Pandemics and socio-economic status. Evidence from the plague of 1630 in northern Italy.

This paper investigates the biological, socio-economic, and institutional factors shaping the individual risk of death during a major pre-industrial epidemic. We use a micro-demographic database for an Italian city (Carmagnola) during the 1630 plague to explore in detail the survival dynamics of the population admitted to the isolation hospital (lazzaretto). We develop a theoretical model of admissions to the lazzaretto, for better interpretation of the observational data. We explore how age and sex shaped the individual risk of death, and we provide a one-of-a-kind study of the impact of socio-economic status. We report an inversion of the normal mortality gradient by status for those interned at the lazzaretto. The rich enjoyed a greater ability to make decisions about their hospitalization, but this backfired. Instead, the poor sent to the lazzaretto faced a relatively low risk of death because they enjoyed better conditions than they would have experienced outside the hospital.

Range-wide evolutionary relationships and historical demography of brown bears (Ursus arctos) revealed by whole-genome sequencing of isolated central Asian populations.

Phylogeographic studies uncover hidden pathways of divergence and inform conservation. Brown bears (Ursus arctos) have one of the broadest distributions of all land mammals, ranging from Eurasia to North America, and are an important model for evolutionary studies. Although several whole genomes were available for individuals from North America, Europe and Asia, limited whole-genome data were available from Central Asia, including the highly imperilled brown bears in the Gobi Desert. To fill this knowledge gap, we sequenced whole genomes from nine Asian brown bears from the Gobi Desert of Mongolia, Northern Mongolia and the Himalayas of Pakistan. We combined these data with published brown bear sequences from Europe, Asia and North America, as well as other bear species. Our goals were to determine the evolutionary relationships among brown bear populations worldwide, their genetic diversity and their historical demography. Our analyses revealed five major lineages of brown bears based on a filtered set of 684,081 single nucleotide polymorphisms. We found distinct evolutionary lineages of brown bears in the Gobi, Himalayas, northern Mongolia, Europe and North America. The lowest level of genetic diversity and the highest level of inbreeding were found in Pakistan, the Gobi Desert and Central Italy. Furthermore, the effective population size (Ne ) for all brown bears decreased over the last 70,000 years. Our results confirm the genetic distinctiveness and ancient lineage of brown bear subspecies in the Gobi Desert of Mongolia and the Himalayas of Pakistan and highlight their importance for conservation.

Amazonian colonization from the Atlantic Forest: New perspectives on the connections of South American tropical forests.

An open and dry vegetation belt separates Amazonia (AM) and the Atlantic Forest (AF). Evidence from palaeoclimatic and phylogenetic studies suggests past connections between these forests during cycles of increased humidity through the formation of forest corridors. The distinctive northern AF avifauna is known to have affinities both with AM and the southern AF. Still, the extent of how these two regions contributed to the assemblage of this avifauna remains poorly understood. Using historical demographic analyses and comparative phylogeography based on sub-genomic genetic sampling, we assessed how past connections between AM and AF led to shared vicariance and colonization events in four avian AF endemic taxa. Our results supported the occurrence of humid forest corridors promoting the contact between AF and AM populations and suggested two vicariant events and two colonization events from AF to AM. Population divergences were mostly non-synchronous and occurred multiple times during the Pleistocene. Historical gene flow was prevalent across study groups, supporting migration flows after the initial separation between AM and AF - a pattern previously unknown in birds between these regions. Idiosyncratic histories and divergent demographic syndromes suggest that organisms' responses to climate-driven habitat shifts broadly depend on their ecological attributes. This study strengthened our knowledge of past connections between AM and AF and provided demographic scenarios amenable for testing in other groups of co-distributed organisms.

Nuclear and chloroplast DNA phylogeography reveals high genetic diversity and postglacial range expansion in Quercus mexicana.

PREMISE: Phylogeographical studies are fundamental for understanding factors that influence the spatial distribution of genetic lineages within species. Population expansions and contractions, distribution shifts, and climate changes are among the most important factors shaping the genetic compositions of populations. METHODS: We investigated the phylogeography of an endemic oak, Quercus mexicana (Fagaceae), which has a restricted distribution in northeastern Mexico along the Sierra Madre Oriental and adjacent areas. Nuclear and chloroplast DNA microsatellite markers were used to describe the genetic diversity and structure of 39 populations of Q. mexicana along its entire distribution area. We tested whether population expansion or contraction events influenced the genetic diversity and structure of the species. We also modeled the historical distributional range of Q. mexicana (for the Mid Holocene, the Last Glacial Maximum, and the Last Interglacial) to estimate the extent to which climate fluctuations have impacted the distribution of this oak species. RESULTS: Our results revealed high genetic diversity and low genetic structure in Q. mexicana populations. Ecological niche models suggested historical fluctuations in the distributional range of Q. mexicana. Historical range changes, gene flow, and physical barriers seem to have played an important role in shaping the phylogeographic structure of Q. mexicana. CONCLUSIONS: Our study indicates that the genetic structure of Q. mexicana may have been the result of responses of oak trees not only to heterogeneous environments present in the Sierra Madre Oriental and adjacent areas, but also to elevational and latitudinal shifts in response to climate changes in the past.

Did the 1918 influenza pandemic cause a 1920 baby boom? Demographic evidence from neutral Europe.

In 1919-20, the European countries that were neutral in the First World War saw a small baby bust followed by a small baby boom. The sparse literature on this topic attributes the 1919 bust to individuals postponing conceptions during the peak of the 1918-20 influenza pandemic and the 1920 boom to recuperation of those conceptions. Using data from six large neutral countries of Europe, we present novel evidence contradicting that narrative. In fact, the subnational populations and maternal birth cohorts whose fertility was initially hit hardest by the pandemic were still experiencing below-average fertility in 1920. Demographic evidence, economic evidence, and a review of post-pandemic fertility trends outside Europe suggest that the 1920 baby boom in neutral Europe was caused by the end of the First World War, not by the end of the pandemic.

Genetic variability and the ecology of geographic range: A test of the central-marginal hypothesis in Australian scincid lizards.

For many species, both local abundance and regional occupancy are highest near the centre of their geographic distributions. One hypothesis for this pattern is that niche suitability declines with increasing distance from a species geographic centre, such that populations near range margins are characterized by reduced density and increased patchiness. In these smaller edge populations, genetic drift is more powerful, leading to the loss of genetic diversity. This simple verbal model has been formalized as the central-marginal hypothesis, which predicts that core populations should have greater genetic diversity than edge populations. Here, we tested the central-marginal hypothesis using a genomic data set of 25 species-level taxa of Australian scincid lizards in the genera Ctenotus and Lerista. A majority of taxa in our data set showed range-wide patterns of genetic variation consistent with central-marginal hypothesis, and eight of 25 taxa showed significantly greater genetic diversity in the centre of their range. We then explored biological, historical, and methodological factors that might predict which taxa support the central-marginal hypothesis. We found that taxa with the strongest evidence for range expansion were the least likely to follow predictions of the central-marginal hypothesis. The majority of these taxa had range expansions that originated at the range edge, which led to a gradient of decreasing genetic diversity from the range edge to the core, contrary to the central-marginal hypothesis.

Population genomic structure in Goodman's mouse lemur reveals long-standing separation of Madagascar's Central Highlands and eastern rainforests.

Madagascar's Central Highlands are largely composed of grasslands, interspersed with patches of forest. The historical perspective was that Madagascar's grasslands had anthropogenic origins, but emerging evidence suggests that grasslands were a component of the pre-human Central Highlands vegetation. Consequently, there is now vigorous debate regarding the extent to which these grasslands have expanded due to anthropogenic pressures. Here, we shed light on the temporal dynamics of Madagascar's vegetative composition by conducting a population genomic investigation of Goodman's mouse lemur (Microcebus lehilahytsara; Cheirogaleidae). These small-bodied primates occur both in Madagascar's eastern rainforests and in the Central Highlands, making them a valuable indicator species. Population divergences among forest-dwelling mammals will reflect changes to their habitat, including fragmentation, whereas patterns of post-divergence gene flow can reveal formerly wooded migration corridors. To explore these patterns, we used RADseq data to infer population genetic structure, demographic models of post-divergence gene flow, and population size change through time. The results offer evidence that open habitats are an ancient component of the Central Highlands, and that widespread forest fragmentation occurred naturally during a period of decreased precipitation near the last glacial maximum. Models of gene flow suggest that migration across the Central Highlands has been possible from the Pleistocene through the recent Holocene via riparian corridors. Though our findings support the hypothesis that Central Highland grasslands predate human arrival, we also find evidence for human-mediated population declines. This highlights the extent to which species imminently threatened by human-mediated deforestation may already be vulnerable from paleoclimatic conditions.

Genetic structure and historic demography of endangered unarmoured threespine stickleback at southern latitudes signals a potential new management approach.

Habitat loss, flood control infrastructure, and drought have left most of southern California and northern Baja California's native freshwater fish near extinction, including the endangered unarmoured threespine stickleback (Gasterosteus aculeatus williamsoni). This subspecies, an unusual morph lacking the typical lateral bony plates of the G. aculeatus complex, occurs at arid southern latitudes in the eastern Pacific Ocean and survives in only three inland locations. Managers have lacked molecular data to answer basic questions about the ancestry and genetic distinctiveness of unarmoured populations. These data could be used to prioritize conservation efforts. We sampled G. aculeatus from 36 localities and used microsatellites and whole genome data to place unarmoured populations within the broader evolutionary context of G. aculeatus across southern California/northern Baja California. We identified three genetic groups with none consisting solely of unarmoured populations. Unlike G. aculeatus at northern latitudes, where Pleistocene glaciation has produced similar historical demographic profiles across populations, we found markedly different demographics depending on sampling location, with inland unarmoured populations showing steeper population declines and lower heterozygosity compared to low armoured populations in coastal lagoons. One exception involved the only high elevation population in the region, where the demography and alleles of unarmoured fish were similar to low armoured populations near the coast, exposing one of several cases of artificial translocation. Our results suggest that the current "management-by-phenotype" approach, based on lateral plates, is incidentally protecting the most imperilled populations; however, redirecting efforts toward evolutionary units, regardless of phenotype, may more effectively preserve adaptive potential.

Population Genomics of New Zealand Pouched Lamprey (kanakana; piharau; Geotria australis).

Pouched lamprey (Geotria australis) or kanakana/piharau is a culturally and ecologically significant jawless fish that is distributed throughout Aotearoa New Zealand. Despite its importance, much remains unknown about historical relationships and gene flow between populations of this enigmatic species within New Zealand. To help inform management, we assembled a draft G. australis genome and completed the first comprehensive population genomics analysis of pouched lamprey within New Zealand using targeted gene sequencing (Cyt-b and COI) and restriction site-associated DNA sequencing (RADSeq) methods. Employing 16 000 genome-wide single nucleotide polymorphisms (SNPs) derived from RADSeq (n = 186) and sequence data from Cyt-b (766 bp, n = 94) and COI (589 bp, n = 20), we reveal low levels of structure across 10 sampling locations spanning the species range within New Zealand. F-statistics, outlier analyses, and STRUCTURE suggest a single panmictic population, and Mantel and EEMS tests reveal no significant isolation by distance. This implies either ongoing gene flow among populations or recent shared ancestry among New Zealand pouched lamprey. We can now use the information gained from these genetic tools to assist managers with monitoring effective population size, managing potential diseases, and conservation measures such as artificial propagation programs. We further demonstrate the general utility of these genetic tools for acquiring information about elusive species.

Demographic inference provides insights into the extirpation and ecological dominance of eusocial snapping shrimps.

Although eusocial animals often achieve ecological dominance in the ecosystems where they occur, many populations are unstable, resulting in local extinction. Both patterns may be linked to the characteristic demography of eusocial species-high reproductive skew and reproductive division of labor support stable effective population sizes that make eusocial groups more competitive in some species, but also lower effective population sizes that increase susceptibility to population collapse in others. Here, we examine the relationship between demography and social organization in Synalpheus snapping shrimps, a group in which eusociality has evolved recently and repeatedly. We show using coalescent demographic modeling that eusocial species have had lower but more stable effective population sizes across 100,000 generations. Our results are consistent with the idea that stable population sizes may enable competitive dominance in eusocial shrimps, but they also suggest that recent population declines are likely caused by eusocial shrimps' heightened sensitivity to environmental changes, perhaps as a result of their low effective population sizes and localized dispersal. Thus, although the unique life histories and demography of eusocial shrimps have likely contributed to their persistence and ecological dominance over evolutionary time scales, these social traits may also make them vulnerable to contemporary environmental change.

The Missing Mortality Advantage for European Immigrants to the United States in the Early Twentieth Century.

Immigrant populations typically have lower mortality rates and longer life expectancies than their nonimmigrant counterparts. This immigrant mortality advantage has been a recurrent finding in demographic and population health research focused on contemporary waves of immigration. However, historical data suggest that European immigrants to the United States in the early twentieth century had worse health and higher rates of mortality, yet it remains unclear why a mortality advantage was absent for immigrants during this period. This article combines Vital Statistics records and Lee-Carter mortality models to analyze mortality by nativity status for the U.S. White population from 1900 to 1960, examining variation by age, sex, time, and place. Contrary to contemporary expectations of a foreign-born mortality advantage, White immigrants had higher mortality rates in the early 1900s, with the largest foreign-born disadvantage among the youngest and oldest populations. Although foreign-born and U.S.-born White mortality rates trended toward convergence over time, the foreign-born mortality penalty remained into the 1950s. A decomposition analysis finds that immigrants' concentration in cities, which had higher rates of infectious disease mortality, accounted for nearly half of the nativity difference in 1900, and this place effect declined in subsequent decades. Additional evidence, such as a spike in mortality inequalities during the 1918 influenza pandemic, suggests that common explanations for the immigrant mortality advantage may be less influential in a context of high risk from infectious disease.

Speciation-by-depth on coral reefs: Sympatric divergence with gene flow or cryptic transient isolation?

The distributions of many sister species in the sea overlap geographically but are partitioned along depth gradients. The genetic changes leading to depth segregation may evolve in geographic isolation as a prerequisite to coexistence or may emerge during primary divergence leading to new species. These alternatives can now be distinguished via the power endowed by the thousands of scorable loci provided by second-generation sequence data. Here, we revisit the case of two depth-segregated, genetically isolated ecotypes of the nominal Caribbean candelabrum coral Eunicea flexuosa. Previous analyses based on a handful of markers could not distinguish between models of genetic exchange after a period of isolation (consistent with secondary contact) and divergence with gene flow (consistent with primary divergence). Analyses of the history of isolation, genetic exchange and population size based on 15,640 new SNP markers derived from RNAseq data best support models where divergence began 800K BP and include epochs of divergence with gene flow, but with an intermediate period of transient isolation. Results also supported the previous conclusion that recent exchange between the ecotypes occurs asymmetrically from the Shallow lineage to the Deep. Parallel analyses of data from two other corals with depth-segregated populations (Agaricia fragilis and Pocillopora damicornis) suggest divergence leading to depth-segregated populations may begin with a period of symmetric exchange, but that an epoch of population isolation precedes more complete isolation marked by asymmetric introgression. Thus, while divergence-with-gene flow may account for much of the differentiation that separates closely related, depth-segregated species, it remains to be seen whether any critical steps in the speciation process only occur when populations are isolated.

Molecular Phylogeny of the Subgenus Karstomys Reveals Genetic Signature of Post-Glacial Colonization of Apodemus mystacinus (Rodentia: Muridae) in the Zagros Mountains from Different Refugia.

Eastern broad-toothed field mouse, Apodemus mystacinus, is a rocky habitat dwelling rodent distributed in Asia Minor, the Levant, the Caucasus, and the Zagros Mountains. In this study, we investigated the phylogenetic relationship between different populations of A. mystacinus throughout its range, based on the mitochondrial cytb marker. Phylogenetic analyses revealed the existence of five separately evolving lineages within A. mystacinus, of which two previously unrecognized lineages were identified in the Zagros Mountains and the Levant. Divergence between two major clades of the subgenus Karstomys, corresponding to A. mystacinus and Apodemus epimelas, is inferred to coincide with the Messinian Salinity Crisis (Late Miocene), whereas the splits between major lineages of A. mystacinus are inferred to have occurred during the Pleistocene. Colonization of the Zagros may have occurred from different refugia via eastward migration of the Turkish population and then again by a more recent colonization from the Caucasus, after reopening of the land corridor between the Caucasus and the Zagros Mountains during the Holocene drought.

The 1918 influenza pandemic did not accelerate tuberculosis mortality decline in early-20th century Newfoundland: Investigating historical and social explanations.

OBJECTIVES: The selective mortality hypothesis of tuberculosis after the 1918 influenza pandemic, laid out by Noymer and colleagues, suggests that acute exposure or pre-existing infection with tuberculosis (TB) increased the probability of pneumonia and influenza (P&I) mortality during the 1918 influenza pandemic, leading to a hastened decline of TB mortality in post-pandemic years. This study describes cultural determinants of the post-pandemic TB mortality patterns in Newfoundland and evaluates whether there is support for this observation. MATERIALS AND METHODS: Death records and historical documents from the Provincial Archives of Newfoundland and Labrador were used to calculate age-standardized island-wide and sex-based TB mortality, as well as region-level TB mortality, for 1900-1939. The Joinpoint Regression Program (version 4.8.0.1) was used to estimate statistically significant changes in mortality rates. RESULTS: Island-wide, females had consistently higher TB mortality for the duration of the study period and a significant shift to lower TB mortality beginning in 1928. There was no similar predicted significant decline for males. On the regional level, no models predicted a significant decline after the 1918 influenza pandemic, except for the West, where significant decline was predicted in the late-1930s. DISCUSSION: Although there was no significant decline in TB mortality observed immediately post-pandemic, as has been shown for other Western nations, the female post-pandemic pattern suggests a decline much later. The general lack of significant decrease in TB mortality rate is likely due to Newfoundland's poor nutrition and lack of centralized healthcare rather than a biological interaction between P&I and TB.

The Influence of Kin Proximity on the Reproductive Success of American Couples, 1900-1910.

Children require a large amount of time, effort, and resources to raise. Physical help, financial contributions, medical care, and other types of assistance from kin and social network members allow couples to space births closer together while maintaining or increasing child survival. We examine the impact of kin availability on couples' reproductive success in the early twentieth-century United States with a panel data set of over 3.1 million couples linked between the 1900 and 1910 U.S. censuses. Our results indicate that kin proximity outside the household was positively associated with fertility, child survival, and net reproduction, and suggest that declining kin availability was an important contributing factor to the fertility transition in the United States. We also find important differences between maternal and paternal kin inside the household-including higher fertility among women residing with their mother-in-law than among those residing with their mother-that support hypotheses related to the contrasting motivations and concerns of parents and parents-in-law.

In the Name of the Father? Fertility, Religion, and Child Naming in the Demographic Transition.

This article shows that parents reveal information about their fertility behavior through how they name their children. I arrive at this finding from a detailed examination of the net fertility of 130,000 married couples in Ireland, a country known for its historically high fertility rate, circa 1911. After stringently accounting for couples' occupation, religion, and location, I find higher fertility rates among couples who chose distinctly Catholic names and traditional names for their children, with the latter being particularly important. Exposure to towns and cities lowered net fertility and weakened preferences for traditional and Catholic names. Cumulatively, these findings highlight the role of traditional rural norms over explicitly religious influences in driving high fertility rates in Ireland. The impact of towns and cities in reducing net fertility suggests that Ireland's sluggish urbanization was a key factor in its high historical fertility rate.

Technological Progress and Health Convergence: The Case of Penicillin in Postwar Italy.

Throughout history, technological progress has transformed population health, but the distributional effects of these gains are unclear. New substitutes for older, more expensive health technologies can produce convergence in population health outcomes but may also be prone to elite capture and thus divergence. We study the case of penicillin using detailed historical mortality statistics and exploiting its abruptly timed introduction in Italy after WWII. We find that penicillin reduced both the mean and standard deviation of infectious disease mortality, leading to substantial convergence across disparate regions of Italy. Our results do not appear to be driven by competing risks or confounded by mortality patterns associated with WWII.

Why a long-term perspective is beneficial for demographers.

Although many contemporary demographers pay attention to historical demography, there is often a surprising lack of appreciation of the demographic circumstances and systems of the past, suggesting an implicit assumption that they are not relevant to the present or that the methods, data, and questions addressed by historical and contemporary demographers are different. This paper provides an overview of historical demography as published in Population Studies and how this has developed over time. Drawing on this, I demonstrate that historical and contemporary demography use similar data sources and identical methods, and they often address comparable questions. I argue that an appreciation of demographic patterns and processes is beneficial for all demographers, even those who work on the most recent time periods, and that better integration of historical and contemporary demography would be beneficial to both. The paper also considers three challenges for historical demography as it moves forward.

Height and health in late eighteenth-century England.

Adult stature has become a widely used indicator of childhood nutritional status in historical populations and may provide insights into health inequalities that are not discernible in mortality rates. However, most pre-twentieth-century British data on heights suffer from selection biases. Here we present unique evidence on heights of adult males by occupation from an unbiased sample of adult males in Dorset in 1798-99. The mean height of fully grown (married) men was very similar to that of older military recruits, and our sample therefore confirms the taller stature of English males relative to males of other European countries in the same period. In contrast to previous evidence of negligible or U-shaped socio-economic gradients in mortality in this period, we found a fairly linear gradient in height by socio-economic status, that is similar in magnitude to class differences in adult height among English males born in the mid-twentieth century.Supplementary material for this article is available at: https://doi.org/10.1080/00324728.2020.1823011.

Global and local correlations of Hajnal's household formation markers in historical Europe: A cautionary tale.

Previous scholarship has assumed global correlations between premarital service in husbandry, marriage age, the extent to which marriage coincided with the attainment of household headship, and the nuclear household structure. According to John Hajnal, these were the four core principles of historical household formation systems. However, whether such correlations applied universally across Europe remains uncertain. We test this possibility by applying both global and local (geographically weighted) measures of correlation to data for 256 rural populations from historical Europe. We demonstrate that local correlations diverge considerably from the global results. The mutual associations between household formation markers exhibit considerable spatial drifts and important spatial gradients, and the numbers of joint combinations of these associations far exceed those predicted by Hajnal. We argue that the global relationship patterns that Hajnal promoted may lead to incorrect interpretations of historical family systems, and may detract from our understanding of their actual mechanics.