The Last Glacial Maximum

Demography and evolutionary history of grey wolf populations around the Bering Strait

Glacial and interglacial periods throughout the Pleistocene have been substantial drivers of change in species distributions. Earlier analyses suggested that modern grey wolves (Canis lupus) trace their origin to a single Late Pleistocene Beringian population that expanded east and westwards, starting c. 25,000 years ago (ya). Here, we examined the demographic and phylogeographic histories of extant populations around the Bering Strait with wolves from two inland regions of the Russian Far East (RFE) and one coastal and two inland regions of North‐western North America (NNA), genotyped for 91,327 single nucleotide polymorphisms. Our results indicated that RFE and NNA wolves had a common ancestry until c. 34,400 ya, suggesting that these populations started to diverge before the previously proposed expansion out of Beringia. Coastal and inland NNA populations diverged c. 16,000 ya, concordant with the minimum proposed date for the ecological viability of the migration route along the Pacific Northwest coast. Demographic reconstructions for inland RFE and NNA populations reveal spatial and temporal synchrony, with large historical effective population sizes that declined throughout the Pleistocene, possibly reflecting the influence of broadscale climatic changes across continents. In contrast, coastal NNA wolves displayed a consistently lower effective population size than the inland populations. Differences between the demographic history of inland and coastal wolves may have been driven by multiple ecological factors, including historical gene flow patterns, natural landscape fragmentation, and more recent anthropogenic disturbance.

Genomic Insights Into the Demographic History of the Southern Chinese

Southern China is the birthplace of rice-cultivating agriculture and different language families and has also witnessed various human migrations that facilitated cultural diffusions. The fine-scale demographic history in situ that forms present-day local populations, however, remains unclear. To comprehensively cover the genetic diversity in East and Southeast Asia, we generated genome-wide SNP data from 211 present-day Southern Chinese and co-analyzed them with ∼1,200 ancient and modern genomes. In Southern China, language classification is significantly associated with genetic variation but with a different extent of predictability, and there is strong evidence for recent shared genetic history particularly in Hmong–Mien and Austronesian speakers. A geography-related genetic sub-structure that represents the major genetic variation in Southern East Asians is established pre-Holocene and its extremes are represented by Neolithic Fujianese and First Farmers in Mainland Southeast Asia. This sub-structure is largely reduced by admixture in ancient Southern Chinese since > ∼2,000 BP, which forms a “Southern Chinese Cluster” with a high level of genetic homogeneity. Further admixture characterizes the demographic history of the majority of Hmong–Mien speakers and some Kra-Dai speakers in Southwest China happened ∼1,500–1,000 BP, coeval to the reigns of local chiefdoms. In Yellow River Basin, we identify a connection of local populations to genetic sub-structure in Southern China with geographical correspondence appearing > ∼9,000 BP, while the gene flow likely closely related to “Southern Chinese Cluster” since the Longshan period (∼5,000–4,000 BP) forms ancestry profile of Han Chinese Cline.

Birds adapted to cold conditions show greater changes in range size related to past climatic oscillations than temperate birds

Investigation of ecological responses of species to past climate oscillations provides crucial information to understand the effects of global warming. In this work, we investigated how past climate changes affected the distribution of six bird species with different climatic requirements and migratory behaviours in the Western Palearctic and in Africa. Species Distribution Models and Marine Isotopic Stage (MIS) 2 fossil occurrences of selected species were employed to evaluate the relation between changes in range size and species climatic tolerances. The Last Glacial Maximum (LGM) range predictions, generally well supported by the MIS 2 fossil occurrences, suggest that cold-dwelling species considerably expanded their distribution in the LGM, experiencing more pronounced net changes in range size compared to temperate species. Overall, the thermal niche proves to be a key ecological trait for explaining the impact of climate change in species distributions. Thermal niche is linked to range size variations due to climatic oscillations, with cold-adapted species currently suffering a more striking range reduction compared to temperate species. This work also supports the persistence of Afro-Palearctic migrations during the LGM due to the presence of climatically suitable wintering areas in Africa even during glacial maxima.

Genomic insights into the origin, adaptive evolution, and herbicide resistance of Leptochloa chinensis, a devastating tetraploid weedy grass in rice fields

Chinese sprangletop (Leptochloa chinensis), belonging to the grass subfamily Chloridoideae, is one of the most notorious weeds in rice ecosystems. Here, we report a chromosome-scale reference genome assembly and a genomic variation map of the tetraploid L. chinensis. The L. chinensis genome is derived from two diploid progenitors that diverged ∼10.9 million years ago, and its two subgenomes display neither fractionation bias nor overall gene expression dominance. Comparative genomic analyses reveal substantial genome rearrangements in L. chinensis after its divergence from the common ancestor of Chloridoideae and, together with transcriptome profiling, demonstrate the important contribution of tetraploidization to the gene sources for the herbicide resistance of L. chinensis. Population genomic analyses of 89 accessions from China reveal that L. chinensis accessions collected from southern/southwestern provinces have substantially higher nucleotide diversity than those from the middle and lower reaches of the Yangtze River, suggesting that L. chinensis spread in China from the southern/southwestern provinces to the middle and lower reaches of the Yangtze River. During this spread, L. chinensis developed significantly increased herbicide resistance, accompanied by the selection of numerous genes involved in herbicide resistance. Taken together, our study generated valuable genomic resources for future fundamental research and agricultural management of L. chinensis, and provides significant new insights into the herbicide resistance as well as the origin and adaptive evolution of L. chinensis.

Ostrich eggshell beads from Ga-Mohana Hill North Rockshelter, southern Kalahari, and the implications for understanding social networks during Marine Isotope Stage 2

Ostrich eggshell (OES) beads from southern African archaeological contexts shed light on past traditions of personal ornamentation, and they are also argued to provide a proxy for understanding past social networks. However, OES beads are often understudied and not reported on in detail. In particular, there has been little research on OES bead variation during Marine Isotope Stage 2 (29,000–12,000 years ago) which includes the Last Glacial Maximum when changing climatic conditions are hypothesized to have significant impact on forager social networks. Here, we present the first technological analysis of terminal Pleistocene OES beads and fragments in the Kalahari from the ~15 ka levels at Ga-Mohana Hill North Rockshelter. We contextualise these findings through comparison with coeval OES bead assemblages across southern Africa during MIS 2. Results indicate that OES beads were manufactured at Ga-Mohana Hill North during the terminal Pleistocene occupation, based on the presence of most stages of bead manufacture. The review shows that OES beads were present across southern Africa through MIS 2, suggesting that culturing of the body was an embodied and persistent practice during that time. While the importance of OES beads as decorative objects was shared by populations across southern Africa, variation in bead diameters indicate that there was stylistic variation.

The genomic origins of the world's first farmers

The precise genetic origins of the first Neolithic farming populations in Europe and Southwest Asia, as well as the processes and the timing of their differentiation, remain largely unknown. Demogenomic modeling of high-quality ancient genomes reveals that the early farmers of Anatolia and Europe emerged from a multiphase mixing of a Southwest Asian population with a strongly bottlenecked western hunter-gatherer population after the last glacial maximum. Moreover, the ancestors of the first farmers of Europe and Anatolia went through a period of extreme genetic drift during their westward range expansion, contributing highly to their genetic distinctiveness. This modeling elucidates the demographic processes at the root of the Neolithic transition and leads to a spatial interpretation of the population history of Southwest Asia and Europe during the late Pleistocene and early Holocene.

We get by with a little help from our friends: shared adaptive variation provides a bridge to novel ecological specialists during adaptive radiation

Adaptive radiations involve astounding bursts of phenotypic, ecological and species diversity. However, the microevolutionary processes that underlie the origins of these bursts are still poorly understood. We report the discovery of an intermediate C. sp. 'wide-mouth' scale-eating ecomorph in a sympatric radiation of Cyprinodon pupfishes, illuminating the transition from a widespread algae-eating generalist to a novel microendemic scale-eating specialist. We first show that this ecomorph occurs in sympatry with generalist C. variegatus and scale-eating specialist C. desquamator on San Salvador Island, Bahamas, but is genetically differentiated, morphologically distinct and often consumes scales. We then compared the timing of selective sweeps on shared and unique adaptive variants in trophic specialists to characterize their adaptive walk. Shared adaptive regions swept first in both the specialist desquamator and the intermediate 'wide-mouth' ecomorph, followed by unique sweeps of introgressed variation in 'wide-mouth' and de novo variation in desquamator. The two scale-eating populations additionally shared 9% of their hard selective sweeps with the molluscivore C. brontotheroides, despite no single common ancestor among specialists. Our work provides a new microevolutionary framework for investigating how major ecological transitions occur and illustrates how both shared and unique genetic variation can provide a bridge for multiple species to access novel ecological niches.

Orphan gene in Littorina: An unexpected role of symbionts in the host evolution

Mechanisms of reproductive isolation between closely related sympatric species are of high evolutionary significance as they may function as initial drivers of speciation and protect species integrity afterwards. Proteins involved in the establishment of reproductive barriers often evolve fast and may be key players in cessation of gene flow between the incipient species. The five Atlantic Littorina (Neritrema) species represent a notable example of recent radiation. The geographic ranges of these young species largely overlap and the mechanisms of reproductive isolation are poorly understood. In this study, we performed a detailed analysis of the reproductive protein LOSP, previously identified in Littorina. We showed that this protein is evolutionary young and taxonomically restricted to the genus Littorina. It has high sequence variation both within and between Littorina species, which is compatible with its presumable role in the reproductive isolation. The strongest differences in the LOSP structure were detected between Littorina subgenera with distinctive repetitive motifs present exclusively in the Neritrema species, but not in L. littorea. Moreover, the sequence of these repetitive structural elements demonstrates a high homology with genetic elements of bacteria, identified as components of Littorina associated microbiomes. We suggest that these elements were acquired from a symbiotic bacterial donor via horizontal genetic transfer (HGT), which is indirectly confirmed by the presence of multiple transposable elements in the LOSP flanking and intronic regions. Furthermore, we hypothesize that this HGT-driven evolutionary innovation promoted LOSP function in reproductive isolation, which might be one of the factors determining the intensive cladogenesis in the Littorina (Neritrema) lineage in contrast to the anagenesis in the L. littorea clade.

Radiocarbon and genomic evidence for the survival of Equus Sussemionus until the late Holocene

The exceptionally rich fossil record available for the equid family has provided textbook examples of macroevolutionary changes. Horses, asses, and zebras represent three extant subgenera of Equus lineage, while the Sussemionus subgenus is another remarkable Equus lineage ranging from North America to Ethiopia in the Pleistocene. We sequenced 26 archaeological specimens from Northern China in the Holocene that could be assigned morphologically and genetically to Equus ovodovi, a species representative of Sussemionus. We present the first high-quality complete genome of the Sussemionus lineage, which was sequenced to 13.4× depth of coverage. Radiocarbon dating demonstrates that this lineage survived until ~3500 years ago, despite continued demographic collapse during the Last Glacial Maximum and the great human expansion in East Asia. We also confirmed the Equus phylogenetic tree and found that Sussemionus diverged from the ancestor of non-caballine equids ~2.3–2.7 million years ago and possibly remained affected by secondary gene flow post-divergence. We found that the small genetic diversity, rather than enhanced inbreeding, limited the species’ chances of survival. Our work adds to the growing literature illustrating how ancient DNA can inform on extinction dynamics and the long-term resilience of species surviving in cryptic population pockets.

Draft Genome Assembly of an Iconic Arctic Species: Muskox (Ovibos moschatus)

Muskoxen (Ovibos moschatus) are Arctic species within the Caprinae subfamily that are economically and culturally significant to northern Indigenous communities. Low genetic diversity from repeated genetic bottlenecks, coupled with the effects of Arctic warming (e.g., heat stress, changing forage, pathogen range expansions), present conservation concerns for this species. Reference genome assemblies enhance our ecological and evolutionary understanding of species (which in turn aid conservation efforts). Herein, we provide a full draft reference genome of muskox using Illumina Hiseq data and cross-species scaffolding. The final reference assembly yielded a genome of 2,621,890,883 bp in length, a scaffold N50 of ~13.2 million, and an annotation identifying ~19.3 k genes. The muskox genome assembly and annotation were then used to reconstruct a phylogenetic tree which estimated muskoxen diverged from other ungulate species~12 Mya. To gain insight into the demographic history of muskoxen we also performed pairwise sequentially Markovian coalescent (PSMC) that identified two population bottlenecks coinciding with major glaciation events contributing to the notoriously low genetic variation observed in muskoxen. Overall, this genome assembly provides a foundation for future population genomic studies, such as latitudinal analyses, to explore the capacity of muskoxen to adapt to rapidly changing environments.

Social ties in the Congo Basin: insights into tropical forest adaptation from BaYaka and their neighbours

Investigating past and present human adaptation to the Congo Basin tropical forest can shed light on how climate and ecosystem variability have shaped human evolution. Here, we first review and synthesize genetic, palaeoclimatological, linguistic and historical data on the peopling of the Congo Basin. While forest fragmentation led to the increased genetic and geographical divergence of forest foragers, these groups maintained long-distance connectivity. The eventual expansion of Bantu speakers into the Congo Basin provided new opportunities for forging inter-group links, as evidenced by linguistic shifts and historical accounts. Building from our ethnographic work in the northern Republic of the Congo, we show how these inter-group links between forest forager communities as well as trade relationships with neighbouring farmers facilitate adaptation to ecoregions through knowledge exchange. While researchers tend to emphasize forager-farmer interactions that began in the Iron Age, we argue that foragers' cultivation of relational wealth with groups across the region played a major role in the initial occupation of the Congo Basin and, consequently, in cultural evolution among the ancestors of contemporary peoples. This article is part of the theme issue 'Tropical forests in the deep human past'.

Population genomics and phylogeography of Colletes gigas , a wild bee specialized on winter flowering plants

Diet specialization may affect the population genetic structure of pollinators by reducing gene flow and driving genetic differentiation, especially in pollen‐specialist bees. Colletes gigas is a pollen‐specialist pollinator of Camellia oleifera, one of the most important staple oil crops in China. Ca. oleifera blooms in cold climates and contains special compounds that make it an unusable pollen source to other pollinators. Thus, C. gigas undoubtedly plays a key role as the main pollinator of Ca. oleifera, with biological and economic significance. Here, we use a population genomic approach to analyze the roles of geography and climate on the genetic structure, genetic diversity, and demographic history of C. gigas. A total of 1,035,407 SNPs were identified from a 582.77 Gb dataset. Clustering and phylogenetic analyses revealed a marked genetic structure, with individuals grouped into nine local clusters. A significant isolation by distance was detected by both the Mantel test (R = .866, p = .008) and linear regression (R² = .616, p < .001). Precipitation and sunshine duration were positively and significantly (R ≥ .765, p ≤ .016) correlated with observed heterozygosity (H_o) and expected heterozygosity (H_e). These results showed that C. gigas populations had a distinct phylogeographic pattern determined by geographical distance and environmental factors (precipitation and sunshine duration). In addition, an analysis of paleogeographic dynamics indicated that C. gigas populations exhibited patterns of glacial expansion and interglacial contraction, likely resulting from post‐glacial habitat contraction and fragmentation. Our results indicated that the peculiar phylogeographic patterns in C. gigas populations may be related to their specialization under long‐term adaptation to host plants. This work improves our understanding of the population genetics in pollen‐specialist bees. The distinct genetic clusters identified in this study should be taken into consideration for the protection and utilization of this specialized crop pollinator.

Late-Glacial and Holocene Lake-Level Fluctuations on the Kenai Lowland, Reconstructed from Satellite-Fen Peat Deposits and Ice-Shoved Ramparts, Kenai Peninsula, Alaska

Recent decades of warmer climate have brought drying wetlands and falling lake levels to southern Alaska. These recent changes can be placed into a longer-term context of postglacial lake-level fluctuations that include low stands that were as much as 7 m lower than present at eight lakes on the Kenai Lowland. Closed-basin lakes on the Kenai Lowland are typically ringed with old shorelines, usually as wave-cut scarps, cut several meters above modern lake levels; the scarps formed during deglaciation at 25–19 ka in a kettle moraine topography on the western Kenai Lowland. These high-water stands were followed by millennia of low stands, when closed-basin lake levels were drawn down by 5–10 m or more. Peat cores from satellite fens near or adjoining the eight closed-basin lakes show that a regional lake level rise was underway by at least 13.4 ka. At Jigsaw Lake, a detailed study of 23 pairs of overlapping sediment cores, seismic profiling, macrofossil analysis, and 58 AMS radiocarbon dates reveal rapidly rising water levels at 9–8 ka that caused large slabs of peat to slough off and sink to the lake bottom. These slabs preserve an archive of vegetation that had accumulated on a lakeshore apron exposed during the preceding drawdown period. They also preserve evidence of a brief period of lake level rise at 4.7–4.5 ka. We examined plant succession using in situ peat sequences in nine satellite fens around Jigsaw Lake that indicated increased effective moisture between 4.6 and 2.5 ka synchronous with the lake level rise. Mid- to late-Holocene lake high stands in this area are recorded by numerous ice-shoved ramparts (ISRs) along the shores. ISRs at 15 lakes show that individual ramparts typically record several shove events, separated by hundreds or thousands of years. Most ISRs date to within the last 5200 years and it is likely that older ISRs were erased by rising lake levels during the mid- to late Holocene. This study illustrates how data on vegetation changes in hydrologically coupled satellite-fen peat records can be used to constrain the water level histories in larger adjacent lakes. We suggest that this method could be more widely utilized for paleo-lake level reconstruction.

Chromosome-level genome of the globe skimmer dragonfly (Pantala flavescens)

BACKGROUND

The globe skimmer dragonfly (Pantala flavescens) is a notable Odonata insect distributed in nature fields and farmlands worldwide, and it is commonly recognized as a natural enemy because it preys on agricultural pests and health pests. As one of the sister groups of winged insects, odonatan species are key to understanding the evolution of insect wings.

FINDINGS

We present a high-quality reference genome of P. flavescens, which is the first chromosome-level genome in the Palaeoptera (Odonata and Ephemeroptera). The assembled genome size was 662 Mb, with a contig N50 of 16.2 Mb. Via Hi-C scaffolding, 648 Mb (97.9%) of contig sequences were clustered, ordered, and assembled into 12 large scaffolds, each corresponding to a natural chromosome. The X chromosome was identified by sequence coverage depth. The repetitive sequences and gene density of the X chromosome are similar to those of autosomal sequences, but the X chromosome shows a much lower degree of heterozygosity. Our analysis shows that the effective population size experienced 3 declining events, which may have been caused by climate change and environmental pollution.

CONCLUSIONS

The genome of P. flavescens provides more information on the biology and evolution of insects and will help for the use of this species in pest control.

Fine-scale genome-wide signature of Pleistocene glaciation in Thitarodes moths (Lepidoptera: Hepialidae), host of Ophiocordyceps fungus in the Hengduan Mountains

The Hengduan Mountains region is a biodiversity hotspot known for its topologically complex, deep valleys and high mountains. While landscape and glacial refugia have been evoked to explain patterns of inter-species divergence, the accumulation of intra-species (i.e. population level) genetic divergence across the mountain-valley landscape in this region has received less attention. We used genome-wide restriction site-associated DNA sequencing (RADseq) to reveal signatures of Pleistocene glaciation in populations of Thitarodes shambalaensis (Lepidoptera: Hepialidae), the host moth of parasitic Ophiocordyceps sinensis (Hypocreales: Ophiocordycipitaceae) or "caterpillar fungus" endemic to the glacier of eastern Mt. Gongga. We used moraine history along the glacier valleys to model the distribution and environmental barriers to gene flow across populations of T. shambalaensis. We found that moth populations separated by less than 10 km exhibited valley-based population genetic clustering and isolation-by-distance (IBD), while gene flow among populations was best explained by models using information about their distributions at the local last glacial maximum (LGM_L , 58 kya), not their contemporary distribution. Maximum likelihood lineage history among populations, and among subpopulations as little as 500 meters apart, recapitulated glaciation history across the landscape. We also found signals of isolated population expansion following the retreat of LGM_L glaciers. These results reveal the fine-scale, long-term historical influence of landscape and glaciation on the genetic structuring of populations of an endangered and economically important insect species. Similar mechanisms, given enough time and continued isolation, could explain the contribution of glacier refugia to the generation of species diversity among the Hengduan Mountains.

Strong and lasting impacts of past global warming on baleen whales and their prey

Global warming is affecting the population dynamics and trophic interactions across a wide range of ecosystems and habitats. Translating these real-time effects into their long-term consequences remains a challenge. The rapid and extreme warming period that occurred after the Last Glacial Maximum (LGM) during the Pleistocene-Holocene transition (7-12 thousand years ago) provides an opportunity to gain insights into the long-term responses of natural populations to periods with global warming. The effects of this post-LGM warming period have been assessed in many terrestrial taxa, whereas insights into the impacts of rapid global warming on marine taxa remain limited, especially for megafauna. In order to understand how large-scale climate fluctuations during the post-LGM affected baleen whales and their prey, we conducted an extensive, large-scale analysis of the long-term effects of the post-LGM warming on abundance and inter-ocean connectivity in eight baleen whale and seven prey (fish and invertebrates) species across the Southern and the North Atlantic Ocean; two ocean basins that differ in key oceanographic features. The analysis was based upon 7032 mitochondrial DNA sequences as well as genome-wide DNA sequence variation in 100 individuals. The estimated temporal changes in genetic diversity during the last 30,000 years indicated that most baleen whale populations underwent post-LGM expansions in both ocean basins. The increase in baleen whale abundance during the Holocene was associated with simultaneous changes in their prey and climate. Highly correlated, synchronized and exponential increases in abundance in both baleen whales and their prey in the Southern Ocean were indicative of a dramatic increase in ocean productivity. In contrast, the demographic fluctuations observed in baleen whales and their prey in the North Atlantic Ocean were subtle, varying across taxa and time. Perhaps most important was the observation that the ocean-wide expansions and decreases in abundance that were initiated by the post-LGM global warming, continued for millennia after global temperatures stabilized, reflecting persistent, long-lasting impacts of global warming on marine fauna.

Late Pleistocene pottery production and exchange: Provenance studies of hunter-gatherer wares from southern Kyushu, Japan by neutron activation analysis

Late Pleistocene hunter-gatherers in East Asia adopted pottery, yet the ability to reconstruct circulation, mobility, and exchange has been hampered, in part, due to problematic regional geochronology. The driving forces behind pottery adoption is unclear. The purpose of this study is to test our results of the first systematic petrographic pottery sourcing from the pre-Younger Dryas by utilizing neutron activation analysis. We examine samples from the Sankauyama I site on Tanegashima Island, southern Japan, dating to the Incipient Jomon, ca. 14,000/13,500-12,800 cal BP, with a well-defined geochronology. Our NAA results corroborate with the petrographic study suggesting that pottery was mainly produced in-situ, but some vessels were transported long distances from another island. Changing from high mobility, sedentary Incipient Jomon foragers made pottery, occasionally investing in long-distance ceramic vessel transportation and exchange likely involving ocean crossing. This may be associated with a risk-buffering strategy in the context of rising sea levels and isolation of Tanegashima.

Pseudomonas syringae on Plants in Iceland Has Likely Evolved for Several Million Years Outside the Reach of Processes That Mix This Bacterial Complex across Earth’s Temperate Zones

Here we report, for the first time, the occurrence of the bacteria from the species complex Pseudomonas syringae in Iceland. We isolated this bacterium from 35 of the 38 samples of angiosperms, moss, ferns and leaf litter collected across the island from five habitat categories (boreal heath, forest, subalpine and glacial scrub, grazed pasture, lava field). The culturable populations of P. syringae on these plants varied in size across 6 orders of magnitude, were as dense as 10⁷ cfu g⁻¹ and were composed of strains in phylogroups 1, 2, 4, 6, 7, 10 and 13. P. syringae densities were significantly greatest on monocots compared to those on dicots and mosses and were about two orders of magnitude greater in grazed pastures compared to all other habitats. The phylogenetic diversity of 609 strains of P. syringae from Iceland was compared to that of 933 reference strains of P. syringae from crops and environmental reservoirs collected from 27 other countries based on a 343 bp sequence of the citrate synthase (cts) housekeeping gene. Whereas there were examples of identical cts sequences across multiple countries and continents among the reference strains indicating mixing among these countries and continents, the Icelandic strains grouped into monophyletic lineages that were unique compared to all of the reference strains. Based on estimates of the time of divergence of the Icelandic genetic lineages of P. syringae, the geological, botanical and land use history of Iceland, and atmospheric circulation patterns, we propose scenarios whereby it would be feasible for P. syringae to have evolved outside the reach of processes that tend to mix this bacterial complex across the planet elsewhere.

Palaeo-Shoreline Configuration of the Adventure Plateau (Sicilian Channel) at the Last Glacial Maximum

The Adventure Plateau, located in the NW sector of the Sicilian Channel, experienced several episodes of exposure/erosion and subsequent drowning, with the most recent occurring after the Last Glacial Maximum (LGM). Unlike other parts of the Sicilian Channel, the Adventure Plateau is relatively tectonically stable and is therefore best suitable for reconstructing its coastal configuration before the post-LGM marine transgression. Here, we use high-resolution seismic data to identify and map the palaeo-coastline at the LGM on the basis of the internal architecture of the prograding wedges (i.e., the location of the subaqueous clinoform rollover point) and the erosional markers such as the subaerial unconformities and the wave ravinement surfaces. These data, which show an extreme variability in the palaeo-morphology of the coastal margins of the Adventure Plateau, have been complemented with vintage seismic profiles in order to entirely cover its perimeter. The mapped LGM coastline has then been compared to predictions from glacial isostatic adjustment (GIA) modeling, which considers the horizontal migration of the shorelines in response to sea level rise and to Earth’s rotational and deformational effects associated with deglaciation. The two shorelines (i.e., the coastline derived from the marine data interpretation and the one derived from the GIA model) are in good agreement at 21 kyears BP, although some discrepancies occur in the southern part of the plateau, where the seabed slope is extremely gentle, which makes the clinoform rollover points and the buried erosional unconformities difficult to detect. After 20 kyears BP, an acceleration in the rate of the sea level rise occurred. The results of this study indicate the importance of comparing experimental data with model predictions in order to refine and calibrate boundary parameters and to gain a better picture of the evolution of sea level rise over various time scales.

Divergence time estimation using ddRAD data and an isolation-with-migration model applied to water vole populations of Arvicola

Molecular dating methods of population splits are crucial in evolutionary biology, but they present important difficulties due to the complexity of the genealogical relationships of genes and past migrations between populations. Using the double digest restriction-site associated DNA (ddRAD) technique and an isolation-with-migration (IM) model, we studied the evolutionary history of water vole populations of the genus Arvicola, a group of complex evolution with fossorial and semi-aquatic ecotypes. To do this, we first estimated mutation rates of ddRAD loci using a phylogenetic approach. An IM model was then used to estimate split times and other relevant demographic parameters. A set of 300 ddRAD loci that included 85 calibrated loci resulted in good mixing and model convergence. The results showed that the two populations of A. scherman present in the Iberian Peninsula split 34 thousand years ago, during the last glaciation. In addition, the much greater divergence from its sister species, A. amphibius, may help to clarify the controversial taxonomy of the genus. We conclude that this approach, based on ddRAD data and an IM model, is highly useful for analyzing the origin of populations and species.

Evolutionary history and colonization patterns of the wing dimorphic grasshopper Dichroplus vittatus in two Argentinean biomes

Quaternary climate oscillations and modification of the environment by humans have played an important role in shaping species distribution and genetic structure of modern species. Here, population genetic parameters were inferred from the analysis of 168 individuals belonging to 11 populations of the South American grasshopper, Dichroplus vittatus, distributed in two Argentinean Biomes (Grassland and Savanna), by sequencing a 543 bp of the mitochondrial COI gene. Overall, we detected considerable haplotype diversity and low nucleotide diversity. AMOVA analyses showed a significant degree of differentiation among Biomes and between populations. Two major mitochondrial lineages can be distinguished. The haplogroup containing the most common haplotype split 17,000 years BP while the haplogroup including the second most common haplotype has a divergence date of about 11,700 years. Approximate Bayesian Computation (ABC) analyses showed that the palaeodemographic scenario that best fitted our data is consistent with a hypothesis of divergence from an ancestral population and subsequent admixture with Grassland-Savanna (South-North) direction. Our results suggest that populations located in both Biomes would derive from a single ancestral population that colonized the region after the Last Glacial Maximum and Grassland would have a more ancestral origin than Savanna. Further, our results emphasize the importance of human-mediated dispersal in the reconfiguration of genetic diversity of species with potential pest capacity.

Genomic Data Reveals Population Genetic and Demographic History of Magnolia fistulosa (Magnoliaceae), a Plant Species With Extremely Small Populations in Yunnan Province, China

Elucidating the genetic background of threatened species is fundamental to their management and conservation, and investigating the demographic history of these species is helpful in the determination of the threats facing them. The woody species of the genus Magnolia (Magnoliaceae) have high economic, scientific and ecological values. Although nearly half of all Magnolia species have been evaluated as threatened, to date there has been no population genetic study employing Next Generation Sequencing (NGS) technology in this genus. In the present study, we investigate the conservation genomics of Magnolia fistulosa, a threatened species endemic to the limestone area along the Sino-Vietnamese border, using a double digest restriction-site-associated DNA-sequencing (ddRAD-seq) approach. To increase the reliability of our statistical inferences, we employed two approaches, Stacks and ipyrad, for SNP calling. A total of 15,272 and 18,960, respectively, putatively neutral SNPs were generated by Stacks and ipyrad. Relatively high genetic diversity and large population divergence were detected in M. fistulosa. Although higher absolute values were calculated using the ipyrad data set, the two data sets showed the same trends in genetic diversity (π, H e), population differentiation (F ST) and inbreeding coefficients (F IS). A change in the effective population size of M. fistulosa within the last 1 Ma was detected, including a population decline about 0.5-0.8 Ma ago, a bottleneck event about 0.2-0.3 Ma ago, population fluctuations during the last glacial stage, and the recovery of effective population size after the last glacial maximum. Our findings not only lay the foundation for the future conservation of this species, but also provide new insights into the evolutionary history of the genus Magnolia in southeastern Yunnan, China.

Population genomic signatures of the oriental fruit moth related to the Pleistocene climates

The Quaternary climatic oscillations are expected to have had strong impacts on the evolution of species. Although legacies of the Quaternary climates on population processes have been widely identified in diverse groups of species, adaptive genetic changes shaped during the Quaternary have been harder to decipher. Here, we assembled a chromosome-level genome of the oriental fruit moth and compared genomic variation among refugial and colonized populations of this species that diverged in the Pleistocene. High genomic diversity was maintained in refugial populations. Demographic analysis showed that the effective population size of refugial populations declined during the penultimate glacial maximum (PGM) but remained stable during the last glacial maximum (LGM), indicating a strong impact of the PGM rather than the LGM on this pest species. Genome scans identified one chromosomal inversion and a mutation of the circadian gene Clk on the neo-Z chromosome potentially related to the endemicity of a refugial population. In the colonized populations, genes in pathways of energy metabolism and wing development showed signatures of selection. These different genomic signatures of refugial and colonized populations point to multiple impacts of Quaternary climates on adaptation in an extant species.

Biogeographic consequences of shifting climate for the western massasauga (Sistrurus tergeminus)

The western massasauga (Sistrurus tergeminus) is a small pit viper with an extensive geographic range, yet observations of this species are relatively rare. They persist in patchy and isolated populations, threatened by habitat destruction and fragmentation, mortality from vehicle collisions, and deliberate extermination. Changing climates may pose an additional stressor on the survival of isolated populations. Here, we evaluate historic, modern, and future geographic projections of suitable climate for S. tergeminus to outline shifts in their potential geographic distribution and inform current and future management. We used maximum entropy modeling to build multiple models of the potential geographic distribution of S. tergeminus. We evaluated the influence of five key decisions made during the modeling process on the resulting geographic projections of the potential distribution, allowing us to identify areas of model robustness and uncertainty. We evaluated models with the area under the receiver operating curve and true skill statistic. We retained 16 models to project both in the past and future multiple general circulation models. At the last glacial maximum, the potential geographic distribution associated with S. tergeminus occurrences had a stronghold in the southern part of its current range and extended further south into Mexico, but by the mid-Holocene, its modeled potential distribution was similar to its present-day potential distribution. Under future model projections, the potential distribution of S. tergeminus moves north, with the strongest northward trends predicted under a climate scenario increase of 8.5 W/m2. Some southern populations of S. tergeminus have likely already been extirpated and will continue to be threatened by shifting availability of suitable climate, as they are already under threat from desertification of grasslands. Land use and habitat loss at the northern edge of the species range are likely to make it challenging for this species to track suitable climates northward over time.

Genome-wide patterns of genetic diversity, population structure and demographic history in mānuka (Leptospermum scoparium) growing on indigenous Māori land

Leptospermum scoparium J. R. Forst et G. Forst, known as mānuka by Māori, the indigenous people of Aotearoa (New Zealand), is a culturally and economically significant shrub species, native to New Zealand and Australia. Chemical, morphological and phylogenetic studies have indicated geographical variation of mānuka across its range in New Zealand, and genetic differentiation between New Zealand and Australia. We used pooled whole genome re-sequencing of 76 L. scoparium and outgroup populations from New Zealand and Australia to compile a dataset totalling ~2.5 million SNPs. We explored the genetic structure and relatedness of L. scoparium across New Zealand, and between populations in New Zealand and Australia, as well as the complex demographic history of this species. Our population genomic investigation suggests there are five geographically distinct mānuka gene pools within New Zealand, with evidence of gene flow occurring between these pools. Demographic modelling suggests three of these gene pools have undergone expansion events, whilst the evolutionary histories of the remaining two have been subjected to contractions. Furthermore, mānuka populations in New Zealand are genetically distinct from populations in Australia, with coalescent modelling suggesting these two clades diverged ~9-12 million years ago. We discuss the evolutionary history of this species and the benefits of using pool-seq for such studies. Our research will support the management and conservation of mānuka by landowners, particularly Māori, and the development of a provenance story for the branding of mānuka based products.

Geological and climatic influences on population differentiation of the Phrynocephalus vlangalii species complex (Sauria: Agamidae) in the northern Qinghai-Tibet Plateau

Extremely heterogeneous topography and complex paleoclimate history of the Qinghai-Tibet Plateau (QTP) have a key role in promoting genetic divergence and lineage/species formation. Here, we sequenced one nuclear and three mitochondrial markers of 532 individuals from the entire range of the Phrynocephalus vlangalii species complex including two species, P. putjatai and P. vlangalii, endemic to the northern QTP. We integrated multilocus phylogeny, demographic analysis and geographic barrier detection to evaluate the population structure and dynamics. We found a new mitochondrial clade (PV-I) in the Gonghe County population of P. vlangalii, partial mitochondrial DNA replacement within P. vlangalii and complete mitochondrial DNA replacement between P. putjatai and P. vlangalii. Neutrality test, mismatch distribution analysis and Extended Bayesian Skyline Plot (EBSP) analysis all supported a significant expansion of the Qaidam Basin population of P. vlangalii (PV-II-2) from 0.091 to 0.026 Ma after Penultimate Glaciation. The uplift of the Arjin and Anyemanqen Mountains during the Kunhuang Movement (∼1.2 Ma) split populations of P. vlangalii in Akesai, Qaidam Basin and source of the Yellow River. The uplift of the Elashan Mountains during the second phase of the Qingzang Movement (∼2.5 Ma) contributed to the divergence of the Gonghe County population of P. vlangalii from other conspecific populations. The third phase of the Qingzang Movement (∼1.7 Ma) contributed to the divergence of the Xinghai population of P. vlangalii from P. putjatai and to the divergence of the northern populations of P. putjatai from the southern conspecific populations. Our data support the idea that the geological and climatic changes following the orogeny of the QTP may have promoted population differentiation and shaped the current population patterns of the P. vlangalii species complex in the northeastern QTP.

Pleistocene mitogenomes reconstructed from the environmental DNA of permafrost sediments

Traditionally, paleontologists have relied on the morphological features of bones and teeth to reconstruct the evolutionary relationships of extinct animals.¹ In recent decades, the analysis of ancient DNA recovered from macrofossils has provided a powerful means to evaluate these hypotheses and develop novel phylogenetic models.² Although a great deal of life history data can be extracted from bones, their scarcity and associated biases limit their information potential. The paleontological record of Beringia³-the unglaciated areas and former land bridge between northeast Eurasia and northwest North America-is relatively robust thanks to its perennially frozen ground favoring fossil preservation.^4,5 However, even here, the macrofossil record is significantly lacking in small-bodied fauna (e.g., rodents and birds), whereas questions related to migration and extirpation, even among well-studied taxa, remain crudely resolved. The growing sophistication of ancient environmental DNA (eDNA) methods have allowed for the identification of species within terrestrial/aquatic ecosystems,^6-12 in paleodietary reconstructions,^13-19 and facilitated genomic reconstructions from cave contexts.^8,20-22 Murchie et al.^6,23 used a capture enrichment approach to sequence a diverse range of faunal and floral DNA from permafrost silts deposited during the Pleistocene-Holocene transition.²⁴ Here, we expand on their work with the mitogenomic assembly and phylogenetic placement of Equus caballus (caballine horse), Bison priscus (steppe bison), Mammuthus primigenius (woolly mammoth), and Lagopus lagopus (willow ptarmigan) eDNA from multiple permafrost cores spanning the last 30,000 years. We identify a diverse metagenomic spectra of Pleistocene fauna and identify the eDNA co-occurrence of distinct Eurasian and American mitogenomic lineages.

Linked selection shapes the landscape of genomic variation in three oak species

Natural selection shapes genome-wide patterns of diversity within species and divergence between species. However, quantifying the efficacy of selection and elucidating the relative importance of different types of selection in shaping genomic variation remain challenging. We sequenced whole genomes of 101 individuals of three closely related oak species to track the divergence history, and to dissect the impacts of selective sweeps and background selection on patterns of genomic variation. We estimated that the three species diverged around the late Neogene and experienced a bottleneck during the Pleistocene. We detected genomic regions with elevated relative differentiation ('F_ST -islands'). Population genetic inferences from the site frequency spectrum and ancestral recombination graph indicated that F_ST -islands were formed by selective sweeps. We also found extensive positive selection; the fixation of adaptive mutations and reduction neutral diversity around substitutions generated a signature of selective sweeps. Prevalent negative selection and background selection have reduced genetic diversity in both genic and intergenic regions, and contributed substantially to the baseline variation in genetic diversity. Our results demonstrate the importance of linked selection in shaping genomic variation, and illustrate how the extent and strength of different selection models vary across the genome.

Genetic assessment reveals inbreeding, possible hybridization, and low levels of genetic structure in a declining goose population

The population numbers of taiga bean goose (Anser fabalis fabalis) have halved during recent decades. Since this subspecies is hunted throughout most of its range, the decline is of management concern. Knowledge of the genetic population structure and diversity is important for guiding management and conservation efforts. Genetically unique subpopulations might be hunted to extinction if not managed separately, and any inbreeding depression or lack of genetic diversity may affect the ability to adapt to changing environments and increase extinction risk. We used microsatellite and mitochondrial DNA markers to study the genetic population structure and diversity among taiga bean geese breeding within the Central flyway management unit using non-invasively collected feathers. We found some genetic structuring with the maternally inherited mitochondrial DNA between four geographic regions (ɸ ST = 0.11-0.20) but none with the nuclear microsatellite markers (all pairwise F ST-values = 0.002-0.005). These results could be explained by female natal philopatry and male-biased dispersal, which completely homogenizes the nuclear genome. Therefore, the population could be managed as a single unit. Genetic diversity was still at a moderate level (average H E = 0.69) and there were no signs of past population size reductions, although significantly positive inbreeding coefficients in all sampling sites (F IS = 0.05-0.10) and high relatedness values (r = 0.60-0.86) between some individuals could indicate inbreeding. In addition, there was evidence of either incomplete lineage sorting or introgression from the pink-footed goose (Anser brachyrhynchus). The current population is not under threat by genetic impoverishment but monitoring in the future is desirable.

The impact of prehistoric human dispersals on the presence of tobacco-related oral cancer in Northeast India

BACKGROUND

Northeast (NE) India is a subject of debate for predicting its involvement in prehistoric anatomically modern human (AMH) dispersal. The unique lifestyle and genetic characteristics of native ethnic groups in this region are believed to be responsible for their susceptibility to tobacco-related oral cancer (TrOC). The present study assessed mitochondrial macro-haplogroup (mHG) diversity and TrOC susceptibility autosomal loci to evaluate the impact of prehistoric AMH dispersal on the present day's high TrOC prevalence in major NE Indian ethnics.

METHODS

We considered 175 unrelated individuals from 35 ethnic groups and previously published 374 sequences for sequencing-based assessment of mtDNA-based marker by subsequent analyses like haplogroup diversity, phylogenetic, genetic structure by AMOVA, and MDS, descriptive statistics of demographic parameters, and migration analysis. Besides, we selected prolonged tobacco-chewing 124 case-control individuals from similar ethnic backgrounds for genotyping 115 autosomal loci in Sequenom iPLEX MassARRAY™ platform and mined 1000genome data (n = 398) for consequent global admixture and ancestry-specific allele frequencies-based analyses.

RESULTS

Our mtDNA-based findings suggested that NE populations were distinct from other Indian populations, owing to the first wave of migration from ancient southern China (∼54kya) and two successive spatial expansion events at ∼45kya and ∼43kya. Consequently, it probably acted as another source for prehistoric AMH dispersal in N/NE Asia. Besides, the second wave of back-migration from SE Asia (∼40kya) probably replaced the mitochondrial footprints of survivors from the first migrants and introduced the TrOC susceptibility traits in this region. Afterward, the autosomal marker-based observations on the transition of the disease-associated admixture component 'K6' from SE Asia reconfirmed these results. Moreover, we also observed that the mitochondrial mHG 'R' is significantly associated with the risk of TrOC (OR > 9.5) in NE India. Furthermore, the possible onset of the phenotypic expression of those traits was predicted at ∼4kya, thus, contributing to present-day's TrOC prevalence.

CONCLUSIONS

This study reflects its uniqueness by revealing an updated AMH dispersal route for the peopling in and out of NE India, which probably introduced the disease-causing traits in the ancestral NE Indian population. Those traits were then imprinted in their genome to get transferred through their respective generations, forming the present-day's TrOC-prevalent NE Indian population.

Integrative geochronology calibrates the Middle and Late Stone Ages of Ethiopia's Afar Rift

Understanding the evolution, dispersals, behaviors, and ecologies of early African Homo sapiens requires accurate geochronological placement of fossils and artifacts. We introduce open-air occurrences of such remains in sediments of the Middle Awash study area in Ethiopia. We describe the stratigraphic and depositional contexts of our discoveries and demonstrate the effectiveness of recently developed uranium-series dating of ostrich eggshell at validating and bridging across more traditional radioisotopic methods (¹⁴C and ⁴⁰Ar/³⁹Ar). Homo sapiens fossils and associated Middle Stone Age artifacts are placed at >158 and ∼96 ka. Later Stone Age occurrences are dated to ∼21 to 24 ka and ∼31 to 32 ka, firmly dating the upper portion of one of the longest records of human evolution.

The Halibee member of the Upper Dawaitoli Formation of Ethiopia’s Middle Awash study area features a wealth of Middle and Later Stone Age (MSA and LSA) paleoanthropological resources in a succession of Pleistocene sediments. We introduce these artifacts and fossils, and determine their chronostratigraphic placement via a combination of established radioisotopic methods and a recently developed dating method applied to ostrich eggshell (OES). We apply the recently developed ²³⁰Th/U burial dating of OES to bridge the temporal gap between radiocarbon (¹⁴C) and ⁴⁰Ar/³⁹Ar ages for the MSA and provide ¹⁴C ages to constrain the younger LSA archaeology and fauna to ∼24 to 21.4 ka. Paired ¹⁴C and ²³⁰Th/U burial ages of OES agree at ∼31 ka for an older LSA locality, validating the newer method, and in turn supporting its application to stratigraphically underlying MSA occurrences previously constrained only by a maximum ⁴⁰Ar/³⁹Ar age. Associated fauna, flora, and Homo sapiens fossils are thereby now fixed between 106 ± 20 ka and 96.4 ± 1.6 ka (all errors 2σ). Additional ⁴⁰Ar/³⁹ results on an underlying tuff refine its age to 158.1 ± 11.0 ka, providing a more precise minimum age for MSA lithic artifacts, fauna, and H. sapiens fossils recovered ∼9 m below it. These results demonstrate how chronological control can be obtained in tectonically active and stratigraphically complex settings to precisely calibrate crucial evidence of technological, environmental, and evolutionary changes during the African Middle and Late Pleistocene.

Collapse of the mammoth-steppe in central Yukon as revealed by ancient environmental DNA

The temporal and spatial coarseness of megafaunal fossil records complicates attempts to to disentangle the relative impacts of climate change, ecosystem restructuring, and human activities associated with the Late Quaternary extinctions. Advances in the extraction and identification of ancient DNA that was shed into the environment and preserved for millennia in sediment now provides a way to augment discontinuous palaeontological assemblages. Here, we present a 30,000-year sedimentary ancient DNA (sedaDNA) record derived from loessal permafrost silts in the Klondike region of Yukon, Canada. We observe a substantial turnover in ecosystem composition between 13,500 and 10,000 calendar years ago with the rise of woody shrubs and the disappearance of the mammoth-steppe (steppe-tundra) ecosystem. We also identify a lingering signal of Equus sp. (North American horse) and Mammuthus primigenius (woolly mammoth) at multiple sites persisting thousands of years after their supposed extinction from the fossil record.

Landscape and climatic variations shaped secondary contacts amid barn owls of the Western Palearctic

The combined actions of climatic variations and landscape barriers shape the history of natural populations. When organisms follow their shifting niches, obstacles in the landscape can lead to the splitting of populations, on which evolution will then act independently. When two such populations are reunited, secondary contact occurs in a broad range of admixture patterns, from narrow hybrid zones to the complete dissolution of lineages. A previous study suggested that barn owls colonized the Western Palearctic after the last glaciation in a ring-like fashion around the Mediterranean Sea, and conjectured an admixture zone in the Balkans. Here, we take advantage of whole-genome sequences of 94 individuals across the Western Palearctic to reveal the complex history of the species in the region using observational and modeling approaches. Even though our results confirm that two distinct lineages colonized the region, one in Europe and one in the Levant, they suggest that it predates the last glaciation and identify a secondary contact zone between the two in Anatolia. We also show that barn owls recolonized Europe after the glaciation from two distinct glacial refugia: a previously identified western one in Iberia and a new eastern one in Italy. Both glacial lineages now communicate via eastern Europe, in a wide and permeable contact zone. This complex history of populations enlightens the taxonomy of Tyto alba in the region, highlights the key role played by mountain ranges and large water bodies as barriers and illustrates the power of population genomics in uncovering intricate demographic patterns.

Phylogeography and Re-Evaluation of Evolutionary Rate of Powassan Virus Using Complete Genome Data

Simple Summary

The evolution of human pathogenic viruses is one of the pressing problems of modern biology and directly relevant to public health. Many important aspects of virus evolution (e.g., evolutionary rate, population size, and migration history) are ‘hidden’ from the naked eye of a researcher. Modern bioinformatics methods make it possible to evaluate and visualize such evolutionary particularities of viruses. In this paper, we reconstructed the migration history and estimated the evolutionary rate of one of the most dangerous neuroinvasive and neurotropic tick-borne flaviviruses—Powassan virus (POWV)—distributed in North America and the Far East of Russia. Using the dates obtained, we hypothesized that the divergence of the most recent common ancestor of POWV into two independent genetic lineages most likely occurred because of the melting of glaciers that began at 11.72 Kya in the Holocene due to the climate warming-caused flooding of the isthmus between Eurasia and North America.

Abstract

In this paper, we revealed the genetic structure and migration history of the Powassan virus (POWV) reconstructed based on 25 complete genomes available in NCBI and ViPR databases (accessed in June 2021). The usage of this data set allowed us to perform a more precise assessment of the evolutionary rate of this virus. In addition, we proposed a simple Bayesian technique for the evaluation and visualization of ‘temporal signal dynamics’ along the phylogenetic tree. We showed that the evolutionary rate value of POWV is 3.3 × 10⁻⁵ nucleotide substitution per site per year (95% HPD, 2.0 × 10⁻⁵–4.7 × 10⁻⁵), which is lower than values reported in the previous studies. Divergence of the most recent common ancestor (MRCA) of POWV into two independent genetic lineages most likely occurred in the period between 2600 and 6030 years ago. We assume that the divergence of the virus lineages happened due to the melting of glaciers about 12,000 years ago, which led to the disappearance of the Bering Land Bridge between Eurasia and North America (the modern Alaskan territory) and spatial division of the viral areal into two parts. Genomic data provide evidence of the virus migrations between two continents. The mean migration rate detected from the Far East of Russia to North America was one event per 1750 years. The migration to the opposite direction occurred approximately once per 475 years.

Late Quaternary dynamics of Arctic biota from ancient environmental genomics

During the last glacial-interglacial cycle, Arctic biotas experienced substantial climatic changes, yet the nature, extent and rate of their responses are not fully understood1-8. Here we report a large-scale environmental DNA metagenomic study of ancient plant and mammal communities, analysing 535 permafrost and lake sediment samples from across the Arctic spanning the past 50,000 years. Furthermore, we present 1,541 contemporary plant genome assemblies that were generated as reference sequences. Our study provides several insights into the long-term dynamics of the Arctic biota at the circumpolar and regional scales. Our key findings include: (1) a relatively homogeneous steppe-tundra flora dominated the Arctic during the Last Glacial Maximum, followed by regional divergence of vegetation during the Holocene epoch; (2) certain grazing animals consistently co-occurred in space and time; (3) humans appear to have been a minor factor in driving animal distributions; (4) higher effective precipitation, as well as an increase in the proportion of wetland plants, show negative effects on animal diversity; (5) the persistence of the steppe-tundra vegetation in northern Siberia enabled the late survival of several now-extinct megafauna species, including the woolly mammoth until 3.9 ± 0.2 thousand years ago (ka) and the woolly rhinoceros until 9.8 ± 0.2 ka; and (6) phylogenetic analysis of mammoth environmental DNA reveals a previously unsampled mitochondrial lineage. Our findings highlight the power of ancient environmental metagenomics analyses to advance understanding of population histories and long-term ecological dynamics.

The population genomic structure of green turtles (Chelonia mydas) suggests a warm-water corridor for tropical marine fauna between the Atlantic and Indian oceans during the last interglacial

The occasional westward transport of warm water of the Agulhas Current, "Agulhas leakage", around southern Africa has been suggested to facilitate tropical marine connectivity between the Atlantic and Indian oceans, but the "Agulhas leakage" hypothesis does not explain the signatures of eastward gene flow observed in many tropical marine fauna. We investigated an alternative hypothesis: the establishment of a warm-water corridor during comparatively warm interglacial periods. The "warm-water corridor" hypothesis was investigated by studying the population genomic structure of Atlantic and Southwest Indian Ocean green turtles (N = 27) using 12,035 genome-wide single nucleotide polymorphisms (SNPs) obtained via ddRAD sequencing. Model-based and multivariate clustering suggested a hierarchical population structure with two main Atlantic and Southwest Indian Ocean clusters, and a Caribbean and East Atlantic sub-cluster nested within the Atlantic cluster. Coalescent-based model selection supported a model where Southwest Indian Ocean and Caribbean populations diverged from the East Atlantic population during the transition from the last interglacial period (130-115 thousand years ago; kya) to the last glacial period (115-90 kya). The onset of the last glaciation appeared to isolate Atlantic and Southwest Indian Ocean green turtles into three refugia, which subsequently came into secondary contact in the Caribbean and Southwest Indian Ocean when global temperatures increased after the Last Glacial Maximum. Our findings support the establishment of a warm-water corridor facilitating tropical marine connectivity between the Atlantic and Southwest Indian Ocean during warm interglacials.

Pleistocene expansion, anthropogenic pressure and ocean currents: Disentangling the past and ongoing evolutionary history of Patella aspera Röding, 1798 in the archipelago of Madeira

AIMS

Rising sea-level following the Last Glacial Maximum lead to fragmentation of coastal limpet populations between islands of the Archipelago of Madeira. This fragmentation is reinforced by recent heavy exploitation reducing effective population size on Madeira Island. We use the limpet P. aspera to understand how the role of processes at different time scales (i.e. changes in the sea level and overexploitation) can influence the genetic composition of an extant species, relating these processes to reproductive phenology and seasonal shifts in ocean currents.

LOCATION

Madeira Island, Porto Santo and Desertas (Archipelago of Madeira, NE Atlantic Ocean).

TAXON

The limpet Patella aspera.

METHODS

Twelve microsatellite genetic markers were used. A power analysis was used to evaluate the power of the microsatellite markers to detect a signal of population differentiation. Long-term past migrations were assessed using a Bayesian Markov Montecarlo approach in the software MIGRATE-n to estimate mutation-scaled migration rates (M = m/μ; m, probability of a lineage immigrating per generation; μ, mutation rate). Two scenarios were evaluated using an Approximate Bayesian Computation (ABC) in the software DIYABC 2.1 (i) Scenario 1: considered a population scenario from a reduced Ne at time t₃ to a higher Ne at time t₂; and (ii) Scenario 2 considering a reduction of Ne from a time t₃ to a time t₂.

RESULTS

Colonization of the archipelago by Portuguese settlers six centuries ago probably led to an important decrease in the genetic diversity of the species (N_e). Contemporary gene flow strongly support a pattern of high asymmetric connectivity explained by the reproductive phenology of the species and spatio-temporal seasonal changes in the ocean currents. Spatio-temporal reconstructions using Bayesian methods, including coalescent and Approximate Bayesian Computation (ABC) approaches, suggest changes in the migration patterns from highly symmetric to highly asymmetric connectivity with subtle population differentiation as consequence of post-glacial maximum sea level rise during the Holocene.

MAIN CONCLUSIONS

Our results suggest that anthropogenic activity could have had serious effects on the genetic diversity of heavily exploited littoral species since the end of the Pleistocene, probably accelerating in recent years.

Decadal-scale onset and termination of Antarctic ice-mass loss during the last deglaciation

Emerging ice-sheet modeling suggests once initiated, retreat of the Antarctic Ice Sheet (AIS) can continue for centuries. Unfortunately, the short observational record cannot resolve the tipping points, rate of change, and timescale of responses. Iceberg-rafted debris data from Iceberg Alley identify eight retreat phases after the Last Glacial Maximum that each destabilized the AIS within a decade, contributing to global sea-level rise for centuries to a millennium, which subsequently re-stabilized equally rapidly. This dynamic response of the AIS is supported by (i) a West Antarctic blue ice record of ice-elevation drawdown >600 m during three such retreat events related to globally recognized deglacial meltwater pulses, (ii) step-wise retreat up to 400 km across the Ross Sea shelf, (iii) independent ice sheet modeling, and (iv) tipping point analysis. Our findings are consistent with a growing body of evidence suggesting the recent acceleration of AIS mass loss may mark the beginning of a prolonged period of ice sheet retreat and substantial global sea level rise.

Next-generation phylogeography resolves post-glacial colonization patterns in a widespread carnivore, the red fox (Vulpes vulpes), in Europe

Carnivores tend to exhibit a lack of (or less pronounced) genetic structure at continental scales in both a geographic and temporal sense and this can confound the identification of post-glacial colonization patterns in this group. In this study we used genome-wide data (using genotyping by sequencing [GBS]) to reconstruct the phylogeographic history of a widespread carnivore, the red fox (Vulpes vulpes), by investigating broad-scale patterns of genomic variation, differentiation and admixture amongst contemporary populations in Europe. Using 15,003 single nucleotide polymorphisms (SNPs) from 524 individuals allowed us to identify the importance of refugial regions for the red fox in terms of endemism (e.g., Iberia). In addition, we tested multiple post-glacial recolonization scenarios of previously glaciated regions during the Last Glacial Maximum using an Approximate Bayesian Computation (ABC) approach that were unresolved from previous studies. This allowed us to identify the role of admixture from multiple source population post-Younger Dryas in the case of Scandinavia and ancient land-bridges in the colonization of the British Isles. A natural colonization of Ireland was deemed more likely than an ancient human-mediated introduction as has previously been proposed and potentially points to a larger mammalian community on the island in the early post-glacial period. Using genome-wide data has allowed us to tease apart broad-scale patterns of structure and diversity in a widespread carnivore in Europe that was not evident from using more limited marker sets and provides a foundation for next-generation phylogeographic studies in other non-model species.

Major population splits coincide with episodes of rapid climate change in a forest-dependent bird

Climate change influences population demography by altering patterns of gene flow and reproductive isolation. Direct mutation rates offer the possibility for accurate dating on the within-species level but are currently only available for a handful of vertebrate species. Here, we use the first directly estimated mutation rate in birds to study the evolutionary history of pied flycatchers (Ficedula hypoleuca). Using a combination of demographic inference and species distribution modelling, we show that all major population splits in this forest-dependent system occurred during periods of increased climate instability and rapid global temperature change. We show that the divergent Spanish subspecies originated during the Eemian-Weichselian transition 115-104 thousand years ago (kya), and not during the last glacial maximum (26.5-19 kya), as previously suggested. The magnitude and rates of climate change during the glacial-interglacial transitions that preceded population splits in pied flycatchers were similar to, or exceeded, those predicted to occur in the course of the current, human-induced climate crisis. As such, our results provide a timely reminder of the strong impact that episodes of climate instability and rapid temperature changes can have on species' evolutionary trajectories, with important implications for the natural world in the Anthropocene.

Evolutionary history of two rare endemic conifer species from the eastern Qinghai-Tibet Plateau

BACKGROUND AND AIMS

Understanding the population genetics and evolutionary history of endangered species is urgently needed in an era of accelerated biodiversity loss. This knowledge is most important for regions with high endemism that are ecologically vulnerable, such as the Qinghai-Tibet Plateau (QTP).

METHODS

The genetic variation of 84 juniper trees from six populations of Juniperus microsperma and one population of Juniperus erectopatens, two narrow-endemic junipers from the QTP that are sister to each other, was surveyed using RNA-sequencing data. Coalescent-based analyses were used to test speciation, migration and demographic scenarios. Furthermore, positively selected and climate-associated genes were identified, and the genetic load was assessed for both species.

KEY RESULTS

Analyses of 149 052 single nucleotide polymorphisms showed that the two species are well differentiated and monophyletic. They diverged around the late Pliocene, but interspecific gene flow continued until the Last Glacial Maximum. Demographic reconstruction by Stairway Plot detected two severe bottlenecks for J. microsperma but only one for J. erectopatens. The identified positively selected genes and climate-associated genes revealed habitat adaptation of the two species. Furthermore, although J. microsperma had a much wider geographical distribution than J. erectopatens, the former possesses lower genetic diversity and a higher genetic load than the latter.

CONCLUSIONS

This study sheds light on the evolution of two endemic juniper species from the QTP and their responses to Quaternary climate fluctuations. Our findings emphasize the importance of speciation and demographic history reconstructions in understanding the current distribution pattern and genetic diversity of threatened species in mountainous regions.

Last glacial temperature reconstructions using coupled isotopic analyses of fossil snails and stalagmites from archaeological caves in Okinawa, Japan

We applied a new geoarchaeological method with two carbonate archives, which are fossil snails from Sakitari Cave and stalagmites from Gyokusen Cave, on Okinawa Island, Japan, to reconstruct surface air temperature changes over the northwestern Pacific since the last glacial period. Oxygen isotope ratios (δ¹⁸O) of modern and fossil freshwater snail shells were determined to infer seasonal temperature variations. The observational and analytical data confirm that δ¹⁸O values of fluid inclusion waters in the stalagmite can be regarded as those of spring waters at the sites where snails lived. Our results indicate that the annual mean, summer, and winter air temperatures were lower by 6–7 °C at ca. 23 thousand years ago (ka) and 4–5 °C at ca. 16–13 ka than those of the present day. Our reconstruction implies that surface air cooling was possibly two times greater than that of seawater around the Ryukyu Islands during the Last Glacial Maximum, which potentially enhanced the development of the East Asian summer monsoon during the last deglaciation. Considering the potential uncertainties in the temperature estimations, the climatic interpretations of this study are not necessarily definitive due to the limited number of samples. Nevertheless, our new geoarchaeological approach using coupled δ¹⁸O determinations of fossil snails and stalagmite fluid inclusion waters will be useful for reconstructing snapshots of seasonally resolved time series of air temperatures during the Quaternary.

Wolbachia-driven selective sweep in a range expanding insect species

Background

Evolutionary processes can cause strong spatial genetic signatures, such as local loss of genetic diversity, or conflicting histories from mitochondrial versus nuclear markers. Investigating these genetic patterns is important, as they may reveal obscured processes and players. The maternally inherited bacterium Wolbachia is among the most widespread symbionts in insects. Wolbachia typically spreads within host species by conferring direct fitness benefits, and/or by manipulating its host reproduction to favour infected over uninfected females. Under sufficient selective advantage, the mitochondrial haplotype associated with the favoured maternally-inherited symbiotic strains will spread (i.e. hitchhike), resulting in low mitochondrial genetic variation across the host species range.

Method

The common bluetail damselfly (Ischnura elegans: van der Linden, 1820) has recently emerged as a model organism for genetics and genomic signatures of range expansion during climate change. Although there is accumulating data on the consequences of such expansion on the genetics of I. elegans, no study has screened for Wolbachia in the damselfly genus Ischnura. Here, we present the biogeographic variation in Wolbachia prevalence and penetrance across Europe and Japan (including samples from 17 populations), and from close relatives in the Mediterranean area (i.e. I. genei: Rambur, 1842; and I. saharensis: Aguesse, 1958).

Results

Our data reveal (a) multiple Wolbachia-strains, (b) potential transfer of the symbiont through hybridization, (c) higher infection rates at higher latitudes, and (d) reduced mitochondrial diversity in the north-west populations, indicative of hitchhiking associated with the selective sweep of the most common strain. We found low mitochondrial haplotype diversity in the Wolbachia-infected north-western European populations (Sweden, Scotland, the Netherlands, Belgium, France and Italy) of I. elegans, and, conversely, higher mitochondrial diversity in populations with low penetrance of Wolbachia (Ukraine, Greece, Montenegro and Cyprus). The timing of the selective sweep associated with infected lineages was estimated between 20,000 and 44,000 years before present, which is consistent with the end of the last glacial period about 20,000 years.

Conclusions

Our findings provide an example of how endosymbiont infections can shape spatial variation in their host evolutionary genetics during postglacial expansion. These results also challenge population genetic studies that do not consider the prevalence of symbionts in many insects, which we show can impact geographic patterns of mitochondrial genetic diversity.

Sex-specific phenotypic effects and evolutionary history of an ancient polymorphic deletion of the human growth hormone receptor

The common deletion of the third exon of the growth hormone receptor gene (GHRd3) in humans is associated with birth weight, growth after birth, and time of puberty. However, its evolutionary history and the molecular mechanisms through which it affects phenotypes remain unresolved. We present evidence that this deletion was nearly fixed in the ancestral population of anatomically modern humans and Neanderthals but underwent a recent adaptive reduction in frequency in East Asia. We documented that GHRd3 is associated with protection from severe malnutrition. Using a novel mouse model, we found that, under calorie restriction, Ghrd3 leads to the female-like gene expression in male livers and the disappearance of sexual dimorphism in weight. The sex- and diet-dependent effects of GHRd3 in our mouse model are consistent with a model in which the allele frequency of GHRd3 varies throughout human evolution as a response to fluctuations in resource availability.

Evidence of humans in North America during the Last Glacial Maximum

[Figure: see text].