Population Bottlenecks Research Articles

Evolutionary Genomics Provides Insights Into Endangerment and Conservation of a Wild Apple Tree Species, Malus sieversii.

Understanding the evolutionary history of a species is essential for effective conservation management. Malus sieversii, a relict broad-leaf forest tree found in arid Central Asian mountains, has a narrow and fragmented distribution and is classified as an endangered species in China. This species is considered one of the ancestors of the domesticated apple trees. In the present study, we sampled five populations of M. sieversii and its wide-ranging congener M. baccata from China. Through deep whole-genome resequencing, we analyzed the population's genetic diversity, genetic structure, demographic history, fixation of deleterious mutations, and genomic divergence. Our results revealed that M. baccata exhibits a higher level of genetic diversity than M. sieversii. The effective population size of M. sieversii decreased, whereas that of M. baccata recovered after the bottleneck effect. In M. sieversii, the genetic structure of the Yili region was distinct from that of the Tacheng region. Populations at the rear edge of the Tacheng region showed a stronger fixation of deleterious mutations than those in the Yili region. Genomic divergence indicated that the positively selected genes were associated with physiological processes within the genomic islands between the Yili and Tacheng regions. Based on these findings, we recommend the establishment of two separate conservation units for the Yili and Tacheng lineages to preserve their genetic resources. Given the limited distribution range and high fixation rate of deleterious mutations, urgent protective measures are recommended for the Tacheng lineage.

Endangered Pinto/Northern Abalone (Haliotis kamtschatkana) are Panmictic Across Their 3700 km Range Along the Pacific Coast of North America.

Connectivity is integral to the dynamics of metapopulations through dispersal and gene flow, and understanding these processes is essential for guiding conservation efforts. Abalone, broadcast-spawning marine snails associated with shallow rocky habitats, have experienced widespread declines, and all seven North American species are threatened. We investigated the connectivity and population genomics of pinto/northern abalone (Haliotis kamtschatkana), the widest-ranging of abalone species. We employed reduced representation sequencing (RADseq) to generate single nucleotide polymorphism (SNP) data, assessing population connectivity and potential adaptive variation at 12 locations across the full range from Alaska to Mexico. Despite depleted populations, our analysis of over 6000 SNPs across nearly 300 individuals revealed that pinto abalone maintains a high genetic diversity with no evidence of a genetic bottleneck. Neutral population structure and isolation by distance were extremely weak, indicating panmixia across the species' range (global F ST = 0.0021). Phylogenetic analysis, principal components analysis, and unsupervised clustering methods all supported a single genetic population. However, slight population differentiation was noted in the Salish Sea and Inside Passage regions, with evidence for higher barriers to dispersal relative to outer coastal areas. This north-central region may also represent the species' ancestral range based on relatively low population-specific F ST values; the northern and southern extremes of the range likely represent range expansions. Outlier analysis did not identify consensus loci implicated in adaptive variation, suggesting limited adaptive differentiation. Our study sheds light on the evolutionary history and contemporary gene flow of this threatened species, providing key insights for conservation strategies, particularly in sourcing broodstock for ongoing restoration efforts.

Density-wave-like gap evolution in La3Ni2O7 under high pressure revealed by ultrafast optical spectroscopy

Density wave (DW) order is believed to be correlated with superconductivity in the recently discovered high-temperature superconductor La3Ni2O7. However, experimental investigations of its evolution under high pressure are still lacking. Here, we explore the quasiparticle dynamics in bilayer nickelate La3Ni2O7 single crystals using ultrafast optical pump-probe spectroscopy under high pressures up to 34.2 GPa. At ambient pressure, the temperature-dependent relaxation dynamics demonstrate a phonon bottleneck effect due to the opening of an energy gap around 151 K. The energy scale of the DW-like gap is determined to be 66 meV by the Rothwarf-Taylor model. Combined with recent experiential results, we propose that this DW-like transition at ambient pressure and low temperature is spin density wave (SDW). With increasing pressure, this SDW order is significantly suppressed up to 13.3 GPa before it completely disappears around 26 GPa. Remarkably, at pressures above 29.4 GPa, we observe the emergence of another DW-like order with a transition temperature of approximately 135 K, which is probably related to the predicted charge density wave (CDW) order. Our study provides the experimental evidences of the evolution of the DW-like gap under high pressure, offering critical insights into the correlation between DW order and superconductivity in La3Ni2O7.

Genome assembly of wisent (Bison bonasus) uncovers a deletion that likely inactivates the THRSP gene

The wisent (Bison bonasus) is Europe’s largest land mammal. We produced a HiFi read-based wisent assembly with a contig N50 value of 91 Mb containing 99.7% of the highly conserved single copy mammalian genes which improves contiguity a thousand-fold over an existing assembly. Extended runs of homozygosity in the wisent genome compromised the separation of the HiFi reads into parental-specific read sets, which resulted in inferior haplotype assemblies. A bovine super-pangenome built with assemblies from wisent, bison, gaur, yak, taurine and indicine cattle identified a 1580 bp deletion removing the protein-coding sequence of THRSP encoding thyroid hormone-responsive protein from the wisent and bison genomes. Analysis of 725 sequenced samples across the Bovinae subfamily showed that the deletion is fixed in both Bison species but absent in Bos and Bubalus. The THRSP transcript is abundant in adipose, fat, liver, muscle, and mammary gland tissue of Bos and Bubalus, but absent in bison. This indicates that the deletion likely inactivates THRSP in bison. We show that super-pangenomes can reveal potentially trait-associated variation across phylogenies, but also demonstrate that haplotype assemblies from species that went through population bottlenecks warrant scrutiny, as they may have accumulated long runs of homozygosity that complicate phasing.

Characterization of the Dynamic Flow Response in Microfluidic Devices.

The purpose of this study is to characterize the dynamic response of fluid flow in microchannels, which can show significant delay times before reaching steady flow conditions. Two main sources of these delays are numerically and experimentally investigated, the hydraulic compliance which originates from the flexibility of the system components (microchannel, tubing, syringe, etc.), and the compressibility of the liquid dead volume in the setup, also known as the "bottleneck effect". A fluid-structure interaction model is presented for the compliance of rectangular PDMS microchannels that is used to form a numerically based relation for the compliance as a function of the pressure and geometry. This relation is successfully able to predict the dynamics of the flow inside PDMS microchannels in stop-flow experiments. The time delays associated with the bottleneck effect is also shown when using different syringe volumes, microchannel resistances, and liquid types. In these tests, the bottleneck effect has a much larger effect compared to the compliance of the PDMS microchannels. This is true even when using softer PDMS by increasing the monomer-to-curing agent mixing ratio. The characterization that is presented here allows for a simple analysis of microfluidic networks using the hydraulic-circuit approach.

Modulating hot carrier relaxation and trapping dynamics in lead halide perovskite nanoplatelets by surface passivation.

Two-dimensional (2D) lead halide perovskite (LHP) nanoplatelets (NPLs) have recently emerged as promising materials for solar cells and light-emitting devices. The reduction of LHP dimensions introduces an abundance of surface defects, which can strongly influence the photophysical properties of these materials. However, an insightful understanding of the effect of surface defects on hot carrier (HC) relaxation, one of the important properties of LHP NPLs, is still inadequate. Herein, the HC relaxation and trapping dynamics in pristine and surface passivated two-layer (2L) CsPbBr3 NPLs have been investigated by using time-resolved spectroscopy. The results reveal that surface defects can trap HCs directly before they relax to the band edge, which accounts for the absence of the hot-phonon bottleneck (HPB) effect in LHP NPLs. After healing surface defects with a passivation agent, the relaxation time of HCs is extended from ∼73 to ∼130 fs in 2L CsPbBr3 NPLs, indicating that the channel of HCs trapped by the surface defects can be effectively blocked. Accordingly, the HPB effect is activated in surface-passivated CsPbBr3 NPLs. The finding of surface defect-related HC relaxation dynamics is important for guiding the development of high-performance LHP NPL devices related to HCs through surface defect engineering.

Population Genetics and Invasion History of the European Starling Across Aotearoa New Zealand.

The expansion of human settlements over the past few centuries is responsible for an unprecedented number of invasive species introductions globally. An important component of biological invasion management is understanding how introduction history and postintroduction processes have jointly shaped present-day distributions and patterns of population structure, diversity and adaptation. One example of a successful invader is the European starling (Sturnus vulgaris), which was intentionally introduced to numerous countries in the 19th century, including Aotearoa New Zealand, where it has become firmly established. We used reduced representation sequencing to characterise the genetic population structure of the European starling in New Zealand, comparing it to that present in sampling locations in the native range and invasive Australian range. The population structure and genetic diversity patterns we found suggested restricted gene flow from the majority of New Zealand to the northmost sampling location (Auckland). We also profiled genetic bottlenecks and shared outlier genomic regions, which supported historical accounts of translocations between both Australian subpopulations and New Zealand, and provided evidence of which documented translocation events were more likely to have been successful. Using these results as well as historic demographic patterns, we demonstrate how genomic analysis complements even well-documented invasion histories to better understand invasion processes, with direct implications for understanding contemporary gene flow and informing invasion management.

Hot Carrier Cooling and Multiphoton Absorption of Quasi-Type II ZnSeTe-Based Quantum Dots.

Ternary ZnSeTe quantum dots (QDs) are regarded as the most promising Cd-free blue emitters, while their fundamental optical properties such as hot carrier (HC) cooling process and multiphoton absorption (MPA) remain unclear, which will hinder their potential application. In this work, we compare the HC cooling processes of ZnSeTe/ZnSeS and ZnSeTe/ZnSeS/ZnS QDs and find that the HC cooling times of ZnSeTe/ZnSeS/ZnS QDs are insensitive to excitation intensity as a result of the suppressed hot-phonon bottleneck and Auger effect. Importantly, we have determined the two- to five-photon absorption cross sections of two kinds of QDs, highlighting the advantages of ZnS shells in enhancing MPA cross sections of ZnSeTe-based QDs. These insightful findings shed light on the underlying optical properties of ZnSeTe-based QDs and emphasize the critical role of the shell in engineering their HC cooling and MPA performance.

Population Genetic Characteristics of Siberian Roe Deer in the Cold Temperate Forest Ecosystem of the Greater Khingan Mountains, Northeast China.

This study focuses on the Siberian roe deer population in the Greater Khingan Mountains, Northeast China. The cold temperate forest ecosystem in this area is distinctive. The Siberian roe deer is a crucial ecological indicator species, and its living conditions hold significant importance for ecological balance. From the winter of 2019 to 2022, 269 fecal samples of Siberian roe deer were collected from four protected areas in the northern part of the Greater Khingan Mountains, Heilongjiang Province. These samples were comprehensively analyzed using mitochondrial DNA and microsatellite markers, combined with conservation genetics evaluation methods. The results revealed that 244 individuals were identified in the fecal samples. The results of a Cyt b genetic analysis of the samples indicated that the haplotype and nucleotide diversity were 88.1% and 20.3%, respectively. The evaluation of 14 pairs of microsatellite loci showed that the average number of alleles was 11.2, and the average expected and observed heterozygosity were 0.672 and 0.506, respectively. Therefore, the overall genetic diversity level is high, but some populations of Siberian roe deer are at risk. AMOVA analysis and STRUCTURE Bayesian clustering confirmed the existence of obvious genetic differentiation among the populations. Historical studies have shown that the HZ and SH populations underwent the earliest diffusion events, and the BJC and SL populations also exhibited related signs (HZ: Huzhong Nature Reserve in the Greater Khingan Mountains; SH: Shuanghe National Nature Reserve in Heilongjiang Province; BJC: Heilongjiang Beijicun National Nature Reserve; SL: Songling District in Heilongjiang Province). Mismatch distribution and neutral tests indicated no expansion events or bottleneck effects in the population, and the inbreeding coefficient was positive, suggesting the possibility of inbreeding. The development potential of the population in the future varies among the various local populations. This study supports the biodiversity of Siberian roe deer at the genetic level to save the population and provides important scientific basis and reference for the protection and management of Siberian roe deer.

A Whole-Genome Survey and the Mitochondrial Genome of Acanthocepola indica Provide Insights into Its Phylogenetic Relationships in Priacanthiformes.

Acanthocepola indica, a deep-sea snake fish, is primarily found in the Indo-west Pacific region, including India, Korea, Japan, and the South China Sea. The taxonomic classification of A. indica based on morphological characteristics remains inaccurate and unclear. In this study, we utilized next-generation sequencing to generate comprehensive genomic data for A. indica. The estimated genome size of A. indica was 422.95 Mb, with a heterozygosity ratio of 1.02% and a sequence repeat ratio of 22.43%. Our analysis suggested that A. indica is diploid, and the draft genome assembly consists of 1,059,784 contigs with a contig N50 of 1942 bp. We identified a total of 444,728 simple sequence repeats in the genome of A. indica. Furthermore, we successfully assembled the complete mitochondrial genome (16,439 bp) of A. indica, which included 13 protein-coding genes, 22 tRNA genes and 2 rRNA genes. Phylogenetic analysis based on mitochondrial genomes revealed that A. indica is closely related to Acanthocepola krusensternii and Cepola schlegelii, providing evidence that the family Cepolidae belongs to the order Priacanthiformes. Population size dynamics analysis indicated that A. indica experienced a bottleneck effect during the Pleistocene Glacial Epoch, likely due to the changes in glacial cycles and sea level fluctuations since ~800 Kya.

Genetic Diversity and Evolutionary Biology of Indian Wildlife- A Review

The genetic diversity and evolutionary biology of Indian wildlife, emphasizing the critical role of genetic variability in ensuring species adaptability and long-term survival. India is one of the world’s megadiverse countries, home to a wide range of unique flora and fauna spread across its biodiversity hotspots, including the Western Ghats and the Eastern Himalayas. However, rapid habitat fragmentation, deforestation, and poaching have severely impacted the genetic health of many wildlife species, leading to reduced gene flow, population bottlenecks, and increased inbreeding. This has heightened the risk of extinction for small, isolated populations such as the Asiatic lion and the Great Indian bustard. Genetic studies using advanced genomic tools have provided key insights into the population structure, phylogenetic relationships, and adaptive potential of species like the Bengal tiger, Asian elephant, and snow leopard. Conservation strategies, including genetic rescue, habitat corridors, and the use of captive breeding programs, are recommended to preserve genetic diversity and prevent further genetic erosion. Technological advances, such as non-invasive sampling and bioinformatics, are transforming wildlife research, enabling more precise and less intrusive genetic monitoring. The integration of genetic data into conservation policies and practices is essential for developing targeted management plans that maintain the evolutionary potential of Indian wildlife.

Delineating genomic features for wild guanaco conservation

Abstract The South American fauna has endured challenges such as illegal hunting, cattle expansion, climate change, and landscape fragmentation. Despite ongoing conservation efforts that aim to address these issues, genetic diversity remains overlooked. We genotyped 126 Lama guanicoe individuals from an area of 2 million km2 in Patagonia and Cuyo using the 60K SNPs Axiom-Camelids, and we assessed population viability through genetic diversity, inbreeding, and population size. We then explored population connectivities through network analyses, genetic differentiation, and Bayesian approaches. Our findings reveal six genetic clusters: Cuyo, Somuncura, North Patagonia, Central Patagonia, South Patagonia, and Tierra del Fuego Island (TDFI). Cuyo and TDFI guanacos differed from others due to isolation-by-distance and geographical barriers, respectively. Cuyo exhibited the highest degree of allele conservation, but TDFI faced heightened vulnerability due to isolation and increased homozygosity. Sharp bottlenecks in Cuyo and North Patagonia coincided with the expansion of sheep farming, while bottlenecks in the other populations occurred during the Little Ice Age. North Patagonia acted as a probable contact zone, facilitating mixing of the Cuyo, Somuncura, and Central Patagonia populations. The Central and South Patagonian populations presented the highest gene flow. Thus, genomic advances help to define distinct conservation units (genetic stocks) to guide management practices and decisions.

Microsatellite Markers & Mitochondrial D-Loop Based Phylogenetic And Diversity Analysis In Gabrali Cattle.

The Gabrali cattle is a multipurpose breed, native to Khyber Pakhtunkhwa, Pakistan. Despite its economic importance, scientific data about its phylogeny and genetic diversity is scarce. To address this issue, the present study was conducted on thirty (30) unrelated Gabrali male and female animals, from which blood samples were collected and DNA was extracted. Twelve (12) microsatellite loci and 1159bp of D-loop region were amplified via PCR and visualized on a 2% agarose gel. Sanger sequencing technique was used to sequence the D-loop amplicons. The microsatellite loci revealed 83 alleles with MNA (mean no of alleles per locus) = 8.8, the Ho (observed heterozygosity) and He (expected heterozygosity) of all loci were 0.58 and 0.50 respectively, mean PIC (Polymorphic Information content) = 0.59 and FIS (Inbreeding coefficient) = 0.056 using GeneAlEx® software. Microsatellite analysis revealed a normal allelic distribution across the breed, consistent with Hardy-Weinberg equilibrium. D-loop sequencing revealed eight haplotypes with 30 SNPs using DNA SP 6.0 software. High AT content was observed than GC content i.e. 55.9% and 44.1% respectively, while the transition to transversion ratio was R = 10:1. The value of Haplotype and Nucleotides diversity was Hd = 0.8601 ± SD = 0.0895 and Π = 0.0136 ± SD = 0.00197 respectively. Phylogenetic analysis done using Neighbor-joining method with bootstraps value of 1000, revealed the monophyletic clade of both Gabrali and Bos indicus haplotypes. Furthermore, the introgression of genes from national cattle breeds into Gabrali cattle was observed. It is concluded that Gabrali cattle have common ancestry with Bos indicus having no threats of genetic bottleneck having substantial genetic diversity.

Tracking the North American Asian Longhorned Beetle Invasion With Genomics.

Biological invasions pose significant threats to ecological and economic stability, with invasive pests like the Asian longhorned beetle (Anoplophora glabripennis Motschulsky, ALB) causing substantial damage to forest ecosystems. Effective pest management relies on comprehensive knowledge of the insect's biology and invasion history. This study uses genomics to address these knowledge gaps and inform existing biosurveillance frameworks. We used 2768 genome-wide single nucleotide polymorphisms to compare invasive A. glabripennis populations in North America, using genomic variation to trace their sources of invasion and spread patterns, thereby refining our understanding of this species' invasion history. We found that most North American A. glabripennis infestations were distinct, resulting from multiple independent introductions from the native range. Following their introduction, all invasive populations experienced a genetic bottleneck which was followed by a population expansion, with a few also showing secondary spread to satellite infestations. Our study provides a foundation for a genome-based biosurveillance tool that can be used to clarify the origin of intercepted individuals, allowing regulatory agencies to strengthen biosecurity measures against this invasive beetle.

Genetic Variation in Jamaican Populations of the Coffee Berry Borer, Hypothenemus hampei.

The coffee berry borer (CBB) Hypothenemus hampei was first described in Africa in 1867 and has spread to all major coffee-producing regions worldwide, including Jamaica. Using long-read sequencing, we produced a new high-quality reference genome (172.7 Mb) for the Jamaican strain of the CBB, with 93% of the genome assembled into 14 scaffolds. Whole genome sequencing of pooled samples from different populations across Jamaica showed that the CBB harbors low levels of genetic diversity alongside an excess of low-frequency alleles, indicative of a recent genetic bottleneck. The analyses also showed a recent surge in the activity of transposable elements (TEs), particularly LINE/R1 and LTR/Gypsy elements, within CBB populations. Our findings offer first insights into the evolutionary genomics of CBB populations in Jamaica, highlighting the potential role of TEs in shaping the genome of this important pest species.

Clonal dynamics after allogeneic haematopoietic cell transplantation

Allogeneic haematopoietic cell transplantation (HCT) replaces the stem cells responsible for blood production with those from a donor1,2. Here, to quantify dynamics of long-term stem cell engraftment, we sequenced genomes from 2,824 single-cell-derived haematopoietic colonies of ten donor–recipient pairs taken 9–31 years after HLA-matched sibling HCT3. With younger donors (18–47 years at transplant), 5,000–30,000 stem cells had engrafted and were still contributing to haematopoiesis at the time of sampling; estimates were tenfold lower with older donors (50–66 years). Engrafted cells made multilineage contributions to myeloid, B lymphoid and T lymphoid populations, although individual clones often showed biases towards one or other mature cell type. Recipients had lower clonal diversity than matched donors, equivalent to around 10–15 years of additional ageing, arising from up to 25-fold greater expansion of stem cell clones. A transplant-related population bottleneck could not explain these differences; instead, phylogenetic trees evinced two distinct modes of HCT-specific selection. In pruning selection, cell divisions underpinning recipient-enriched clonal expansions had occurred in the donor, preceding transplant—their selective advantage derived from preferential mobilization, collection, survival ex vivo or initial homing. In growth selection, cell divisions underpinning clonal expansion occurred in the recipient’s marrow after engraftment, most pronounced in clones with multiple driver mutations. Uprooting stem cells from their native environment and transplanting them to foreign soil exaggerates selective pressures, distorting and accelerating the loss of clonal diversity compared to the unperturbed haematopoiesis of donors.

Genetic polymorphism of merozoite surface protein 1 and merozoite surface protein 2 in the Vietnam Plasmodium falciparum population

BackgroundPlasmodium falciparum merozoite surface proteins 1 (PfMSP1) and 2 (PfMSP2) are potential candidates for malaria vaccine development. However, the genetic diversity of these genes in the global P. falciparum population presents a significant challenge in developing an effective vaccine. Hence, understanding the genetic diversity and evolutionary trends in the global P. falciparum population is crucial.MethodsThis study analyzed the genetic variations and evolutionary changes of pfmsp1 and pfmsp2 in P. falciparum isolates from the Central Highland and South-Central regions of Vietnam. DNASTAR and MEGA7 programs were utilized for analyses. The polymorphic nature of global pfmsp1 and pfmsp2 was also investigated.ResultsA total of 337 sequences of pfmsp1 and 289 sequences of pfmsp2 were obtained. The pfmsp1 and pfmsp2 from Vietnam revealed a higher degree of genetic homogeneity compared to those from other malaria-endemic countries. Remarkably, the allele diversity patterns of Vietnam pfmsp1 and pfmsp2 differed significantly from those of neighboring countries in the Greater Mekong Subregion. Declines in allele diversity and polymorphic patterns of Vietnam pfmsp1 and pfmsp2 were observed.ConclusionsThe Vietnam P. falciparum population might be genetically isolated from the parasite populations in other neighboring GMS countries, likely due to geographical barriers and distinct evolutionary pressures. Furthermore, bottleneck effects or selective sweeps may have contributed to the genetic homogeneity of Vietnam pfmsp1 and pfmsp2.

Antibonding valence states induce low lattice thermal conductivity in metal halide semiconductors

Reduction of phonon mediated thermal transport properties, i.e., lattice thermal conductivity (κL), of semiconductors can strongly affect the performance of thermoelectrics and optoelectronics. Although extrinsic routes to reduce κL have been achieved through selective scattering of phonons via doping, alloying, and hierarchical nano-structuring, semiconductors with intrinsically low κL have recently gained widespread attention due to their ability to decouple electronic and phonon transports. While innate low κL in crystalline semiconductors is a desired requirement to achieve high performance thermoelectrics, the solar upconversion efficiency of photovoltaics based on metal halide perovskites (MHPs) have been shown to increase due to their ultralow κL through the hot-phonon bottleneck effect. Therefore, understanding the microscopic mechanisms underlying ultralow κL in crystalline semiconductors is extremely important. Several structural factors that are intrinsic to a material have been shown to strongly influence the reduction of κL. Among them, the presence of rattling atoms, lone-pair electrons, and large lattice anharmonicity have been widely studied. Here, we bring out yet another largely unexplored intrinsic characteristic of materials related to the filled antibonding valence states (AVS) near the Fermi level, which are shown to induce low κL in crystalline compounds. We focus our review on an emerging class of compounds–metal halide semiconductors including MHPs and investigate the interplay between structures, chemical bonding and κL, carefully curating from literature a list of 33 compounds having different structure dimensionality with known κL. We established a universal connection between the elastic moduli, speeds of sound, and κL with the presence of AVS just below the Fermi level. We found that large peak in the AVS correlates positively with lower values of elastic moduli, speeds of sound, and κL, providing antibonding states based design criteria of low-κL compounds. Furthermore, we discuss different synthesis strategies, which are crucial for experimental realization of ultralow κL through structure manipulation. Additionally, we outline how chemical bonding data can be utilized in machine learning models for predictive modeling of κL. We hope that our approach of understanding low-κL through the viewpoint of chemical bonding theory would encourage exploration of phonon transport properties in other families of materials having filled AVS that can provide further insights on the structure-bonding-property relationships aiding novel materials design approaches.

Abundant genetic variation is retained in many laboratory schistosome populations.

Schistosomes are obligately sexual blood flukes that can be maintained in the laboratory using freshwater snails as intermediate and rodents as definitive hosts. The genetic composition of laboratory schistosome populations is poorly understood: whether genetic variation has been purged due to serial inbreeding or retained is unclear. We sequenced 19 - 24 parasites from each of five laboratory Schistosoma mansoni populations and compared their genomes with published exome data from four S. mansoni field populations. We found abundant genomic variation (0.897 - 1.22 million variants) within laboratory populations: these retained on average 49% (π = 3.27e-04 - 8.94e-04) of the nucleotide diversity observed in the four field parasite populations (π = 1.08e-03 - 2.2e-03). However, the pattern of variation was very different in laboratory and field populations. Tajima's D was positive in all laboratory populations except SmBRE, indicative of recent population bottlenecks, but negative in all field populations. Current effective population size estimates of laboratory populations were lower (2 - 258) compared to field populations (3,174 - infinity). The distance between markers at which linkage disequilibrium (LD) decayed to 0.5 was longer in laboratory populations (59 bp - 180 kb) compared to field populations (9 bp - 9.5 kb). SmBRE was the least variable; this parasite also shows low fitness across the lifecycle, consistent with inbreeding depression. The abundant genetic variation present in most laboratory schistosome populations has several important implications: (i) measurement of parasite phenotypes, such as drug resistance, using laboratory parasite populations will determine average values and underestimate trait variation; (ii) genome-wide association studies (GWAS) can be conducted in laboratory schistosome populations by measuring phenotypes and genotypes of individual worms; (iii) genetic drift may lead to divergence in schistosome populations maintained in different laboratories. We conclude that the abundant genetic variation retained within many laboratory schistosome populations can provide valuable, untapped opportunities for schistosome research.

Population Genetic Investigation of Hypophthalmichthys nobilis in the Yangtze River Basin Based on RAD Sequencing Data.

The Bighead carp (Hypophthalmichthys nobilis), a primary freshwater aquaculture species in China, faces challenges due to over-exploitation and environmental changes. We leveraged RAD-seq to perform a comprehensive population genetic analysis on 14 H. nobilis populations sampled from the Yangtze River (13 populations) and the Marseilles Reach of the Illinois River (one population). Analysis of genetic diversity showed that different parameters demonstrated varied inferences, and notably, Zhongxian (ZX2), Wanhzou (WZ2), Yangzhou hatchery (YZYZ), Yangzhou (YZ), and Taihu (TH) populations showed apparent heterozygote deficiency. Linkage disequilibrium (LD) analysis exhibited a trend of higher linkage disequilibrium in populations from the upper reaches of the Yangtze River, followed by those from the middle reaches and then those from the lower reaches. Additionally, the reconstructed polygenetic tree and PCA plot clustered all populations into 2 major subgroups, while the results of structure analysis indicated 4 ancestors. The pairwise FST values ranged from 0 to 0.5530. Among these, high FST values (0.1931-0.5530) were only observed between populations WZ2, YZ, YZYZ, and the remaining 11 populations. Furthermore, genetic bottlenecks were observed in all populations 20-30 thousand years ago. Overall, the research offers insights essential for genetic management practices for sustainable aquaculture and biodiversity conservation of bighead carp.