Palaeogenomics reveal a hybrid origin of the world's largest Camelus species

The extinct Camelus knoblochi is known as the largest camel in genus Camelus, but its relationship to modern Camelus species remains unclear. In this study, we reported the first mitochondrial and nuclear analyses of seven Late Pleistocene C. knoblochi samples from Northeastern China. We found that they are inseparable to wild Bactrian camel on the matrilineal side, but belong to a distinct cluster on the biparental nuclear side. Further admixture proportion analyses suggested hybrid ancestry between both the ancestors of the modern wild and domesticated Bactrian camels, with ~65% contribution from the former and ~35% from the later. By calculating the coalescence time for three Camelus species above, we estimated the hybridization event occurred between approximately 0.8 and 0.33 Ma. We also used Bayesian skyline to reconstruct the maternal demographic trajectories for different Camelus to better compare their evolutionary histories. Our results provide molecular insights into C. knoblochi and fill in a vital piece in understanding the genus Camelus.

Applying comparative methods to different databases: lessons from demographic analyses across mammal species

Comparative demographic analyses aim to identify axes of variation in vital rates and the factors that determine the position of species along these axes. These analyses can be performed using different primary data sets, with marked heterogeneity in data quality and structure. Whether the outcome of demographic comparative analyses depends on the database used because theoretical predictions of evolutionary ecology are not that robust and depend on the set of species analysed or because data limitation prevents the identification of the expected patterns has never been investigated. This chapter fills this knowledge gap by performing a comparative demographic analysis across mammalian species from two distinct databases (Comadre and Malddaba) that were built for different purposes. The chapter first estimates some demographic metrics for each database, analyses their allometric relationships, and compares the estimates with theoretical expectations by performing phylogenetic regressions. Using Malddaba led to stronger allometric relationships closer to the expectation than Comadre. Moreover, the contribution of dimensionless demographic metrics to axes of variation in the shape of demographic trajectories was different between databases. The findings in the chapter demonstrate the key role of age dependence in vital rates for shaping demographic tactics across mammalian species and highlight the need for carefully choosing the database and the metrics to use depending on the question asked. Instead of opposing databases, the authors’ analysis nicely illustrates that different databases could be used to address different questions about life history variation.

Conserved genomic landscapes of differentiation across Populus speciation continuum

Investigating genome-wide variation patterns along a speciation continuum is of central importance to understand the evolutionary processes contributing to lineage diversification. To identify which forces have shaped the genomic landscapes in Populus, we resequenced 201 whole-genomes from eight closely related species, with pairs of species at different stages along the speciation continuum. Using population structure and identity by descent analyses, we show extensive introgression between some species pairs, especially those with parapatric distributions. Inference of historical changes in effective population sizes support species-specific demographic trajectories, including recent population expansions in species characterized by broad present-day distributions. We observe highly conserved genomic landscapes, either focusing on within-species (genetic diversity: π and recombination rate: ρ) or among-species variation (relative divergence: FST and absolute divergence: DXY). Independent of the stage across the divergence continuum, we recovered positive correlations between the pair π and ρ and the pair DXY and ρ across all species pairs, which is consistent with a substantial contribution of linked selection in shaping these genomic landscapes. However, the positive correlations between π and DXY became weaker as the overall divergence level (da) increased, suggesting that background selection is not the only factor at play. Positive correlations between FST and DXY in all species pairs, regardless of the rate of gene flow, also indicates the high FST could be due to divergent sorting of ancient polymorphism before speciation. Our study showcases the importance of investigating genomic patterns on multiple species across the speciation continuum to better understand the genomic landscapes of diversity and differentiation.

Cycles in Stone Mining and Copper Circulation in Europe 5500–2000 bc: A View from Space

The authors of this article consider the relationship in European prehistory between the procurement of high-quality stones (for axeheads, daggers, and other tools) on the one hand, and the early mining, crafting, and deposition of copper on the other. The data consist of radiocarbon dates for the exploitation of stone quarries, flint mines, and copper mines, and of information regarding the frequency through time of jade axeheads and copper artefacts. By adopting a broad perspective, spanning much of central-western Europe from 5500 to 2000 bc, they identify a general pattern in which the circulation of the first copper artefacts was associated with a decline in specialized stone quarrying. The latter re-emerged in certain regions when copper use decreased, before declining more permanently in the Bell Beaker phase, once copper became more generally available. Regional variations reflect the degrees of connectivity among overlapping copper exchange networks. The patterns revealed are in keeping with previous understandings, refine them through quantification and demonstrate their cyclical nature, with additional reference to likely local demographic trajectories.

Long-Term Mass Displacements—The Main Demographic Consequence of Nuclear Disasters?

Human history has witnessed several major disasters that have affected the economic, social and environmental conditions of their respective regions. The nuclear disaster of Chernobyl (1986, Ukraine, that time the Soviet Union) and Fukushima (2011, Japan) appears to be the most significant disasters in terms of negative outcomes produced for their population over a long time. Despite this, the analysis of the socio-economic outcomes of these disasters has attracted much less scientific attention than health or radiation-related issues (UNDP 2002a; Lehman and Wadsworth 2009, 2011). Although nuclear accidents are deemed to be rare events, the Fukushima disaster occurred only 25 years after Chernobyl. These disasters highlighted the need for a detailed long-term socio-economic analysis of these accidents to acquire sufficient knowledge to be applied when considering new construction sites for nuclear power facilities (Lehman and Wadsworth 2011). This chapter focuses on the problem of permanent resettlement resulting from nuclear disasters and its effects on regional demographic trajectories and spatial shifts. Based on the results of this study we argue that mass displacement after a nuclear disaster rather than the radiation itself has a much more significant impact on deteriorating health, natural reproduction and economic performance of the affected population. Furthermore, given the differences in radio-ecological conditions, reconstruction policy and the time framework, Fukushima may demonstrate demographic consequences that are different from the Chernobyl case.

Genome-wide analyses reveal drivers of penguin diversification

Penguins are the only extant family of flightless diving birds. They currently comprise at least 18 species, distributed from polar to tropical environments in the Southern Hemisphere. The history of their diversification and adaptation to these diverse environments remains controversial. We used 22 new genomes from 18 penguin species to reconstruct the order, timing, and location of their diversification, to track changes in their thermal niches through time, and to test for associated adaptation across the genome. Our results indicate that the penguin crown-group originated during the Miocene in New Zealand and Australia, not in Antarctica as previously thought, and thatAptenodytesis the sister group to all other extant penguin species. We show that lineage diversification in penguins was largely driven by changing climatic conditions and by the opening of the Drake Passage and associated intensification of the Antarctic Circumpolar Current (ACC). Penguin species have introgressed throughout much of their evolutionary history, following the direction of the ACC, which might have promoted dispersal and admixture. Changes in thermal niches were accompanied by adaptations in genes that govern thermoregulation and oxygen metabolism. Estimates of ancestral effective population sizes (Ne) confirm that penguins are sensitive to climate shifts, as represented by three different demographic trajectories in deeper time, the most common (in 11 of 18 penguin species) being an increasedNebetween 40 and 70 kya, followed by a precipitous decline during the Last Glacial Maximum. The latter effect is most likely a consequence of the overall decline in marine productivity following the last glaciation.

The impact of bottlenecks and inbreeding on the genome of the endangered Pyrenean desman

The Pyrenean desman (Galemys pyrenaicus) is a small semiaquatic mammal endemic to the Iberian Peninsula. Despite its limited range, this species presents a strong genetic structure due to past isolation in glacial refugia and subsequent bottlenecks. Additionally, some populations are highly fragmented today as a consequence of river barriers, causing substantial levels of inbreeding. These features make the Pyrenean desman a unique model in which to study the genomic footprints of differentiation, bottlenecks and extreme isolation in an endangered species. The complete genome of the Pyrenean desman was assembled using a Bloom filter-based approach. An analysis of the 1.83 Gb reference genome and the sequencing of five additional individuals from different evolutionary units allowed us to detect its main genomic characteristics. The population differentiation of the species was reflected in highly distinctive demographic trajectories. A severe population bottleneck during the postglacial recolonization of the eastern Pyrenees created the lowest genomic heterozygosity ever recorded in a mammal. Moreover, isolation and inbreeding gave rise to a high proportion of runs of homozygosity (ROH). Despite these extremely low levels of genetic diversity, two key multigene families from an eco-evolutionary perspective that need to be genetically variable, the major histocompatibility complex and olfactory receptor genes, showed heterozygosity excess in the majority of individuals. Furthermore, these two classes of genes were significantly less abundant than expected within ROH. These results allow us to characterize important genomic health indicators for each individual, information that may be crucial for the conservation and management of the species.

Recent Demographic History Inferred by High-Resolution Analysis of Linkage Disequilibrium

Inferring changes in effective population size (Ne) in the recent past is of special interest for conservation of endangered species and for human history research. Current methods for estimating the very recent historical Ne are unable to detect complex demographic trajectories involving multiple episodes of bottlenecks, drops, and expansions. We develop a theoretical and computational framework to infer the demographic history of a population within the past 100 generations from the observed spectrum of linkage disequilibrium (LD) of pairs of loci over a wide range of recombination rates in a sample of contemporary individuals. The cumulative contributions of all of the previous generations to the observed LD are included in our model, and a genetic algorithm is used to search for the sequence of historical Ne values that best explains the observed LD spectrum. The method can be applied from large samples to samples of fewer than ten individuals using a variety of genotyping and DNA sequencing data: haploid, diploid with phased or unphased genotypes and pseudohaploid data from low-coverage sequencing. The method was tested by computer simulation for sensitivity to genotyping errors, temporal heterogeneity of samples, population admixture, and structural division into subpopulations, showing high tolerance to deviations from the assumptions of the model. Computer simulations also show that the proposed method outperforms other leading approaches when the inference concerns recent timeframes. Analysis of data from a variety of human and animal populations gave results in agreement with previous estimations by other methods or with records of historical events.

The mining resource cycle and settlement demography in Malå, Northern Sweden

Research on the demographic impacts of mining in sparsely populated areas has focused primarily on relatively large towns. Less attention has been paid to smaller villages, which may experience different impacts because of their highly concentrated economies and their small populations, making them more vulnerable to demographic “boom and bust” effects. This paper examines demographic change in four small villages in northern Sweden, which are located close to several mining projects but have evolved through different degrees of integration with or separation from mining. Using a longitudinal “resource cycle” perspective, the demographic trajectories of the villages are compared to understand how different types of settlement and engagement with mining have led to different demographic outcomes in the long term. While the four villages experienced similar trajectories in terms of overall population growth and decline, their experiences in relation to more nuanced indicators, including age and gender distributions and population mobilities, were different, and potential reasons for this are discussed. Due to data limitations, however, the long-term demographic consequences of mining for local Sami people remain unclear. The paper problematises this research gap in light of general concerns about mining impacts on traditional Sami livelihoods.

A High-quality Draft Genome Assembly of the Black-necked Crane (Grus nigricollis) Based on Nanopore Sequencing

The black-necked crane (Grus nigricollis) which inhabits high-altitude areas has the largest body size of the world’s 15 crane species, and is classified as threatened by the IUCN. To support further studies on population genetics and genomics, we present a high-quality genome assembly based on both Illumina and nanopore sequencing. In total, 54.59 Gb Illumina short reads and 116.5 Gb nanopore long reads were generated. The 1.23 Gb assembled genome has a high contig N50 of 17.89 Mb, and has a longest contig of 87.83 Mb. The completeness (97.7%) of the draft genome was evaluated with single-copy orthologous genes using BUSCO. We identified 17,789 genes and found that 8.11% of the genome is composed of repetitive elements. In total, 84 of the 2,272 one-to-one orthologous genes were under positive selection in the black-necked crane lineage. SNP-based inference indicated two bottlenecks in the recent demographic trajectories of the black-necked crane. The genome information will contribute to future study of crane evolutionary history and provide new insights into the potential adaptation mechanisms of the black-necked crane to its high-altitude habitat.