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Neil J Gemmell

Publications and source records attributed to Neil J Gemmell.

At least 19 recordsLinked to original sources
PubMed2026

Evaluating sampling strategies for the detection of avian influenza viruses in the environment.

Highly pathogenic avian influenza (HPAI) viruses pose an increasing threat to wildlife, livestock and human health, underscoring the need for scalable and early-warning surveillance systems. Environmental RNA (eRNA) monitoring offers a non-invasive, cost-effective alternative to traditional host-based sampling by detecting viral genetic material shed into the environment. Despite its utility, the relative performance of different environmental sampling approaches for avian influenza virus (AIV) detection remains poorly resolved. Here, we conducted a longitudinal study with monthly sampling over approximately one year across two urban waterfowl ponds in Aotearoa New Zealand to evaluate four eRNA sampling strategies - fresh faeces, sediment, active-filtered water and passive-filtered water - for their ability to detect AIV. Using a combination of metagenomic sequencing and RT-qPCR, we show that all sample types can detect AIV, although detections were highly inconsistent across sampling methods, locations and time points. While metagenomic sequencing provided valuable genomic data, including subtype identification and phylogenetic context, RT-qPCR exhibited greater sensitivity, with active-filtered water yielding the highest detection rates, and is currently the more cost-effective approach for large-scale surveillance. Notably, AIV detections were asynchronous among sample types and frequently lacked temporal concordance, suggesting that environmental heterogeneity, RNA persistence, and methodological detection limits strongly influence surveillance outcomes. Despite these inconsistencies, phylogenetic analyses revealed that detected viruses belong to established Australasian lineages, highlighting the ability of environmental surveillance to capture ecologically relevant viral diversity. Our findings demonstrate that while eRNA-based surveillance holds substantial promise as a complementary tool for AIV monitoring, its effectiveness is highly dependent on the environmental sampling strategies and laboratory detection methods used.

Ducks↗
PubMed2006

Heterozygote advantage for fecundity.

Heterozygote advantage, or overdominance, remains a popular and persuasive explanation for the maintenance of genetic variation in natural populations in the face of selection. However, despite being first proposed more than 80 years ago, there remain few examples that fit the criteria for heterozygote advantage, all of which are associated with disease resistance and are maintained only in the presence of disease or other gene-by-environment interaction. Here we report five new examples of heterozygote advantage, based around polymorphisms in the BMP15 and GDF9 genes that affect female fecundity in domesticated sheep and are not reliant on disease for their maintenance. Five separate mutations in these members of the transforming growth factor beta (TGFbeta) superfamily give phenotypes with fitness differentials characteristic of heterozygous advantage. In each case, one copy of the mutant allele increases ovulation rate, and ultimately litter size per ewe lambing, relative to the wildtype. However, homozygous ewes inheriting mutant alleles from both parents have impaired oocyte development and maturation, which results in small undeveloped ovaries and infertility. Using data collected over many years on ovulation rates, litter size, and lambing rates, we have calculated the equilibrium solution for each of these polymorphisms using standard population genetic theory. The predicted equilibrium frequencies obtained for these mutant alleles range from 0.11 to 0.23, which are amongst the highest yet reported for a polymorphism maintained by heterozygote advantage. These are amongst the most frequent and compelling examples of heterozygote advantage yet described and the first documented examples of heterozygote advantage that are not reliant on a disease interaction for their maintenance.

Animals↗
PubMed2006

Gender differences in publication output: towards an unbiased metric of research performance.

We examined the publication records of a cohort of 168 life scientists in the field of ecology and evolutionary biology to assess gender differences in research performance. Clear discrepancies in publication rate between men and women appear very early in their careers and this has consequences for the subsequent citation of their work. We show that a recently proposed index designed to rank scientists fairly is in fact strongly biased against female researchers, and advocate a modified index to assess men and women on a more equitable basis.

Australia↗
PubMed2006

Deciphering past human population movements in Oceania: provably optimal trees of 127 mtDNA genomes.

The settlement of the many island groups of Remote Oceania occurred relatively late in prehistory, beginning approximately 3,000 years ago when people sailed eastwards into the Pacific from Near Oceania, where evidence of human settlement dates from as early as 40,000 years ago. Archeological and linguistic analyses have suggested the settlers of Remote Oceania had ancestry in Taiwan, as descendants of a proposed Neolithic expansion that began approximately 5,500 years ago. Other researchers have suggested that the settlers were descendants of peoples from Island Southeast Asia or the existing inhabitants of Near Oceania alone. To explore patterns of maternal descent in Oceania, we have assembled and analyzed a data set of 137 mitochondrial DNA (mtDNA) genomes from Oceania, Australia, Island Southeast Asia, and Taiwan that includes 19 sequences generated for this project. Using the MinMax Squeeze Approach (MMS), we report the consensus network of 165 most parsimonious trees for the Oceanic data set, increasing by many orders of magnitude the numbers of trees for which a provable minimal solution has been found. The new mtDNA sequences highlight the limitations of partial sequencing for assigning sequences to haplogroups and dating recent divergence events. The provably optimal trees found for the entire mtDNA sequences using the MMS method provide a reliable and robust framework for the interpretation of evolutionary relationships and confirm that the female settlers of Remote Oceania descended from both the existing inhabitants of Near Oceania and more recent migrants into the region.

DNA, Mitochondrial↗
PubMed2006

Association of poly-purine/poly-pyrimidine sequences with meiotic recombination hot spots.

BACKGROUND: Meiotic recombination events have been found to concentrate in 1-2.5 kilo base regions, but these recombination hot spots do not share a consensus sequence and why they occur at specific sites is not fully understood. Some previous evidence suggests that poly-purine/poly-pyrimidine (poly-pu/py) tracts (PPTs), a class of sequence with distinctive biochemical properties, could be involved in recombination, but no general association of PPTs with meiotic recombination hot spots has previously been reported. RESULTS: We used computational methods to investigate in detail the relationship between PPTs and hot spots. We show statistical associations of PPT frequency with hot spots of meiotic recombination initiating lesions, double-strand breaks, in the genome of the yeast S. cerevisiae and with experimentally well characterized human meiotic recombination hot spots. Supporting a possible role of poly-pu/py-rich sequences in hot spot recombination, we also found that all three single nucleotide polymorphisms previously shown to be associated with human hot spot activity changes occur within sequence contexts of 14 bp or longer that are 85% or more poly-pu/py and at least 70% G/C. These polymorphisms are all close to the hot spot mid points. Comparing the sequences of experimentally characterized human hot spots with the orthologous regions of the chimpanzee genome previously shown not to contain hot spots, we found that in all five cases in which comparisons for the hot spot central regions are possible with publicly available sequence data, there are differences near the human hot spot mid points within sequences 14 bp or longer consisting of more than 80% poly-pu/py and at least 50% G/C. CONCLUSION: Our results, along with previous evidence for the unique biochemical properties and recombination-stimulating potential of poly-pu/py-rich sequences, suggest that the possible functional involvement of this type of sequence in meiotic recombination hot spots deserves further experimental exploration.

Algorithms↗
PubMed2006

Sex allocation theory aids species conservation.

Supplementary feeding is often a key tool in the intensive management of captive and threatened species. Although it can increase such parameters as breeding frequency and individual survival, supplementary feeding may produce undesirable side effects that increase overall extinction risk. Recent attempts to increase breeding frequency and success in the kakapo Strigops habroptilus using supplementary feeding inadvertently resulted in highly male-biased chick sex ratios. Here, we describe how the inclusion of sex allocation theory has remedied this conservation dilemma. Our study is the first to manipulate chick sex ratios in an endangered species by altering maternal condition and highlights the importance of incorporating evolutionary theory into modern conservation practice.

Animals↗
PubMed2006

Entanglement of New Zealand fur seals in man-made debris at Kaikoura, New Zealand.

New Zealand fur seals in the Kaikoura region breed near a town with expanding tourist and fishing industries and commonly come ashore entangled in nets and plastic debris. However, the rate at which entanglement occurs was previously unknown. A decade of Department of Conservation seal callout data was analysed to determine the level of entanglement in the region and the most common debris type. Monitoring of adult female fur seals released from entanglement provided information on the potential for serious wounds to heal and survivorship of released individuals. Entanglement rates of pinnipeds in Kaikoura are some of the highest reported world-wide (average range: 0.6-2.8%) with green trawl net (42%), and plastic strapping tape (31%) together contributing the most to debris types. Nearly half of the reported entangled seals are successfully released (43%) and post-release monitoring shows that with appropriate intervention the chance of an individual surviving even with a significant entanglement wound is high. Our study demonstrates that while entanglement in the region is high, a successful intervention protocol may help reduce the potential for entanglement-related mortality in the region.

Animal Population Groups↗
PubMed2006

The rise, fall and renaissance of microsatellites in eukaryotic genomes.

Microsatellites are among the most versatile of genetic markers, being used in an impressive number of biological applications. However, the evolutionary dynamics of these markers remain a source of contention. Almost 20 years after the discovery of these ubiquitous simple sequences, new genomic data are clarifying our understanding of the structure, distribution and variability of microsatellites in genomes, especially for the eukaryotes. While these new data provide a great deal of descriptive information about the nature and abundance of microsatellite sequences within eukaryotic genomes, there have been few attempts to synthesise this information to develop a global concept of evolution. This review provides an up-to-date account of the mutational processes, biases and constraints believed to be involved in the evolution of microsatellites, particularly with respect to the creation and degeneration of microsatellites, which we assert may be broadly viewed as a life cycle. In addition, we identify areas of contention that require further research and propose some possible directions for future investigation.

Animals↗
PubMed2006

Comparative phylogeography of coastal limpets across a marine disjunction in New Zealand.

Cook Strait, which separates the North and South Island of New Zealand, has been a transient, but re-occurring feature of the New Zealand land mass throughout the Pleistocene, maintaining its current width and depth for the past 5000 years. Historic land fragmentation coupled with the complex hydrography of the Greater Cook Strait region has created both biogeographic and phylogeographic disjunctions between the North and South Island in several marine species. Here we use mitochondrial cytochrome b DNA sequences of three endemic intertidal limpets, Cellana ornata, Cellana radians and Cellana flava to assess intraspecific phylogeographic patterns across Cook Strait and to look for interspecific concordance of ecological and evolutionary processes among closely related taxa. We sequenced 328-359 bp in 85-321 individuals from 8-31 populations spanning the biogeographic range of the three species. Intraspecific phylogeographic analyses show moderate to strong genetic discontinuity among North and South Island populations due to allopatric fragmentation. This pattern was broadly concordant across the three species and the observed divergence among this group of intertidal limpets (0.3-2.0%) is similar to that of previously studied subtidal organisms. For each species, divergence time calculations suggest contemporary North and South Island lineages diverged from their respective most recent common ancestor approximately 200 000 to 300 000 years before present (bp), significantly earlier than previous estimates in other coastal marine taxa that arose from a miscalculation of divergence time.

Animals↗
PubMed2005

Are invasive species the drivers of ecological change?

Invasive species are widely accepted as one of the leading direct causes of biodiversity loss. However, much of the evidence for this contention is based on simple correlations between exotic dominance and native species decline in degraded systems. Although appealing, direct causality is not the only possible interpretation. A plausible alternative hypothesis is that exotic dominance could be the indirect consequence of habitat modification driving native species loss. In a new paper, MacDougall and Turkington now provide the first direct test of whether invasive species are the drivers of community change, or merely 'passengers' along for the environmental ride.

Journal Article↗
PubMed2004

Moa were many.

Until a few hundred years ago, New Zealand hosted several species of flightless ratite birds, collectively known as the moa. We have used mitochondrial sequence data for Dinornis, the largest of the moa, and new coalescent approaches to estimate its population size prior to human arrival ca. 1000-6000 years BP. We show that, as little as 1000 years ago, Dinornis numbered between 300,000 and 1.4 million and that the standing population of all moa species was ca. 3-12 million. This estimate is an order of magnitude larger than the accepted population estimate (ca. 159,000) for all moa species at the arrival of humans and suggests that moa numbers had already declined prior to human settlement.

Animals↗
PubMed2004

Host isolation and patterns of genetic variability in three populations of Teladorsagia from sheep.

We have used a mitochondrial marker to explore the population genetics of an economically important parasite of sheep, Teladorsagia. We examined diversity within and between parasites from three very different host populations, as well as within and between individual hosts. One of our study populations, the Soay sheep on Hirta, St Kilda, is unusually isolated with no sheep having been introduced to the island since 1932. Worm haplotypes from Hirta were compared with those from two other host populations. Remarkably, despite its historical isolation the Hirta population shows similar levels of within-population diversity to the other study populations. No divergence between the three Teladorsagia populations was found, consistent with gene flow between the populations. The high diversity within Teladorsagia populations provides compelling evidence that this variability is a general feature of parasitic nematode populations. Such diversity may be caused by high effective population size, coupled with an increased mutation rate for mtDNA, which has important implications for the spread of anthelmintic resistance in nematode populations.

Animals↗
PubMed2004

Mother's curse: the effect of mtDNA on individual fitness and population viability.

The mitochondrial genome is considered generally to be an innocent bystander in adaptive evolution; however, there is increasing evidence that mitochondrial DNA (mtDNA) is an important contributor to viability and fecundity. Some of this evidence is now well documented, with mtDNA mutations having been shown to play a causal role in degenerative diseases, ageing, and cancer. However, most research on mtDNA has ignored the possibility that other instances exist where mtDNA mutations could have profound fitness consequences. Recent work in humans and other species now indicates that mtDNA mutations play an important role in sperm function, male fertility, and male fitness. Ironically, deleterious mtDNA mutations that affect only males, such as those that impair sperm function, will not be subject to natural selection because mitochondria are generally maternally inherited and could reach high frequencies in populations if the mutations are not disadvantageous in females. Here, we review how such mtDNA mutations might affect the viability of natural populations. We consider factors that increase or decrease the strength of the effect of mtDNA mutations on population viability and discuss what mechanisms exist to mitigate deleterious mtDNA effects.

Journal Article↗
PubMed2004

Adaptive radiation within New Zealand endemic species of the cockroach genus Celatoblatta Johns (Blattidae): a response to Plio-Pleistocene mountain building and climate change.

The South Island of New Zealand offers unique opportunities to study insect evolution due to long-term physical isolation, recent alpine habitats and high levels of biotic endemism. Using DNA sequence data from cytochrome oxidase subunit 1, we investigated the phylogeographical pattern among 10 endemic cockroach species within the genus Celatoblatta Johns (Blattidae). We tested the hypothesis that an ancestral cockroach species underwent rapid speciation in response to major climatic differentiation induced by mountain building. Results suggest that speciation was a twofold process, with an interspecific radiation of Pliocene/Pleistocene age followed by intraspecific diversification during the mid Pleistocene. Average genetic distance (maximum likelihood GTR + I + Gamma) was 9.17%, with a maximum of 14.5%. Data revealed eight deep well-supported branches, each with terminal clades. Six clades were differentiated according to morphological species, while the seventh was composed of three sympatric species. We consider the latter to be a phylogenetic species, possibly as a result of hybridization within a defined geographical area. This finding seriously challenges species distinctions for these three cockroach species. Correlation between genetic distances and a Climate Similarity Index (CSI) was negative, suggesting that species found in similar habitats are also genetically closely related. A Mantel test on within-clade genetic distances vs. linear geographical distance was positive, suggesting allopatric isolation for those haplotypes. We present a model of speciation for South Island Celatoblatta.

Adaptation, Biological↗
PubMed2004

Measuring vertebrate telomeres: applications and limitations.

Telomeres are short tandem repeated sequences of DNA found at the ends of eukaryotic chromosomes that function in stabilizing chromosomal end integrity. In vivo studies of somatic tissue of mammals and birds have shown a correlation between telomere length and organismal age within species, and correlations between telomere shortening rate and lifespan among species. This result presents the tantalizing possibility that telomere length could be used to provide much needed information on age, ageing and survival in natural populations where longitudinal studies are lacking. Here we review methods available for measuring telomere length and discuss the potential uses and limitations of telomeres as age and ageing estimators in the fields of vertebrate ecology, evolution and conservation.

Aging↗