed, paraffin-embedded (FFPE) samples from historical post-mortem cases. The presence of C. psittaci in all samples had been confirmed using a quantitative PCR assay. The C. psittaci ompA gene was amplified and sequenced from samples from 26 native and introduced infected birds comprising 12 different species. These sequences were compared to published available C. psittaci genotypes.
RESULTS: Genotypes A and C of C. psittaci were identified in the samples. Genotype A was identified in samples from nine birds, including various native and introduced species. Genotype C was identified in samples from 16 different waterfowl species, and a mixed infection of both genotypes was found in a kaka (Nestor meridionalis). In native birds, C. psittaci infection was confirmed in seven new host species.
CONCLUSIONS AND CLINICAL RELEVANCE: Two genotypes (A and C) of C. psittaci were found in samples from a wider range of both native and introduced species of birds in New Zealand than previously reported. Both genotypes have been globally associated with significant disease in birds and humans. These initial results suggest the host range of C. psittaci in New Zealand birds is under-reported. However, the prevalence of C. psittaci infection in New Zealand, and the associated impact on avian and public health, remains to be determined. There are biosecurity implications associated with the importation of birds to New Zealand if there is a limited diversity of C. psittaci genotypes present.
through the creation of barriers and connections that have resulted in speciation and dispersal events,
respectively. One of the most conspicuous groups of anuran fauna in the Andes and surrounding areas
is the direct-developing species of the genus Pristimantis. We investigated the molecular phylogenetic
placement of 12 species from the montane Andes of Colombia in a broader geographical context with
a new genus-level phylogeny in order to identify the role of Andean orogeny over the last 40 million years
and the effect of elevational differences in diversification of Pristimantis. We examined the biogeographic
history of the genus using ancestral range reconstruction by biogeographic regions and elevational
ranges. We recognized the middle elevational band (between 1000 and 3000 m) in the Northwestern
Andes region of Colombia and Ecuador as a focal point for the origin and radiation of Pristimantis species.
Additionally, we found several Andean migrations toward new habitats in Central Andes and Merida
Andes for some species groups. We suggest that the paleogeological changes in the Northwestern Andes
were the main promoter of speciation in Pristimantis, and may have served as a corridor for the dispersion
of lowland species.
of organisms. We used molecular phylogenetics, divergence time estimates, and population genetics to reconstruct
the mode, pattern, and tempo of diversification within the wide-ranging purple swamphens (genus Porphyrio), with
emphasis on the ‘‘supertramp’’ P. porphyrio. Our results suggest that the Porphyrio clade arose during the Middle
Miocene in Africa, with a single colonization in the Americas and several other colonizations in Southeast Asia and the
Indo-Pacific around 10 mya. We found that the widespread P. porphyrio is not monophyletic. Indeed, several
subspecies and subspecies groups may represent species-level lineages. The P. p. melanotus lineage probably reached
Australasia during the Pleistocene (600 kya), although some islands were colonized only in the past few hundred years.
New Zealand, and some other islands, had previously been colonized (~2.5 mya) by flying Porphyrio that evolved into
flightless endemic species. Early and recent lineages are now sympatric. Widespread occupation of oceanic islands
implies high dispersal and colonization rates, but gene flow probably occurs episodically and follows varying routes at
different times. This pattern of colonization enables populations to differentiate and, ultimately, speciate.
Cryptosporidium from humans and other animals may have important implications for understanding disease dynamics and transmission. We analyse sequences from four loci (gp60, HSP-70, COWP and actin) representing multiple Cryptosporidium species reported in humans. We predicted low genetic diversity in species that present unusual human infections due to founder events and bottlenecks. High genetic diversity was observed in isolates from humans of C. meleagridis, C. cuniculus, C. hominis and C. parvum. A deviation of expected values of neutrality using Tajima’s D was observed in C. cuniculus and C. meleagridis. The
high genetic diversity in C. meleagridis and C. cuniculus did not match our expectations but deviations from neutrality indicate a recent decrease in genetic variability through a population bottleneck after an expansion event. Cryptosporidium hominis was also found with a significant Tajima’s D positive value likely caused by recent population expansion of unusual genotypes in humans. These insights indicate that changes in genetic diversity can help us to understand host-parasite adaptation and evolution.
The aim of our study was to assess the presence and risk of waterborne pathogens in the drinking water of outdoor facilities in New Zealand and track potential sources of microbial contamination in water sources.
Methods and results
A serial cross‐sectional study with a risk‐based sample collection strategy was conducted at 15 public campgrounds over two summer seasons (2011–2012 and 2012–2013). Drinking water supplied to these campgrounds was not compliant with national standards, based on Escherichia coli as an indicator organism, in more than half of the sampling occasions. Campylobacter contamination of drinking water at the campgrounds was likely to be of wild bird origin. Faecal samples from rails (pukeko and weka) were 35 times more likely to return a Campylobacter‐positive result compared to passerines. Water treatment using ultraviolet (UV) irradiation or a combination of filtration and UV irradiation or chemicals was more likely to result in water that was compliant with the national standards than water from a tap without any treatment. The use of filters alone was not associated with the likelihood of compliance.
Conclusions
Providing microbiologically safe drinking water at outdoor recreational facilities is imperative to avoid gastroenteritis outbreaks. This requires an in‐depth understanding of potential sources of contamination in drinking water sources and the installation of adequate water treatment facilities.
Significance and Impact of the Study
Our study provides evidence that drinking water without treatment or filter‐only treatment in public campgrounds is unlikely to comply with national standards for human consumption and extra water treatment measures such as UV irradiation or chemical treatment are needed.
METHODS: DNA was extracted from samples collected from a non-random sample of birds; either swabs from live asymptomatic birds or birds with clinical signs, or formalin-fixed, paraffin-embedded (FFPE) samples from historical post-mortem cases. The presence of C. psittaci in all samples had been confirmed using a quantitative PCR assay. The C. psittaci ompA gene was amplified and sequenced from samples from 26 native and introduced infected birds comprising 12 different species. These sequences were compared to published available C. psittaci genotypes.
RESULTS: Genotypes A and C of C. psittaci were identified in the samples. Genotype A was identified in samples from nine birds, including various native and introduced species. Genotype C was identified in samples from 16 different waterfowl species, and a mixed infection of both genotypes was found in a kaka (Nestor meridionalis). In native birds, C. psittaci infection was confirmed in seven new host species.
CONCLUSIONS AND CLINICAL RELEVANCE: Two genotypes (A and C) of C. psittaci were found in samples from a wider range of both native and introduced species of birds in New Zealand than previously reported. Both genotypes have been globally associated with significant disease in birds and humans. These initial results suggest the host range of C. psittaci in New Zealand birds is under-reported. However, the prevalence of C. psittaci infection in New Zealand, and the associated impact on avian and public health, remains to be determined. There are biosecurity implications associated with the importation of birds to New Zealand if there is a limited diversity of C. psittaci genotypes present.
through the creation of barriers and connections that have resulted in speciation and dispersal events,
respectively. One of the most conspicuous groups of anuran fauna in the Andes and surrounding areas
is the direct-developing species of the genus Pristimantis. We investigated the molecular phylogenetic
placement of 12 species from the montane Andes of Colombia in a broader geographical context with
a new genus-level phylogeny in order to identify the role of Andean orogeny over the last 40 million years
and the effect of elevational differences in diversification of Pristimantis. We examined the biogeographic
history of the genus using ancestral range reconstruction by biogeographic regions and elevational
ranges. We recognized the middle elevational band (between 1000 and 3000 m) in the Northwestern
Andes region of Colombia and Ecuador as a focal point for the origin and radiation of Pristimantis species.
Additionally, we found several Andean migrations toward new habitats in Central Andes and Merida
Andes for some species groups. We suggest that the paleogeological changes in the Northwestern Andes
were the main promoter of speciation in Pristimantis, and may have served as a corridor for the dispersion
of lowland species.
of organisms. We used molecular phylogenetics, divergence time estimates, and population genetics to reconstruct
the mode, pattern, and tempo of diversification within the wide-ranging purple swamphens (genus Porphyrio), with
emphasis on the ‘‘supertramp’’ P. porphyrio. Our results suggest that the Porphyrio clade arose during the Middle
Miocene in Africa, with a single colonization in the Americas and several other colonizations in Southeast Asia and the
Indo-Pacific around 10 mya. We found that the widespread P. porphyrio is not monophyletic. Indeed, several
subspecies and subspecies groups may represent species-level lineages. The P. p. melanotus lineage probably reached
Australasia during the Pleistocene (600 kya), although some islands were colonized only in the past few hundred years.
New Zealand, and some other islands, had previously been colonized (~2.5 mya) by flying Porphyrio that evolved into
flightless endemic species. Early and recent lineages are now sympatric. Widespread occupation of oceanic islands
implies high dispersal and colonization rates, but gene flow probably occurs episodically and follows varying routes at
different times. This pattern of colonization enables populations to differentiate and, ultimately, speciate.