Jessica J. Hayward

Genetic recombination is targeted towards gene promoter regions in dogs

The identification of the H3K4 trimethylase, PRDM9, as the gene responsible for recombination hotspot localization has provided considerable insight into the mechanisms by which recombination is initiated in mammals. However, uniquely amongst mammals, canids appear to lack a functional version of PRDM9 and may therefore provide a model for understanding recombination that occurs in the absence of PRDM9, and thus how PRDM9 functions to shape the recombination landscape. We have constructed a fine-scale genetic map from patterns of linkage disequilibrium assessed using high-throughput sequence data from 51 free-ranging dogs, Canis lupus familiaris. While broad-scale properties of recombination appear similar to other mammalian species, our fine-scale estimates indicate that canine highly elevated recombination rates are observed in the vicinity of CpG rich regions including gene promoter regions, but show little association with H3K4 trimethylation marks identified in spermatocytes. By comparison to genomic data from the Andean fox, Lycalopex culpaeus, we show that biased gene conversion is a plausible mechanism by which the high CpG content of the dog genome could have occurred.

Factors influencing the distribution patterns of Recent deep-sea benthic foraminifera, east of New Zealand, Southwest Pacific Ocean

Abstract This study investigates which combination of environmental factors most strongly influences the distribution patterns of benthic foraminferal tests (>0.63 μm) in a region bisected by the Subtropical Front, east of New Zealand. Seafloor sample sites extend from outer shelf (90 m) to abyssal (4700 m) depths, across substrates ranging from biogenic/terrigenous gravelly sand to hemipelagic mud, and occur under the influence of Antarctic intermediate water (AAIW) and circumpolar deep waters as well as receiving detritus from both Subtropical and Subantarctic surface water masses. Elevated values of the planktic foraminiferal fragmentation index and reworked small Paleogene planktic foraminifera at outer shelf and bathyal depths coincide with areas of strong bottom currents. Q-mode cluster analysis on the census counts of 398 benthic species clusters the 66 samples into three large groups (shallow, bathyal, abyssal), and at a lower level 10 mappable associations are recognised. A combination of canonical correspondence analysis and a correlation coefficient matrix was used to relate the faunal data to a set of measured environmental proxies. These analyses show that factors that have a relationship with depth are the most significant in determining foraminiferal distribution. The principal environmental factors which appear to most strongly influence this benthic foraminiferal distribution are: dissolved oxygen content in bottom waters; sustainability of organic carbon flux rates; seasonality of food supply; lateral advection of water masses; bottom water carbonate corrosiveness; energetic state at the benthic boundary layer; grain-size composition of substrate; salinity and temperature of the bottom waters. Shallow water associations (90–1250 m), dominated by Cassidulina carinata and Trifarina angulosa, occur within coarse substrates under well-oxygenated, high energy regimes and sustained food input. The occurrence of the bathyal associations (230–2840 m), dominated by C. carinata, Alabaminella weddellensis and Abditodentrix pseudothalmanni, closely mirrors the distribution of AAIW within a region of variable food supply. The sustainability of food supply combined with bottom water type and associated ventilation and dissolution strongly influence the composition of abyssal associations (1200–4700 m), mostly dominated by Epistominella exigua and A. weddellensis.

Genetic structure in village dogs reveals a Central Asian domestication origin

Significance Dogs were the first domesticated species, but the precise timing and location of domestication are hotly debated. Using genomic data from 5,392 dogs, including a global set of 549 village dogs, we find strong evidence that dogs were domesticated in Central Asia, perhaps near present-day Nepal and Mongolia. Dogs in nearby regions (e.g., East Asia, India, and Southwest Asia) contain high levels of genetic diversity due to their proximity to Central Asia and large population sizes. Indigenous dog populations in the Neotropics and South Pacific have been largely replaced by European dogs, whereas those in Africa show varying degrees of European vs. indigenous African ancestry. Dogs were the first domesticated species, originating at least 15,000 y ago from Eurasian gray wolves. Dogs today consist primarily of two specialized groups—a diverse set of nearly 400 pure breeds and a far more populous group of free-ranging animals adapted to a human commensal lifestyle (village dogs). Village dogs are more genetically diverse and geographically widespread than purebred dogs making them vital for unraveling dog population history. Using a semicustom 185,805-marker genotyping array, we conducted a large-scale survey of autosomal, mitochondrial, and Y chromosome diversity in 4,676 purebred dogs from 161 breeds and 549 village dogs from 38 countries. Geographic structure shows both isolation and gene flow have shaped genetic diversity in village dog populations. Some populations (notably those in the Neotropics and the South Pacific) are almost completely derived from European stock, whereas others are clearly admixed between indigenous and European dogs. Importantly, many populations—including those of Vietnam, India, and Egypt—show minimal evidence of European admixture. These populations exhibit a clear gradient of short-range linkage disequilibrium consistent with a Central Asian domestication origin.

Complex disease and phenotype mapping in the domestic dog

The domestic dog is becoming an increasingly valuable model species in medical genetics, showing particular promise to advance our understanding of cancer and orthopaedic disease. Here we undertake the largest canine genome-wide association study to date, with a panel of over 4,200 dogs genotyped at 180,000 markers, to accelerate mapping efforts. For complex diseases, we identify loci significantly associated with hip dysplasia, elbow dysplasia, idiopathic epilepsy, lymphoma, mast cell tumour and granulomatous colitis; for morphological traits, we report three novel quantitative trait loci that influence body size and one that influences fur length and shedding. Using simulation studies, we show that modestly larger sample sizes and denser marker sets will be sufficient to identify most moderate- to large-effect complex disease loci. This proposed design will enable efficient mapping of canine complex diseases, most of which have human homologues, using far fewer samples than required in human studies.

A review of genetic analyses of hybridisation in New Zealand

Abstract Hybridisation between related taxa has a range of possible biological consequences, ranging from the production of sterile offspring, through introgression of alleles into populations, to the formation of new species. Examples of plant and animal species hybridising with related taxa abound in the New Zealand region. We review New Zealand examples of hybridisation that have been verified with chromosomal, protein or DNA data. Contemporary hybridisation has been studied at hybrid zones where distinct populations meet and mate in a defined and stable zone of contact. The role of human habitat modification is highlighted with examples of recent range changes that have led to hybridisation and subsequent conservation problems. Hybridisation can result in the swamping of endangered species, although it can also act as a bridge for the transfer of adaptations among lineages. Historical hybridisation in New Zealand has been examined with phylogenetics and there are many examples of organelle introgression or capture. The origin of new species of New Zealand stick insects, ferns and daisies via hybridisation has been demonstrated with cytogenetic and DNA sequence evidence. Thus the importance of hybridisation in the evolution of New Zealands flora and fauna is highlighted.

Microevolution of Canine Influenza Virus in Shelters and Its Molecular Epidemiology in the United States

ABSTRACT Canine influenza virus (CIV) emerged around 2000 when an equine influenza virus (EIV) was transmitted to dogs in Florida. After 2003, the canine virus was carried by infected greyhounds to various parts of the United States and then became established in several large animal shelters, where it has continued to circulate. To better understand the evolution of CIV since its emergence, and particularly its microevolution in spatially restricted populations, we examined multiple gene segments of CIV from dogs resident in two large animal shelters in New York City during the period 2006 to 2009. In particular, we focused on viruses circulating in the two shelters in 2008 and 2009, which we found shared a common ancestor. While viruses in each shelter were generally monophyletic, we observed some gene flow between them. These shelter sequences were compared to earlier CIV isolates. The shelter viruses differed in 1 to 6 amino acids in each gene segment compared to viruses isolated in Florida between 2003 and 2005 and in Colorado in 2006 and 2008. A comparison of the sequences of equine and canine viruses revealed amino acid replacements that distinguished the viruses from the two hosts, but no clear evidence of positive selection indicative of host adaptation was detected, suggesting that any host range adaptation in CIV occurred early in the emergence of this virus or even before it transferred to dogs.

Phylogenetic analysis of feline immunodeficiency virus in feral and companion domestic cats of New Zealand.

ABSTRACT Nested PCR was used to amplify envelope V3-V6 gene fragments of feline immunodeficiency virus (FIV) from New Zealand cats. Phylogenetic analyses established that subtypes A and C predominate among New Zealand cats, with clear evidence of intersubtype recombination. In addition, 17 sequences were identified that were distinct from all known FIV clades, and we tentatively suggest these belong to a novel subtype.

Depth distribution of recent deep-sea benthic foraminifera east of New Zealand, and their potential for improving paleobathymetric assessments of Neogene microfaunas

Abstract Paleobathymetric assessments of fossil foraminiferal faunas play a significant role in the analysis of the paleogeographic, sedimentary, and tectonic histories of New Zealands Neogene marine sedimentary basins. At depths >100 m, these assessments often have large uncertainties. This study, aimed at improving the precision of paleodepth assessments, documents the present‐day distribution of deep‐sea foraminifera (>63 μm) in 66 samples of seafloor sediment at 90–4700 m water depth (outer shelf to mid‐abyssal), east of New Zealand. One hundred and thirty‐nine of the 465 recorded species of benthic foraminifera are new records for the New Zealand region. Characters of the foraminiferal faunas which appear to provide the most useful information for estimating paleobathymetry are, in decreasing order of reliability: relative abundance of common benthic species; benthic species associations; upper depth limits of key benthic species; and relative abundance of planktic foraminifera. R‐mode cluster analysis on the quantitative census data of the 58 most abundant species of benthic foraminifera produced six species associations within three higher level clusters: (1) calcareous species most abundant at mid‐bathyal to outer shelf depths (<1000 m); (2) calcareous species most abundant at mid‐bathyal and greater depths (>600 m); (3) agglutinated species mostly occurring at deep abyssal depths (>3000 m). A detrended correspondence analysis ordination plot exhibits a strong relationship between these species associations and bathymetry. This is manifest in the bathymetric ranges of the relative abundance peaks of many of the common benthic species (e.g., Abditodentrix pseudothalmanni 500–2800 m, Bolivina robusta 200–650 m, Bulimina marginata f. marginata 20–600 m, B. marginata f. aculeata 400–3000 m, Cassidulina norvangi 1000–4500 m, Epistominella exigua 1000–4700 m, and Trifarina angulosa 10–650 m), which should prove useful in paleobathymetric estimates. The upper depth limits of 28 benthic foraminiferal species (e.g., Fursenkoina complanata 200 m, Bulimina truncana 450 m, Melonis affinis 550 m, Eggerella bradyi 750 m, and Cassidulina norvangi 1000 m) have potential to improve the precision of paleobathymetric estimates based initially on the total faunal composition. The planktic percentage of foraminiferal tests increases from outer shelf to upper abyssal depths followed by a rapid decline within the foraminiferal lysocline (below c. 3600 m). A planktic percentage <50% is suggestive of shelf depths, and >50% is suggestive of bathyal or abyssal depths above the CCD. In the abyssal zone there is dramatic taphonomic loss of most agglutinated tests (except some textulariids) at burial depths of 0.1–0.2 m, which negates the potential usefulness of these taxa in paleobathymetric assessments.

Benthic foraminiferal proxy evidence for the Neogene palaeoceanographic history of the Southwest Pacific, east of New Zealand

Abstract Canonical correspondence analysis indicates that the distribution of Neogene benthic foraminiferal faunas (>63 μm) in seven DSDP and ODP sites (500–4500 m water depth) east of New Zealand (38–51°S, 170°E–170°W) is most strongly influenced by depth (water mass stratification), and secondly by age (palaeoceanographic changes influencing faunal composition and biotic evolution). Stratigraphic faunal changes are interpretted in terms of the pulsed sequential development of southern, and later northern, polar glaciation and consequent cooling of bottom waters, increased vertical and lateral stratification of ocean water masses, and increased overall and seasonal surface water productivity. Oligocene initiation of the Antarctic Circumpolar Current and Deep Western Boundary Current (DWBC), flowing northwards past New Zealand, resulted in extensive hiatuses throughout the Southwest Pacific, some extending through into the Miocene. Planktic foraminiferal fragmentation index values indicate that carbonate dissolution was significant at abyssal depths throughout most of the Neogene, peaking at upper abyssal depths in the late Miocene (11–7 Ma), with the lysocline progressively deepened thereafter. Miocene abyssal faunas are dominated by Globocassidulina subglobosa and Oridorsalis umbonatus , with increasing Epistominella exigua after 16 Ma at upper abyssal depths. Peak abundances of Epistominella umbonifera indicate increased input of cold Southern Component Water to the DWBC at 7–6 Ma. Faunal association changes imply establishment of the modern Oxygen Minimum Zone (upper Circumpolar Deep Water) in the latest Miocene. Significant latitudinal differences between the benthic foraminiferal faunas at lower bathyal depths indicate the existence of an oceanic front along the Chatham Rise (location of present Subtropical Front), since the early late Miocene at least, with more pulsed productivity (higher E. exigua ) along the south side. Modern Antarctic Intermediate Water faunal associations were established north of the Chatham Rise at 10–9 Ma, and south of it at 3–1.5 Ma. Middle–upper bathyal faunas on the Campbell Plateau are dominated by reticulate bolivinids during the early and middle Miocene, indicative of sustained productivity above relatively sluggish, suboxic bottom waters. Faunal changes and hiatuses indicate increased current vigour over the Campbell Plateau from the latest Miocene on. Surface water productivity (food supply) appears to have increased in three steps (at times of enhanced global cooling) marked by substantially increased relative abundance of: (1) Abditodentrix pseudothalmanni , Alabaminella weddellensis , Cassidulina norvangi (16–15 Ma, increased pulsed productivity); (2) Bulimina marginata f. aculeata , Nonionella auris , Trifarina angulosa , Uvigerina peregrina (3–1.5 Ma, increased overall productivity); and (3) Cassidulina carinata (1–0.5 Ma, increased overall productivity). Three intervals of deep-sea benthic foraminiferal taxonomic turnover are recognised (16–15, 11.5–10, 2–0.5 Ma) corresponding to intervals of enhanced global cooling and possible productivity changes. The late Pliocene–middle Pleistocene extinction, associated with increasing Northern Hemisphere glaciation, culminating in the middle Pleistocene climatic transition, was more significant in the study area than the earlier Neogene turnovers.

Molecular epidemiology of feline immunodeficiency virus in the domestic cat (Felis catus).

Studying the evolutionary mechanisms of feline immunodeficiency virus in the domestic cat (Felis catus), FIV(Fca), provides a good comparison to other lentiviruses, such as HIV and FIV(Pco) in the cougar (Puma concolor). We review the current epidemiological and evolutionary findings of FIV(Fca). In addition to the five accepted FIV(Fca), subtypes, several recent phylogenetic studies have found strains that form separate clades, indicative of novel subtypes. In New Zealand cats, these strains of unknown subtype have been found to be involved in complex patterns of intergenic recombination, and whole genome sequences are required to resolve these. Evidence of recombination events has been documented with the highest levels in the env gene, the region involved in host cell receptor recognition. Several cases of FIV(Fca) multiple infections, both inter- and intra-subtype, have been reported. The findings of both unknown subtypes and relatively high levels of recombination suggest the need for further testing of the current vaccine. Limited studies on the evolutionary rate of FIV(Fca) document a value twice to three times that of FIV in the cougar, a result suggesting the different levels of co-adaptation between the viruses and their respective hosts. We studied the tissue distribution of FIV(Fca) in feral domestic cats, finding the first case of FIV compartmentalisation, a phenomenon well documented in HIV-1 patients.