A review and analysis of cryptosporidiosis outbreaks in New Zealand.

Cryptosporidium is a leading global cause of diarrhoea with many reported outbreaks related to water and zoonotic transmission. This study summarizes data from Public Health Surveillance reports since 2010 in New Zealand to describe exposures associated with human diarrhoea outbreaks caused by Cryptosporidium. We investigate the species and subtypes of cases involved in some of the outbreaks to elucidate transmission routes and the predominant aetiological agents of cryptosporidiosis. For the period 2010­2017, 318 cryptosporidiosis outbreaks were reported in New Zealand resulting in 1634 cases and 20 hospitalizations. The most important mode of transmission was person-to-person (primary infections and secondary or close contacts infections), relating to 260 outbreaks and 1320 cases, followed by 113 outbreaks associated with animals, resulting in 436 human cases. From 2018 to 2021, there were 37 cryptosporidiosis outbreaks associated with 324 cases. We identified the subtypes by using polymerase chain reaction targeting the gp60 gene and the likelihood of mixed subtype infections with the Tracking of Indels by DEcomposition (TIDE) algorithm. Subtype families Ib and Ig of Cryptosporidium hominis and IIa and IId of Cryptosporidium parvum were found among cases; however, C. hominis subtypes occurred in 8 of the 11 outbreaks reviewed where molecular data were available. Examination of the chromatograms showed no mixed subtype infections in the samples assessed. Subtyping data need to be routinely incorporated into national surveillance programmes to better understand the epidemiology, sources, transmission and extent of cryptosporidiosis outbreaks in New Zealand. Our study highlights the value of integrating epidemiological information and molecular typing to investigate and manage clusters of cryptosporidiosis cases.

Mammal-related Cryptosporidium infections in endemic reptiles of New Zealand.

New Zealand's endemic reptile fauna is highly threatened and pathogens causing infectious diseases may be a significant risk to already endangered species. Here, we investigate Cryptosporidium infection in captive endemic New Zealand reptiles. We found two mammal-related Cryptosporidium species (C. hominis and C. parvum) and six subtypes from three gp60 families (Ib, Ig and IIa) in 12 individuals of captive endemic Tuatara, Otago and Grand skinks, and Jewelled and Rough geckos. Cryptosporidium serpentis was identified in two Jewelled geckos using 18S. In New Zealand, C. hominis and C. parvum are associated with infections in humans and introduced domestic animals but have also been recently found in wildlife. Our finding of Cryptosporidium infection in endemic reptiles can help inform strategies to monitor the conservation of species and manage potential introductions of pathogens to in-situ and ex-situ populations.

Trait-dependent dispersal in rails (Aves: Rallidae): Historical biogeography of a cosmopolitan bird clade.

The ability of lineages to disperse over evolutionary timescales may be influenced by the gain or loss of traits after adaptation to new ecological conditions. For example, rails (Aves: Rallidae) have many cases of flightless insular endemic species that presumably evolved after flying ancestors dispersed over large ocean barriers and became isolated. Nonetheless, the details of how flying and its loss have influenced the clade's historical biogeography are unknown, as is the importance of other predictors of dispersal such as the geographic distance between regions. Here, we used a dated phylogeny of 158 species of rails to compare trait-dependent and trait-independent biogeography models in BioGeoBEARS. We evaluated a probabilistic historical biogeographical model that allows geographic range and flight to co-evolve and influence dispersal ability on a phylogeny. The best-fitting dispersal model was a trait-dependent dispersal (DEC + j + x + t21 + m1) that accrued 85.2% of the corrected Akaike Information Criterion (AICc) model weight. The distance-dependence parameter, x was estimated at -0.54, ranging from -0.49 to -0.65 across models, suggesting that a doubling of dispersal distance results in an approximately 31% decrease in dispersal rate (2-0.54 = 0.69). The estimated rate of loss of flight (t21) was similar across all models (~0.029 loss events per lineage per million years). The multiplier on dispersal rate when a lineage is non-flying, m1, is estimated to be 0.38 under this model. Surprisingly, the estimate of m1 was not 0.0, probably because the loss of flight is so common in the rails that entire clades of flightless species are found in the data, forcing the model to attribute some dispersal to flightless lineages. These results indicate that long-distance dispersal over macroevolutionary timespans can be modelled, rather than simply attributed to chance, allowing support for different hypotheses to be quantified and limitations to be identified. Overall, by combining new analytical methods with a comprehensive phylogeny, we use a quantitative framework to show how traits influence dispersal capacity and eventually shape geographical distributions at a macroevolutionary scale.

Comparative genetic diversity of Cryptosporidium species causing human infections.

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 Cryptosporidium meleagridis, Cryptosporidium cuniculus, Cryptosporidium hominis and Cryptosporidium 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.

Species and genotypes causing human cryptosporidiosis in New Zealand.

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.

Evolutionary processes in populations of Cryptosporidium inferred from gp60 sequence data.

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.

Origin of a major infectious disease in vertebrates: The timing of Cryptosporidium evolution and its hosts.

Protozoan parasites of the genus Cryptosporidium infect all vertebrate groups and display some host specificity in their infections. It is therefore possible to assume that Cryptosporidium parasites evolved intimately aside with vertebrate lineages. Here we propose a scenario of Cryptosporidium-Vertebrata coevolution testing the hypothesis that the origin of Cryptosporidium parasites follows that of the origin of modern vertebrates. We use calibrated molecular clocks and cophylogeny analyses to provide and compare age estimates and patterns of association between these clades. Our study provides strong support for the evolution of parasitism of Cryptosporidium with the rise of the vertebrates about 600 million years ago (Mya). Interestingly, periods of increased diversification in Cryptosporidium coincides with diversification of crown mammalian and avian orders after the Cretaceous-Palaeogene (K-Pg) boundary, suggesting that adaptive radiation to new mammalian and avian hosts triggered the diversification of this parasite lineage. Despite evidence for ongoing host shifts we also found significant correlation between protozoan parasites and vertebrate hosts trees in the cophylogenetic analysis. These results help us to understand the underlying macroevolutionary mechanisms driving evolution in Cryptosporidium and may have important implications for the ecology, dynamics and epidemiology of cryptosporidiosis disease in humans and other animals.

A likelihood inference of historical biogeography in the world's most diverse terrestrial vertebrate genus: diversification of direct-developing frogs (Craugastoridae: Pristimantis) across the Neotropics.

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 40million 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 3000m) 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.

Deep global evolutionary radiation in birds: diversification and trait evolution in the cosmopolitan bird family Rallidae.

Sufficient breadth of taxon sampling in major organisms groups is important to identify more realistic biological diversification processes that reveal the degree of historical biogeographic signal and net diversification retained in the current lineage distribution. We examine the mechanisms driving diversity in one of the major avian clades with an exceptional large-scale radiation, the family Rallidae, using the most complete species-level (∼70%) time calibrated hypothesis of evolutionary relationships produced to date. We find that Rallidae exhibit a pattern of diversification involving episodes of range expansion and regional speciation that results in most clades represented in all habitable continents. Our results suggest that several features may have played an important role on the diversification rates in Rallidae. Lineage accumulation is nearly constant and morphology (frontal shield and body size), innovate (flightlessness), habitat (forest) and distribution (insular) traits are possibly associated with increasing diversification rates along with spatial and ecological processes during the Miocene and Pliocene. Diversification and the global retention of lineage diversity have occurred in multiple lineages in Rallidae due to their dispersal ability and exploitation of ecological opportunities.

First report of novel assemblages and mixed infections of Giardia duodenalis in human isolates from New Zealand.

Giardia duodenalis (syn. G. intestinalis and G. lamblia) is a protozoan parasite that cause disease (giardiasis) in humans and other animals. The pathogen is classified into eight assemblages, further divided into sub-assemblages, based on genetic divergence and host specificities. There are two zoonotic subtypes known as assemblages A and B, whilst assemblages from C to H are mainly found in domesticated animals, rodents and marine mammals. Here, we report for the first time the presence of assemblage E and sub-assemblage AIII in human isolates from the South Island in New Zealand. We identified a > 99% nucleotide similarity of assemblage E and sub-assemblage AIII with sequences of the gdh gene available in GenBank from individual human samples collected in Dunedin and Christchurch, respectively. We also performed a deep sequencing approach to assess intra-host assemblage variation. The sample from Dunedin showed evidence of mixed assemblage E and zoonotic sub-assemblage BIV. The report of two novel assemblages and mixed infections provides insights into the genetic diversity, epidemiology and transmission dynamics of Giardia duodenalis in New Zealand.

Deep Macroevolutionary Impact of Humans on New Zealand's Unique Avifauna.

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 [9-11]. 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.

Local and global genetic diversity of protozoan parasites: Spatial distribution of Cryptosporidium and Giardia genotypes.

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 heterogeneity 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. erinacei) 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.

The Global Phylogeography of Lyssaviruses - Challenging the 'Out of Africa' Hypothesis.

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 lyssaviruses, 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 phylogenetic 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.

Eocene diversification of crown group rails (Aves: Gruiformes: Rallidae).

Central to our understanding of the timing of bird evolution is debate about an apparent conflict between fossil and molecular data. A deep age for higher level taxa within Neoaves is evident from molecular analyses but much remains to be learned about the age of diversification in modern bird families and their evolutionary ecology. In order to better understand the timing and pattern of diversification within the family Rallidae we used a relaxed molecular clock, fossil calibrations, and complete mitochondrial genomes from a range of rallid species analysed in a Bayesian framework. The estimated time of origin of Rallidae is Eocene, about 40.5 Mya, with evidence of intrafamiliar diversification from the Late Eocene to the Miocene. This timing is older than previously suggested for crown group Rallidae, but fossil calibrations, extent of taxon sampling and substantial sequence data give it credence. We note that fossils of Eocene age tentatively assigned to Rallidae are consistent with our findings. Compared to available studies of other bird lineages, the rail clade is old and supports an inference of deep ancestry of ground-dwelling habits among Neoaves.

Comparative phylogeography of direct-developing frogs (Anura: Craugastoridae: Pristimantis) in the southern Andes of Colombia.

The Andes of South America hosts perhaps the highest amphibian species diversity in the world, and a sizable component of that diversity is comprised of direct-developing frogs of the genus Pristimantis (Anura: Craugastoridae). In order to better understand the initial stages of species formation in these frogs, this study quantified local-scale spatial genetic structuring in three species of Pristimantis. DNA sequences of two mitochondrial gene fragments (16S and COI) were obtained from P. brevifrons, P. palmeri and P. jubatus at different locations in the Cordillera Occidental. We found high levels of genetic diversity in the three species, with highly structured populations (as measured by F(ST)) in P. brevifrons and P. palmeri while P. jubatus showed panmixia. Large effective population sizes, inferred from the high levels of genetic diversity, were found in the three species and two highly divergent lineages were detected within P. jubatus and P. palmeri. Estimated divergence times among populations within P. brevifrons and P. palmeri coincide with the Pleistocene, perhaps due to similar responses to climatic cycling or recent geological history. Such insights have important implications for linking alpha and beta diversity, suggesting regional scale patterns may be associated with local scale processes in promoting differentiation among populations in the Andes.