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As a globally distributed perennial Gramineae, Phragmites australis can adapt to harsh ecological environments and has significant economic and environmental values. Here, we performed a complete assembly and annotation of the mitogenome of P. australis using genomic data from the PacBio and BGI platforms. The P. australis mitogenome is a multibranched structure of 501,134 bp, divided into two circular chromosomes of 325,493 bp and 175,641 bp, respectively. A sequence-simplified succinate dehydrogenase 4 gene was identified in this mitogenome, which is often translocated to the nuclear genome in the mitogenomes of gramineous species. We also identified tissue-specific mitochondrial differentially expressed genes using RNAseq data, providing new insights into understanding energy allocation and gene regulatory strategies in the long-term adaptive evolution of P. australis mitochondria. In addition, we studied the mitogenome features of P. australis in more detail, including repetitive sequences, gene Ka/Ks analyses, codon preferences, intracellular gene transfer, RNA editing, and multispecies phylogenetic analyses. Our results provide an essential molecular resource for understanding the genetic characterisation of the mitogenome of P. australis and provide a research basis for population genetics and species evolution in Arundiaceae. [ABSTRACT FROM AUTHOR]

Anthropogenic pressures such as hunting are increasingly driving the localised functional extinctions of large‐ and medium‐sized wildlife in tropical forests, a phenomenon broadly termed 'defaunation'. Concurrently in these areas, smaller‐bodied species benefit from factors such as competitive release and increase in numbers. This transformation of the wildlife community can impact species interactions and ecosystem services such as seed dispersal and seed‐mediated geneflow with far‐reaching consequences. Evidence for negative genetic effects following defaunation is well‐documented in large‐seeded plants that require large frugivores for long‐distance seed dispersal. However, how defaunation affects plants with small or medium‐small seeds (< 1.5 cm), which tend to be consumed and dispersed by frugivorous mutualists of a range of body sizes and responses to anthropogenic threats, is not well understood. To better understand defaunation's impacts on tropical plant communities, we investigated spatial and genetic patterns in a hyperabundant medium‐to‐small‐seeded palm, Euterpe precatoria in three sites with different defaunation levels. Results indicate that defaunation is associated with higher fine‐scale spatial genetic structure among seedlings and increased spatial clustering within seedling cohorts and between seedlings and conspecific adults, as well as a reduction in nearest‐neighbour distances between seedlings and conspecific adults. There were no clear effects on inbreeding or genetic diversity. However, we caution these trends may indicate that defaunation reduces seed dispersal services for species previously presumed to be robust to deleterious effects of losing large frugivores by virtue of having smaller seeds and broad suites of dispersal agents, and negative downstream effects on genetic diversity could occur. [ABSTRACT FROM AUTHOR]

Adaptive radiations are rich laboratories for exploring, testing, and understanding key theories in evolution and ecology because they offer spectacular displays of speciation and ecological adaptation. Particular challenges to the study of adaptive radiation include high levels of species richness, rapid speciation, and gene flow between species. Over the last decade, high‐throughput sequencing technologies and access to population genomic data have lessened these challenges by enabling the analysis of samples from many individual organisms at whole‐genome scales. Here we review how population genomic data have facilitated our knowledge of adaptive radiation in five key areas: (1) phylogenetics, (2) hybridization, (3) timing and rates of diversification, (4) the genomic basis of trait evolution, and (5) the role of genome structure in divergence. We review current knowledge in each area, highlight outstanding questions, and focus on methods that facilitate detection of complex patterns in the divergence and demography of populations through time. It is clear that population genomic data are revolutionising the ability to reconstruct evolutionary history in rapidly diversifying clades. Additionally, studies are increasingly emphasising the central role of gene flow, re‐use of standing genetic variation during adaptation, and structural genomic elements as facilitators of the speciation process in adaptive radiations. We highlight hybridization—and the hypothesized processes by which it shapes diversification—and questions seeking to bridge the divide between microevolutionary and macroevolutionary processes as rich areas for future study. Overall, access to population genomic data has facilitated an exciting era in adaptive radiation research, with implications for deeper understanding of fundamental evolutionary processes across the tree of life. [ABSTRACT FROM AUTHOR]

Background: Ginkgo biloba L., an iconic living fossil, challenges traditional views of evolutionary stasis. While nuclear genomic studies have revealed population structure across China, the evolutionary patterns reflected in maternally inherited plastomes remain unclear, particularly in the Sichuan Basin - a potential glacial refugium that may have played a crucial role in Ginkgo's persistence. Results: Analysis of 227 complete plastomes, including 81 newly sampled individuals from the Sichuan Basin, revealed three distinct maternal lineages differing from known nuclear genome patterns. We identified 170 sequence variants and extensive RNA editing (235 sites) with a bias toward hydrophobic amino acid conversions, suggesting active molecular evolution. A previously undocumented haplotype (IIA2), predominant in western Sichuan Basin populations, showed close genetic affinity with rare refugial haplotypes. Western populations exhibited higher haplotypic diversity and distinctive genetic structure, supporting the basin's role as both glacial refugium and corridor for population expansion. Ancient trees (314–784 years) provided evidence for interaction between natural processes and historical human dispersal in shaping current genetic patterns. Conclusions: Our findings demonstrate substantial genetic diversity within Sichuan Basin Ginkgo populations and reveal dynamic molecular evolution through plastome variation and RNA editing patterns, challenging the notion of evolutionary stasis in this living fossil. This study provides crucial genomic resources for understanding Ginkgo's evolution and informs conservation strategies for this endangered species. [ABSTRACT FROM AUTHOR]

Tequila bats (genus Leptonycteris) have gained attention for their critical role in pollinating different plant species, especially Agave spp. and columnar cacti. Leptonycteris nivalis is the largest nectar-feeding bat in the Americas, and the females exhibit migratory behavior during the breeding season. Due to its relatively small and seemingly declining population sizes, this species is protected by government agencies in the United States and Mexico. We conducted population genetics and phylogeographic analyses to elucidate the genetic structure and demographic history of the species using two mitochondrial markers and a Y chromosome-associated gene, to describe both maternal and paternal lineages. We estimated high haplotypic diversity measures for the different markers (Dloop—Hd = 0.775; Cyt-b—Hd = 0.937; DBY -Hd = 0.946). We found that geographic genetic differentiation is very low, and there is high connectivity among localities. The estimated divergence time between L. nivalis and L. yerbabuenae, the other species in the genus found in Mexico, aligns with previous estimates for the genus (6.91–9.43 mya). A demographic expansion was detected approximately at 600 ka—700 ka (thousands of years ago). The historical demographic changes observed in L. nivalis appear to be associated with environmental shifts during the Pleistocene, which likely impacted the distribution range of the plants that these bats feed on, such as Agave species. [ABSTRACT FROM AUTHOR]

Nepal, largely covered by the Himalayan mountains, hosts indigenous populations with distinct linguistic, cultural, and genetic characteristics. Among these populations, the Raute, Nepal's last nomadic hunter-gatherers, offer a unique insight into the genetic and demographic history of Himalayan foragers. Despite strong cultural connections to other regional foragers, the genetic history of this population remains understudied. This study presents newly genotyped genome-wide SNP data of the Raute to explore their genetic isolation, their origins and potential as an older foraging lineage, and their genetic connections to other regional foragers. Our results show that high levels of inbreeding in the Raute indicate recent genetic isolation. Effective population size estimates suggest a dramatic population decline around 50 generations ago. Strong genetic similarity to Nepalese populations of various subsistence styles highlights a dynamic history of genetic interactions prior to isolation, with particular closeness to historical foragers like the Kusunda and Tharu, but excludes an ancient foraging lineage origin. The study underscores the complexity of human population dynamics in the Himalayas, suggesting a history of extensive interaction between foragers and farmers, followed by isolation and demographic decline among the Raute. [ABSTRACT FROM AUTHOR]

The flat-headed loach (Oreonectes platycephalus) is a small fish inhabiting headwaters of hillstreams of southern China. Its local populations are characterized by low genetic diversity and exceptionally high differentiation, making it an ideal model for studying small population isolates' persistence and adaptive potential. However, the lack of Oreonectes reference genomes limits endeavours toward these ambitions. We assembled the first haplotype-resolved chromosome-level genome of the genus Oreonectes using PacBio HiFi and Hi-C technologies. This genome consists of two haplotypes (24 pseudo-chromosomes in each), with sizes of 565.68 Mb (haplotype A) and 521.13 Mb (haplotype B) and scaffold N50 lengths of 22.80 Mb and 21.91 Mb, respectively. Chr01 was identified as the likely sex chromosome pair. After masking repetitive elements which accounted for 34.43% to 36.44% of the genome, there are 27,127 protein-coding genes in haplotype A and 25,576 in haplotype B. The availability of this haplotype-resolved chromosome-level reference genome will facilitate the study of population and conservation genetics of the flat-headed loach and other Oreonectes species. [ABSTRACT FROM AUTHOR]

Liogenys is a neotropical genus widely distributed in South America and characterized by rhizophagous feeding habits. Taxonomy survey of Liogenys from Chile revealed a species complex consisting of L. palpalis, L. obesula and an undescribed morphotype. Morphological data alone are not sufficient to distinguish between them. The three-species hypothesis was tested using phylogenetic and preliminary phylogeographic analyses, as well as unilocus delimitation methods using mitochondrial (COI) and nuclear (ITS2) markers. The tree-based PTP method based on ITS2 considers both L. obesula and the undescribed morphotype to be variants of L. palpalis , a single, polymorphic species. Haplotypes from 12 localities along central Chile revealed four genetically structured populations, with statistical variance (54.34%) only within them. Isolated populations occur in Southern Santiagan Region and coastal desert. There are eight species of Liogenys in Chile. Diagnoses are provided for five species. Liogenys elguetai sp. nov. is described. Five synonyms are proposed for three species. Liogenys pubisternis , a new synonym of L. palpalis , is transferred from Diplotaxis. Lectotypes are provided for four names (L. castaneus, L. grandis, L. pubisternis , and Melolontha palpalis). Liogenys boliviensis is recorded for the first time from Chile and Peru, extending the distribution of Liogenys to northernmost Chile. [ABSTRACT FROM AUTHOR]

The influence of long-term climatic changes such as glacial cycles on the history of living organisms has been a subject of research for decades, but the detailed population dynamics during the environmental fluctuations and their effects on genetic diversity and genetic load are not well understood on a genome-wide scale. The Japanese macaque (Macaca fuscata) is a unique primate adapted to the cold environments of the Japanese archipelago. Despite the past intensive research for the Japanese macaque population genetics, the genetic background of Japanese macaques at the whole-genome level has been limited to a few individuals, and the comprehensive demographic history and genetic differentiation of Japanese macaques have been underexplored. We conducted whole-genome sequencing of 64 Japanese macaque individuals from 5 different regions, revealing significant genetic differentiation and functional variant diversity across populations. In particular, Japanese macaques have low genetic diversity and harbor many shared and population-specific gene loss, which might contribute to population-specific phenotypes. Our estimation of population demography using phased haplotypes suggested that, after the strong population bottleneck shared among all populations around 400 to 500 kya, the divergence among populations initiated around 150 to 200 kya, but there has been the time with strong gene flow between some populations after the split, indicating multiple population split and merge events probably due to habitat fragmentation and fusion during glacial cycles. These findings not only present a complex population history of Japanese macaques but also enhance their value as research models, particularly in neuroscience and behavioral studies. This comprehensive genomic analysis sheds light on the adaptation and evolution of Japanese macaques, contributing valuable insights to both evolutionary biology and biomedical research. [ABSTRACT FROM AUTHOR]

The nocturnal aye-aye, Daubentonia madagascariensis , is one of the most elusive lemurs on the island of Madagascar. The timing of its activity and arboreal lifestyle has generally made it difficult to obtain accurate assessments of population size using traditional census methods. Therefore, alternative estimates provided by population genetic inference are essential for yielding much needed information for conservation measures and for enabling ecological and evolutionary studies of this species. Here, we utilize genomic data from 17 individuals—including 5 newly sequenced, high-coverage genomes—to estimate this history. Essential to this estimation are recently published annotations of the aye-aye genome which allow for variation at putatively neutral genomic regions to be included in the estimation procedures, and regions subject to selective constraints, or in linkage to such sites, to be excluded owing to the biasing effects of selection on demographic inference. By comparing a variety of demographic estimation tools to develop a well-supported model of population history, we find strong support for two demes, separating northern Madagascar from the rest of the island. Additionally, we find that the aye-aye has experienced two severe reductions in population size. The first occurred rapidly, ∼3,000 to 5,000 years ago, and likely corresponded with the arrival of humans to Madagascar. The second occurred over the past few decades and is likely related to substantial habitat loss, suggesting that the species is still undergoing population decline and remains at great risk for extinction. [ABSTRACT FROM AUTHOR]

Population structure provides essential information for developing meaningful conservation plans. This is especially important in remote places, such as oceanic islands, where limited population sizes and genetic isolation can make populations more susceptible and self-dependent. In this study, we assess and compare the relatedness, population genetics and molecular ecology of two sympatric Acropora species, A. surculosa sensu Randall & Myers (1983) and A. cf. verweyi Veron & Wallace, 1984 around Guam, using genome-wide sequence data (ddRAD). We further contrast our findings with the results of a recent study on back reef A. cf. pulchra (Brook, 1891) to assess the impact of habitat, colony morphology, and phylogenetic relatedness on these basic population genetic characteristics and generate testable hypotheses for future studies. Both target species were found to have small effective population sizes, low levels of genetic diversity, and minimal population structure around Guam. Nonetheless, A. cf. verweyi had significantly higher levels of genetic diversity, some population structure as well as more clones, close relatives and putative loci under selection. Comparisons with A. cf. pulchra indicate a potentially significant impact by habitat on population structure and genetic diversity while colony morphology seems to significantly impact clonality. This study revealed significant differences in the basic population genetic makeup of two sympatric Acropora species on Guam. Our results suggest that colony morphology and habitat/ecology may have a significant impact on the population genetic makeup in reef corals, which could offer valuable insights for future management decisions in the absence of genetic data. [ABSTRACT FROM AUTHOR]

Subacute sclerosing panencephalitis (SSPE) is a lethal neurological disorder occurring several years after measles. Reconstruction of the evolution of the measles virus (MeV) genome in an SSPE case suggested that the matrix (M) protein mutation M-F50S, when added to other mutations, drove neuropathogenesis. However, whether and how M-F50S would promote spread independently from other mutations was in question. We investigated here the cell specificity of MeV spread in this brain and documented that both neurons and astrocytes were heavily infected. We then generated recombinant MeV with individual mutations in the three proteins of the viral membrane fusion apparatus, M, fusion (F), and hemagglutinin (H). These viruses reached similar titers as the parental wild-type virus, kept the respective mutations upon passage, and infected cells expressing the tissue-specific MeV receptors SLAM and nectin-4 with similar efficiencies. However, after inoculation of receptor-negative neurons and astrocytes differentiated from human induced pluripotent stem cells, only MeV M-F50S spread with moderate efficiency; the parental virus and its derivatives coding for a hyperfusogenic F protein, or for a cytoplasmic tail-mutated H protein, did not spread. When delivered to primary mouse neurons by cell-mediated neurite overlay, MeV M-F50S frequently reached the cell bodies and occasionally formed small infectious centers, while the other MeV reached the cell bodies only sporadically. These results demonstrate that, in neuronal cell cultures, M-F50S can enable receptor-independent spread in the absence of other mutations, and validate the inference that this single amino acid change initiated ubiquitous MeV brain spread. IMPORTANCE Measles virus (MeV), a non-integrating negative-strand RNA virus, rarely causes subacute sclerosing panencephalitis (SSPE) several years after acute infection. During brain adaptation, the MeV genome acquires multiple mutations reducing the dependence of its membrane fusion apparatus (MFA) from an activating receptor. It was proposed that one of these mutations, matrix protein F50S, drove neuropathogenesis in an SSPE case. We report here that, in two types of neuronal cultures, a recombinant MeV with only this mutation gained receptor-independent spread, whereas viruses expressing MFA proteins with other mutations acquired during brain adaptation did not. Our results validate the inference that M-F50S initiated ubiquitous MeV brain spread resulting in lethal disease. They also prompt studies of the impact of analogous amino acid changes of the M proteins of other nonsegmented negative-strand RNA viruses on their interactions with membrane lipids and cytoskeletal components. [ABSTRACT FROM AUTHOR]

Major changes in genetic variation are generally considered deleterious to populations. The massive biodiversity of insects distinguishes them from other animal groups. Insect deviant effective population sizes, alternative modes of reproduction, advantageous inbreeding, endosymbionts, and other factors translate to highly specific inbreeding and outbreeding outcomes. We review the evidence for inbreeding and outbreeding depression and consequences across wild and captive insect populations, highlighting conservation, invasion, and commercial production entomology. We not only discern patterns but also explain why they are often inconsistent or absent. We discuss how insect inbreeding and outbreeding depression operates in complex, sometimes contradictory directions, such as inbreeding being detrimental to individuals but beneficial to populations. We conclude by giving recommendations to (a) more comprehensively account for important variables in insect inbreeding and outbreeding depression, (b) standardize the means of measuring genetic variation and phenotypic impacts for insect populations so as to more reliably predict when inbreeding or outbreeding depression applies, and (c) outline possible remediation options, both nongenetic and genetic, including revision of restrictive international trade laws. [ABSTRACT FROM AUTHOR]

Simple Summary: The present study employed a total of twenty-two microsatellite loci for the purpose of assessing and analyzing the genetic diversity between and within different populations of honeybees in the Czech Republic. A total of 3647 samples of bees from hives and 553 samples from flowers were collected uniformly from 77 geographical regions (districts). All investigated microsatellite markers demonstrated sufficient variability and moderate heterozygosity. Additionally, the population structure was identified. The findings of this study indicate that there is moderate genetic diversity among honeybee populations defined by districts, but this is independent of evidence for at least three major genetic clusters. To date, no study has been conducted to investigate the diversity in honeybee populations of Apis mellifera in the Czech Republic. Between 2022 and 2023, worker bees were collected from colonies distributed throughout the Czech Republic in 77 districts, and their genetic differences were examined using 22 microsatellite loci. The samples were obtained from hives (n = 3647) and through the process of capture on flowers (n = 553). Genetic diversity parameters were assessed for both populations in all 77 districts. The findings demonstrated that honeybee populations exhibit moderate genetic diversity, as evidenced by the number of observed alleles, the Shannon index, and heterozygosity values. There was no discrepancy in diversity between hive and flower samples. Diversity characteristics were determined: mean observed heterozygosity 0.55 (hives) and 0.56 (flowers), and fixation index 0.58 for both populations. The average number of alleles per locus was 13.77 and 11.18 from hives and flowers, respectively. The low FST and FIS values (they measured the level of genetic differentiation between populations and the level of inbreeding, respectively) suggest the absence or minimal genetic diversity within and among studied populations. The genetic variation was calculated as 2% and 1% between populations, 8% and 6% between individuals within populations, and 91% and 93% between all individuals in samples from hives and flowers, respectively. Cluster and DAPC (discriminant analysis principal component) analysis classified the bee samples collected from across the country into three and five to six distinguishable groups, respectively. The honeybee population in the Czech Republic displays sufficient diversity and a partial structure. However, there appears to be no correlation between the genetic groups and the geographic regions to which they are assigned. [ABSTRACT FROM AUTHOR]

The species Niphon spinosus (Cuvier, 1829) is the only representative of the family Niphonidae and the genus Niphon, and its taxonomic history is complicated; it is still unclear in a phylogenetic sense. In this study, we report the complete mitochondrial genome of N. spinosus (OP391482), which was determined to be 16,503 bp long with biased A + T contents (53.8%) using next-generation technology. The typical set of 13 protein-coding genes (PCGs), 2 rRNA genes, 22 tRNA genes, and one control region (D-loop) are included in the mitochondrial genome. The H-strand encoded 28 genes (14 tRNA, 2 rRNA, and 12 PCGs), and D-loop, whereas the L-strand encoded the remaining 9 genes (8 tRNA and ND6). Its nucleotide composition, gene arrangement, codon usage patterns, and tRNA secondary structures are identical with other members of the Percoidei suborder. Furthermore, we reconstructed phylogenetic trees based on the 13 PCGs. The resulting phylogenetic trees showed N. spinosus placing as a separate lineage within the family Niphonidae, its close relationship to Trachinus draco (Trachinidae), and the clustering of major subfamilies like Luciopercinae and Percinae of the Percoidei suborder. These findings will contribute to future studies on the evolutionary history, population genetics, molecular taxonomy, and phylogeny of N. spinosus and related species. [ABSTRACT FROM AUTHOR]

Simple Summary: This study highlights the genetic diversity of Bulinus globosus in Kenya, demonstrating that the AkInt3 intron is a valuable marker for detecting detailed intra-specific genetic variation, surpassing COI sequences. The presence of DNA recombination between AkInt3 haplogroups suggests that cross-fertilization is a common reproductive strategy, which may reduce inbreeding effects. Additionally, evidence of potential polyploidy points to further genetic complexity, warranting more studies. The findings indicate that AkInt3 primers could aid genetic studies in other Bulinus species, with distinct haplogroups suggesting significant genetic diversity. Future research across Africa will be essential for understanding B. globosus evolution and its role in disease transmission. Urinary schistosomiasis is caused by the blood fluke Schistosoma haematobium, which is predominantly found in Africa. The freshwater snail Bulinus globosus is its main intermediate host. The species that make up the B. globosus group are genetically complex, and their taxonomic status remains controversial. Genetic variation, heterozygosity, and DNA recombination in B. globosus were examined using the mitochondrial cytochrome c oxidase subunit 1 (COI) and the intron 3 region of the arginine kinase gene (AkInt3). A total of 81 B. globosus snails were collected from three different localities in Kwale County, Kenya. Genomic diversity, heterozygosity, DNA recombination, and haplotype network were calculated using AkInt3 sequences. Low polymorphism in the COI sequence divided B. globosus into six haplotypes (C1–C6). However, AkInt3 sequencing studies showed high polymorphisms, classifying 81 B. globosus snails into 44 haplotypes (H1–H44). These haplotypes were separated into three haplogroups (I–III). AkInt3 sequence heterozygosity was also found. DNA recombination haplotypes between haplogroups were commonly found in heterozygous samples. AkInt3 sequence studies showed high levels of genetic polymorphism and heterozygosity, supporting its use as a genetic marker for elucidating the population genetics of B. globosus. Furthermore, our study showed that B. globosus populations in Kenya form a "species complex". [ABSTRACT FROM AUTHOR]

Simple Summary: The invasive charru mussel, Mytella strigata, has been spreading rapidly in the West Pacific, including the South China Sea. This study analyzed genetic variations in seven populations sampled in both spring and autumn 2023 using mitochondrial nad2 gene fragments. Results revealed high haplotype diversity but low nucleotide diversity for all populations, suggesting recent rapid expansion after a genetic bottleneck. On the whole, genetic diversity was higher in spring populations compared to autumn populations. These findings highlight seasonal differences in genetic variation and provide insights into the molecular characteristics of M. strigata population expansion in China. Native to tropical America, the charru mussel, Mytella strigata, has been spreading rapidly in the West Pacific Ocean, including the South China Sea. In order to study the adaptive evolution of M. strigata and examine the present status of invasion in China, the mitochondrial nad2 gene fragment was employed to analyze the genetic variations of seven populations sampled in both spring and autumn 2023. Results showed that all the populations had high haplotype diversity (>0.5) and low nucleotide diversity (<0.005), suggesting the ongoing rapid expansion following a genetic bottleneck. The Zhanjiang population had the highest genetic diversity in spring with 22 haplotypes, 37 polymorphic sites, and haplotype diversity, nucleotide diversity, and the average number of nucleotide differences being 0.911, 0.00623, and 4.341, respectively. However, in autumn, the Shanwei population had the most haplotypes (11) and polymorphic sites (19), with the highest haplotype diversity value of 0.891, while the Qunjian population had the highest nucleotide diversity (0.00392) and average number of nucleotide differences (2.809). Combining geographic populations by seasons confirmed lower genetic diversity in autumn compared to spring, evidenced by fewer haplotypes and polymorphic sites, reduced haplotype diversity and nucleotide diversity, and lower genetic distance within populations. These findings provided evidence for understanding the molecular characteristics of M. strigata population expansion in China. [ABSTRACT FROM AUTHOR]

Theoretical studies from diverse areas of population biology have shown that demographic stochasticity can substantially impact evolutionary dynamics in finite populations, including scenarios where traits that are disfavored by natural selection can nevertheless increase in frequency through the course of evolution. Here, we analytically describe the eco-evolutionary dynamics of finite populations from demographic first principles. We investigate how noise-induced effects can alter the evolutionary fate of populations in which total population size may vary stochastically over time. Starting from a generic birth-death process, we derive a set of stochastic differential equations (SDEs) that describe the eco-evolutionary dynamics of a finite population of individuals bearing discrete traits. Our equations recover well-known descriptions of evolutionary dynamics, such as the replicator-mutator equation, the Price equation, and Fisher's fundamental theorem in the infinite population limit. For finite populations, our SDEs reveal how stochasticity can predictably bias evolutionary trajectories to favor certain traits, a phenomenon we call "noise-induced biasing." We show that noise-induced biasing acts through two distinct mechanisms, which we call the "direct" and "indirect" mechanisms. While the direct mechanism can be identified with classic bet-hedging theory, the indirect mechanism is a more subtle consequence of frequency- and density-dependent demographic stochasticity. Our equations reveal that noise-induced biasing may lead to evolution proceeding in a direction opposite to that predicted by natural selection in the infinite population limit. By extending and generalizing some standard equations of population genetics, we thus describe how demographic stochasticity appears alongside, and interacts with, the more well-understood forces of natural selection and neutral drift to determine the eco-evolutionary dynamics of finite populations of nonconstant size. [ABSTRACT FROM AUTHOR]

Population genetics often assumes that random mutations lead to a uniform distribution of phenotypic variation, which is then acted upon by natural selection. However, growing evidence suggests that the phenotypic variation available to natural selection is not isotropic, but rather constrained and biased by various factors, including genetic architecture, mutation, and developmental systems. Such limitations and biases in the variability of phenotypic characters are referred to as variational bias. It is critical to clarify what we measure when we measure variational bias, and how different types of variational bias relate to one another. A more rigorous investigation into the role of developmental bias in the genotype-to-phenotype map is needed to bridge micro-evolution and macro-evolution. The extraordinary diversity and adaptive fit of organisms to their environment depends fundamentally on the availability of variation. While most population genetic frameworks assume that random mutations produce isotropic phenotypic variation, the distribution of variation available to natural selection is more restricted, as the distribution of phenotypic variation is affected by a range of factors in developmental systems. Here, we revisit the concept of developmental bias – the observation that the generation of phenotypic variation is biased due to the structure, character, composition, or dynamics of the developmental system – and argue that a more rigorous investigation into the role of developmental bias in the genotype-to-phenotype map will produce fundamental insights into evolutionary processes, with potentially important consequences on the relation between micro- and macro-evolution. We discuss the hierarchical relationships between different types of variational biases, including mutation bias and developmental bias, and their roles in shaping the realized phenotypic space. Furthermore, we highlight the challenges in studying variational bias and propose potential approaches to identify developmental bias using modern tools. The extraordinary diversity and adaptive fit of organisms to their environment depends fundamentally on the availability of variation. While most population genetic frameworks assumes that random mutations produce isotropic phenotypic variation, the distribution of variation available to natural selection is more restricted, as the distribution of phenotypic variation is affected by a range of factors in developmental systems. Here, we revisit the concept of developmental bias – the observation that the generation of phenotypic variation is biased due to the structure, character, composition, or dynamics of the developmental system – and argue that a more rigorous investigation into the role of developmental bias in the genotype-to-phenotype map will produce fundamental insights into evolutionary processes, with potentially important consequences on the relation between micro- and macro-evolution. We discuss the hierarchical relationships between different types of variational biases, including mutation bias and developmental bias, and their roles in shaping the realized phenotypic space. Furthermore, we highlight the challenges in studying variational bias and propose potential approaches to identify developmental bias using modern tools. [ABSTRACT FROM AUTHOR]

Aspergillus fumigatus is a globally distributed mold and a major cause of opportunistic infections in humans. Because most infections are from environmental exposure, it is critical to understand environmental populations of A. fumigatus. Soil is a major ecological niche for A. fumigatus. Here, we analyzed 748 soil isolates from 21 locations in six provinces and one territory in Canada. All isolates were genotyped using nine microsatellite markers. Due to small sample size and/or close proximities for some local samples, these isolates were grouped into 16 local geographic and ecological populations. Our results indicated high allelic and genotypic diversities within most local and provincial populations. Interestingly, low but statistically significant genetic differentiations were found among geographic populations within Canada, with relatively similar proportions of strains and genotypes belonging to two large genetic clusters. In Hamilton, Ontario, and Vancouver, BC, where two and three ecological populations were analyzed, respectively, we found limited genetic difference among them. Most local and provincial populations showed evidence of both clonality and recombination, with no population showing random recombination. Of the 748 soil isolates analyzed here, two were resistant to triazole antifungals. We discuss the implications of our results to the evolution and epidemiology of A. fumigatus. [ABSTRACT FROM AUTHOR]

Microsatellite markers are cost-effective, rapid, efficient, and show great advantages in in large-sample kinship analysis and population structure studies. However, microsatellite loci are seriously underdeveloped in non-model organisms. The plateau zokor (Eospalax baileyi) is a key species living underground in the Tibetan Plateau, the effective management of which has long been challenging. In this study, we analyzed the distribution characteristics and functions of microsatellites in the genome of plateau zokors, and their polymorphic sites. The mononucleotide and dinucleotide types being the most abundant in the genome. The largest number of microsatellites and their abundance in the intergenic region whereas the smallest number of microsatellites and their abundance in the coding region. The coding sequences containing microsatellites were annotated to 52 major functional genes and assigned 19,358 Gene Ontology entries. The Kyoto Encyclopedia of Genes and Genomes pathway was the most enriched in the signal transduction pathway. Thirteen pairs of polymorphic loci were successfully amplified, with the number of alleles ranging from 3 to 8, observed heterozygosity ranging from 0.059 to 0.810, and expected heterozygosity ranging from 0.469 to 0.854. These microsatellite markers provide a cornerstone for studies on the identification of parentage and population genetics of plateau zokors. [ABSTRACT FROM AUTHOR]

Cercospora leaf spot (CLS), caused by Cercospora beticola, is a major foliar disease impacting sugar beet production worldwide. The development of new resistant sugar beet hybrids is a powerful tool to better manage the disease, but it is unclear how these hybrids affect CLS epidemiology. We used a molecular epidemiology approach to study natural epidemics of CLS affecting two susceptible and two resistant sugar beet hybrids at two field sites. Infected plants were geotagged on a weekly basis. Isolations of C. beticola were made from infected leaves and genotyped using six simple‐sequence repeat loci to identify clones. We determined that CLS epidemics had a later onset in plots planted to resistant hybrids, but once the pathogen established an infection, there was little difference between resistant and susceptible hybrids in the probability of localized spread and dispersal. We found that different clones often infected the same leaf and that clusters of infected plants were often colonized by a mixture of clones. There was little overall difference in genetic diversity of C. beticola collected on resistant and susceptible hybrids; however, genotypic diversity was lower on the resistant hybrid at one site, suggestive of a selection bottleneck. At the end of the epidemic infections were not randomly distributed across the fields and we found that a single clone could spread over a distance of 100 m during a growing season. [ABSTRACT FROM AUTHOR]

Mirror-image flowers (enantiostyly) involve a form of sexual asymmetry in which a flower's style is deflected either to the left or right side, with a pollinating anther orientated in the opposite direction. This curious floral polymorphism, which was known but not studied by Charles Darwin, occurs in at least 11 unrelated angiosperm families and represents a striking example of adaptive convergence in form and function associated with cross-pollination by insects. In several lineages, dimorphic enantiostyly (one stylar orientation per plant, both forms occurring within populations) has evolved from monomorphic enantiostyly, in which all plants can produce both style orientations. We use a modelling approach to investigate the emergence of dimorphic enantiostyly from monomorphic enantiostyly under gradual evolution. We show using adaptive dynamics that depending on the balance between inbreeding depression following geitonogamy, pollination efficiency, and plant density, dimorphism can evolve from an ancestral monomorphic population. In general, the newly emergent dimorphic population is stable against invasion of a monomorphic mutant. However, our model predicts that under certain ecological conditions, for example, a decline of pollinators, dimorphic enantiostyly may revert to a monomorphic state. We demonstrate using population genetics simulations that the observed evolutionary transitions are possible, assuming a plausible genetic architecture. [ABSTRACT FROM AUTHOR]

"Molecular Ecology" is a highly influential journal in evolution and ecology, ranking fourth in Evolutionary Biology and eighth in Ecology based on published citable items and citation counts. The journal's impact factor, EigenFactor score, and Google Scholar's h5-index are all impressive. Updates to subject categories reflect advancements in genomic tools and resources, including areas like microbiome and epigenetic research. The journal is also working to reconcile FAIR and CARE principles regarding data sharing, Indigenous rights, and interests. The editorial board has undergone changes, with Dr. Ben Sibbett being promoted to co-Editor-in-Chief alongside Loren Rieseberg. The journal's social media presence remains strong, and it continues to publish valuable reviews and special issues. Notable awards include the 2024 Molecular Ecology Prize awarded to Professor Michael Whitlock and the Harry Smith Prize awarded to Robert Masaki Hechler. The journal expresses gratitude to all contributors and welcomes suggestions for improvement. [Extracted from the article]

The Notomicrus traili species group (Coleoptera: Noteridae) is a lineage of aquatic beetles distributed throughout South America and extends into Mexico and the West Indies. Previous research has revealed a species complex within this group, with multiple distinct clades sharing overlapping distributions and lineages attributed to N. traili and the closely related Notomicrus gracilipes recovered as polyphyletic. Here, we perform targeted capture of ultraconserved elements (UCEs) to examine relationships and patterns of evolution within the N. traili group. First, we use short‐read whole‐genome sequencing of four noterid genera to design a noterid‐specific UCE probe set (Noteridae 3.4Kv1) targeting over 3400 unique loci. Using this probe set, we capture UCE data from population‐level sampling of 44 traili group specimens from across the Neotropics, with an emphasis on the Guiana Shield where distributions of several putative N. traili group populations overlap. We subject the resulting data matrix to various trimming and data completeness treatments and reconstruct the phylogeny with both concatenated maximum likelihood and coalescent congruent methods. We recover robust phylogenetic estimates that identify several phylogenetically distinct clades within the traili group that share overlapping distributions. To test for the genetic distinctiveness of populations, we extract single nucleotide polymorphism (SNP) data from UCE alignments using a chimeric reference method to map UCE‐enriched reads and examine patterns of genetic clustering using principal component analyses (PCAs) and STRUCTURE. Population genetic results are highly concordant with recovered phylogenetic structure, revealing a high degree of co‐ancestry shared within identified clades, contrasting with limited ancestry sharing between clades. We recover a pattern consistent with repeated diversification and dispersal of the traili group in the Neotropics, highlighting the efficacy of a tailored UCE approach for facilitating shallow‐scale phylogenetic reconstructions and population genetic analyses, which can reveal novel aspects of coleopteran phylogeography. [ABSTRACT FROM AUTHOR]

Understanding population genetic diversity and evolutionary dynamics of marine fish species can provide theoretical bases for fishery management and germplasm conservation, especially facing a changing environment. The rockfish species in genus Sebastiscus are economically important species for farming and sport fisheries in China, Japan and Korea. In this study, inter-annual and inter-specific comparisons on genetic diversity, population differentiation and historical demography of S. marmoratus and S. tertius collected from coastal waters of Zhangzhou, China were conducted using mitochondrial control region sequences. High levels of genetic diversity were observed in both species, indicating high adaptive potential to environmental changes. Demographic analyses detected recent population expansion in population S. tertius (Ste-2020) and population S. marmoratus collected in 2020 (Sma-2020), yet failed in population collected in 2016 (Sma-2016). Moreover, in population Sma-2020, novel haplotypes were detected and grouped into a separate sub-branch, revealed by neighbour-joining topology. Detected recent population expansion and novel haplotypes might be considered as a response to environmental changes. Besides, results of genetic differentiation analysis suggested high intra-specific genetic variation in both species. These genetic data and information will provide novel implications for strengthening the management of S. marmoratus and S. tertius fisheries in climate change scenarios. [ABSTRACT FROM AUTHOR]

The Japanese Archipelago comprises a chain of islands; therefore, gaps between islands can represent potential dispersal barriers for coastal species, especially those inhabiting tidal flats. This study investigates the population genetic structure of the soldier crab Mictyris guinotae (Brachyura: Thoracotremata: Mictyridae) using mitochondrial COI gene sequences. Specimens were collected from Tanegashima Island and five Ryukyu Islands, covering the species' known geographic distribution. Although the Mantel test identified a moderate trend (r2 = 0.41, P < 0.01) for isolation by distance, all populations exhibited high haplotype and nucleotide diversities, with neither analysis of molecular variance nor ΦST detecting genetic differences among populations. Notably, the northernmost population (Tanegashima Island), approximately 260 km from the nearest known geographic distribution on Amami-Oshima Island, shared haplotypes with other populations, although the number of specimens from Tanegashima Island is only four due to its small population size. This absence of genetic differences among populations of M. guinotae differs from other intertidal organisms in the region examined in previous studies. Mismatch distributions suggest contrasting demographic history in M. guinotae and the sand bubbler crab Scopimera ryukyuensis, which has been revealed to show population genetic structuring despite its similar geographic distribution to M. guinotae. The present study provides another case of genetic diversity among intertidal organisms in the Ryukyu Islands. [ABSTRACT FROM AUTHOR]

Yellowstone National Park is home to the only plains bison population that has continually existed as wildlife, on the same landscape, through the population bottleneck of the late 19th century. Nevertheless, by the early 1900s, only 23 wild bison were known to have survived poaching. Salvation efforts included the addition of 18 females from Montana and 3 bulls from Texas to augment this population. A century later, nuclear microsatellite-based population-level assessment revealed two genetically distinct bison subpopulations. However, in 2016, an analysis of mitochondrial haplotypes showed the two founding lineages were distributed throughout the park. This study is designed to delineate any current substructure in the Yellowstone bison population by strategically sampling the two major summer breeding herds and the two major winter ranges. Population-level metrics were derived using the same microsatellite loci as the original study along with a newly developed set of highly informative bison-specific single nucleotide polymorphisms. Our analyses reveal that the modern bison in Yellowstone National Park currently consists of one interbreeding population, composed of two subunits. [ABSTRACT FROM AUTHOR]

The identification of positive selection has been framed as a classification task, with Convolutional Neural Networks (CNNs) already outperforming summary statistics and likelihood-based approaches in accuracy. Despite the prevalence of CNN-based methods that manipulate the pixels of images representing raw genomic data as a preprocessing step to improve classification accuracy, the efficacy of these pixel-rearrangement techniques remains inadequately examined, particularly in the presence of confounding factors like population bottlenecks, migration and recombination hotspots. We introduce a set of pixel rearrangement algorithms aimed at enhancing CNN classification accuracy in detecting selective sweeps. These algorithms are employed to assess the performance of four CNN models for selective sweep detection. Our findings illustrate that the judicious application of rearrangement algorithms notably enhances the overall classification accuracy of a CNN across various datasets simulating confounding factors. We observed that sorting the columns of the genomic matrices has higher on CNN performance than rearranging the sequences. To some extent, these rearrangement algorithms are more robust to misspecified demographic models compared with the utilization of the default preprocessing algorithm as suggested by the respective authors of each CNN architecture. We provide the data rearrangement algorithms as a distinct package available for download at: https://github.com/Zhaohq96/Genetic-data-rearrangement. • Data rearrangement algorithms can boost the overall classification accuracy of CNNs in identifying selective sweeps. • To some extent, data rearrangement algorithms improve classification robustness to demographic model misspecification. • Suitable rearrangement algorithms per CNN are robust to varying genomic window sizes. [ABSTRACT FROM AUTHOR]

GenoTools, a Python package, streamlines population genetics research by integrating ancestry estimation, quality control, and genome-wide association studies capabilities into efficient pipelines. By tracking samples, variants, and quality-specific measures throughout fully customizable pipelines, users can easily manage genetics data for large and small studies. GenoTools' "Ancestry" module renders highly accurate predictions, allowing for high-quality ancestry-specific studies, and enables custom ancestry model training and serialization specified to the user's genotyping or sequencing platform. As the genotype processing engine that powers several large initiatives, including the NIH's Center for Alzheimer's and Related Dementias and the Global Parkinson's Genetics Program, GenoTools was used to process and analyze the UK Biobank and major Alzheimer's disease and Parkinson's disease datasets with over 400,000 genotypes from arrays and 5,000 whole genome sequencing samples and has led to novel discoveries in diverse populations. It has provided replicable ancestry predictions, implemented rigorous quality control, and conducted genetic ancestry-specific genome-wide association studies to identify systematic errors or biases through a single command. GenoTools is a customizable tool that enables users to efficiently analyze and scale genotyping and sequencing (whole genome sequencing and exome) data with reproducible and scalable ancestry, quality control, and genome-wide association studies pipelines. [ABSTRACT FROM AUTHOR]

The phylogeography of many forest-dwelling species in Europe is well understood. However, our knowledge regarding the genetics of saproxylic beetles remains insufficient. This knowledge gap extends to understanding the influence of both quaternary history and contemporary forest dynamics on population genetics. To fill this gap, we conducted a systematic review and meta-analysis of recent literature concerning saproxylic beetle taxa with available genetic data. We include both threatened and common species in our study, which enabled us to generalize our findings to the whole saproxylic community. Results suggest a latitudinal decrease in diversity in most species, likely influenced by Pleistocene glaciation and subsequent population expansions from southern refugia. Additionally, we observed an east–west gradient in diversity, with threatened species exhibiting higher diversity towards the east. This may reflect historical forest dynamics and anthropogenic pressures, such as heavy wood logging in Western Europe. Similarly, we found a pattern along altitude, with populations in higher elevation forests, which are often more natural, exhibiting higher diversity. Furthermore, we identified distinct phylogenetic units or genetic clusters in southern Europe reflecting the distribution of glacial refugia. For some taxa, distinct units were also reported in eastern Europe where populations spread from Asian refugia. Central Europe showed a high number of phylogenetic units, although unique (private) clades or clusters were absent. Most likely it is an effect of the presence of beetles that originated from various refugia belonging to different phylogenetic units. This study brings insights into general phylogeographic patterns, which have previously been examined only for single representatives of saproxylic beetles. It should also help in the proper planning of conservation and management efforts for wood-dwelling beetles. [ABSTRACT FROM AUTHOR]

Sea turtles are highly migratory and predominantly inhabit oceanic environments, which poses significant challenges to the study of their life cycles. Research has traditionally focused on nesting females, utilizing nest counts and mark-recapture methods, while male behavior remains understudied. To address this gap, previous studies have analyzed the genotypes of females and hatchlings to indirectly infer male genotypes and evaluate the extent of multiple paternity within populations. Our research aimed to investigate the presence of multiple paternity in loggerhead turtle (Caretta caretta) nests for the first time in Brazil. We analyzed 534 hatchlings from 43 nests associated with 42 females during the 2017/18 to 2019/20 nesting seasons, using four highly polymorphic, species-specific microsatellite markers (nDNA). Parentage tests were conducted to reconstruct paternal genotypes and determine the rates of multiple paternity within clutches. Our results revealed that 72.09% of clutches were sired by multiple males, with contributions ranging from one to six males per clutch. Additionally, seven out of 88 males (7.95%) were found to have sired clutches from multiple females, with some males contributing to more than one clutch within and across breeding seasons. The breeding sex ratio (BSR) was calculated to be 2.09 males per female. While multiple paternity is a common phenomenon among sea turtles, this study is the first to document polyandry in loggerheads in Brazil and the first to provide evidence of polygyny in this species globally. This research establishes a crucial database for future studies in Brazil, with a focus on the BSR of the Southwest Atlantic subpopulation, offering essential insights for developing effective management strategies for this vulnerable population. [ABSTRACT FROM AUTHOR]

Simple Summary: Gastric carcinoma is a type of cancer with a strong breed predisposition in the Tervueren and Groenendael long-haired varieties of the Belgian Shepherd dog. We conducted a study of the incidence of gastric carcinoma in Tervueren and Groenendael dogs that were born in the Netherlands between 2000 and 2010. We found that on average during this period 3.8% of long-haired Belgian Shepherds develop gastric carcinoma during their lifetime. For the Tervueren variety the percentage of reported dogs that developed gastric carcinoma during their lifetime was 4.7% and for the Groenendael 2.1%. No sex predilection was demonstrated. The median age at death from gastric carcinoma in these dogs was 9.0 years. The heritability was calculated to be 0.53, indicating a strong hereditary component to development of the disease. The odds of developing gastric carcinoma in offspring are higher if at least one parent is affected compared to if parents are not known to be affected. Effective selection against this disease in this dog population is challenging, as dogs are often diagnosed with this disease after they have been used for breeding. Background: Gastric carcinoma in the Tervueren and Groenendael varieties of the Belgian Shepherd dog is commonly recognized and carries a grave prognosis. Information on incidence and heritability is necessary to design an effective selection strategy against this disease. Methods: A database of cases and controls was built including cases with Tier 1 (confirmed via endoscopy or post-mortem) and Tier 2 evidence of gastric carcinoma. From the database, a birth cohort of dogs born in the Netherlands in the period 2000–2010 was used, together with pedigree information to calculate heritability using a mixed models approach. Univariate linear regression was used to test the influence of the gastric carcinoma status of the parents on gastric carcinoma occurrence in offspring. Results: For Tervueren the 10-year cumulative incidence was 4.7%, and for the Groenendael this was 2.1%. There was no sex predilection. The odds of gastric carcinoma were 5.0 (2.4–11.0) in offspring where at least one parent was known to be affected versus at least one parent was known to be unaffected. Heritability, based on analysis using pedigree information from 338 dogs with gastric carcinoma and 159 controls, was 0.53 (SE 0.15). Conclusions: Gastric carcinoma in the Belgian Shepherd Tervueren and Groenendael varieties has a high incidence in the Dutch population and a strong genetic component. Because it is a late onset disease, dogs have often already been used for breeding before they are diagnosed. An effective breeding strategy for reducing disease incidence therefore relies on the identification of genetic risk factors influencing its development. [ABSTRACT FROM AUTHOR]

Introduction: Malaria molecular surveillance (MMS) can provide insights into transmission dynamics, guiding national control programs. We previously designed AmpliSeq assays for MMS, which include different traits of interest (resistance markers and pfhrp2/3 deletions), and SNP barcodes to provide population genetics estimates of Plasmodium vivax and Plasmodium falciparum parasites in the Peruvian Amazon. The present study compares the genetic resolution of the barcodes in the AmpliSeq assays with widely used microsatellite (MS) panels to investigate population genetics of Amazonian malaria parasites. Methods: We analyzed 51 P. vivax and 80 P. falciparum samples from three distinct areas in the Loreto region of the Peruvian Amazon: Nueva Jerusalén (NJ), Mazan (MZ), and Santa Emilia (SE). Population genetics estimates and costs were compared using the SNP barcodes (P. vivax : 40 SNPs and P. falciparum: 28 SNPs) and MS panels (P. vivax : 16 MS and P. falciparum : 7 MS). Results: The P. vivax genetic diversity (expected heterozygosity, He) trends were similar for both markers: He MS = 0.68–0.78 (p > 0.05) and He SNP = 0.36–0.38 (p > 0.05). P. vivax pairwise genetic differentiation (fixation index, FST) was also comparable: FST-MS = 0.04–0.14 and FST-SNP = 0.03–0.12 (pairwise p > 0.05). In addition, P. falciparum genetic diversity trends (He MS = 0–0.48, p < 0.05; He SNP = 0–0.09, p < 0.05) and pairwise FST comparisons (FST-MS = 0.14–0.65, FST-SNP = 0.19–0.61, pairwise p > 0.05) were concordant between both panels. For P. vivax , no geographic clustering was observed with any panel, whereas for P. falciparum , similar population structure clustering was observed with both markers, assigning most parasites from NJ to a distinct subpopulation from MZ and SE. We found significant differences in detecting polyclonal infections: for P. vivax , MS identified a higher proportion of polyclonal infections than SNP (69% vs. 33%, p = 3.3 × 10−5), while for P. falciparum , SNP and MS detected similar rates (46% vs. 31%, p = 0.21). The AmpliSeq assay had a higher estimated per-sample cost compared to MS ($183 vs. $27–49). Discussion: The SNP barcodes in the AmpliSeq assays offered comparable results to MS for investigating population genetics in P. vivax and P. falciparum populations, despite some discrepancies in determining polyclonality. Given both panels have their respective advantages and limitations, the choice between both should be guided by research objectives, costs, and resource availability. [ABSTRACT FROM AUTHOR]

ABSTRACT In this computer note I introduce software, PopCluster, that implements a new likelihood method for unsupervised population structure analysis from marker data. To infer a coarse population structure, it assumes the mixture model and adopts a simulated annealing algorithm to make a maximum likelihood clustering analysis, partitioning the sampled individuals into a predefined number of clusters. To deduce a fine population structure, it further assumes the admixture model and employs an expectation maximisation algorithm to estimate individual admixture proportions. PopCluster has many features. First, it is one of just a couple of model‐based methods that can handle both biallelic and multiallelic markers in the same framework. Second, it is the first population structure analysis method that uses both Message Passing Interface (MPI) and openMP to exploit multiple CPUs with both shared and distributed memories and has the capacity to handle genomic data with millions of individuals and millions of loci. Third, the algorithms for both mixture and admixture analyses are fast, rendering PopCluster favourably in computational efficiency over previous methods in analysing genomic data. Fourth, PopCluster is built for Windows, Linux and Mac platforms, and its Windows version has an integrated GUI that can conveniently visualise analysis results and facilitate data input. Fifth, its Windows version has a built‐in simulation module designed to simulate genotype data under admixture, hybridization or migration models. PopCluster provides a valuable toolset for researchers to simulate, infer and visualise individual admixture and population genetic structure, hybridization and migration using marker data. [ABSTRACT FROM AUTHOR]

RESEARCH HIGHLIGHTSEimeria are globally enzootic parasites that can cause coccidiosis in chickens. Until recently, remarkably little had changed over the last 40 years in the fundamental biology that underpins detection and control of Eimeria. Tools such as microscopy and lesion scoring remain central to diagnosis, and control still relies on routine supplementation of diets with anticoccidial drugs or application of live vaccines. However, refocusing on aspects of economics, molecular biology, and bacteriology that relate to coccidiosis has prompted considerable change in dogma. The cost of coccidiosis in chickens has been difficult to define, but updating models created in the 1990s suggested an annual cost to the global poultry industry of £10.4 billion in 2016, rising to a peak of £12.9 billion in 2022 under the influence of the COVID-19 pandemic and regional wars. Surveillance using genomic sequence-based diagnostics has suggested the presence of three new Eimeria species, supported by subsequent biological characterization of each line. Use of microbiome sequencing pipelines has revealed the breadth of impact Eimeria infection exerts on enteric microbiota, contributing to dysbiosis and deteriorating litter conditions. Enhanced understanding of Eimeria and the consequences of infection can be used to improve control and diagnosis with relevance to productivity and welfare, creating opportunities to optimize anticoccidial drug use.The cost of coccidiosis in chickens fluctuates considerably, peaking in 2022.Three new Eimeria species can infect chickens and escape current vaccines.Eimeria infection exerts wide-ranging effects on enteric microbiota.The cost of coccidiosis in chickens fluctuates considerably, peaking in 2022.Three new Eimeria species can infect chickens and escape current vaccines.Eimeria infection exerts wide-ranging effects on enteric microbiota. [ABSTRACT FROM AUTHOR]

AbstractNavigating the challenges in apomixis population genetics requires a comprehensive understanding of its unique genetic consequences. This review explores the population genetics of apomixis, comparing sexual and apomictic populations, research challenges, and outlining future directions. Apomictic plants form clonal seeds, and arise from sexual species through hybridization and/or polyploidy. Sexual species generate genetic variation via meiotic recombination, random mating, and gradual accumulation of beneficial mutations. In contrast, apomicts rely on similar mechanisms to generate genetic variation but at a much slower rate, primarily through ´residual´ sexuality. Clonality in apomicts also promotes the accumulation of deleterious mutations. Additionally, recurrent origins of apomicts from sexual progenitors, especially via hybridization contribute to genetic diversity in apomictic populations. These processes, with varying rates of recombination, gene flow, and genotype fixation, lead to distinct genetic structures between sexual and apomictic populations. Reevaluating the evolutionary mechanisms like gene flow, genetic drift, mutation rates, and selection pressures is, therefore, crucial for understanding the processes driving genetic differentiation and genomic structure in apomictic populations. Research on apomixis has advanced from early documentation in the 18th century to modern cytological and genomic approaches. Early theoretical models of apomixis inheritance, adjusted for polyploid and nonsexual populations, provided foundational insights, while recent genome-wide studies have shed light on the genetic basis and evolutionary dynamics of apomixis across taxa. However, significant gaps remain in understanding population-level evolutionary forces shaping apomixis. Future research in comparative genomics of apomictic and sexual relatives will help identify genes and epigenetic marks of adaptive significance. Functional evaluation of genes associated with selective advantages, coupled with specialized bioinformatic tools, will improve our understanding of genotype-phenotype interactions. Integrative approaches combining multi-omics, morphology, and ecological information are key to resolving the population genetic complexities of apomictic taxa and their adaptation and speciation processes. Moreover, machine learning offers promise for analyzing large genomic datasets and uncovering hidden patterns, while interdisciplinary collaborations could translate findings into conservation, agriculture, and biotechnology applications. [ABSTRACT FROM AUTHOR]

ABSTRACT Species with high connectivity usually lack genetic differentiation. We tested for the presence of multiple populations of jumbo squid (Dosidicus gigas) on the Southeastern Pacific Ocean. Samples were collected from Ecuador to southern Chile (1.5° S–38° S). Two mitochondrial genes were sequenced (COI and ND2). Jumbo squids from all sampled locations in Ecuador, Peru, and Chile, as a whole, were characterized by low genetic diversity and an absence of spatial genetic structure, which suggest the presence of a population genetic unit in the Southeastern Pacific Ocean. Absence of spatial genetic structure was associated with high vagility of adults, eggs, and paralarvae of jumbo squid. We conclude that jumbo squid should be managed as a single biological stock along the Southeastern Pacific Ocean. [ABSTRACT FROM AUTHOR]

Background: Strongyloides nematodes are livestock parasites, and Strongyloides papillosus infecting ruminant livestock can cause disease. Recent genomic analysis of several Strongyloides species is now facilitating population genomic analyses of natural Strongyloides infections, for example finding that Strongyloides ratti in wild UK rats exists as an assemblage of long-lived, asexual lineages. Methods: Here we have initiated an investigation into the population genomics of S. papillosus in goats in Pakistan. We sampled Strongyloides from goat faeces and then whole genome sequenced individual larvae. Results: We find that S. papillosus is common, with a prevalence of 28%; that the population is genetically diverse and that individual goats commonly have mixed-genotype infections, and that there is evidence of admixture in only ca. 20% of worms. Conclusions: These results now provoke further questions about the host range of different S. papillosus genotypes that can be investigated by further population genomic analyses in the future. [ABSTRACT FROM AUTHOR]

Background: Intestinal schistosomiasis was confirmed endemic in Mangochi District, Malawi, in May of 2018 following an unexpected encounter with discreet populations of Biomphalaria spp. freshwater snails during routine malacological surveillance activities. Since then, only limited malacological surveillance of Biomphalaria has been carried out, and so the distribution of Biomphalaria populations in this area is currently unclear. Additionally, sites of active Schistosoma mansoni transmission in this area are also unknown. In the present study, through extensive malacological surveillance, we aimed to formally document the distribution of Biomphalaria in Mangochi District. We also aimed to identify active intestinal schistosomiasis transmission sites in this area through subjecting all collected Biomphalaria to a recently developed S. mansoni-specific molecular xenomonitoring PCR. Methods: Three malacological surveys were carried out along the southern shoreline of Lake Malawi, Mangochi District, Malawi, in November 2021, July 2022 and October/November 2022. All collected Biomphalaria were subjected to cercarial shedding analysis to identify active Schistosoma infections. Shed cercariae were then genotyped to species level using a standard multi-locus PCR and Sanger sequencing protocol. Following this, a subset of Biomphalaria from each collection site were also genotyped to species level using a standard PCR and Sanger sequencing protocol. All collected Biomphalaria were then subjected to a recently developed S. mansoni-specific molecular xenomonitoring PCR to identify infected, but non-shedding, Biomphalaria. Results: A total of 589 Biomphalaria were collected across all three surveys. One single Biomphalaria (0.17%) specimen was found to be actively shedding Schistosoma cercariae, which were molecularly confirmed as S. mansoni. All genotyped Biomphalaria (n = 42) were molecularly identified as B. pfeifferi. A further 19 Biomphalaria specimens, collected from four different surveillance sites, were found to be infected with S. mansoni through molecular xenomonitoring. Intestinal schistosomiasis transmission was therefore identified at four different foci in Mangochi District. Conclusions: Our study highlights the importance of molecular approaches to investigate Biomphalaria populations and monitor Biomphalaria-associated intestinal schistosomiasis transmission in endemic areas. As such, the continued development and use of such approaches, in particular the development and use of molecular xenomonitoring assays that can be carried out in resource-poor schistosomiasis-endemic settings, is encouraged. The revision of ongoing schistosomiasis control programmes in Mangochi District, in line with WHO recommendations, is also encouraged. [ABSTRACT FROM AUTHOR]

Background: Tibetan Plateau is credited as the "Third Pole" after the Arctic and the Antarctic, and lakes there represent a pristine habitat ideal for studying microbial processes under climate change. Results: Here, we collected 169 samples from 54 lakes including those from the central Tibetan region that was underrepresented previously, grouped them to freshwater, brackish, and saline lakes, and generated a genome atlas of the Tibetan Plateau Lake Microbiome. This genomic atlas comprises 8271 metagenome-assembled genomes featured by having significant phylogenetic and functional novelty. The microbiomes of freshwater lakes are enriched with genes involved in recalcitrant carbon degradation, carbon fixation, and energy transformation, whereas those of saline lakes possess more genes that encode osmolyte transport and synthesis and enable anaerobic metabolism. These distinct metabolic features match well with the geochemical properties including dissolved organic carbon, dissolved oxygen, and salinity that distinguish between these lakes. Population genomic analysis suggests that microbial populations in saline lakes are under stronger functional constraints than those in freshwater lakes. Although microbiomes in the Tibet lakes, particularly the saline lakes, may be subject to changing selective regimes due to ongoing warming, they may also benefit from the drainage reorganization and metapopulation reconnection. Conclusions: Altogether, the Tibetan Plateau Lake Microbiome atlas serves as a valuable microbial genetic resource for biodiversity conservation and climate research. 9n3SXpnTm6EbgSwcGAa_6c Video Abstract [ABSTRACT FROM AUTHOR]

Supergenes are genetic architectures resulting in the segregation of alternative combinations of alleles underlying complex phenotypes. The co‐segregation of alleles at linked loci is often facilitated by polymorphic chromosomal rearrangements suppressing recombination locally. Supergenes are involved in many complex polymorphisms, including sexual, colour or behavioural polymorphisms in numerous plants, fungi, mammals, fish, and insects. Despite a long history of empirical and theoretical research, the formation of supergenes remains poorly understood. Here, using a two‐island population genetic model, we explore how gene flow and the evolution of overdominant chromosomal inversions may jointly lead to the formation of supergenes. We show that the evolution of inversions in differentiated populations, both under disruptive selection, leads to an increase in frequency of poorly adapted, immigrant haplotypes. Indeed, rare allelic combinations, such as immigrant haplotypes, are more frequently reshuffled by recombination than common allelic combinations, and therefore benefit from the recombination suppression generated by inversions. When an inversion capturing a locally adapted haplotype spreads but is associated with a fitness cost hampering its fixation (e.g. a recessive mutation load), the maintenance of a non‐inverted haplotype in the population is enhanced; under certain conditions, the immigrant haplotype persists alongside the inverted local haplotype, while the standard local haplotype disappears. This establishes a stable, local polymorphism with two non‐recombining haplotypes encoding alternative adaptive strategies, that is, a supergene. These results bring new light to the importance of local adaptation, overdominance, and gene flow in the formation of supergenes and inversion polymorphisms in general. [ABSTRACT FROM AUTHOR]

Large‐scale chromosome rearrangements, such as fissions and fusions, are a common feature of eukaryote evolution. They can have considerable influence on the evolution of populations, yet it remains unclear exactly how rearrangements become established and eventually fix. Rearrangements could fix by genetic drift if they are weakly deleterious or neutral, or they may instead be favoured by positive natural selection. Here, we compare genome assemblies of three closely related Brenthis butterfly species and characterize a complex history of fission and fusion rearrangements. An inferred demographic history of these species suggests that rearrangements became fixed in populations with large long‐term effective size (Ne), consistent with rearrangements being selectively neutral or only very weakly underdominant. Using a recently developed analytic framework for characterizing hard selective sweeps, we find that chromosome fusions are not enriched for evidence of past sweeps compared to other regions of the genome. Nonetheless, we do infer a strong and recent selective sweep around one chromosome fusion in the B. daphne genome. Our results suggest that rearrangements in these species likely have weak absolute fitness effects and fix by genetic drift. However, one putative selective sweep raises the possibility that natural selection may sometimes play a role in the fixation of chromosome fusions. [ABSTRACT FROM AUTHOR]

ABSTRACT Landscape genomic approaches for detecting genotype‐environment associations (GEA), isolation by distance (IBD) and isolation by environment (IBE) have seen a dramatic increase in use, but there have been few thorough analyses of the influence of sampling strategy on their performance under realistic genomic and environmental conditions. We simulated 24,000 datasets across a range of scenarios with complex population dynamics and realistic landscape structure to evaluate the effects of the spatial distribution and number of samples on common landscape genomics methods. Our results show that common analyses are relatively robust to sampling scheme as long as sampling covers enough environmental and geographic space. We found that for detecting adaptive loci and estimating IBE, sampling schemes that were explicitly designed to increase coverage of available environmental space matched or outperformed sampling schemes that only considered geographic space. When sampling does not cover adequate geographic and environmental space, such as with transect‐based sampling, we detected fewer adaptive loci and had higher error when estimating IBD and IBE. We found that IBD could be detected with as few as nine sampling sites, while large sample sizes (e.g., greater than 100 individuals) were crucial for detecting adaptive loci and IBE. We also demonstrate that, even with optimal sampling strategies, landscape genomic analyses are highly sensitive to landscape structure and migration—when spatial autocorrelation and migration are weak, common GEA methods fail to detect adaptive loci. [ABSTRACT FROM AUTHOR]

Background and Aims Species delimitation can be challenging when analysing recently diverged species, especially those taxonomically synonymized owing to morphological similarities. We aimed to untangle the relationships between two grassland species, Petunia guarapuavensis and Petunia scheideana , exploring the dynamics of fast divergence and addressing their species delimitation. Methods We used a low-coverage genome sequencing and population genomic approach to distinguish species and populations between P. guarapuavensis and P. scheideana. Our analysis focused on detecting structuration, hybridization/introgression and phylogenetic patterns. We used demographic models to support species delimitation while exploring potential phylogeographical barriers influencing gene flow. Key Results Our findings indicated differentiation between the two species and revealed another lineage, which was phylogenetically distinct from the others and had no evidence of gene flow with them. The presence of a river acted as a phylogeographical barrier, limiting gene flow and allowing for structuration between closely related lineages. The optimal species delimitation scenario involved secondary contact between well-established lineages. Conclusions The rapid divergence observed in these Petunia species explains the lack of significant morphological differences, because floral diagnostic traits in species sharing pollinators tend to evolve more slowly. This study highlights the complexity of species delimitation in recently diverged groups and emphasizes the importance of genomic approaches in understanding evolutionary relationships and speciation dynamics. [ABSTRACT FROM AUTHOR]

Human activity generates new global processes, including range expansions caused by landscape transformations, climate change, and biological invasions. The study of the causes and processes that accompany the colonization of new areas, as well as the ecological and evolutionary consequences, has been developing rapidly in the last 20 years at the junction of such domains of biology as spatial ecology, ecology of movement, ecology of invasions, metapopulation theory, behavioral ecology, evolutionary ecology, population genetics, and personality research. In this review, we summarize theoretical ideas and empirical studies to answer two main questions: what distinguishes colonists from the residents of source populations and what specific demographic and genetic processes drive and accompany the wave of population expansion? [ABSTRACT FROM AUTHOR]

ABSTRACT Aim Location Taxon Methods Results Main Conclusions The impact of Pleistocene climate fluctuations on the biogeographical history of aquatic species has been a topic of enduring debate. This issue poses particular challenges for parapatric closely related species, especially those situated in transition zones where species assemblages occur between distinct zoogeographic boundaries.Eastern China.Five closely related Sinopotamon species and subspecies, S. shensiense, S. honanense, S. y. yangtsekiense, S. y. shanxianense, and S. y. tongbaiense.These parapatric Sinopotamon species and subspecies, distributed along the boundary between the Palaearctic and Oriental realms in eastern China, offer an ideal model for addressing these challenges. We explored the biogeographic history of these species by conducting a comparative phylogeographic analysis using nine microsatellite loci and two mitochondrial DNA sequences, combined with morphological variation and fine‐tuned ecological niche modelling.Our phylogeographic analyses consistently revealed two well‐supported clades: clade A, for S. y. yangtsekiense, and clade B, which includes other species showing polyphyletic patterning and significant gene introgression. The Nanyang Basin and surrounding mountains regions (NBSM) was identified as a critical shared refuge and hybrid zone, facilitating interspecific introgression through at least two putative hybridisation events. During the Late Pleistocene glacial cycles, introgressive hybridisation of these species occurred in the NBSM, followed by rapid expansion and colonisation of heterogenous habitats during interglacial cycles, with dispersal corridors largely aligning with the local river system. In particular, the diffusion corridor of S. honanense significantly disrupted the continuous distribution of S. y. shanxianense and S. y. tongbaiense, indicating that S. honanense has replaced S. y. shanxianense and S. y. tongbaiense in the NYSM and caused a disruption in its distribution.The biogeographic histories of the species in clade B are consistent with a mixing–isolation–mixing model, which suggests that populations experienced repeated introgressive hybridisation during glacial periods and regional habitat isolation during interglacial periods. Our findings represent a classic case of fine tracking biogeographical scenarios in parapatric species and provide unprecedented insights into the evolutionary radiation of the freshwater fauna that occupies zoogeographic boundaries. [ABSTRACT FROM AUTHOR]

ABSTRACT 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. [ABSTRACT FROM AUTHOR]

Dermestes frischii Kugelann, 1792 is a storage pest worldwide, and is important for estimating the postmortem interval in forensic entomology. However, because of the lack of transcriptome and genome resources, population genetics and biological control studies on D. frischii have been hindered. Here, single‐molecule real‐time sequencing and next‐generation sequencing were combined to generate the full‐length transcriptome of the five developmental stages of D. frischii, namely egg, young larva, mature larva, pupa and adult. A total of 41,665 full‐length non‐chimeric sequences and 59,385 non‐redundant transcripts were generated, of which 42,756 were annotated in public databases. Using the weighted gene co‐expression network analysis, gene co‐expression modules related to the five developmental stages were constructed and screened, and the genes in these modules were subjected to Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses. The expression patterns of the differentially expressed genes (DEGs) related to olfaction and insect hormone biosynthesis were also explored. Transcription of most odorant binding proteins was up‐regulated in the adult stage, suggesting they are important for foraging in adults. Many genes encoding for the ecdysone‐inducible protein were up‐regulated in the pupal stage, may be mainly responsible for the tissue remodelling of metamorphosis. The results of the quantitative real‐time polymerase chain reaction (qRT‐PCR) were consistent with the RNA‐seq results. This is the first full‐length transcriptome sequencing of dermestids, and the data obtained here are vital for understanding the stage‐specific development and olfactory system of D. frischii, providing valuable resources for storage pest and forensic research. [ABSTRACT FROM AUTHOR]

Introduction: Mitochondrial DNA (mtDNA) has been extensively utilized in archeology, human evolutionary genetics, and forensic genetic for over three decades, primarily due to its maternal inheritance and relatively high mutation rate. The Chinese Han, the largest and most widely distributed ethnic group in China, have been the focus of numerous genetic studies. However, the forensic parameters and genetic structure of the Shandong Han, specifically in relation to the whole mitochondrial genome, remain undocumented. Methods: We performed whole mitochondrial genome sequencing on 141 unrelated Han individuals from Shandong province using massively parallel sequencing. Results: A total of 135 unique mtDNA haplotypes were identified, classified into 105 haplogroups, resulting in a haplotype diversity value of 0.9993. The discriminatory capacity of whole mitochondrial genome was calculated at 0.9574, compared to 0.8936 when only the control region was analyzed. The majority of the haplogroups observed were specific to East Asian lineages, including D4, D5 and F1. Population comparisons revealed that the modern Shandong Han share genetic connections with ancient populations from the Yellow River and West Liao River basins. Additionally, the Shandong Han may have integrated a significant number of maternal lineages from other regions during their development. The demographic expansion of the Shandong Han is estimated to have occurred approximately 9,000 years ago, corresponding to the Neolithic period, a time of significant cultural and technological development. Discussion: The dataset generated in this study is available in the EMPOP database under the accession number EMP00886 and will serve as an important mtDNA reference for forensic casework in China. The study of whole mitochondrial genome based on the analysis of matrilineal genetic structure of the Shandong Han population can help to enrich the forensic mtDNA reference database in East Asia and provide reference for future archeology and forensic genetics research. [ABSTRACT FROM AUTHOR]