Population Bottlenecks Research Articles

Extreme founder effect associated with hyperglycemia and hyperlipidemia on the island of NIAS/Indonesia

The island of Nias/Indonesia shows an extremely reduced genetic diversity indicating a strong founder effect. As a consequence, the prevalence of some disease genes should significantly differ among populations depending on the gene pool passed on to the founder population and their successive expansion as it has already been documented for several monogenic diseases. Results of the current study based on routine laboratory blood examination give rise to the notion that this might also hold true for polygenic disorders. We observed very high prevalence of hyperglycemia (non-fasting glucose above 200 mg/dL in 14 % Nias population compared to 1.5 % in the population of the neighboring island of Sumatra) accompanied by hypertriglyceridemia, high non-HDL-cholesterol, and low HDL-cholesterol levels. These findings suggest that the Nias population may be disproportionally affected by prediabetes and type 2 diabetes mellitus. By contrast, laboratory parameters potentially indicative of other polygenic disorders such as total plasma cholesterol, electrolytes, creatinine, urea, and uric acid were comparable between the inhabitants of Nias and Sumatra islands. To our knowledge this is the first study suggesting that the extremely strong genetic bottleneck seen in the Nias population translates into the widespread metabolic disease with potentially deleterious influence on public health.

Unveiling Spatiotemporal Diffusion of Hot Carriers Influenced by Spatial Nonuniform Hot Phonon Bottleneck Effect in Monolayer MoS2.

The exceptional semiconducting properties of two-dimensional (2D) transition metal dichalcogenides (TMDs) have made them highly promising for the development of future electronic and optoelectronic devices. Extensive studies of TMDs are partly associated with their ability to generate 2D-confined hot carriers above the conduction band edges, enabling potential applications that rely on such transient excited states. In this work, room-temperature spatiotemporal hot carrier dynamics in monolayer MoS2 is studied by transient absorption microscopy (TAM), featuring an initial ultrafast expansion followed by a rapid negative diffusion, and ultimately a slow long-term expansion of the band edge C-excitons. We provide direct experimental evidence to identify the abnormal negative diffusion process as a spatial contraction of the hot carriers resulting from spatial variation in the hot phonon bottleneck effect due to the Gaussian intensity distribution of the pump laser beam.

Transmission-Blocking Strategies for Malaria Eradication: Recent Advances in Small-Molecule Drug Development.

Malaria drug research and development efforts have resurged in the last decade following the decelerating rate of mortality and malaria cases in endemic regions. The inefficiency of malaria interventions is largely driven by the spreading resistance of the Plasmodium falciparum parasite to current drug regimens and that of the malaria vector, the Anopheles mosquito, to insecticides. In response to the new eradication agenda, drugs that act by breaking the malaria transmission cycle (transmission-blocking drugs), which has been recognized as an important and additional target for intervention, are being developed. These drugs take advantage of the susceptibility of Plasmodium during population bottlenecks before transmission (gametocytes) and in the mosquito vector (gametes, zygotes, ookinetes, oocysts, sporozoites). To date, compounds targeting stage V gametocytes predominate in the chemical library of transmission-blocking drugs, and some of them have entered clinical trials. The targeting of Plasmodium mosquito stages has recently renewed interest in the development of innovative malaria control tools, which hold promise for the application of compounds effective at these stages. In this review, we highlight the major achievements and provide an update on the research of transmission-blocking drugs, with a particular focus on their chemical scaffolds, antiplasmodial activity, and transmission-blocking potential.

Population genetic structure of the European pond turtle (Emys orbicularis) at the northern edge of the Pannonian Basin

Populations of plants and animals at the edge of a species’ range may exhibit lower genetic diversity due to a combination of historical (e.g., postglacial dispersal) and contemporary (e.g., low effective population size, strong genetic drift or bottlenecks) processes. In this study, we analysed the genetic structure of populations of the European pond turtle (Emys orbicularis) in the northern part of the Pannonian Basin (Slovakia, Hungary, Austria), which represents the edge of the species’ range. Using mitochondrial DNA (mtDNA) and microsatellite markers, we aimed to assign individuals and populations into phylogeographic lineages and to determine genetic variation and population structure. Our study revealed that most individuals from natural populations belong to mtDNA lineage II (widely distributed haplotype IIa, and likely endemic haplotypes IIl and IIo), which is typical for the whole Pannonian region. However, non-native haplotypes were detected in one Slovak population (haplotype Ib) and in the Austrian Donau Auen National Park (haplotype IVa). Microsatellite markers revealed high variability comparable to that in other parts of the range, suggesting that marginal populations may not necessarily have reduced genetic diversity. A genetically mixed population was found in the Donau Auen National Park, consisting of turtles belonging to mtDNA lineage II (taxonomically assessed as subspecies E. orbicularis orbicularis) and lineage IV (taxonomically assessed as E. orbicularis hellenica), which is native to the circum-Adriatic region. The admixture suggests intense hybridization and introgression between the two lineages (subspecies).

Microsatellite-based bottleneck analysis and migration events among four native Turkish goat breeds

Abstract. Molecular data analyzed by accurate statistical approaches not only have the potential to investigate demographic events faced in the past, e.g., migration, but they also offer significant hints such as bottleneck effects to take suitable measures for sustainable breeding in farm animals. In this study, the genetic bottleneck and migration events among four native Turkish goat populations, i.e., Hair, Honamlı, Kabakulak, and Norduz, were assessed using 367 multi-allelic data belonging to 28 microsatellite loci. The null hypothesis was not rejected for the Wilcoxon sign rank test in the infinite allele model, two-phase model, and stepwise mutation model, while a normal L-shaped distribution of allele frequencies was observed in terms of mode-shift indicators in four native Turkish goat populations. Both the Wilcoxon sign rank test and the mode-shift indicator demonstrated that Anatolian goat populations have had a lack of recent genetic bottlenecks and have maintained their effective population sizes over the generations. Moreover, the 95 % confidence interval confirmed that the effective population sizes of Hair, Honamlı, and Kabakulak may reach infinity, while the highest effective population size for Norduz was estimated at 794.5, when the lowest allele frequency was considered to be 0.01. Up to four migration events revealed a significant migration from Norduz to Hair and Kabakulak populations. In contrast, no migration from other populations to Norduz was observed, most probably due to its geographic isolation. The bottleneck results may serve as a guide for future management practices, whereas further studies, especially on a whole-genome basis, are needed to confirm migration events among Anatolian goat breeds.

Combined demographic, ecological and genetic tools reveal connectivity within a fragmented butterfly population

Protected species require targeted studies to establish population sizes, their dispersal capacity and the possible genetic bottleneck effect that could impair the future of the remaining populations. In this study, we used the genotyping-by-sequencing technique (SNP: single nucleotide polymorphism) combined with Capture-Mark-Recapture (CMR) method to measure the dispersal ability and subpopulation sizes of the protected butterfly Zerynthia polyxena in 14 sites of NW Italian Alps. The study species form a metapopulation divided into several small subpopulations (ranging from 90 to 859 estimated subpopulation sizes). The species showed low mobility, likely due to habitat fragmentation, with individuals travelling an average of 80 m from their original capture site. SNPs highlighted high observed heterozygosity, low genetic substructuring at short distances, and large genetic differentiation only for individuals found in sites located at 46 km distance, suggesting high gene flow at short distances and limited gene flow between distant populations. Although CMR data did not detect movement beyond 700 m, the genetic results revealed remarkable connectivity among nearby subpopulations. The results indicate that gene flow still exists among the subpopulations despite the fragmented habitat. Considering that the species is locally threatened by habitat loss due to the planning of a European high-speed railway, our data suggest that it is not too late to adopt conservation measures. In conclusion, combining genetic and ecological studies can be utilised to design proper conservation plans for protected and threatened insect metapopulations.

Assessing the population structure and genetic variability of Kenyan native goats under extensive production system

Indigenous goats are important to many livelihoods. Despite this, they are subjected to indiscriminate crossbreeding. This affects their genetic variability which is needed to survive in current regime of climate change. The study assessed population structure and genetic diversity of Galla and Small East African goats (SEA) using pedigree information. A total of 7384 animals, 5222 of the Galla and 2162 of the SEA breeds, born between the years 1983 and 2022, were utilized. Individuals with known parents were defined as reference population. From the results, the maximum generation traced for Galla and SEA populations was 14.6 and 14.5, respectively. However, only 6 and 5 generations for Galla and SEA were complete. Pedigree completeness increased with the increasing number of generations. The average generation interval (GI) for Galla and SEA was 3.84 ± 0.04 and 4.4 ± 0.13 years. The average increase in the rate of inbreeding per generation for Galla and SEA was 0.04 and 0.05, with the effective ancestors and founders (fa/fe) ratio being same (1.00) for both breeds. Fifty percent (50%) of the genetic variability in the populations was contributed by 3 and 1 ancestor for Galla SEA, respectively. The effective population size (Ne) was 5.19 and 4.77 for Galla and SEA. Therefore, the current breeding programs should be changed to avoid future genetic bottlenecks in this population. These findings offer an opportunity to enhance the current genetic status and management of Kenyan native goats and other regions with similar production systems.

Genetic assessment and monitoring of wild, captive, and reintroduced northern leopard frog populations

The northern leopard frog (Lithobates pipiens) has undergone dramatic declines in population size and range over recent decades in western Canada and the United States. In British Columbia, only a single population remains at the Creston Valley Wildlife Management Area. Yet, the continuing viability of this population is uncertain. In this paper, the current genetic structure of northern leopard frog populations in western Canada was assessed using microsatellite markers. Historical samples from the extinct population of Fort Steele in British Columbia were compared with the Creston Valley population to understand changes in population genetic parameters over time. Genotypic data from four populations (Creston Valley, Drain K, Prince Spring, and Cypress Hill) sampled in 2004 and 2019 were compared. To evaluate changes in the genetic diversity of the Creston Valley population over time, allelic richness and expected heterozygosity of the population were compared at three time points using genotypes from 2000, 2004, and 2019. Northern leopard frog populations in western Canada showed high genetic differentiation, with genetic diversity decreasing from east to west. Although there weren’t notable changes in genetic parameters between 2004 and 2019, there was evidence of a decline in diversity between 2000 and 2019. The extinct population of Fort Steele had private alleles, while the current Creston Valley population did not, suggesting a genetic bottleneck in the Creston Valley population. Therefore, genetic rescue, specifically for the endangered Creston Valley population, can be considered as an action to support recovery. Additionally, continued genetic monitoring will help in the effective management of the species by providing information on the success of conservation actions.

Climatic fluctuations, geographic features, and evolutionary forces: Shaping high genomic diversity and local adaptation in Muntiacus reevesi

AbstractAimGenetic diversity is crucial for species adaptability. Understanding the mechanisms behind its formation and maintenance is essential for effective conservation. Recent studies have demonstrated that despite experiencing severe population bottlenecks, Muntiacus reevesi retains high genetic diversity and continues its northward migration, indicative of ongoing adaptive evolution. However, our comprehension of this phenomenon remains incomplete. The objective of this study is to explore the mechanisms underlying the formation of high genetic diversity and the genomic characteristics associated with local adaptation, using M. reevesi as a case study.LocationSouthern China.MethodsWe analysed resequencing data from 62 genomes and identified 29,124,081 high‐quality single‐nucleotide polymorphisms (SNPs). We used population genetics, demographic history, population differentiation, gene flow analysis software, and genotype‐environment association (GEA) models to assess the factors that have contributed to high genetic diversity and environmental adaptability in the historical climate and geographical context.ResultsThe study identified that during Pleistocene climatic fluctuations, M. reevesi diverged into eastern (DB and WJW populations) and western lineages (WL, BA, and QL populations), all displayed high genetic diversity. Historically, M. reevesi maintained large effective populations, but contemporary human‐induced threats have led to a significant decline. Population differentiation models suggest distinct expansion pathways for eastern and western lineages, resulting in population admixture, with mountain corridors facilitating gene flow and maintaining high genetic diversity. Additionally, environmental‐genotype analysis revealed local adaptation in the QL‐BA population, highlighting candidate adaptive genes (ME3 and PRKG1) potentially linked to cold adaptation and foraging behaviour.ConclusionThis study enhances our understanding of the mechanisms behind the high genetic diversity and environmental adaptability of M. reevesi, offering insights into how bottleneck populations maintain diversity, crucial for biogeographic research and conservation strategies for similar species.

Cryptic Diversity of Barred Mudskippers, <i>Periophthalmus argentilineatus</i> (Valenciennes, 1837), from the Southern Coast of Java and East Lombok, Indonesia inferred by <i>COI</i> Mitochondrial Gene

The Barred Mudskipper (P. argentilineatus) is an amphibious fish species that displays fully terrestrial behaviour during low tides. Previous studies have indicated the existence of cryptic species of the barred mudskipper, leading to difficulties in taxonomic identification due to similarities in morphological characteristics. Therefore, this study aimed to generate DNA barcodes for Indonesian barred mudskipper populations. We collected ten specimens from Clungup Beach and Kondang Bandung Beach, representing our samples. Additionally, we incorporated 25 previously collected COI sequences from Indonesia into our analysis. The mitochondrial COI gene was amplified using PCR and analysed using various bioinformatics programs. This study provides evidence for the presence of three genetically distinct clades (A, B, and C) within the P. argentilineatus population in Indonesia, with a deep genetic divergence of 2.41% to 6.12%. Clade A showed a high genetic divergence of 5.51-6.12%, suggesting the presence of a cryptic species consistent with previous studies. The high level of haplotype diversity and low nucleotide diversity observed in each clade suggest a population bottleneck followed by a rapid expansion. The lack of geographical separation in the haplotype network analysis indicates that gene flow between populations may have been facilitated by glaciation events in the past. These findings contribute to a better understanding of the biodiversity of the barred mudskipper species in Indonesia and will aid in the accurate identification of cryptic species. This study highlights the importance of using molecular techniques to complement morphological identification in understanding the evolution and diversity of mudskipper fish species.

Interrogating Genomes and Geography to Unravel Multiyear Vesicular Stomatitis Epizootics.

We conducted an integrative analysis to elucidate the spatial epidemiological patterns of the Vesicular Stomatitis New Jersey virus (VSNJV) during the 2014-15 epizootic cycle in the United States (US). Using georeferenced VSNJV genomics data, confirmed vesicular stomatitis (VS) disease cases from surveillance, and a suite of environmental factors, our study assessed environmental and phylogenetic similarity to compare VS cases reported in 2014 and 2015. Despite uncertainties from incomplete virus sampling and cross-scale spatial processes, patterns suggested multiple independent re-invasion events concurrent with potential viral overwintering between sequential seasons. Our findings pointed to a geographically defined southern virus pool at the US-Mexico interface as the source of VSNJV invasions and overwintering sites. Phylodynamic analysis demonstrated an increase in virus diversity before a rise in case numbers and a pronounced reduction in virus diversity during the winter season, indicative of a genetic bottleneck and a significant narrowing of virus variation between the summer outbreak seasons. Environment-vector interactions underscored the central role of meta-population dynamics in driving disease spread. These insights emphasize the necessity for location- and time-specific management practices, including rapid response, movement restrictions, vector control, and other targeted interventions.

First Record of Malformation in Seahorses Attributed to the Oil Spill off the Brazilian Coast in 2019.

In 2019, there was an environmental catastrophe in Brazil, when more than 5000 tons of unknown origin crude oil invaded beaches and mangroves. Two years later, two monitoring areas were selected to study seahorses' offspring: Massangana River estuary (apparently healthy area) and Cocaia Island (affected area). Thirty-six reproductive events of Hippocampus reidi (Syngnathidae) couples from these two areas were monitored to analyze the offspring. At the apparently healthy area, no newborns with malformations were found. However, the offspring from Cocaia Island showed a mean of 19.73% (±5.23) malformations in newborns. It is argued that the toxic/teratogenic effects of polycyclic aromatic hydrocarbons have affected the population in two ways: directly through the induction of mutations in the germ cells of the species and through a drastic reduction of the population (bottleneck effect) whose density observed today recovered through consanguineous couplings, potentiating deleterious genotypes in the offspring. Environ Toxicol Chem 2024;43:1996-2004. © 2024 SETAC.

Repeated horizontal acquisition of lagriamide-producing symbionts in Lagriinae beetles.

Microbial symbionts associate with multicellular organisms on a continuum from facultative associations to mutual codependency. In some of the oldest intracellular symbioses there is exclusive vertical symbiont transmission, and co-diversification of symbiotic partners over millions of years. Such symbionts often undergo genome reduction due to low effective population sizes, frequent population bottlenecks, and reduced purifying selection. Here, we describe multiple independent acquisition events of closely related defensive symbionts followed by genome erosion in a group of Lagriinae beetles. Previous work in Lagria villosa revealed the dominant genome-eroded symbiont of the genus Burkholderia produces the antifungal compound lagriamide and protects the beetle's eggs and larvae from antagonistic fungi. Here, we use metagenomics to assemble 11 additional genomes of lagriamide-producing symbionts from seven different host species within Lagriinae from five countries, to unravel the evolutionary history of this symbiotic relationship. In each host species, we detected one dominant genome-eroded Burkholderia symbiont encoding the lagriamide biosynthetic gene cluster (BGC). Surprisingly, however, we did not find evidence for host-symbiont co-diversification, or for a monophyly of the lagriamide-producing symbionts. Instead, our analyses support at least four independent acquisition events of lagriamide-encoding symbionts and subsequent genome erosion in each of these lineages. By contrast, a clade of plant-associated relatives retained large genomes but secondarily lost the lagriamide BGC. In conclusion, our results reveal a dynamic evolutionary history with multiple independent symbiont acquisitions characterized by high degree of specificity. They highlight the importance of the specialized metabolite lagriamide for the establishment and maintenance of this defensive symbiosis.

Population structure and genetic diversity in males of the autochthonous Busha cattle in Croatia

Busha is recognized as the most numerous autochthonous cattle breed in Croatia. In small populations, using the same sire repeatedly can increase inbreeding rates. This can lead to fewer high-quality, and high inbred breeding sires over time. Genealogical records of the Busha cattle breed registered from 1987 to 2022 were used to investigate the population structure and the genetic variability of the male individuals. The dataset included 10,411 animals, of which 3,962 were males. The average equivalent complete generation reached 2.92 in the total population and 3.05 in the reference population, when considering only living animals. The average inbreeding coefficient in the male population was 1.59%. Over the studied period, inbreeding rose to an average value of 2.07% in the last birth year cohort (2017-2022). The unequal contribution of the effective number of founders indicates the more frequent use of particular breeding sire lines. Nevertheless, despite the controlled inbreeding rate observed among breeding sires, and the absence of any evident population bottleneck, our study highlighted the need for breeding strategies to optimize the contribution of breeding animals in the next generations to ensure long-term conservation of the Busha cattle breed.

Molecular Assessment of Genetic Diversity and Bottleneck in Hair Goat Reared in Türkiye

Objective: Being the most preferred and geographically distributed in Türkiye, the Hair goat was screened at a molecular level to evaluate genetic diversity and population structure via microsatellite DNA markers. This paper also aimed to investigate the effects of genetic bottleneck to evaluate whether the Hair goat has maintained its effective population size in recent past. Material and Methods: A total of 411 Hair goats were sampled from farms participating in the "Hair Goat Breeding" project, initiated by the General Directorate of Agricultural Research and Policies in Aydın and Denizli provinces. Sampled animals were genotyped with 18 microsatellite loci to assess genetic diversity, population structure, and genetic bottleneck. Results: A total of 341 different alleles were observed across 18 microsatellite loci in which the highest number of alleles (26) and effective alleles (10.18) were detected in INRA005 and HSC loci, respectively. The average observed heterozygosity (0.73) was lower than the expected value (0.83), whereas all loci turned out to be highly informative (PIC>0.50). Factorial correspondence analysis separated animals into two groups, while a genetic admixture was detected between these groups. STRUCTURE analysis, on the other hand, confirmed that 411 animals were derived from three ancestral populations in which the third group is drawn due to admixed individuals. The Wilcoxon test and mode-shift indicator detected a lack of genetic bottleneck indicating that Hair goats reared in Türkiye have maintained their effective population size in recent past. Conclusion: This study validates that used microsatellite markers are highly polymorphic and could be utilized for revealing genetic diversity in different local goat breeds. The findings recovered in this study could be integrated into breeding and conservation programs, while further studies should adopt SNP array technologies and next-generation sequencing platforms to reveal deeper knowledge about the genetic diversity and population structure of Anatolian goat breeds.

Conserved Evolutionary Trajectory Can Be Perturbed to Prevent Resistance Evolution under Norfloxacin Pressure by Forcing Mycobacterium smegmatis on Alternate Evolutionary Paths.

Antibiotic resistance is a pressing health issue, with the emergence of resistance in bacteria outcompeting the discovery of novel drug candidates. While many studies have used Adaptive Laboratory Evolution (ALE) to understand the determinants of resistance, the influence of the drug dosing profile on the evolutionary trajectory remains understudied. In this study, we employed ALE on Mycobacterium smegmatis exposed to various concentrations of Norfloxacin using both cyclic constant and stepwise increasing drug dosages to examine their impact on the resistance mechanisms selected. Mutations in an efflux pump regulator, LfrR, were found in all of the evolved populations irrespective of the drug profile and population bottleneck, indicating a conserved efflux-based resistance mechanism. This mutation appeared early in the evolutionary trajectory, providing low-level resistance when present alone, with a further increase in resistance resulting from successive accumulation of other mutations. Notably, drug target mutations, similar to those observed in clinical isolates, were only seen above a threshold of greater than 4× the minimum inhibitory concentration (MIC). A combination of three mutations in the genes, lfrR, MSMEG_1959, and MSMEG_5045, was conserved across multiple lineages, leading to high-level resistance and preceding the appearance of drug target mutations. Interestingly, in populations evolved from parental strains lacking the lfrA efflux pump, the primary target of the lfrR regulator, no lfrR gene mutations are selected. Furthermore, evolutional trajectories originating from the ΔlfrA strain displayed early arrest in some lineages and the absence of target gene mutations in those that evolved, albeit delayed. Thus, blocking or inhibiting the expression of efflux pumps can arrest or delay the fixation of drug target mutations, potentially limiting the maximum attainable resistance levels.

Genetic variability and population genetic structure in the Caucasian Parsley Frog, Pelodytes caucasicus (Boulenger, 1896) based on microsatellite markers

The Caucasian Parsley Frog, Pelodytes caucasicus (Boulenger, 1896), is endemic to Caucasia, and its population is decreasing. Here, we present information on the genetic structure and diversity of populations from four provinces of Türkiye (Giresun, Trabzon, Rize, and Artvin) using microsatellite markers. Despite their small geographic range, the species’ populations showed moderate genetic differentiation, which could be a result of rapid genetic drift. Our results show that Trabzon and Giresun populations are genetically different from those of Rize and Artvin. We found considerably low genetic diversity in Artvin, Trabzon, and Giresun populations. The inbreeding co-efficient is also high in those localities (HO<HE). Despite low genetic diversity and a high inbreeding coefficient, we could not find any sign of a genetic bottleneck.

Low genetic differentiation despite high habitat fragmentation in an endemic and endangered species of Iridaceae from South America: implications for conservation

Abstract To conserve threatened species effectively, it is crucial to map the genetic variation of the remaining populations. Thus, using 15 microsatellites markers, from which 10 were specially developed for this study, we investigated genetic structure and gene flow patterns of Herbertia zebrina Deble, a critically endangered species endemic from grasslands of southern Brazil. We also investigated the degree of habitat fragmentation and the impacts on levels of genetic diversity, mating system and pollinators of the species. STRUCTURE and discriminant analysis of principal components identified the existence of three genetic clusters. Populations were not isolated by distance, and genetic differentiation among populations was low (7.0%). Migration rates were also low, but no evidence of genetic bottlenecks was found. However, effective population-scaled mutation rates (Θ) were &amp;lt; 1, suggesting that populations could be experiencing genetic drift, but the reason remains unknown. The results indicate that measurements of habitat fragmentation were not significantly correlated with genetic diversity estimates, which tend to increase with fragment size. H. zebrina was identified as an outcrossing species and specialized pollinators, such as Chalepogenus goeldianus and Lanthanomelissa betinae were rarely observed. Our findings suggest that genetic differentiation across multiple populations within the entire geographic distribution of H. zebrina is very low and populations may struggle to adapt to the current environmental and pollination changes. However, habitat fragmentation is still too recent to detect significant impacts on the levels of genetic variation. Thus, conservation plans are necessary to avoid further declines of this species.

Genomic stasis over millions of years in subseafloor sediment.

One of the significant challenges in microbiology is to understand the extent and mechanisms of evolution within life beneath the surface of the Earth. The population bottleneck that microbes in deep marine sediment experience implies that mutational and population genetic forces could lead to higher levels of relaxed selection and an increase in pseudogenes. To investigate this hypothesis, a group of Thalassospira strains were isolated from subseafloor sediment that is 3 to 6 million years old, as reported by Orsi and colleagues in 2021. These isolates, representing lineages that have been buried for millions of years, offer an excellent opportunity to study the evolution of life beneath the seafloor over a long period. The existence of closely related strains from environments on the surface of the Earth enabled us to examine the impact of selection within each group. We discovered that isolates from beneath the seafloor show lineage-specific similarities to Thalassospira from the surface world, both in the overall intensity of selection on the genome and in the specific genes affected by mutation. We found no signs of increased relaxed selection or other notable genomic changesin the genomes of the Thalassospira isolates from beneath the seafloor, suggesting that these subseafloor isolates were awakened from a million-year near-stasis. The unique genomic characteristics of each Thalassospira lineage from beneath the seafloor must then reflect genetic changes that surface-inhabiting decendants acquired in the past 3-6 million years. Remarkably, Thalassospira lineages beneath the surface appear to have stably maintained their genomes in the midst of metabolic dormancy and extremely long generation times.

Single-nucleotide polymorphisms and copy number variations drive adaptive evolution to freezing stress in a subtropical evergreen broad-leaved tree: Hexaploid wild Camellia oleifera

Subtropical evergreen broad-leaved trees are usually vulnerable to freezing stress, while hexaploid wild Camellia oleifera shows strong freezing tolerance. As a valuable genetic resource of woody oil crop C. oleifera, wild C. oleifera can serve as a case for studying the molecular bases of adaptive evolution to freezing stress. Here, 47 wild C. oleifera from 11 natural distribution sites in China and 4 relative species of C. oleifera were selected for genome sequencing. “Min Temperature of Coldest Month” (BIO6) had the highest comprehensive contribution to wild C. oleifera distribution. The population genetic structure of wild C. oleifera could be divided into two groups: in cold winter (BIO6 ≤ 0 °C) and warm winter (BIO6 > 0 °C) areas. Wild C. oleifera in cold winter areas might have experienced stronger selection pressures and population bottlenecks with lower Ne than those in warm winter areas. 155 single-nucleotide polymorphisms (SNPs) were significantly correlated with the key bioclimatic variables (106 SNPs significantly correlated with BIO6). Twenty key SNPs and 15 key copy number variation regions (CNVRs) were found with genotype differentiation > 50% between the two groups of wild C. oleifera. Key SNPs in cis-regulatory elements might affect the expression of key genes associated with freezing tolerance, and they were also found within a CNVR suggesting interactions between them. Some key CNVRs in the exon regions were closely related to the differentially expressed genes under freezing stress. The findings suggest that rich SNPs and CNVRs in polyploid trees may contribute to the adaptive evolution to freezing stress.