Identifying glacial refugia in a geographic parthenogen using palaeoclimate modelling and phylogeography: the New Zealand stick insect Argosarchus horridus (White)

We have used phylogeographic analysis of mitochondrial DNA (COI and COII genes) and ecological niche modelling (ENM) to reconstruct the population history of Argosarchus horridus (White), a widespread species of New Zealand stick insect. These data were used to address outstanding questions on the role of glacial refugia in determining the distribution and genetic structure of New Zealand species. Phylogeographic analysis shows a general pattern of high diversity in upper North Island and reduced diversity in lower North Island and South Island. The ENM indicates that during the last glacial maximum, A. horridus was largely restricted to refugia around coastal areas of North Island. The ENM also suggests refugia on the northeast coast of South Island and southeast coast of North Island and this prediction is verified by phylogeographic analysis, which shows a clade restricted to this region. Argosarchus horridus is also most likely a geographic parthenogen where males are much rarer at higher latitudes. The higher levels of genetic variation in northern, bisexual populations suggest southern and largely unisexual populations originated from southwardly expanding parthenogenetic lineages. Bayesian skyline analysis also provides support for a recent population size increase consistent with a large increase in geographic distribution in the late Pleistocene. These results exemplify the utility of integrating ENM and phylogeographic analysis in testing hypotheses on the origin of geographic parthenogenesis and effects of Pleistocene environmental change on biodiversity.     

The Genetic Legacy of Religious Diversity and Intolerance: Paternal Lineages of Christians, Jews, and Muslims in the Iberian Peninsula

Most studies of European genetic diversity have focused on large-scale variation and interpretations based on events in prehistory, but migrations and invasions in historical times could also have had profound effects on the genetic landscape. The Iberian Peninsula provides a suitable region for examination of the demographic impact of such recent events, because its complex recent history has involved the long-term residence of two very different populations with distinct geographical origins and their own particular cultural and religious characteristics—North African Muslims and Sephardic Jews. To address this issue, we analyzed Y chromosome haplotypes, which provide the necessary phylogeographic resolution, in 1140 males from the Iberian Peninsula and Balearic Islands. Admixture analysis based on binary and Y-STR haplotypes indicates a high mean proportion of ancestry from North African (10.6%) and Sephardic Jewish (19.8%) sources. Despite alternative possible sources for lineages ascribed a Sephardic Jewish origin, these proportions attest to a high level of religious conversion (whether voluntary or enforced), driven by historical episodes of social and religious intolerance, that ultimately led to the integration of descendants. In agreement with the historical record, analysis of haplotype sharing and diversity within specific haplogroups suggests that the Sephardic Jewish component is the more ancient. The geographical distribution of North African ancestry in the peninsula does not reflect the initial colonization and subsequent withdrawal and is likely to result from later enforced population movement—more marked in some regions than in others—plus the effects of genetic drift.     

Kiore (Rattus exulans) distribution and relative abundance on a small highly modified island

ABSTRACT

Kiore (Pacific rat; Rattus exulans) is both a target for eradication and a taonga or highly valued species in New Zealand, and its abundance and distribution vary considerably throughout the country. We investigated reports of an abundant kiore population on Slipper Island (Whakahau), off the east coast of New Zealand’s North Island, in March 2017. We trapped kiore to examine their distribution across a range of habitats with varying degrees of human activity. Kiore were captured in all habitats, with particularly high abundance at a campground with a fruiting fig tree (50 kiore per 100 trap nights corrected for sprung traps). We found no evidence of other rat species; Slipper Island appears to remain one of few New Zealand islands with kiore but without ship rats (Rattus rattus) and Norway rats (R. norvegicus), the two other rat species present in New Zealand. Slipper Island potentially provides opportunities to research kiore behaviour and population dynamics in a New Zealand commensal environment, and genetics of an isolated island population.     

Immunoglobulin allotypes in Jewish populations living in Israel and the United States

The ongoing interest in the interrelationships of Jewish populations justifies inclusion of the immunoglobulin allotypes in an ethnohistorical analysis. A total of 2,184 serum specimens obtained from unrelated Israeli Jewish and self-identified Milwaukee, WI, Jewish blood donors were classified as Ashkenazi, Sephardi, Asiatic, or North African and tested for G1m (a, x, z, and f), G3m (b0, b1, b3, b5, g), A2m (1 and 2), and Km (1). Selected sera were also tested for G3m (s, t, c3, c5). The estimated maximum likelihood Gm-Am haplotype frequencies were used in a heterogeneity chi-square analysis. The results indicate that there is less heterogeneity within Jewish populations from Europe, Middle East, and North Africa than in corresponding non-Jewish populations representing the same geographical areas. In order to avoid the hazards of a univariate focus, previously published data were incorporated into two additional analyses: 15 populations with information on 16 genetic loci and 24 populations with information on five genetic loci. Both sets of data were analyzed using principal-components and cluster analysis. In both sets of analyses, with the exception of the Yemenite Jews, Jewish populations grouped together. These analyses support the belief that Jewish populations appear to be derived from a common gene pool, and there has been some genetic drift and minimal gene flow with surrounding populations.     

Patterns of mortality and causes of death among Rhode Island Jews, 1979–1981

Abstract

Using information provided by institutions handling Jewish deaths, this study identified 735 deaths among Jewish residents of Rhode Island during 1979–81. Official death records then provided data on the characteristics of the deceased and on cause of death, allowing comparisons of Jewish/non‐ Jewish patterns of mortality and cause of death, as well as analysis of differentials among the Jewish decedents, taking account of birthplace and occupation. The findings indicate that relatively fewer Jewish males die at ages below 65, and more at ages 85 and over than is true of total white males. Jewish females exhibit an age‐at‐death pattern more similar to that of all white women. These sex differences characterize cause of death as well. Differences are more pronounced between Jewish and non‐Jewish males than between the female groups. Most noteworthy, Jewish male deaths from diabetes are significantly higher and deaths from respiratory disease significantly lower than among total white men. Differentials in age of death between Jewish native‐born and foreign‐born are largely a function of their differential age composition, and socioeconomic status showed no clear relation to age at death or cause of death.     

Counting the founders: the matrilineal genetic ancestry of the Jewish Diaspora

The history of the Jewish Diaspora dates back to the Assyrian and Babylonian conquests in the Levant, followed by complex demographic and migratory trajectories over the ensuing millennia which pose a serious challenge to unraveling population genetic patterns. Here we ask whether phylogenetic analysis, based on highly resolved mitochondrial DNA (mtDNA) phylogenies can discern among maternal ancestries of the Diaspora. Accordingly, 1,142 samples from 14 different non-Ashkenazi Jewish communities were analyzed. A list of complete mtDNA sequences was established for all variants present at high frequency in the communities studied, along with high-resolution genotyping of all samples. Unlike the previously reported pattern observed among Ashkenazi Jews, the numerically major portion of the non-Ashkenazi Jews, currently estimated at 5 million people and comprised of the Moroccan, Iraqi, Iranian and Iberian Exile Jewish communities showed no evidence for a narrow founder effect, which did however characterize the smaller and more remote Belmonte, Indian and the two Caucasus communities. The Indian and Ethiopian Jewish sample sets suggested local female introgression, while mtDNAs in all other communities studied belong to a well-characterized West Eurasian pool of maternal lineages. Absence of sub-Saharan African mtDNA lineages among the North African Jewish communities suggests negligible or low level of admixture with females of the host populations among whom the African haplogroup (Hg) L0-L3 sub-clades variants are common. In contrast, the North African and Iberian Exile Jewish communities show influence of putative Iberian admixture as documented by mtDNA Hg HV0 variants. These findings highlight striking differences in the demographic history of the widespread Jewish Diaspora.     

Variation in mandible shape and body size of house mice Mus musculus in five separate New Zealand forest habitats

This study investigates variation in house mouse Mus musculus body size and mandible shape across New Zealand, using geometric morphometrics and biomechanical advantage analyses. The Mus phylogroups currently known in New Zealand include Mus musculus domesticus, M. m. musculus and M. m. castaneus. We examined samples of house mice inhabiting five different podocarp and beech forest environments across the North and South Islands (Pureora Forest, Zealandia Wildlife Sanctuary, Craigieburn Forest Park, Eglinton Valley and Hollyford Valley). Significant variation in mandible shape and body size was found between all five forest populations. South Island mice had larger bodies and greater mechanical advantage in the temporalis muscle compared with their North Island counterparts. Zealandia Sanctuary mouse mandibles were broader and shorter than South Island mouse mandibles, and had greater masseter muscle advantage. Centroid size and body weight, but not head-body length, varied significantly with two distinct genetic haplotypes. Finally, annual rainfall was the most significant covariate with mandible shape. Higher rainfall locations were generally associated with soft-food related mandible shapes, while lower rainfall correlated with hard-food mandible shapes. This preliminary investigation provides the framework for further research into mandible shape and body size variation in New Zealand house mice.     

Phylogeography reveals a North Island range extension for New Zealand's only sexually wing-dimorphic stonefly (Stenoperla helsoni)

Stenoperla helsoni is an endemic New Zealand stonefly characterised by distinctive sexually dimorphic wing loss. Previous distribution records indicated that this species was restricted to the South Island's Southern Alps, although our recent collections of wing-reduced specimens from a site in the Tararua Ranges suggest that this species may extend into the lower North Island. We amplified the mitochondrial COI gene to confirm the identity of North Island specimens, and to assess phylogeographic structuring within the species and genus. North Island specimens were confirmed as S. helsoni, indicating that this species has a much wider geographic range than previously thought. This broad distribution, combined with low levels of intraspecific divergence, suggests that female S. helsoni may be strong fliers, despite males being flightless. Distinct North Island and South Island populations were identified, with a 1.5% divergence between the two populations.     

Phylogeography of a high‐dispersal New Zealand sea‐star: does upwelling block gene‐flow?

New Zealand's (NZ) geographical isolation, extensive coastline and well-characterized oceanography offer a valuable system for marine biogeographical research. Here we use mtDNA control region sequences in the abundant endemic sea-star Patiriella regularis to test the following literature-based predictions: that coastal upwelling disrupts north-south gene flow and promotes population differentiation (hypothesis 1); and that an invasive Tasmanian population of the species was introduced anthropogenically from southern New Zealand (hypothesis 2). We sequenced 114 samples from 22 geographical locations, including nine sites from North Island, nine from South Island, one from Stewart Island and three from Tasmania. Our analysis of these sequences revealed an abundance of shallow phylogenetic lineages within P. regularis (68 haplotypes, mean divergence 0.9%). We detected significant genetic heterogeneity between pooled samples from northern vs. southern New Zealand (FST = 0.072; P = 0.0002), consistent with the hypothesis that upwelling disrupts gene flow between these regions (hypothesis 1). However, we are currently unable to rule out the alternative hypothesis that Cook Strait represents a barrier to dispersal (North Island vs. South Island; FST = 0.031; P = 0.0467). The detection of significant spatial structure in NZ samples is consistent with restricted gene flow, and the strong structure evident in northern NZ may be facilitated by distinct ocean current systems. Four shared haplotypes and nonsignificant differentiation (FST = 0.025; P = 0.2525) between southern New Zealand and Tasmanian samples is consistent with an anthropogenic origin for the latter population (hypothesis 2).     

BRCA1 and BRCA2 mutation analysis of 208 Ashkenazi Jewish women with ovarian cancer

Ovarian cancer is a component of the autosomal-dominant hereditary breast-ovarian cancer syndrome and may be due to a mutation in either the BRCA1 or BRCA2 genes. Two mutations in BRCA1 (185delAG and 5382insC) and one mutation in BRCA2 (6174delT) are common in the Ashkenazi Jewish population. One of these three mutations is present in approximately 2% of the Jewish population. Each mutation is associated with an increased risk of ovarian cancer, and it is expected that a significant proportion of Jewish women with ovarian cancer will carry one of these mutations. To estimate the proportion of ovarian cancers attributable to founding mutations in BRCA1 and BRCA2 in the Jewish population and the familial cancer risks associated with each, we interviewed 213 Jewish women with ovarian cancer at 11 medical centers in North America and Israel and offered these women genetic testing for the three founder mutations. To establish the presence of nonfounder mutations in this population, we also completed the protein-truncation test on exon 11 of BRCA1 and exons 10 and 11 of BRCA2. We obtained a detailed family history on all women we studied who had cancer and on a control population of 386 Ashkenazi Jewish women without ovarian or breast cancer. A founder mutation was present in 41.3% of the women we studied. The cumulative incidence of ovarian cancer to age 75 years was found to be 6.3% for female first-degree relatives of the patients with ovarian cancer, compared with 2.0% for the female relatives of healthy controls (relative risk 3.2; 95% CI 1.5-6.8; P=.002). The relative risk to age 75 years for breast cancer among the female first-degree relatives was 2.0 (95% CI 1.4-3.0; P=.0001). Only one nonfounder mutation was identified (in this instance, in a woman of mixed ancestry), and the three founding mutations accounted for most of the observed excess risk of ovarian and breast cancer in relatives.     

Evidence for breeding of Megadyptes penguins in the North Island at the time of human arrival

The arrival of humans in New Zealand around 750 years ago resulted in widespread faunal extinctions including the endemic Waitaha penguin (Megadyptes waitaha). Previously thought to have only bred on coastal South Island and Stewart Island, recent genetic reanalysis of prehistoric large penguin bones from the lower North Island indicates that the Waitaha penguin may have been a common resident. Here we synthesise previous studies and present new palaeontological and archaeological evidence to suggest that the Waitaha penguin was probably breeding in the lower North Island at the time of human arrival, and did not represent vagrant individuals from more southerly breeding colonies. The elimination of breeding Megadyptes from the North Island would add to the already significant avifaunal losses from New Zealand, of which the North Island suffered the greatest biodiversity loss after the arrival of humans.     

Distance sampling techniques compared for a New Zealand endemic passerine (

The effectiveness of line- and point-transect distance sampling methods was compared for estimating the density of a conspicuous endemic passerine, the North Island saddleback Philesturnus carunculatus rufusater, in two forest habitats on Tiritiri Matangi Island, Hauraki Gulf, New Zealand. The reference population abundance in each habitat was calculated through an intensive capture, colour-banding, and resighting effort. Line transects consistently produced unbiased estimates of density for both sites at two time periods (morning and afternoon), and proved to be the most efficient of the distance sampling methods tested. Point-transect methods proved to be biased in this instance, consistently producing overestimates of density for this species, and were unreliable as indices of the small differences in density between habitats. Transect counts conducted from established walking tracks underestimated both density and the variance of estimated density. We conclude that in situations requiring estimates of absolute density for North Island saddleback, a series of randomly positioned line transects will accurately represent the density of individuals. Furthermore, this study highlights the need to pilot distance survey techniques on the species of interest to detect possible violation of the assumptions underlying these methods. We question the widespread use of point-transect counts for censusing avian species without such preliminary investigation, and recommend further comparisons of distance sampling methods in New Zealand with reference populations where opportunity provides.     

Phylogeography and ecological niche modelling of the New Zealand stick insect Clitarchus hookeri (White) support survival in multiple coastal refugia

Aim Increasing our understanding of the effects of the Last Glacial Maximum (LGM) and determining the location of refugia requires studies on widely distributed species with dense sampling of populations. We have reconstructed the biogeographic history of Clitarchus hookeri (White), a widespread species of New Zealand stick insect that exhibits geographic parthenogenesis, using phylogeographic analysis and ecological niche modelling. Location New Zealand. Methods We used DNA sequence data from the mitochondrial cytochrome c oxidase subunit I gene to reconstruct phylogenetic relationships among haplotypes from C. hookeri and two undescribed Clitarchus species. We also used distribution data from our own field surveys and museum records to reconstruct the geographic distribution of C. hookeri during the present and the LGM, using ecological niche modelling. Results The ecological niche models showed that the geographic distribution of C. hookeri has expanded dramatically since the LGM. Our model predicted large areas of suitable LGM habitat in upper North Island, and small patches along the east coast of South Island. The phylogeographic analysis shows that populations in the northern half of North Island contain much higher levels of genetic variation than those from southern North Island and South Island, and is congruent with the ecological niche model. The distribution of bisexual populations is also non-random, with males completely absent from South Island and very rare in southern North Island. Main conclusions During the LGM C. hookeri was most likely restricted to several refugia in upper North Island and one or more smaller refugia along the east coast of South Island. The unisexual populations predominate in post-glacial landscapes and are clearly favoured in the recolonization of such areas. Our study exemplifies the utility of integrating ecological niche modelling and phylogeographic analysis.     

Development,characterization and cross-amplification of microsatellite markers for <Emphasis Type="Italic">Chrysolaena obovata</Emphasis>, an important Asteraceae from Brazilian Cerrado

Feral cattle residing in Chirikof Island, Alaska, are relatively distinct from breeds used in commercial production in North America. However, preliminary evidence suggested that they exhibit substantial genetic relationship with cattle from Yakutian region of Siberia. Thus, our objective was to further elucidate quantify the origins, admixture and divergence of the Chirikof Island cattle relative to cattle from Siberia and USA. Subject animals were genotyped at 15 microsatellite loci. Compared with Turano–Mongolian and North American cattle, Chirikof Island cattle had similar variation, with slightly less observed heterozygosity, fewer alleles per locus and a positive fixation index. Analysis of the genetic distances revealed two primary clusters; one that contained the North American breeds and the Kazakh White head, and a second that contained the Yakutian and Kalmyk breeds, and the Chirikof population. Thus, it is suggested that Chirikof Island cattle may be a composite of British breeds emanating from North America and Turano–Mongolian cattle. A potential founder effect, consistent with historical records of the Russian–American period, may contribute to the adaptation of the Chirikof Island cattle to their harsh high-latitude environment. Further study of adaptive mechanisms manifest by these cattle is warranted.     

Avian arboviruses of the Witless Bay seabird Sanctuary, Newfoundland, Canada.

A virologic and serologic survey of arbovirus infections among seabirds and seabird ticks, Ixodes uriae, on Great Island. Witless Bay, Newfoundland, Canada, was conducted during 1971 and 1972. Kermerovo (Great Island, Bauline) and Sakhalin (Avalon) group viruses previously reported from birds and/or ticks on Great Island were prevalent among avian populations, while conclusive evidence of known nonindigenous serotypes was lacking. Circumstantial evidence-hemagglutination inhibiting antibody-of an unidentified member of the group B tick-borne encephalitis complex transmitted among marine birds of North America by I. uriae is reported. No evidence of human infections with any of these viruses was detected in a small number of biologists doing research on Great Island.     

Changes in Jewish mortality and survival, 1963–1987

Abstract

From information on mortality of Jews obtained from individual death certificates and population data from surveys of the Jewish population undertaken in 1963 and 1987, age‐specific death rates and life expectancy of the Jewish population of Rhode Island are compared with those of the total white population for 1963 and 1987 to assess changing differentials. The Jewish mortality experience continues to differ from that of the larger population even while both groups have experienced noticeable improvements. For males, the age standardized rates have widened in favor of Jews as have the life expectancies at birth and the percentage surviving to old age. By contrast, for females, the standardized death rate has widened considerably in favor of whites, while life expectancy has improved almost identically for both groups and therefore remained about equal, as it was in 1963. Reasons for these patterns are explored through attention to differences between Jews and the general white population in death rates at particular stages of the life cycle. Jews tend to be more advantaged at all but the most advanced ages, age groups in which proportionally more of the Jewish population and Jewish deaths are concentrated.     

Severe pollen limitation in populations of the New Zealand shrub Alseuosmia macrophylla (Alseuosmiaceae) can be attributed to the loss of pollinating bird species

The loss of bird species following human colonization of New Zealand has raised concerns about the consequences for crucial ecosystem functions such as pollination. The understorey shrub Alseuosmia macrophylla (Alseuosmiaceae) exhibits characteristics typical of a bird pollination syndrome, but populations still persist in northern North Island forest remnants despite the local extinction of most endemic bird pollinators, leading to the suggestion that moths – rather than birds – may be the primary pollinators. The aim of this study was to quantify the importance of endemic birds as pollinators of A. macrophylla over several years by comparing plants on Little Barrier Island (LBI), where all extant endemic bird pollinators still occur, to plants at sites on the adjacent North Island in the Waitakere Ranges (WTK), where only one of these species remains common. Flowers on LBI were visited by endemic bellbirds (Anthornis melanura) and stitchbirds (Notiomystis cincta), while at WTK sites the most common visitors were the recently arrived silvereye (Zosterops lateralis) and the introduced honeybee (Apis mellifera), both of which acted principally as nectar robbers. Caged flowers on LBI had significantly lower fruit set than open flowers, and plants at WTK were significantly more pollen‐limited than plants on LBI. This provides evidence that the loss of endemic pollinating birds is the most likely reason for the high pollen limitation found in some North Island A. macrophylla populations, and the very low seed set of these populations could have serious implications for the long‐term persistence of this species.     

Genetic relationships between feral cattle from Chirikof Island, Alaska and other breeds

The origin of cattle on Chirikof Island, off the coast of Alaska, is not well documented. We assessed genetic differentiation of cattle isolated on Chirikof Island from several breeds commonly used for commercial production in North America including breeds popularly believed to have contributed to the Chirikof Island population. A set of 34 microsatellite loci was used to genotype Angus, Charolais, Hereford, Highland, Limousin, Red Angus, Salers, Shorthorn, Simmental, Tarentaise and Texas Longhorn cattle sampled from North America and the Chirikof Island population. Resulting F(ST) statistics for these loci ranged from 0.06 to 0.22 and on average, 14% of total genetic variation was between breeds. Whether population structure was modelled as a bifurcating tree or genetic network, Chirikof Island cattle appeared to be unique and strongly differentiated relative to the other breeds that were sampled. Bayesian clustering for multiple-locus assignment to genetic groups indicated low levels of admixture in the Chirikof Island population. Thus, the Chirikof Island population may be a novel genetic resource of some importance for conservation and industry.     

The breeding season of three species of kiwi (Apteryx) in captivity as determined from egg-laying dates

Records from kiwi ( Apteryx spp.) breeding centres were used to obtain laying dates of 403 North Island brown kiwi ( Apteryx australis mantelli ) eggs, 24 great spotted kiwi ( Apteryx haastii ) eggs and 25 little spotted kiwi ( Apteryx owenii ) eggs. North Island brown kiwi outdoors had an annual cycle of egg-laying with 88.5% of eggs laid from June to January. Eggs were laid in every month of the year, with fewest eggs in April (2.1 % of all eggs). The greatest number of eggs was laid in July (15.6% of all eggs), with a second peak of laying in October (13.5% of all eggs). Both the great spotted kiwi and little spotted kiwi had annual cycles of egg-laying, with the main egg-laying seasons being August-January (87.5% of eggs) for the former and July-December (96.0% of eggs) for the latter. The highest peaks of laying were in October and August, respectively. Kiwi eggs were considered to belong to the same clutch if they were laid no more than 40 days apart. Clutch size in the North Island brown and little spotted kiwi was most commonly one or two eggs. In the great spotted kiwi only clutches of one egg were found. The mean clutch size of North Island brown kiwi outdoors (1.51±0.05) did not differ from that of free-living North Island brown kiwi (1.33±0.09). Similarly, there was no difference in the mean clutch size of captive and free-living little spotted kiwi (1.39±0.14 and 1.10±0.07). The mean interval between eggs for kiwi outdoors did not differ between North Island brown kiwi and little spotted kiwi (27.4±0.5 and 30.7±1.8 days). The results indicate that all three species of kiwi maintain annual cycles of egg-laying in captivity, with the main egg-laying season being longer than in free-living birds.     

LRRK2 G2019S in families with Parkinson disease who originated from Europe and the Middle East: evidence of two distinct founding events beginning two millennia ago

The leucine-rich repeat kinase 2 (LRRK2) G2019S mutation is the most common genetic determinant of Parkinson disease (PD) identified to date. It accounts for 1%-7% of PD in patients of European origin and 20%-40% in Ashkenazi Jews and North African Arabs with PD. Previous studies concluded that patients from these populations all shared a common Middle Eastern founder who lived in the 13th century. We tested this hypothesis by genotyping 25 microsatellite and single-nucleotide-polymorphism markers in 22 families with G2019S and observed two distinct haplotypes. Haplotype 1 was present in 19 families of Ashkenazi Jewish and European ancestry, whereas haplotype 2 occurred in three European American families. Using a maximum-likelihood method, we estimated that the families with haplotype 1 shared a common ancestor 2,250 (95% confidence interval 1,650-3,120) years ago, whereas those with haplotype 2 appeared to share a more recent founder. Our data suggest two separate founding events for G2019S in these populations, beginning at a time that coincides with the Jewish Diasporas.