The Last Glacial Maximum

Pleistocene Glaciation Drove Shared Population Coexpansion in Eastern North American Snakes

Glacial cycles during the Pleistocene had profound impacts on local environments and climatic conditions. In North America, some regions that currently support diverse biomes were entirely covered by ice sheets, while other regions were environmentally unsuitable for the organisms that live there now. Organisms that occupy these regions in the present day must have expanded or dispersed into these regions since the last glacial maximum, leading to the possibility that species with similar geographic distributions may show temporally concordant population size changes associated with these warming trends. We examined 17 lineages from 9 eastern North American snake species and species complexes to test for a signal of temporally concordant coexpansion using a machine learning approach. We found that the majority of lineages show population size increases towards the present, with evidence for coexpansion in five out of fourteen lineages, while expansion in others was idiosyncratic. We also examined relationships between genetic distance and current environmental predictors and showed that genomic responses to environmental predictors are not consistent among species. We, therefore, conclude that Pleistocene warming resulted in population size increases in most eastern North American snake species, but variation in environmental preferences and other species-specific traits results in variance in the exact timing of expansion.

Population Genomics and Morphology Provide Insights into the Conservation and Diversity of Apis laboriosa

In recent decades, honeybee populations have declined, dramatically owing to destructive honey harvesting practices and the loss of foraging grounds and nesting sites. Among them, Apis laboriosa Smith, 1871 (Hymenoptera, Apidae), an important pollinator species found in the Himalayan region, holds significant economic and ecological value. However, conservation efforts and intraspecific taxonomic studies regarding it have been rather limited, and thus its full geographic range remains elusive. This study is the first to research A. laboriosa in Sichuan. Through a systematic study integrating morphological feature analysis and genomic data, the following conclusions are drawn. Whole-genome resequencing data analysis reveals that the Sichuan population forms a new monophyletic group (Bootstraps = 100). In the past ten thousand years, the population sizes of A. laboriosa in four different regions of China have been decreasing rapidly. Measures should be taken to protect them across the entire distribution range, especially the populations in Tibet and Sichuan, due to their relatively large genetic differences and low intra-population genetic diversity. Based on the significant difference analysis, the following four wing vein morphological features with extremely significant differences were identified: the width of the right forewing (FB), the cubital index a/b (Ci), the forewing vein angle (E9), and the forewing vein angle (K19). These findings are expected to offer a valuable reference for future A. laboriosa conservation endeavors, particularly in protecting populations with a high level of genetic differentiation.

Submerged Corridors of Ancient Gene Flow in an Island Amphibian

Many island archipelagos sit on shallow continental shelves, and during the Pleistocene, these islands were often connected as global sea levels dropped following glaciation. Given a continental shelf only 30-60 m below sea level, the terrestrial biota of the Seychelles Archipelago likely dispersed amongst now isolated islands during the Pleistocene. Hypogeophis rostratus is an egg-laying, direct-developing caecilian amphibian found on 10 islands in the granitic Seychelles. Despite the seemingly limited dispersal abilities of this salt-intolerant amphibian, its distribution on multiple islands suggests likely historic dispersal across now submerged continental shelf corridors. We tested for the genetic signature of these historic corridors using fine-scale genomic data (ddRADseq). We found that genomic clusters often did not correspond to islands in the archipelago and that isolation-by-distance patterns were more consistent with gene flow across a continuous landscape than with isolated island populations. Using effective migration surfaces and ancestral range expansion prediction, we found support for contemporary populations originating near the large southern island of Mahé and dispersing to northern islands via the isolated Frégate island, with additional historic migration across the flat expanse of the Seychelles bank. Collectively, our results suggest that biogeographic patterns can retain signals from Pleistocene 'palaeo-islands' and that present-day islands can be thought of as hosting bottlenecks or transient refugia rather than discrete genetic units. Thus, the signatures of gene flow associated with palaeo-islands may be stronger than the isolating effects of contemporary islands in terrestrial species distributed on continental shelf islands.

An update on Aenocyon dirus in the interior of North America: new records, radiocarbon dates, ZooMS spectra, and isotopic data for an iconic late Pleistocene carnivore

Aenocyon dirus played a crucial role as a predator in late Quaternary megafaunal communities throughout southern North America. This article presents two new occurrences of the species from southwest Iowa on the eastern Great Plains, updates the Peccary Cave record in the southern Ozark Highlands, and amends the fossil record of the species. In southern North America, there are 166 occurrences of A. dirus, spanning Marine Isotope Stage (MIS) 2-19, with at least two-thirds (n = 112) of the occurrences dating to MIS 2-3 (11,600-57,000 cal B.P.). A. dirus fossils are found across this region, with notable concentrations in California, Florida, the Ozark Highlands, and broadly across the southern Great Plains. Consideration of Canis specimens from the lead region (covering contiguous parts of Illinois, Wisconsin, and Iowa) previously identified as Canis mississippiensis (and sometimes synonymized with A. dirus or C. lupus) reveals they are actually C. lupus. The terminal extinction of A. dirus occurred sometime after 12,800 cal B.P. The Iowa finds, consisting of a radius and a partial cranium, are the first records for the state. Zooarchaeology by mass spectrometry confirms these records, as well as the Peccary Cave record, are A. dirus, as opposed to C. lupus. The Iowa specimens are directly dated to 29,040-28,410 cal B.P. and 14,325-14,075 cal B.P., while Peccary Cave is dated to 25,350-21,405 cal B.P. These results place A. dirus in the interior of southern North America before, during, and after the Last Glacial Maximum (26,500-19,000 cal B.P.). Stable nitrogen isotope (δ15N) values of bone collagen from the younger of the two Iowa records suggest this individual did not regularly compete for prey with Smilodon fatalis during the Bølling-Allerød Chronozone (14,640-12,850 cal B.P.). To the south, at Peccary Cave, considerations of prey size, prey abundance, and isotopic data strongly suggest Platygonus compressus was the focal prey species.

Phenotypic and genomic signatures across wild Rosa species open new horizons for modern rose breeding

The cultivation and domestication of roses reflects cultural exchanges and shifts in aesthetics that have resulted in today's most popular ornamental plant group. However, the narrow genetic foundation of cultivated roses limits their further improvement. Wild Rosa species harbour vast genetic diversity, yet their utilization is impeded by taxonomic confusion. Here we generated a phased and gap-free reference genome of Rosa persica for phylogenetic and population genomic analyses of a large collection of Rosa samples. The robust nuclear and plastid phylogenies support most of the morphology-based traditional taxonomy of Rosa. Population genomic analyses disclosed potential genetic exchanges among sections, indicating the northwest and southwest of China as two independent centres of diversity for Rosa. Analyses of domestication traits provide insights into selection processes related to flower colour, fragrance, double flower and resistance. This study provides a comprehensive understanding of rose domestication and lays a solid foundation for future re-domestication and innovative breeding efforts using wild resources.

Distribution Patterns of Platycodon grandiflorus From the Last Interglacial Period to the Future by Ecological Niche Modeling

Global climate change may represent a significant threat to the distribution and quality of medicinal plants, altering cultivation areas and compromising the quality of medical materials. Platycodon grandiflorus, a traditional Chinese medicinal herb, has a millennia-long medicinal and culinary use history in East Asia. Given its escalating demand, accurately evaluating the changes under different climate scenarios and predicting its potential distribution are imperative for ensuring its conservation and sustainable utilization. By integrating MaxEnt with ArcGIS, this study advances previous approaches by incorporating historical, present, and future climate data to model the distribution dynamics of P. grandiflorus across China. The results indicated: (1) The species' distribution strongly correlates with environmental variables, particularly bio13, prec07, prec09, and tmin07, whose cumulative value of percent contribution was 78.5%; (2) The centroids of potential geographic distribution during the LIG, LGM, and MH periods were situated further westward compared to the present distribution, with substantial contraction observed in highly suitable habitats throughout these historical periods; (3) Under present climatic conditions, the overall suitable habitat encompasses 4,185,964 km2, with highly suitable habitats constituting one-third of this expanse, predominantly concentrated in central, southern, and northeastern China; (4) Future climate change scenarios predict that the total suitable habitat will expand to varying degrees (7% increase on average), albeit with potential reductions in highly suitable areas (3% decrease on average); and (5) The distribution of P. grandiflorus is likely to move toward higher latitudes in the future due to climate changes. Our findings fill a critical knowledge gap by quantifying the impact of climate change on the distribution of P. grandiflorus. These results offer crucial insights for developing effective conservation strategies, promoting sustainable utilization, and establishing standardized cultivation protocols for P. grandiflorus resources.

Natural selection shaped the protective effect of the mtDNA lineage against obesity in Han Chinese populations

Mitochondria play a key role in lipid metabolism, and mitochondrial DNA (mtDNA) mutations are thus considered to affect obesity susceptibility by altering oxidative phosphorylation and mitochondrial function. In this study, we investigate mtDNA variants that may affect obesity risk in 2877 Han Chinese individuals from 3 independent populations. The association analysis of 16 basal mtDNA haplogroups with body mass index, waist circumference, and waist-to-hip ratio reveals that only haplogroup M7 is significantly negatively correlated with all three adiposity-related anthropometric traits in the overall cohort, verified by the analysis of a single population, i.e., the Zhengzhou population. Furthermore, subhaplogroup analysis suggests that M7b1a1 is the most likely haplogroup associated with a decreased obesity risk, and the variation T12811C (causing Y159H in ND5) harbored in M7b1a1 may be the most likely candidate for altering the mitochondrial function. Specifically, we find that proportionally more nonsynonymous mutations accumulate in M7b1a1 carriers, indicating that M7b1a1 is either under positive selection or subject to a relaxation of selective constraints. We also find that nuclear variants, especially in DACT2 and PIEZO1, may functionally interact with M7b1a1.

Chromosomal-Level Genome Suggests Adaptive Constraints Leading to the Historical Population Decline in an Extremely Endangered Plant

Increased human activity and climate change have significantly impacted wild habitats and increased the number of endangered species. Exploring evolutionary history and predicting adaptive potential using genomic data will facilitate species conservation and biodiversity recovery. Here, we examined the genome evolution of a critically endangered tree Pellacalyx yunnanensis, a plant species with extremely small populations (PSESP) that is narrowly distributed in Xishuangbanna, China. The species has neared extinction due to economic exploitation in recent decades. We assembled a chromosome-level genome of 334 Mb, with the N50 length of 20.5 Mb. Using the genome, we discovered that P. yunnanensis has undergone several population size reductions, leading to excess deleterious mutations. The species may possess low adaptive potential due to reduced genetic diversity and the loss of stress-responsive genes. We estimate that P. yunnanensis is the basal species of its genus and diverged from its relatives during global cooling, suggesting it was stranded in unsuitable environments during periods of dramatic climate change. In particular, the loss of seed dormancy leads to germination under unfavourable conditions and reproduction challenges. This dormancy loss may have occurred through genetic changes that suppress ABA signalling and the loss of genes involved in seed maturation. The high-quality genome has also enabled us to reveal phenotypic trait evolution in Rhizophoraceae and identify divergent adaptation to intertidal and inland habitats. In summary, our study elucidates mechanisms underlying the decline and evaluates the adaptive potential of P. yunnanensis to future climate change, informing future conservation efforts.

Evaluating Past Range Shifts and Niche Dynamics of Giant Pandas Since the Last Interglacial

Understanding the response of species to past climate change provides great opportunities to know their adaptive capacity for resilience under future climate change. Since the Late Pleistocene, dramatic climate fluctuations have significantly impacted the distribution of giant pandas (Ailuropoda melanoleuca). However, how the spatial distribution and climatic niche of giant pandas shifted in response to past climate change remain poorly understood. Based on the known distribution records (fossil and present day) and the most updated climate projections for the Last Interglacial (LIG; ~120 ka), Last Glacial Maximum (LGM; ~22 ka), Mid-Holocene (MH; ~6 ka), and the present day, we predicted and compared the distribution and climatic niche of giant pandas. The results show that giant pandas have undergone a considerable range contraction (a 28.27% reduction) followed by a marked range expansion (a 75.8% increase) during the LIG-LGM-MH period, while its climatic niche remained relatively stable. However, from the MH to the current, both the distribution area and climatic niche of giant pandas have undergone significant changes. Our findings suggest that the giant panda may adjust its distribution to track stable climatic niches in response to future climate change. Future conservation planning should designate accessible areas for giant pandas and adjust priority conservation areas as needed.

Green revolution gene drives adaptation of Arabidopsis to the extremely high altitude

To elucidate the process of adaptation, particularly the traits subject to natural selection and the molecular mechanisms underlying their natural variation, is one of the primary objectives of evolutionary biology. The uplifted landscape offers an excellent framework for understanding how organisms adapt to dramatic climatic gradients. To investigate the genetic basis of plant adaptation to the extremely high altitude, we first compared the genomic and phenotypic variations of two closely related Arabidopsis thaliana accessions from high altitude (Xizang, also known as "Tibet") and low altitude (Yunnan), respectively. The Xizang population represents a relict group characterized by a small effective population size. Notably, the Xizang genome has more transposable elements (TEs) and more gene loss-of-function (LoF) mutations. Differentially expressed genes were enriched in biological processes of cellular response to oxygen-containing compound, regulation of defense response, and response to light intensity. Intriguingly, the phenotypic selection analysis revealed that silique density was under natural selection. Furthermore, we genetically mapped and validated that the LoF mutation of GA20ox1, the homologous gene of green revolution in rice, resulted in a higher silique density in Xizang Arabidopsis. Given that GA20ox1 is linked to Arabidopsis adaptation to the Alps Mountains, its parallel evolution plays an important role in the adaptation to Alpine habitats. Overall, our results highlight that identifying adaptive traits and elucidating the molecular mechanisms underlying natural variation of these traits is crucial for unraveling the mystery of adaptive evolution and has significant implications for crop breeding.

Upward and Northwest Range Shifts for Four Endemic Lamiaceae Medicinal Herbs in the Third Pole

In response to climate warming, alpine plants are migrating to higher elevations and latitudes to track suitable habitats. In mountainous systems, the contraction of land area toward mountaintops is causing plant habitats to shrink as plants migrate upwards. The Tibetan Plateau (TP) and its adjacent Himalaya-Hengduan Mountains (HHMs) constitute the world's highest flora, known as the "Third Pole" To predict the responses to climate change of alpine plants in the Third Pole, we utilized four endemic Lamiaceae alpine herbs as an Ecological Niche Modeling (ENM) based on comprehensive data comprising 740 occurrence records and 26 environmental variables using Biomod2. The primary results revealed that climate-related factors, particularly temperature variability, shape the distribution patterns of the study species and drive them to migrate upward and northward in the future. The heterogeneous topography of the HHM and the TP leads to distinct distribution dynamics. The TP can provide substantial new potential distribution areas to mitigate habitat loss in the adjacent HHM under climate warming. Meanwhile, stable areas in the high-elevation regions within HHM can serve as refugia to ensure species survival under climate change.

Deep-water corals indicate the Red Sea survived the last glacial lowstand

The Red Sea, a nascent ocean basin connected to the Indian Ocean via a shallow strait, is assumed to have experienced significant environmental changes during the last glacial period due to a sea-level drop likely exceeding 110 m. This study investigates the hypothesis that hydrodynamic restriction led to severe ecological impacts, including basin-wide extinction due to elevated salinity followed by a short time of oxygen depletion. Uranium-Thorium dating of deep-water corals (DWCs) from 26 northern Red Sea sites reveals coral growth during and after the Last Glacial sea-level lowstand, indicating tolerable seawater chemistry. Additional geochemical data show no significant difference in Red Sea chemistry or temperature between the Latest Pleistocene and Holocene. A meta-analysis of 27 deep-sea cores reveals that while planktonic foraminifera experienced local extinction, other microfossil groups seemingly persisted. These findings suggest that the Red Sea survived the last sea-level lowstand, challenging the paradigm of a complete ecological collapse and providing insights into the resilience of marine ecosystems.

Polar bears and expanding sea ice in the Mid Holocene Aleutian Islands, Alaska

The archaeological record offers the opportunity to infer the effects of regional climatic shifts on species distributions and human-animal interactions. In Alaska's temperate Aleutian Islands, the archaeological record suggests that the Neoglacial climate phase (ca. 4700 - 2500 rcyr BP) was significantly colder and the region likely supported sea ice and ice-dependent animals. Previous analyses have identified polar bear (Ursus maritimus) remains in archaeological sites in Unalaska Bay, which have been used to infer bear range expansion and significant climate changes during this period. However, morphological similarities between polar and brown (Ursus arctos) bears make it difficult to distinguish between the two species, and the presence of bear material in Unalaska Bay could be the result of long-distance travel or trade rather than local harvest. Here, we applied zooarchaeological methods to address potential morphological and size differences, to age the bears, and to interpret human use of the bears. Our results suggest that the small assemblage is likely composed of both brown and polar bear remains, but that morphological analyses alone are insufficient to definitively reconstruct bear distributions in this context. Bear age profiles and butchery patterns suggest that the animals were harvested locally and the extension of sea ice in the Neoglacial phase likely facilitated their presence around Unalaska Island. Future analyses that use ancient DNA, collagen fingerprinting, and stable isotopes to determine the species, sex, number of individuals, and relationships to modern populations will be necessary to illuminate regional bear population dynamics in the Neoglacial.

Sea level since the Last Glacial Maximum from the Atlantic coast of Africa

Constraining sea level at the Last Glacial Maximum (LGM) is spatially restricted to a few locations. Here, we reconstruct relative sea-level (RSL) changes along the Atlantic coast of Africa for the last ~30 ka BP using 347 quality-controlled sea-level datapoints. Data from the continental shelves of Guinea Conakry and Cameroon indicate a progressive lowering of RSL during the LGM from -99.4 ± 5.2 m to -104.0 ± 3.2 m between ~26.7 ka and ~19.1 ka BP. From ~15 ka to ~7.5 ka BP, RSL shows phases of major accelerations up to ~25 mm a-1 and a significant RSL deceleration by ~8 ka BP. In the mid to late Holocene, data indicate the emergence of a sea-level highstand, which varied in magnitude (0.8 ± 0.8 m to 4.0 ± 2.4 m above present mean sea level) and timing (5.0 ± 1.0 to 1.7 ± 1.0 ka BP). We further identified misfits between glacial isostatic adjustment models and the highstand, suggesting the interplay of different ice-sheet meltwater contributions and hydro-isostatic processes along the wide region of Atlantic Africa are not fully resolved.

Footprints of Human Migration in the Population Structure of Wild Baker's Yeast

Humans have a long history of fermenting food and beverages that led to domestication of the baker's yeast, Saccharomyces cerevisiae. Despite their tight companionship with humans, yeast species that are domesticated or pathogenic can also live on trees. Here we used over 300 genomes of S. cerevisiae from oaks and other trees to determine whether tree-associated populations are genetically distinct from domesticated lineages and estimate the timing of forest lineage divergence. We found populations on trees are highly structured within Europe, Japan, and North America. Approximate estimates of when forest lineages diverged out of Asia and into North America and Europe coincide with the end of the last ice age, the spread of agriculture, and the onset of fermentation by humans. It appears that migration from human-associated environments to trees is ongoing. Indeed, patterns of ancestry in the genomes of three recent migrants from the trees of North America to Europe could be explained by the human response to the Great French Wine Blight. Our results suggest that human-assisted migration affects forest populations, albeit rarely. Such migration events may even have shaped the global distribution of S. cerevisiae. Given the potential for lasting impacts due to yeast migration between human and natural environments, it seems important to understand the evolution of human commensals and pathogens in wild niches.

Genomic insights into demographic history, structural variation landscape, and complex traits from 514 Hu sheep genomes

Hu sheep is an indigenous breed from the Taihu Lake Plain in China, known for its high fertility. Although Hu sheep belong to the Mongolian group, their demographic history and genetic architecture remain inconclusive. Here, we analyze 697 sheep genomes from representatives of Mongolian sheep breeds. Our study suggests that the ancestral Hu sheep first separated from the Mongolian group approximately 3000 years ago. As Hu sheep migrated from the north and flourished in the Taihu Lake Plain around 1000 years ago, they developed a unique genetic foundation and phenotypic characteristics, which are evident in the genomic footprints of selective sweeps and structural variation landscape. Genes associated with reproductive traits (BMPR1B and TDRD10) and horn phenotype (RXFP2) exhibit notable selective sweeps in the genome of Hu sheep. A genome-wide association analysis reveals that structural variations at LOC101110773, MAST2, and ZNF385B may significantly impact polledness, teat number, and early growth in Hu sheep, respectively. Our study offers insights into the evolutionary history of Hu sheep and may serve as a valuable genetic resource to enhance the understanding of complex traits in Hu sheep.

Paleorecords Reveal Biological Mechanisms Crucial for Reliable Species Range Shift Projections Amid Rapid Climate Change

The recent acceleration of global climate warming has created an urgent need for reliable projections of species distributions, widely used by natural resource managers. Such projections have been mainly produced by species distribution models with little information on their performances in novel climates. Here, we hindcast the range shifts of forest tree species across Europe over the last 12,000 years to compare the reliability of three different types of models. We show that in the most climatically dissimilar conditions, process-explicit models (PEMs) tend to outperform correlative species distribution models (CSDMs), and that PEM projections are likely to be more reliable than those made with CSDMs by the end of the 21st century. These results demonstrate for the first time the often promoted albeit so far untested idea that explicit description of mechanisms confers model robustness, and highlight a new avenue to increase model projection reliability in the future.

Late Holocene "Turn-Off" of Coral Reef Growth in the Northern Red Sea and Implications for a Sea-Level Fall

Coral reefs, known for their remarkable diversity, serve a pivotal function in modulating the global oceanic carbon cycle and act as natural barriers that protect coastlines from erosion and storm surges by dissipating wave energy. Despite their importance, their sensitivity to temperature fluctuations, sea-level shifts and anthropogenic changes in the future is highly unknown. In this study, we create a comprehensive documentation of coral growth, sedimentology and ecology spanning the middle to late Holocene in the Gulf of Eilat/Aqaba, northern Red Sea. We then integrate these findings with a reconstruction of the area's environmental conditions over time. The findings reveal a noticeable hiatus of reef growth between 4400 and 1000 years BP (Before Present; "present" being defined as 1950), aligning well with comparable observations made across various locations in the Southern Hemisphere. The coral diversity and abundance along the cores display surprisingly similar patterns before and after the hiatus. This implies that the distinctive coral community thriving during the initial growth phase reappeared nearly 4000 years later, presumably sourced from the deeper reefs. The results are evaluated in the context of a potential sea-level drop and the resilience of coral communities to perturbations of this magnitude. We conclude that the hiatus at this site is due to a combination of factors, including tectonic activity and glacio-eustatic sea-level changes. Our research highlights the critical importance of understanding and managing coral reef ecosystems' responses to sea-level fluctuations to mitigate future impacts on these vulnerable environments.

Spatiotemporal glacier retreat on the Tibetan Plateau since the LGMG to early holocene based on compilation of moraine boulder ages

Tibetan Plateau and its surrounding mountains (TPSM) have experienced prominent glacier retreat since the Global Last Glacial Maximum, while the detailed deglaciation process remains unclear. To investigate the spatiotemporal pattern of the glacier retreat history, we compiled 196 moraines dating from 26.5 to 10 ka based on 994 boulder 10Be exposure age from seven regions on the TPSM and calculated the separated component Gaussians of moraine ages. The result shows that synchronous glacier retreat across the entire TPSM began around 22 ka in response to onset of rising local summer insolation. Moraine abandonment centered at five stages, i.e., 22-20, 19-18 ka, 17-16, 14.5-12.9, and 11.6-10 ka. Synchronous retreat occurred at 22-20 ka and 14.5-12.9 ka in all seven regions, while at 19-18 ka, it occurred in all regions except Tianshan. Pamir and NE Tibet showed no retreat at 17-16 ka, likely due to the sustained influence of the Westerlies. The stage at 11.6-10 ka was absent in Central Tibet due to lack of chronology from the perched moraines therein. This work offers new insights into the evolution of the cryosphere and adjustments in atmospheric circulation on the TPSM.

Potential plant extinctions with the loss of the Pleistocene mammoth steppe

During the Pleistocene-Holocene transition, the dominant mammoth steppe ecosystem across northern Eurasia vanished, in parallel with megafauna extinctions. However, plant extinction patterns are rarely detected due to lack of identifiable fossil records. Here, we introduce a method for detection of plant taxa loss at regional (extirpation) to potentially global scale (extinction) and their causes, as determined from ancient plant DNA metabarcoding in sediment cores (sedaDNA) from lakes in Siberia and Alaska over the past 28,000 years. Overall, potential plant extinctions track changes in temperature, in vegetation, and in megafauna extinctions at the Pleistocene-Holocene transition. Estimated potential plant extinction rates were 1.7-5.9 extinctions per million species years (E/MSY), above background extinction rates but below modern estimates. Major potential plant extinction events were detected around 17,000 and 9000 years ago which lag maximum vegetation turnover. Our results indicate that herbaceous taxa and taxa contributing less to beta diversity are more vulnerable to extinction. While the robustness of the estimates will increase as DNA reference libraries and ancient sedaDNA data expand, the available data support that plants are more resilient to environmental changes than mammals.

Impact of global environmental changes on the range contraction of Eurasian moose since the Late Pleistocene

Climatic oscillations are considered primary factors influencing the distribution of various life forms on Earth. Large species adapted to cold climates are particularly vulnerable to extinction due to climate changes. In our study, we investigated whether temperature increase since the Late Pleistocene and the contraction of environmental niche during the Holocene were the main factors contributing to the decreasing range of moose (Alces alces) in Europe. We also examined whether there were significant differences in environmental conditions between areas inhabited by moose in Europe and Asia, that could support the division of moose into western and eastern forms, as suggested by genetic and morphological data. We analysed environmental conditions in the locations of 655 subfossil and modern moose occurrences over the past 50,000 years in Eurasia. We found that the most limiting climatic factor for the moose distribution since the Late Pleistocene was July temperature. More than 90 % of moose records were found in areas where mean summer temperature was below 19 °C, with July temperatures showing over 3 times narrower interquartile range compared to January temperatures. We identified significant differences in environmental conditions between areas inhabited by the European and Asiatic moose. In Europe, the species occurred in regions with milder climates, higher primary productivity, and more frequently within forest biomes compared to Asiatic individuals. The moose range shifted more in the west-east than in the south-north direction during the Holocene climate warming in Europe. We conclude that although the area of suitable moose habitat has increased since 12-8 ka years BP, as demonstrated by environmental niche modeling, the retreat of A. alces in large areas of Europe was likely caused by anthropogenic landscape change (e.g., deforestation) and overhunting by humans during the late Holocene rather than by climate warming during the Pleistocene to Holocene transition.

How does communication evolve? Insights from geographic variation in facial signaling in Polistes paper wasps

Communication systems require coordination between senders and receivers; therefore, understanding how novel signals arise is challenging. Intraspecific geographic variation in signaling provides an opportunity to investigate the factors that shape signal evolution. Facial signals in Polistes paper wasps provide an interesting case study for the causes and consequences of geographic variation in signaling systems. Two species of paper wasps, Polistes dominula and Polistes fuscatus, have been well studied for their facial patterns that signal quality and individual identity, respectively. Remarkably, whether or not facial patterns are used as signals at all appears to vary geographically in both species. The relative evidence for the roles of phenotypic plasticity versus genetic differentiation is discussed. Future research directions that leverage geographic variation in Polistes hold promise to substantially contribute to understanding the links between signals and behavior, as well as the evolution of cognition.

The 1000 Chinese Indigenous Pig Genomes Project provides insights into the genomic architecture of pigs

Pigs play a central role in human livelihoods in China, but a lack of systematic large-scale whole-genome sequencing of Chinese domestic pigs has hindered genetic studies. Here, we present the 1000 Chinese Indigenous Pig Genomes Project sequencing dataset, comprising 1011 indigenous individuals from 50 pig populations covering approximately two-thirds of China's administrative divisions. Based on the deep sequencing (~25.95×) of these pigs, we identify 63.62 million genomic variants, and provide a population-specific reference panel to improve the imputation performance of Chinese domestic pig populations. Using a combination of methods, we detect an ancient admixture event related to a human immigration climax in the 13th century, which may have contributed to the formation of southeast-central Chinese pig populations. Analyzing the haplotypes of the Y chromosome shows that the indigenous populations residing around the Taihu Lake Basin exhibit a unique haplotype. Furthermore, we find a 13 kb region in the THSD7A gene that may relate to high-altitude adaptation, and a 0.47 Mb region on chromosome 7 that is significantly associated with body size traits. These results highlight the value of our genomic resource in facilitating genomic architecture and complex traits studies in pigs.

Evolution and legacy of East Asian aurochs

Aurochs (Bos primigenius), once widely distributed in Afro-Eurasia, became extinct in the early 1600 s. However, their phylogeography and relative contributions to domestic cattle remain unknown. In this study, we analyzed 16 genomes of ancient aurochs and three mitogenomes of ancient bison (Bison priscus) excavated in East Asia, dating from 43,000 to 3,590 years ago. These newly generated data with previously published genomic information on aurochs as well as ancient/extant domestic cattle worldwide through genome analysis. Our findings revealed significant genetic divergence between East Asian aurochs and their European, Near Eastern, and African counterparts on the basis of both mitochondrial and nuclear genomic data. Furthermore, we identified evidence of gene flow from East Asian aurochs into ancient and present-day taurine cattle, suggesting their potential role in facilitating the environmental adaptation of domestic cattle.

Mosaic of Somatic Mutations in Earth's Oldest Living Organism, Pando

Understanding how mutations arise and spread through individuals and populations is fundamental to evolutionary biology. Most organisms have a life cycle with unicellular bottlenecks during reproduction. However, some organisms like plants, fungi, or colonial animals can grow indefinitely, changing the manner in which mutations spread throughout both the individual and the population. Furthermore, clonally reproducing organisms may also achieve exceedingly long lifespans, making somatic mutation an important mechanism of creating heritable variation for Darwinian evolution by natural selection. Yet, little is known about intra-organism mutation rates and evolutionary trajectories in long-lived species. Here, we study the Pando aspen clone, the largest known quaking aspen (Populus tremuloides) clone founded by a single seedling and thought to be one of the oldest studied organisms. Aspen reproduce vegetatively via new root-borne stems forming clonal patches, sometimes spanning several hectares. To study the evolutionary history of the Pando clone, we collected and sequenced over 500 samples from Pando and neighboring clones, as well as from various tissue types within Pando, including leaves, roots, and bark. We applied a series of filters to distinguish somatic mutations from the pool of both somatic and germline mutations, incorporating a technical replicate sequencing approach to account for uncertainty in somatic mutation detection. Despite root spreading being spatially constrained, we observed only a modest positive correlation between genetic and spatial distance, suggesting the presence of a mechanism preventing the accumulation and spread of mutations across units. Phylogenetic models estimate the age of the clone to between ~16,000-80,000 years. This age is generally corroborated by the near-continuous presence of aspen pollen in a lake sediment record collected from Fish Lake near Pando. Overall, this work enhances understanding of mutation accumulation and dispersal within and between ramets of long-lived, clonally-reproducing organisms.

Heterochronous mitogenomes shed light on the Holocene history of the Scandinavian brown bear

Following glacial retreat after the last ice age, brown bears (Ursus arctos) recolonised Scandinavia. Previous research based on mitochondrial markers suggests that bears recolonised from both the north and the south, with a contact zone in central Scandinavia. More recently, the Scandinavian brown bear was subjected to a strong population decline with only ca. 130 remaining individuals, due to intense human persecution approximately 100 years ago. Here, we analyse 41 ancient, historical, and modern mitochondrial genomes, to examine the number of female lineages involved in the postglacial recolonisation event and temporal changes in the Scandinavian brown bears' mitochondrial genetic diversity. Our results support the bi-directional recolonisation hypothesis, indicating multiple mitochondrial lineages from clade 1a possibly followed a southern route, while only a single lineage from clade 3a appears to have followed a northern route. Furthermore, we found that the recent bottleneck had a strong impact on the southern subpopulation, resulting in only one remaining haplotype in the contemporary brown bears. For the northern subpopulation, the impact was moderate, and most haplotypes were retained throughout the bottleneck. By exploring the postglacial recolonisation and recent population pressures, our study enhances understanding of how these factors have influenced the genetic diversity of Scandinavian brown bears.

Geological inference of channel and polka-dot seismic anomalies in Yeongil bay, Pohang

The Engineering Ocean Seismic 3D system, which enables ultra-high-resolution seismic surveys on a smaller survey scale, was deployed in Yeongil Bay, Pohang, South Korea. The region is renowned for abundant shallow gas deposits and faults. Based on acoustic impedance contrast and abnormal behavior observations, two seismic anomalies termed channel and polka-dot anomalies have been identified in the seismic volume. Seismic attribute analysis based on the signal amplitude and structural characteristics reveals that these anomalies correspond to shallow biogenic gas deposits. Structural interpretation of the seismic volume revealed that the contractional deformation resulting from post-Miocene neotectonics has resulted in uplift and reverse faulting in the Pohang region, contributing to the formation of anomalies. The channel anomalies correspond to gas-saturated tidal channels that formed during eustatic sea-level changes in the post-Last Glacial Maximum period. The polka-dot anomalies are located in topographic lows and are overlain by neotectonic sediment. The different behaviors of these anomalies in a seismic volume can be attributed to the different thicknesses of overburden overlying each of the anomalies.

Genetic relationships of populations of the Black Kite Milvus migrans (Accipitriformes: Accipitridae) in the east of its range in Asia and Australia

While the Black Kite Milvus migrans is one of the most widespread birds of prey, occurring over Eurasia, Africa and Australia, it remains poorly understood outside of Europe, with southeast Asian populations particularly mysterious as their taxonomy is based on outdated morphological data. The subspecies M. m. formosanus, described in 1920, is thought to inhabit Taiwan and Hainan; however, populations in these areas have experienced dramatic changes over the past fifty years. Furthermore, M. m. formosanus is the only officially recognised subspecies for which almost no genetic data is yet available. Based on two mitochondrial genes, we compared Taiwanese Black Kites with northeast Asian and Japanese M. m. lineatus, Indian M. m. govinda and Australian M. m. affinis to reconstruct details of their population history. While Indian and Australian Black Kites are descendants of the same population, they do not share common haplotypes, probably having diverged by the end of the last glaciation. The Japanese population is distinctive in showing genetic uniformity, and it may be isolated from the mainland population. Nesting Taiwanese kites carry two previously known M. m. lineatus haplogroups and a new haplogroup possibly inherited from M. m. formosanus previously occurring in the area. A recent decline in the local population, along with expansion of M. m. lineatus, most likely led to Taiwan now being inhabited by descendants of both subspecies, which form two genetically isolated populations in southern and northern Taiwan.

Genetic Insights into the Giant Keyhole Limpet (Megathura crenulata), an Eastern Pacific Coastal Endemic: Complete Mitogenome, Phylogenetics, Phylogeography, and Historical Demography

BACKGROUND

The giant keyhole limpet Megathura crenulata is a gastropod mollusk (Fissurella superfamily) that is endemic to the eastern Pacific coast from southern California, USA, to Baja California Sur, Mexico. M. crenulata is socioeconomically important as it produces a potent immune-stimulating protein, called Keyhole Limpet Hemocyanin, which is extracted in vivo and utilized for vaccine development. However, ecological studies are scarce and genetic knowledge of the species needs to be improved. Our objectives were to assemble and annotate the mitogenome of M. crenulata, and to assess its phylogenetic relationships with other marine gastropods and to evaluate its population genetic diversity and structure.

METHODS

Samples were collected for mitogenome assembly (n = 3) spanning its geographic range, Puerto Canoas (PCA) and Punta Eugenia (PEU), Mexico, and California (CAL), USA. Total DNA was extracted from gills sequenced using Illumina paired-end 150-bp-read sequencing. Reads were cleaned, trimmed, assembled de novo, and annotated. In addition, 125 samples from eight locations were analyzed for genetic diversity and structure analysis at the 16s rRNA and COX1 genes.

RESULTS

The M. crenulata mitogenomes had lengths of 16,788 bp (PCA) and 16,787 bp (PEU) and were composed of 13 protein-coding regions, 22 tRNAs, two rRNAs, and the D-Loop region. In terms of phylogeographic diversity and structure, we found a panmictic population that has experienced recent demographic expansion with low nucleotide diversity (0.002), high haplotypic diversity (0.915), and low φST (0.047).

CONCLUSIONS

Genetic insights into the giant keyhole limpet provides tools for its management and conservation by delimiting fishing regions with low genetic diversity and/or genetically discrete units.

Revealing the evolutionary history and contemporary population structure of Pacific salmon in the Fraser River through genome resequencing

The Fraser River once supported massive salmon returns. However, over the last century, the largest returns have consistently been less than half of the recorded historical maximum. There is substantial interest from surrounding communities and governments to increase salmon returns for both human use and functional ecosystems. To generate resources for this endeavor, we resequenced genomes of Chinook (Oncorhynchus tshawytscha), coho (Oncorhynchus kisutch), and sockeye salmon (Oncorhynchus nerka) from the Fraser River at moderate coverage (∼16×). A total of 954 resequenced genomes were analyzed, with 681 collected specifically for this study from tissues sampled between 1997 and 2021. An additional 273 were collected from previous studies. At the species level, Chinook salmon appeared to have 1.6-2.1× more SNPs than coho or sockeye salmon, respectively. This difference may be attributable to large historical declines of coho and sockeye salmon. At the population level, 3 Fraser River genetic groups were identified for each species using principal component and admixture analyses. These were consistent with previous research and supports the continued use of these groups in conservation and management efforts. Environmental factors and a migration barrier were identified as major factors influencing the boundaries of these genetic groups. Additionally, 20 potentially adaptive loci were identified among the genetic groups. This information may be valuable in new management and conservation efforts. Furthermore, the resequenced genomes are an important resource for contemporary genomics research on Fraser River salmon and have been made publicly available.

Combined climate change and dispersal capacity positively affect Hoplobatrachus chinensis occupancy of agricultural wetlands

Global warming significantly impacts amphibian populations globally, and modeling helps understand these effects. Here, we used MaxEnt and MigClim models to predict the impact of climate change on habitat suitability for Hoplobatrachus chinensis. Our results indicate that temperature is a key factor affecting H. chinensis distribution. Increasing temperatures positively correlated with habitat suitability, with suitable habitat expanding northward by 2060 while maintaining suitability in the southern parts of the range. We found a 25.18% overlap between the current potential suitable habitat of H. chinensis and agricultural wetlands. Our model indicated that H. chinensis might be able to track shifts in suitable habitats under climate change given a 15 km dispersal ability per generation. Climate change will likely expand suitable habitat for H. chinensis. Our predictions offer important guidance for the conservation of the species, especially for the integrated role of natural and agricultural wetlands such as rice paddies.

Magnetic enhancement in paleosols with hydroclimatic and vegetation cover variabilities (Holocene vs. late MIS 3) in the central Korean Peninsula

Magnetic susceptibility enhancement (kE) is useful for reconstructing terrestrial paleohydroclimate variabilities. However, kE and its driving process(es) in the Korean Peninsula remain uninvestigated. Therefore, this study investigated two kEs of similar magnitudes, dated MIS 1 (Holocene) and late MIS 3 (~ 29-36 ka), from a paleosol sequence in the upland of paleo-fluvial terrace in the central Korean Peninsula. We observed increased ferri- and antiferro-magnetic mineral components,including ultrafine particles, and stronger chlorite weathering for the two kEs, suggesting pedogenic component predominance. The Fe-bearing (phyllo)silicate weathering mechanism proposed for the Chinese Loess Plateau sequences can explain the pedogenesis-induced kEs for the studied site. Superparamagnetic-domain (SPD) to pseudo-single-domain sized particles of pedogenic magnetite are likely major contributors to kEs. Moreover, we recognized the younger kE interval as more SPD contribution but less in total ferrimagnetic contribution, and more antiferromagnetic contribution than the older ones. The magnetic differences between the periods can result from vegetation cover impact and surrounding hydroclimate conditions, consistent with the recent suggestion for part of the southeast Chinese sites with relatively more rainfall. Consequently, our study provides a baseline for improving the relationship between mineral magnetic signals and local/regional hydroclimatic and environmental variabilities.

Central China as LGM plant refugia: Insights from biome reconstruction for palaeoclimate information

The demonstration of survival of forest stands in relatively stable refugia during cold glacial stages has offered an increased understanding of the response of vegetation to climate change, but also provides insight into considerations for the conversation of biodiversity hotspots. However, refugia studies in China remain in question due to the lack of plant macrofossils, especially those of endemic and relict species. Palynology, while more broad brush, provides a method for exploring whether refugia occur, and can provide some details of palaeovegetation composition and temporal dynamics. Here, three pollen records derived from subalpine wetlands in central China, spanning the Last Glacial Maximum (LGM), have been coupled with biome and mean annual precipitation (MAP) reconstructions to identify the presence of trees that endured cold climate. The results indicated that some forest, including temperate deciduous broadleaf forest and cool mixed forest, survived the LGM at the three locations, and was thus at odds with the hypothesis that forests were replaced by herbs and grasses in central China at that time. Refugia favored by protection from cold air drainage and the availability of adequate water can explain the survival of the trees during otherwise harsh episodes. Our findings are consistent with other records from central China that argue for tree dominated refugia during the LGM.

Conservation genomic study of Hopea hainanensis (Dipterocarpaceae), an endangered tree with extremely small populations on Hainan Island, China

Introduction

Hopea hainanensis Merrill & Chun is considered a keystone and indicator species in the tropical lowland rainforests of Hainan Island. Owing to its high-quality timber, H. hainanensis has been heavily exploited, leading to its classification as a first-class national protected plant in China and a plant species with extremely small populations (PSESPs).

Methods

This study analyzed genome-wide single nucleotide polymorphisms obtained through restriction site-associated DNA sequencing from 78 adult trees across 10 H. hainanensis populations on Hainan Island.

Results and discussion

The nucleotide diversity of the sampled populations ranged from 0.00096 to 0.00138, which is lower than that observed in several other PSESPs and endangered tree species. Bayesian unsupervised clustering, principal component analysis, and neighbor-joining tree reconstruction identified three to five genetic clusters in H. hainanensis, most of which were geographically widespread and shared by multiple populations. Demographic history analysis based on pooled samples indicated that the decline in the H. hainanensis population began approximately 20,000 years ago, starting from an ancestral population size of approximately 10,000 individuals. The reduction in population size accelerated approximately 4,000 years ago and has continued to the present, resulting in a severely reduced population on Hainan Island. Intensified genetic drift in small and isolated H. hainanensis populations may contribute to moderate differentiation between some of them, as revealed by pairwise F st. In conclusion, our conservation genomic study confirms a severe population decline and an extremely low level of nucleotide variation in H. hainanensis on Hainan Island. These findings provide critical insights for the sustainable management and genetic restoration of H. hainanensis on Hainan Island.

Mitochondrial DNA Genomes Reveal Relaxed Purifying Selection During Human Population Expansion after the Last Glacial Maximum

Modern humans have experienced explosive population growth in the past thousand years. We hypothesized that recent human populations have inhabited environments with relaxation of selective constraints, possibly due to the more abundant food supply after the Last Glacial Maximum. The ratio of nonsynonymous to synonymous mutations (N/S ratio) is a useful and common statistic for measuring selective constraints. In this study, we reconstructed a high-resolution phylogenetic tree using a total of 26,419 East Eurasian mitochondrial DNA genomes, which were further classified into expansion and nonexpansion groups on the basis of the frequencies of their founder lineages. We observed a much higher N/S ratio in the expansion group, especially for nonsynonymous mutations with moderately deleterious effects, indicating a weaker effect of purifying selection in the expanded clades. However, this observation on N/S ratio was unlikely in computer simulations where all individuals were under the same selective constraints. Thus, we argue that the expanded populations were subjected to weaker selective constraints than the nonexpanded populations were. The mildly deleterious mutations were retained during population expansion, which could have a profound impact on present-day disease patterns.

Human population dynamics in Upper Paleolithic Europe inferred from fossil dental phenotypes

Despite extensive archaeological research, our knowledge of the human population history of Upper Paleolithic Europe remains limited, primarily due to the scarce availability and poor molecular preservation of fossil remains. As teeth dominate the fossil record and preserve genetic signatures in their morphology, we compiled a large dataset of 450 dentitions dating between ~47 and 7 thousand years ago (ka), outnumbering existing skeletal and paleogenetic datasets. We tested a range of competing demographic scenarios using a coalescent-based machine learning Approximate Bayesian Computation (ABC) framework that we modified for use with phenotypic data. Mostly in agreement with but also challenging some of the hitherto available evidence, we identified a population turnover in western Europe at ~28 ka, isolates in western and eastern refugia between ~28 and 14.7 ka, and bottlenecks during the Last Glacial Maximum. Methodologically, this study marks the pioneering application of ABC to skeletal phenotypes, paving the way for exciting future research avenues.

Genomic variation, environmental adaptation, and feralization in ramie, an ancient fiber crop

Feralization is an important evolutionary process, but the mechanisms behind it remain poorly understood. Here, we use the ancient fiber crop ramie (Boehmeria nivea (L.) Gaudich.) as a model to investigate genomic changes associated with both domestication and feralization. We first produced a chromosome-scale de novo genome assembly of feral ramie and investigated structural variations between feral and domesticated ramie genomes. Next, we gathered 915 accessions from 23 countries, comprising cultivars, major landraces, feral populations, and the wild progenitor. Based on whole-genome resequencing of these accessions, we constructed the most comprehensive ramie genomic variation map to date. Phylogenetic, demographic, and admixture signal detection analyses indicated that feral ramie is of exoferal or exo-endo origin, i.e., descended from hybridization between domesticated ramie and the wild progenitor or ancient landraces. Feral ramie has higher genetic diversity than wild or domesticated ramie, and genomic regions affected by natural selection during feralization differ from those under selection during domestication. Ecological analyses showed that feral and domesticated ramie have similar ecological niches that differ substantially from the niche of the wild progenitor, and three environmental variables are associated with habitat-specific adaptation in feral ramie. These findings advance our understanding of feralization, providing a scientific basis for the excavation of new crop germplasm resources and offering novel insights into the evolution of feralization in nature.

Deeper and stronger North Atlantic Gyre during the Last Glacial Maximum

Subtropical gyre (STG) depth and strength are controlled by wind stress curl and surface buoyancy forcing1,2. Modern hydrographic data reveal that the STG extends to a depth of about 1 km in the Northwest Atlantic, with its maximum depth defined by the base of the subtropical thermocline. Despite the likelihood of greater wind stress curl and surface buoyancy loss during the Last Glacial Maximum (LGM)3, previous work suggests minimal change in the depth of the glacial STG4. Here we show a sharp glacial water mass boundary between 33° N and 36° N extending down to between 2.0 and 2.5 km-approximately 1 km deeper than today. Our findings arise from benthic foraminiferal δ18O profiles from sediment cores in two depth transects at Cape Hatteras (36-39° N) and Blake Outer Ridge (29-34° N) in the Northwest Atlantic. This result suggests that the STG, including the Gulf Stream, was deeper and stronger during the LGM than at present, which we attribute to increased glacial wind stress curl, as supported by climate model simulations, as well as greater glacial production of denser subtropical mode waters (STMWs). Our data suggest (1) that subtropical waters probably contributed to the geochemical signature of what is conventionally identified as Glacial North Atlantic Intermediate Water (GNAIW)5-7 and (2) the STG helped sustain continued buoyancy loss, water mass conversion and northwards meridional heat transport (MHT) in the glacial North Atlantic.

Genome resequencing reveals population divergence and local adaptation of blacklegged ticks in the United States

Tick vectors and tick-borne disease are increasingly impacting human populations globally. An important challenge is to understand tick movement patterns, as this information can be used to improve management and predictive modelling of tick population dynamics. Evolutionary analysis of genetic divergence, gene flow and local adaptation provides insight on movement patterns at large spatiotemporal scales. We develop low coverage, whole genome resequencing data for 92 blacklegged ticks, Ixodes scapularis, representing range-wide variation across the United States. Through analysis of population genomic data, we find that tick populations are structured geographically, with gradual isolation by distance separating three population clusters in the northern United States, southeastern United States and a unique cluster represented by a sample from Tennessee. Populations in the northern United States underwent population contractions during the last glacial period and diverged from southern populations at least 50 thousand years ago. Genome scans of selection provide strong evidence of local adaptation at genes responding to host defences, blood-feeding and environmental variation. In addition, we explore the potential of low coverage genome sequencing of whole-tick samples for documenting the diversity of microbial pathogens and recover important tick-borne pathogens such as Borrelia burgdorferi. The combination of isolation by distance and local adaptation in blacklegged ticks demonstrates that gene flow, including recent expansion, is limited to geographical scales of a few hundred kilometres.

Widespread horse-based mobility arose around 2200 BCE in Eurasia

Horses revolutionized human history with fast mobility1. However, the timeline between their domestication and their widespread integration as a means of transport remains contentious2-4. Here we assemble a collection of 475 ancient horse genomes to assess the period when these animals were first reshaped by human agency in Eurasia. We find that reproductive control of the modern domestic lineage emerged around 2200 BCE, through close-kin mating and shortened generation times. Reproductive control emerged following a severe domestication bottleneck starting no earlier than approximately 2700 BCE, and coincided with a sudden expansion across Eurasia that ultimately resulted in the replacement of nearly every local horse lineage. This expansion marked the rise of widespread horse-based mobility in human history, which refutes the commonly held narrative of large horse herds accompanying the massive migration of steppe peoples across Europe around 3000 BCE and earlier3,5. Finally, we detect significantly shortened generation times at Botai around 3500 BCE, a settlement from central Asia associated with corrals and a subsistence economy centred on horses6,7. This supports local horse husbandry before the rise of modern domestic bloodlines.

Human Y chromosome haplogroup L1-M22 traces Neolithic expansion in West Asia and supports the Elamite and Dravidian connection

West and South Asian populations profoundly influenced Eurasian genetic and cultural diversity. We investigate the genetic history of the Y chromosome haplogroup L1-M22, which, while prevalent in these regions, lacks in-depth study. Robust Bayesian analyses of 165 high-coverage Y chromosomes favor a West Asian origin for L1-M22 ∼20.6 thousand years ago (kya). Moreover, this haplogroup parallels the genome-wide genetic ancestry of hunter-gatherers from the Iranian Plateau and the Caucasus. We characterized two L1-M22 harboring population groups during the Early Holocene. One expanded with the West Asian Neolithic transition. The other moved to South Asia ∼8-6 kya but showed no expansion. This group likely participated in the spread of Dravidian languages. These South Asian L1-M22 lineages expanded ∼4-3 kya, coinciding with the Steppe ancestry introduction. Our findings advance the current understanding of Eurasian historical dynamics, emphasizing L1-M22's West Asian origin, associated population movements, and possible linguistic impacts.

Geomorphic impacts within Red River Fault and island shifting as witnessed by the phylogeography of the largest water strider

Palaeogeological events and climate oscillations profoundly impact the demographics and distributions of small-range species, increasing the extinction risk. The largest water strider worldwide, Gigantometra gigas (Hemiptera: Gerridae), exhibits restricted distributions in Vietnam and southern China. Herein, we generated three genomic datasets (mitogenomes, 146 nuclear protein-coding genes and single nucleotide polymorphisms) with ecological niche modelling (ENM) to explicitly test whether the present-day distribution of G. gigas actually resulted from geographical and climatic effects. We found that the origin of this largest water strider reached the divergence time of the genus within Gerridae, providing a greater opportunity to explore its response to geographic movements. The right-lateral motion of the Red River Fault facilitated the divergence of two phylogeographic lineages, resulting in the "north-south component" genetic pattern in G. gigas. The Hainan and southeast Vietnam populations of the southern linage were completely separated by the Beibu Gulf but exhibited similar genetic compositions, confirming that Hainan had a continental origin and that Hainan Island joined with the Indo-China Peninsula to promote gene exchange among populations. Additionally, we noticed the low genetic diversity but long demographic history of the northern lineage, which displayed population dynamics opposite to those of other organisms. Integrating the demographic changes and ENM findings revealed that suitable habitat contraction and rapid demographic decline during the Last Glacial Maximum (LGM) triggered the low genetic diversity of the northern lineage. Overall, the demographic history of the largest water strider was mainly shaped by geographical features, and first provided evidence from the phylogeographic perspective of aquatic insects to support the hypothesis of Hainan Island shifting.

Inferences about the population history of Rangifer tarandus from Y chromosome and mtDNA phylogenies

Reindeer, called caribou in North America, has a circumpolar distribution and all extant populations belong to the same species (Rangifer tarandus). It has survived the Holocene thanks to its immense adaptability and successful coexistence with humans in different forms of hunting and herding cultures. Here, we examine the paternal and maternal history of Rangifer based on robust Y-chromosomal and mitochondrial DNA (mtDNA) trees representing Eurasian tundra reindeer, Finnish forest reindeer, Svalbard reindeer, Alaska tundra caribou, and woodland caribou. We first assembled Y-chromosomal contigs, representing 1.3 Mb of single-copy Y regions. Based on 545 Y-chromosomal and 458 mtDNA SNPs defined in 55 males, maximum parsimony trees were created. We observed two well separated clades in both phylogenies: the "EuroBeringian clade" formed by animals from Arctic Islands, Eurasia, and a few from North America and the "North American clade" formed only by caribou from North America. The time calibrated Y tree revealed an expansion and dispersal of lineages across continents after the Last Glacial Maximum. We show for the first time unique paternal lineages in Svalbard reindeer and Finnish forest reindeer and reveal a circumscribed Y haplogroup in Fennoscandian tundra reindeer. The Y chromosome in domesticated reindeer is markedly diverse indicating that several male lineages have undergone domestication and less intensive selection on males. This study places R. tarandus onto the list of species with resolved Y and mtDNA phylogenies and builds the basis for studies of the distribution and origin of paternal and maternal lineages in the future.

A chromosome-level genome of Chenghua pig provides new insights into the domestication and local adaptation of pigs

As a country with abundant genetic resources of pigs, the domestication history of pigs in China and the adaptive evolution of Chinese pig breeds at different latitudes have rarely been elucidated at the genome-wide level. To fill this gap, we first assembled a high-quality chromosome-level genome of the Chenghua pig and used it as a benchmark to analyse the genomes of 272 samples from three genera of three continents. The divergence of the three species belonging to three genera, Phacochoerus africanus, Potamochoerus porcus, and Sus scrofa, was assessed. The introgression of pig breeds redefined that the migration routes were basically from southern China to central and southwestern China, then spread to eastern China, arrived in northern China, and finally reached Europe. The domestication of pigs in China occurred ∼12,000 years ago, earlier than the available Chinese archaeological domestication evidence. In addition, FBN1 and NR6A1 were identified in our study as candidate genes related to extreme skin thickness differences in Eurasian pig breeds and adaptive evolution at different latitudes in Chinese pig breeds, respectively. Our study provides a new resource for the pig genomic pool and refines our understanding of pig genetic diversity, domestication, migration, and adaptive evolution at different latitudes.

Hot spring oases in the periglacial desert as the Last Glacial Maximum refugia for temperate trees in Central Europe

Northern glacial refugia are a hotly debated concept. The idea that many temperate organisms survived the Last Glacial Maximum (LGM; ~26.5 to 19 thousand years) in several sites across central and northern Europe stems from phylogeographic analyses, yet direct fossil evidence has thus far been missing. Here, we present the first unequivocal proof that thermophilous trees such as oak (Quercus), linden (Tilia), and common ash (Fraxinus excelsior) survived the LGM in Central Europe. The persistence of the refugium was promoted by a steady influx of hydrothermal waters that locally maintained a humid and warm microclimate. We reconstructed the geological and palaeohydrological factors responsible for the emergence of hot springs during the LGM and argue that refugia of this type, allowing the long-term survival and rapid post-LGM dispersal of temperate elements, were not exceptional in the European periglacial zone.

Whole-genome resequencing reveals genetic diversity and adaptive evolution in Chinese honeybee (Apis cerana cerana) in Guizhou, China

Introduction: Guizhou Province, characterized by complex and diverse geographic and climatic environments, has rich genetic resources for the Chinese honeybee (Apis cerana cerana) and is one of the main bee-producing areas in China. However, research on the genetic diversity of Chinese honeybee in the Guizhou region is very limited, despite implications for conservation of biodiversity. Methods: In this study, we analyzed the genetic diversity, differentiation, and selection signals based on 116 Chinese honeybees from 12 regions in Guizhou Province using whole-genome sequencing. Results: We identified 1,400,430 high-quality SNPs across all samples. A population structure analysis revealed two independent genetic subgroups of Chinese honeybees in Guizhou, a Yunnan-Guizhou Plateau population in western Guizhou and a hilly-mountainous population in eastern Guizhou. The average nucleotide diversity (Pi) ranged from 0.00138 to 0.00161 and average expected heterozygosity (He) ranged from 0.2592 to 0.2604. The average genetic differentiation index (F ST) for Chinese honeybees in pairwise comparisons of 12 regions ranged from 0.0094 to 0.0293. There was clear genetic differentiation between the western plateau and the eastern hilly mountainous areas of Guizhou; however, F ST values between the eastern and western populations ranged from 0.0170 to 0.0293, indicating a low degree of differentiation. A genome-wide scan revealed a number of genes under selection in the Yunnan-Guizhou Plateau environment. These genes were related to growth and development, reproduction, and cold resistance, and several candidate genes involved in environmental adaptation were identified, including CTR, MAPK, MAST, HSF, and MKKK. Discussion: The results of the present study provide important theoretical bases for the conservation, evaluation, development, and utilization of genetic resources for Chinese honeybees in the Guizhou region and for further investigations of environmental adaptation and underlying mechanisms in the species.

Mid-Holocene marine faunas from the Bangkok Clay deposits in Nakhon Nayok, the Central Plain of Thailand

Based on several field investigations, many molluscan shells and chondrichthyan teeth, together with other invertebrate and actinopterygian remains were found from the marine Bangkok Clay deposits in Ongkharak, Nakhon Nayok, at a depth of ~ 5-7 m below the topsoil surface. Animal macrofossils recovered from these Holocene marine deposits were identified and their chronological context was investigated in order to reconstruct the paleoenvironments of the area at that time. The majority of marine fossils recovered from the site consist of molluscs, with a total of 63 species identified. Other invertebrate species include a stony coral, a mud lobster, barnacles, and a sea urchin. The vertebrates are represented by fish remains, including carcharhinid shark teeth from at least nine species, stingray and trichiurid teeth, and one sciaenid otolith. The molluscan fauna indicates that the paleoenvironments of the area corresponded to intertidal to sublittoral zones, where some areas were mangrove forests and intertidal mudflats. The fish fauna is dominated by the river shark Glyphis, indicating freshwater influences and possibly occasional brackish conditions. The carbon-14 analysis of mollusc and charcoal remains shows that deposition of the marine sediment sequence began during the mid-Holocene, spanning approximately from 8,800 to 5,300 cal yr BP. This study provides in-depth insights into the diversity of fishes, marine molluscs, and other invertebrates from the Bangkok Clay deposits, supporting the existence of a marine transgression onto the Lower Central Plain of Thailand during the mid-Holocene.

Survival in nunatak and peripheral glacial refugia of three alpine plant species is partly predicted by altitudinal segregation

Mountain biota survived the Quaternary cold stages most probably in peripheral refugia and/or ice-free peaks within ice-sheets (nunataks). While survival in peripheral refugia has been broadly demonstrated, evidence for nunatak refugia is still scarce. We generated RADseq data from three mountain plant species occurring at different elevations in the southeastern European Alps to investigate the role of different glacial refugia during the Last Glacial Maximum (LGM). We tested the following hypotheses. (i) The deep Piave Valley forms the deepest genetic split in the species distributed across it, delimiting two peripheral refugia. (ii) The montane to alpine species Campanula morettiana and Primula tyrolensis survived the LGM in peripheral refugia, while high-alpine to subnival Saxifraga facchinii likely survived in several nunatak refugia. (iii) The lower elevation species suffered a strong population decline during the LGM. By contrast, the higher elevation species shows long-term stability of population sizes due to survival on permanently ice-free peaks and small population sizes at present. We found peripheral refugia on both sides of the Piave Valley, which acted as a major genetic barrier. Demographic modelling confirmed nunatak survival not only for S. facchinii but also for montane to alpine C. morettiana. Altitudinal segregation influenced the species' demographic fluctuations, with the lower elevation species showing a significant population increase at the end of the LGM, and the higher elevation species either showing decrease towards the present or stable population sizes with a short bottleneck. Our results highlight the role of nunatak survival and species ecology in the demographic history of mountain species.