Demographic History Research Articles

Population genetic structure and demographic history reconstruction of introduced flathead catfish (Pylodictis olivaris) in two US Mid-Atlantic rivers.

Population genetic analysis of invasive populations can provide valuable insights into the source of introductions, pathways for expansion, and their demographic histories. Flathead catfish (Pylodictis olivaris) are a prolific invasive species with high fecundity, long-distance dispersal, and piscivorous feeding habits that can lead to declines in native fish populations. In this study, we analyse the genetics of invasive P. olivaris in the Mid-Atlantic region to assess their connectivity and attempt to reconstruct the history of introduced populations. Based on an assessment across 13 microsatellite loci, P. olivaris from the Susquehanna River system (N = 537), Schuylkill River (N = 33), and Delaware River (N = 1) have low genetic diversity (global Hobs = 0.504), although we detected no evidence of substantial inbreeding (FIS = -0.083 to 0.022). P. olivaris from these different river systems were genetically distinct, suggesting separate introductions. However, population structure was much weaker within each river system and exhibited a pattern of high connectivity, with some evidence of isolation by distance. P. olivaris from the Susquehanna and Schuylkill rivers showed evidence for recent genetic bottlenecks, and demographic models were consistent with historical records, which suggest that populations were established by recent founder events consisting of a small number of individuals. Our results show the risk posed by small introductions of P. olivaris, which can spread widely once a population is established, and highlight the importance of prevention and sensitive early detection methods to prevent the spread of P. olivaris in the future.

Origin of the Laurentian Great Lakes fish fauna through upward adaptive radiation cascade prior to the Last Glacial Maximum

The evolutionary histories of adaptive radiations can be marked by dramatic demographic fluctuations. However, the demographic histories of ecologically-linked co-diversifying lineages remain understudied. The Laurentian Great Lakes provide a unique system of two such radiations that are dispersed across depth gradients with a predator-prey relationship. We show that the North American Coregonus species complex (“ciscoes”) radiated rapidly prior to the Last Glacial Maximum (80–90 kya), a globally warm period, followed by rapid expansion in population size. Similar patterns of demographic expansion were observed in the predator species, Lake Charr (Salvelinus namaycush), following a brief time lag, which we hypothesize was driven by predator-prey dynamics. Diversification of prey into deep water created ecological opportunities for the predators, facilitating their demographic expansion, which is consistent with an upward adaptive radiation cascade. This study provides a new timeline and environmental context for the origin of the Laurentian Great Lakes fish fauna, and firmly establishes this system as drivers of ecological diversification and rapid speciation through cyclical glaciation.

Contrasting demographic history and mutational load in three threatened whitebark pines (Pinus subsect. Gerardianae): implications for conservation.

Demographic history and mutational load are of paramount importance for the adaptation of the endangered species. However, the effects of population evolutionary history and genetic load on the adaptive potential in endangered conifers remain unclear. Here, using population transcriptome sequencing, whole chloroplast genomes and mitochondrial DNA markers, combined with niche analysis, we determined the demographic history and mutational load for three threatened whitebark pines having different endangered statuses, Pinus bungeana, P. gerardiana and P. squamata. Demographic inference indicated that severe bottlenecks occurred in all three pines at different times, coinciding with periods of major climate and geological changes; in contrast, while P. bungeana experienced a recent population expansion, P. gerardiana and P. squamata maintained small population sizes after bottlenecking. Abundant homozygous-derived variants accumulated in the three pines, particularly in P. squamata, while the species with most heterozygous variants was P. gerardiana. Abundant moderately and few highly deleterious variants accumulated in the pine species that have experienced the most severe demographic bottlenecks (P. gerardiana and P. squamata), most likely because of purging effects. Finally, niche modeling showed that the distribution of P. bungeana might experience a significant expansion in the future, and the species' identified genetic clusters are also supported by differences in the ecological niche. The integration of genomic, demographic and niche data has allowed us to prove that the three threatened pines have contrasting patterns of demographic history and mutational load, which may have important implications in their adaptive potential and thus are also key for informing conservation planning.

Demography and environment modulate the effects of genetic diversity on extinction risk in a butterfly metapopulation

Linking genetic diversity to extinction is a common goal in genomic studies. Recently, a debate has arisen regarding the importance of genetic variation in conservation as some studies have failed to find associations between genome-wide genetic diversity and extinction risk. However, only rarely are genetic diversity and fitness measured together in the wild, and typically demographic history and environment are ignored. It is therefore difficult to infer whether a lack of an association is real or obscured by confounding factors. To address these shortcomings, we analyzed genetic data from 7,501 individuals with extinction data from 279 meadows and mortality of 1,742 larval nests in a butterfly metapopulation. We found a strong negative association between genetic diversity and extinction when considering only heterozygosity in models. However, this association disappeared when accounting for ecological covariates, suggesting a confounding between demography and genetics and a more complex role for heterozygosity in extinction risk. Modeling interactions between heterozygosity and demographic variables revealed that associations between extinction and heterozygosity were context-dependent. For example, extinction declined with increasing heterozygosity in large, but not currently small populations, although negative associations between heterozygosity, extinction, and mortality were detected in small populations with a recent history of decline. We conclude that low genetic diversity is an important predictor of extinction, predicting >25% increase in extinction beyond ecological factors in certain contexts. These results highlight that inferences about the importance of genetic diversity for population viability should not rely on genomic data alone but require investments in obtaining demographic and environmental data from natural populations.

Divergent lineages in a young species: The case of datilillo (Yucca valida), a broadly distributed plant from the Baja California Peninsula.

Globally, barriers triggered by climatic changes have caused habitat fragmentation and population allopatric divergence. Across North America, oscillations during the Quaternary have played important roles in the distribution of wildlife. Notably, diverse plant species from the Baja California Peninsula in western North America, isolated during the Pleistocene glacial-interglacial cycles, exhibit strong genetic structure and highly concordant divergent lineages across their ranges. A representative plant genus of the peninsula is Yucca, with Y. valida having the widest range. Although a dominant species, it has an extensive distribution discontinuity between 26° N and 27° N, suggesting restricted gene flow. Moreover, historical distribution models indicate the absence of an area with suitable conditions for the species during the Last Interglacial, making it an interesting model for studying genetic divergence. We assembled 4411 SNPs from 147 plants of Y. valida throughout its range to examine its phylogeography to identify the number of genetic lineages, quantify their genetic differentiation, reconstruct their demographic history and estimate the age of the species. Three allopatric lineages were identified based on the SNPs. Our analyses support that genetic drift is the driver of genetic differentiation among these lineages. We estimated an age of less than 1 million years for the common ancestor of Y. valida and its sister species. Habitat fragmentation caused by climatic changes, low dispersal, and an extensive geographical range gap acted as cumulative mechanisms leading to allopatric divergence in Y. valida.

Human genetic structure in Northwest France provides new insights into West European historical demography

The demographical history of France remains largely understudied despite its central role toward understanding modern population structure across Western Europe. Here, by exploring publicly available Europe-wide genotype datasets together with the genomes of 3234 present-day and six newly sequenced medieval individuals from Northern France, we found extensive fine-scale population structure across Brittany and the downstream Loire basin and increased population differentiation between the northern and southern sides of the river Loire, associated with higher proportions of steppe vs. Neolithic-related ancestry. We also found increased allele sharing between individuals from Western Brittany and those associated with the Bell Beaker complex. Our results emphasise the need for investigating local populations to better understand the distribution of rare (putatively deleterious) variants across space and the importance of common genetic legacy in understanding the sharing of disease-related alleles between Brittany and people from western Britain and Ireland.

Usefulness of estimated glucose disposal rate in detecting heart failure: results from national health and nutrition examination survey 1999–2018

BackgroundEstimated glucose disposal rate (eGDR) is a novel, clinically available, and cost-effective surrogate of insulin resistance. The current study aimed to assess the association between eGDR and prevalent heart failure (HF), and further evaluate the value of eGDR in detecting prevalent HF in a general population.Methods25,450 subjects from the National Health and Nutrition Examination Survey 1999–2018 were included. HF was recorded according to the subjects’ reports. Logistic regression was employed to analyze the association between eGDR and HF, the results were summarized as Per standard deviation (SD) change. Then, subgroup analysis tested whether the main result from logistic regression was robust in several conventional subpopulations. Finally, receiver-operating characteristic curve (ROC) and reclassification analysis were utilized to evaluate the potential value of eGDR in improving the detection of prevalent HF.ResultsThe prevalence of reported HF was 2.96% (753 subjects). After adjusting demographic, laboratory, anthropometric, and medical history data, each SD increment of eGDR could result in a 43.3% (P < 0.001) risk reduction for prevalent HF. In the quartile analysis, the top quartile had a 31.1% (P < 0.001) risk of prevalent HF compared to the bottom quartile in the full model. Smooth curve fitting demonstrated that the association was linear in the whole range of eGDR (P for non-linearity = 0.313). Subgroup analysis revealed that the association was robust in age, sex, race, diabetes, and hypertension subgroups (All P for interaction > 0.05). Additionally, ROC analysis displayed a significant improvement in the detection of prevalent HF (0.869 vs. 0.873, P = 0.008); reclassification analysis also confirmed the improvement from eGDR (All P < 0.001).ConclusionOur study indicates that eGDR, a costless surrogate of insulin resistance, may have a linear and robust association with the prevalent HF. Furthermore, our findings implicate the potential value of eGDR in refining the detection of prevalent HF in the general population.

Draft Genome of Akame (Lates Japonicus) Reveals Possible Genetic Mechanisms for Long-Term Persistence and Adaptive Evolution with Low Genetic Diversity.

It is known that some endangered species have persisted for thousands of years despite their very small effective population sizes and low levels of genetic polymorphisms. To understand the genetic mechanisms of long-term persistence in threatened species, we determined the whole genome sequences of akame (Lates japonicus), which has survived for a long time with extremely low genetic variations. Genome-wide heterozygosity in akame was estimated to be 3.3 to 3.4 × 10-4/bp, one of the smallest values in teleost fishes. Analysis of demographic history revealed that the effective population size in akame was around 1,000 from 30,000 years ago to the recent past. The relatively high ratio of nonsynonymous to synonymous heterozygosity in akame indicated an increased genetic load. However, a detailed analysis of genetic diversity in the akame genome revealed that multiple genomic regions, including genes involved in immunity, synaptic development, and olfactory sensory systems, have retained relatively high nucleotide polymorphisms. This implies that the akame genome has preserved the functional genetic variations by balancing selection, to avoid a reduction in viability and loss of adaptive potential. Analysis of synonymous and nonsynonymous nucleotide substitution rates has detected signs of positive selection in many akame genes, suggesting adaptive evolution to temperate waters after the speciation of akame and its close relative, barramundi (Lates calcarifer). Our results indicate that the functional genetic diversity likely contributed to the long-term persistence of this species by avoiding the harmful effects of the population size reduction.

Genetic diversity, demographic history, and selective signatures of Silkie chicken

BackgroundSilkie is a traditional Chinese chicken breed characterized by its unique combination of specialized morphological traits. While previous studies have focused on the genetic basis of these traits, the overall genomic characteristics of the Silkie breed remain largely unexplored. In this study, we employed whole genome resequencing data to examine the genetic diversity, selective signals and demographic history of the Silkie breed through comparative analyses with seven other Chinese indigenous breeds (IDGBs), a commercial breed, and the wild ancestor Red Jungle Fowl.ResultsIn total, 20.8 million high-quality single nucleotide polymorphisms and 86 large structural variations were obtained. We discovered that Silkie exhibits a relatively high level of inbreeding and is genetically distinct from other IDGBs. Furthermore, our analysis indicated that Silkie has experienced a stronger historical population bottleneck and has a smaller effective population size compared with other IDGBs. We identified 45 putatively selected genes that are enriched in the melanogenesis pathway, which probably is related to the feather color. Among these genes, LMBR1 and PDSS2 have been previously associated with the extra toe and the hookless feathers, respectively. Six of the selected genes (KITLG, GSK3B, SOBP, CTBP1, ELMO2, SNRPN) are known to be associated with neurodevelopment and mental diseases in human, and are possibly related to the distinct behavior of Silkie. We further identified structural variants in Silkie and found previously reported variants linked to hyperpigmentation (END3), muff and beard (HOXB8), and Rose-comb phenotype (MNR2). Additionally, we found a 0.61 Mb inversion overlapping with the GMDS gene, which was previously linked to neurodevelopmental defects in zebrafish and humans. This may also be related to the behavior distinctiveness of Silkie.ConclusionsOur study revealed that Silkie is genetically distinct and relatively highly inbred compared to other IDGB chicken populations, possibly attributed to more prolong population bottlenecks and selective breeding practice. These results enhance our understanding of how domestication and selective breeding have shaped the genome of Silkie. These findings contribute to the broader field of domestication and avian genomics, and have implications for the future conservation and breeding efforts.

Reconstructing a Lay Individual’s Elbow Fracture at Santa Caterina Friary, Barcelona (15th–16th Century): The Contribution of Paleopathology to the Valorization of Bioarcheological Heritage

The paleopathological literature notably lacks the description and analysis of distal humeral fractures and their associated complications. The objectives of this study were (1) to evaluate a distal humerus fracture associated with cubitus valgus observed in the articulated right elbow of an adult male buried in the Santa Caterina Friary site in Barcelona, dating back to the modern period (15th to early 16th century), and (2) to contribute to the valorization of bioarcheological heritage. Employing macroscopic and radiographic studies, the injury was assessed. The results indicated a healed antemortem fracture, probably associated with a fall. In the AO/OTA classification, it corresponds to type 13C1.1 (complete articular fracture, articular simple, metaphyseal simple, above the transcondylar axis), accompanied by a coronoid process fracture due to anterior trochlear dislocation impact (O’Driscoll type 1 classification: transverse fracture of the distal apophysis with involvement of the sublime tubercle). This fracture, resulting in a 28° cubitus valgus and significant elbow changes, infers community support in healing and highlights the socio-economic dynamics of guilds and adaptive strategies to physical adversities. This study is one of the first to describe cubitus valgus in a historical Spanish population, offering a comprehensive view of the complexities, physical adversities, and adaptive strategies employed by individuals following an elbow fracture.

Genetic Variation among Rare Florida Endemic Hymenocallis henryae Populations and the Implication for Conservation and Management

Hymenocallis henryae is a rare, charismatic spider lily endemic to the Florida panhandle. Currently under review to determine if listing under the Endangered Species Act is warranted, this species has undescribed genetic diversity, information crucial to the listing process. We conducted field observations of 21 historic populations across the species’ geographical range and performed genomic analyses of 279 individuals from 19 extant populations. Most populations had fewer than 40 individuals, while populations with &gt;100 individuals were found exclusively on managed lands. Genetic diversity was uniformly low within populations (HE: 0.074–0.093), with low to moderate inbreeding coefficients (FIS: 0.068–0.431). Genetic differentiation was relatively low among most populations (FST: 0–0.098), although there was statistical support for isolation by distance. In addition, we found high genetic similarity and lack of population structure across the species range. Clonal propagation through fused bulbs is a common reproductive strategy. We confirmed current threats (habitat change, residential development, fire suppression) and identified several coastal populations threatened by sea level rise. It is recommended to continue with in situ protection and management as well as the establishment of ex situ living collections to preserve populations most at risk of extirpation from habitat loss and degradation.

Extreme genetic signatures of local adaptation in a notorious rice pest, Chilo suppressalis

ABSTRACT Climatic variation stands as a significant driving force behind genetic differentiation and the evolution of adaptive traits. Chilo (C.) suppressalis, commonly known as the rice stem borer, is a highly destructive pest that crucially harms rice production. The lack of natural population genomics data has hindered a more thorough understanding of its climate adaptation, particularly the genetic basis underlying adaptive traits. To overcome this obstacle, our study employed completely resequenced genomes of 384 individuals to explore the population structure, demographic history, and gene flow of C. suppressalis in China. This study observed that its gene flow occurred asymmetrically, moving from central populations to peripheral populations. Using genome-wide selection scans and genotype-environment association studies, we identified potential loci that may be associated with climatic adaptation. The most robust signal was found to be associated with cold tolerance, linked to a homeobox gene, goosecoid (GSC), whose expression level was significantly different in low and high latitudes. Moreover, downregulating the expression of this gene by RNAi enhances its cold tolerance phenotypes. Our findings have uncovered and delved into the genetic foundation of the ability of C. suppressalis to adapt to its environment. This is essential in ensuring the continued effectiveness and sustainability of novel control techniques.

Prevalence, Features, and Outcomes of Type 1 Neovascularization in Eyes with Angioid Streaks

This study aimed to delineate the characteristics, prevalence, and outcomes of neovascularization (NV), particularly aneurysmal Type 1 NV, in patients with angioid streaks (AS) secondary to pseudoxanthoma elasticum (PXE), and to introduce a clinical classification based on multimodal imaging (MMI). Retrospective longitudinal cohort study. 85 patients (168 eyes) with AS secondary to PXE at two tertiary referral centers. Data collection included demographic, medical, and ocular histories. Diagnostic methods comprised fundus photography, autofluorescence, indocyanine green angiography, optical coherence tomography (OCT), and OCT angiography. Prevalence of Type 1 NV, visual acuity (VA), risk of exudation. Type 1 NV was identified in 127 eyes (76%), with 85 of these (67%) showing exclusively Type 1 NV. These lesions often originated around the disc, at sites of Bruch's membrane dehiscences, and followed the path of AS, extending to the posterior pole in 101 eyes (80%). Despite 65% of Type 1 NV remaining non-exudative, 36% evolved into exudative over five years, and 11 eyes experienced mid-peripheral subretinal hemorrhages. Aneurysmal dilations, observed in 57% of cases, substantially increased exudation risk (hazard ratio = 3.86, p=0.02). Despite treatment, VA significantly deteriorated in exudative Type 1 NV (p=0.02). Type 2 NV, detected in 56 eyes (33%), often coexisted with Type 1 NV and was associated with poorer visual outcomes and higher rates of macular atrophy. A classification of AS was developed, ranging from empty AS (stage 0, no NV) to advanced NV (stage 3, both Type 1 and Type 2 NV). Type 1 NV predominates in AS. Although predominantly non-exudative, its progression correlates with substantial visual impairment, similar to the deficits observed with Type 2 NV. Aneurysmal Type 1 NV poses a significant exudation risk, underscoring the need for vigilant monitoring.

A map of canine sequence variation relative to a Greenland wolf outgroup.

For over 15years, canine genetics research relied on a reference assembly from a Boxer breed dog named Tasha (i.e., canFam3.1). Recent advances in long-read sequencing and genome assembly have led to the development of numerous high-quality assemblies from diverse canines. These assemblies represent notable improvements in completeness, contiguity, and the representation of gene promoters and gene models. Although genome graph and pan-genome approaches have promise, most genetic analyses in canines rely upon the mapping of Illumina sequencing reads to a single reference. The Dog10K consortium, and others, have generated deep catalogs of genetic variation through an alignment of Illumina sequencing reads to a reference genome obtained from a German Shepherd Dog named Mischka (i.e., canFam4, UU_Cfam_GSD_1.0). However, alignment to a breed-derived genome may introduce bias in genotype calling across samples. Since the use of an outgroup reference genome may remove this effect, we have reprocessed 1929 samples analyzed by the Dog10K consortium using a Greenland wolf (mCanLor1.2) as the reference. We efficiently performed remapping and variant calling using a GPU-implementation of common analysis tools. The resulting call set removes the variability in genetic differences seen across samples and breed relationships revealed by principal component analysis are not affected by the choice of reference genome. Using this sequence data, we inferred the history of population sizes and found that village dog populations experienced a 9-13 fold reduction in historic effective population size relative to wolves.

Montane rainforest dynamics under changes in climate and human impact during the past millennia in northern Madagascar.

Although it is well known that humans substantially altered the Malagasy ecosystems, the timing of the human arrival as well as the extension of their environmental impact is yet not well understood. This research aims to study the influence of early human impact and climate change on rainforests and wildlife in northern Madagascar during the past millennia. Results obtained from the lake sediment in a montane environment showed significant changes in vegetation within the lake catchment associated with a major drought that started approximately 1100 years ago. Human impact, revealed by fires, began at roughly the same time and occurred outside the lake catchment. Although this does not dismiss the impacts that humans had at a regional scale, this result demonstrates that the late Holocene natural drought also significantly impacted the ecosystems independently of anthropogenic activities. At a regional scale, a review of species demographic history revealed a substantial number of population bottlenecks during the last millennia, probably resulting from this combination of human-related impact and natural climate changes. This research highlights the importance of a multi-site and multi-proxy comparison for deciphering the nature and succession of environmental changes.

Early-Life Disease Exposure and Its Heterogeneous Effects on Mortality Throughout Life: Sweden, 1905–2016

Exposure to infectious diseases in early life has been linked to increased mortality risk in later life in high-disease settings, such as eighteenth- and nineteenth-century Europe. Less is known about the long-term effects of early-life disease exposure in milder disease environments. This study estimates heterogeneous effects from disease exposure in infancy on later-life mortality in twentieth-century Sweden, by socioeconomic status at birth and sex. Using historical population data for southern Sweden, we study 11,515 individuals who were born in 1905–1929 from age 1 until age 85. We measure exposure to disease using the local post–early neonatal mortality rate in the first 12 months after birth and apply flexible parametric survival models. For females, we find a negative effect on life expectancy (scarring) at ages 1–85 following high disease exposure in infancy, particularly for those born to unskilled workers. For males, we find no negative effect on later-life survival, likely because stronger mortality selection in infancy outweighs scarring. Thus, even as the incidence of infectious diseases declined at the start of the twentieth century, early-life disease exposure generated long-lasting negative but heterogeneous population health effects.

Assessing the information-content of messy data to reconstruct population recovery dynamics for the world's rarest primate.

Understanding the dynamics of population recovery in threatened species requires robust longitudinal monitoring datasets. However, evidence-based decision-making is often impeded by variable data collection approaches, necessitating critical evaluation of restricted available baselines. The Hainan gibbon, the world's rarest primate, had possibly declined to only seven or eight individuals in 1978 at Bawangling National Nature Reserve but has experienced subsequent population growth. Past population estimates lack detailed reporting of survey effort, and multiple conflicting estimates are available, hindering assessment of gibbon recovery. We investigated all reported estimates of Bawangling gibbon population size from 1978 to 2022, to evaluate the biological signal of population trends and the extent to which noise associated with varying survey effort, reporting and estimation may mask or misrepresent any underlying signal. This longitudinal dataset demonstrates that the Bawangling population experienced a series of bottlenecks and recoveries, with three successive periods of growth interspersed by population crashes (1978-1989, 1989-2000 and 2000-2022). The rate of gibbon population recovery was progressively slower over time in each successive period of growth, and this potential decline in recovery rate following serial bottlenecks suggests that additional management strategies may be required alongside "nature-based solutions" for this species. However, population viability analysis suggests the 1978 founder population is unlikely to have been as low as seven individuals, raising concerns for interpreting reported historical population counts and understanding the dynamics of the species' recovery. We caution against overinterpreting potential signals within "messy" conservation datasets, and we emphasise the crucial importance of standardised replicable survey methods and transparent reporting of data and effort in all future surveys of Hainan gibbons and other highly threatened species.

Nutritional Status of Under-Five Children in the Climate Vulnerable Area of Bangladesh

Children, due to their physiological and metabolic vulnerabilities, are particularly sensitive to climate-related changes. Factors such as heat waves, extreme weather events, temperature variations, increased precipitation, and drought directly impact food and nutrition. This cross-sectional study was aimed to assess the nutritional status of under-5 children in a flood-prone district in northern Bangladesh. A total of 207 children aged 24-59 months were conveniently selected for the study. Data collection involved face-to-face interviews and observations using a semi-structured questionnaire. Data analysis was performed using SPSS version 16.0. Demographic information, educational background, immunization status, breastfeeding practices, health history, and dietary intake were considered for assessing nutritional status. More than half (55.6%) of the children was in age group 48-59 months, and the male-female ratio was 1.25:1. Most of the (70%) children belonged to nuclear families and more female children (53.6%) had completed their primary education than male (44%). All children were immunized, where three-fifth (60.4%) of the mothers acknowledged breastfeeding after birth, and three-fourth (75.4%) had completed exclusive breastfeeding. The majority were not ill in the month preceding the data collection. Dietary assessment revealed that most of the (94%) children consumed rice in the morning as breakfast, 97% at midday as lunch, and 94% at night as dinner. Among the children all of them had experienced flooding (100%) and significant proportion had experienced river bank erosion (97.6%). According to measurements, 81.2% were normal by MUAC, 62.8% by height for age Z scores, 71% by weight for age Z scores, and 83.1% by weight for height Z scores. The study identified higher proportions of underweight and severe wasted cases in male children, severe stunted cases with mothers having primary education, and severe wasted cases in extended families. Although certain trends were observed, the relationships between nutritional status and variables such as gender, maternal education, family type, and duration of residence were not statistically significant. Given the potential long-term impact of malnutrition, early intervention, and prioritization of nutritional considerations during the under-five age group are imperative. Bangladesh Med J. 2023 May; 52(2): 29-39

Molecular Evolutionary Dynamics of Coxsackievirus A6 Causing Hand, Foot, and Mouth Disease From 2021 to 2023 in China: Genomic Epidemiology Study.

Hand, foot, and mouth disease (HFMD) is a global public health concern, notably within the Asia-Pacific region. Recently, the primary pathogen causing HFMD outbreaks across numerous countries, including China, is coxsackievirus (CV) A6, one of the most prevalent enteroviruses in the world. It is a new variant that has undergone genetic recombination and evolution, which might not only induce modifications in the clinical manifestations of HFMD but also heighten its pathogenicity because of nucleotide mutation accumulation. The study assessed the epidemiological characteristics of HFMD in China and characterized the molecular epidemiology of the major pathogen (CV-A6) causing HFMD. We attempted to establish the association between disease progression and viral genetic evolution through a molecular epidemiological study. Surveillance data from the Chinese Center for Disease Control and Prevention from 2021 to 2023 were used to analyze the epidemiological seasons and peaks of HFMD in Henan, China, and capture the results of HFMD pathogen typing. We analyzed the evolutionary characteristics of all full-length CV-A6 sequences in the NCBI database and the isolated sequences in Henan. To characterize the molecular evolution of CV-A6, time-scaled tree and historical population dynamics regarding CV-A6 sequences were estimated. Additionally, we analyzed the isolated strains for mutated or missing amino acid sites compared to the prototype CV-A6 strain. The 2021-2023 epidemic seasons for HFMD in Henan usually lasted from June to August, with peaks around June and July. The monthly case reporting rate during the peak period ranged from 20.7% (4854/23,440) to 35% (12,135/34,706) of the total annual number of cases. Analysis of the pathogen composition of 2850 laboratory-confirmed cases identified 8 enterovirus serotypes, among which CV-A6 accounted for the highest proportion (652/2850, 22.88%). CV-A6 emerged as the major pathogen for HFMD in 2022 (203/732, 27.73%) and 2023 (262/708, 37.01%). We analyzed all CV-A6 full-length sequences in the NCBI database and the evolutionary features of viruses isolated in Henan. In China, the D3 subtype gradually appeared from 2011, and by 2019, all CV-A6 virus strains belonged to the D3 subtype. The VP1 sequences analyzed in Henan showed that its subtypes were consistent with the national subtypes. Furthermore, we analyzed the molecular evolutionary features of CV-A6 using Bayesian phylogeny and found that the most recent common ancestor of CV-A6 D3 dates back to 2006 in China, earlier than the 2011 HFMD outbreak. Moreover, the strains isolated in 2023 had mutations at several amino acid sites compared to the original strain. The CV-A6 virus may have been introduced and circulating covertly within China prior to the large-scale HFMD outbreak. Our laboratory testing data confirmed the fluctuation and periodic patterns of CV-A6 prevalence. Our study provides valuable insights into understanding the evolutionary dynamics of CV-A6.

Comparative phylogeography and genetic diversity of two co-occurring anti-tropical krill species Hansarsia megalops and Thysanoessa gregaria in the Atlantic Ocean

Abstract Hansarsia megalops and Thysanoessa gregaria are two abundant krill species in the warm-temperate belts in the North and South Atlantic. This pattern of disjunct distribution, often referred to as anti-tropical (or bipolar), is a regular phenomenon among marine organisms that can appear at different taxonomic levels. Analysis of spatial genetic diversity based on variation of the mitochondrial cytochrome oxidase I (COI) gene was carried out to understand whether these broadly sympatric krill species have similar patterns in population structure and demographic history. The results suggested that the anti-tropical distribution of both species was driven by trans-equatorial migrations during different historical periods. We observed contrasting differences in genetic diversity between species coupled with similar patterns of genetic diversity and structure in disjunct populations on both sides of the equator. We also found additional genetically distinctive populations of T. gregaria in the South Atlantic in Subantarctic waters and showed that the Southern Subtropical Frontal Zone acts as a strong boundary between two genetically distinctive populations of T. gregaria. The results suggest that both species-specific habitat preferences and interactions between closely related species (congeners) may shape differences in population genetic diversity and structure among species.