Phenotypic divergence of Glossina morsitans (Diptera: Glossinidae) populations in Zambia: Application of landmark-based wing geometric morphometrics to discriminate population-level variation.

An important consequence of the discontinuous distribution of insect populations within their geographic range is phenotypic divergence. Detection of this divergence can be challenging when it occurs through subtle shifts in morphological traits with complex geometries, such as insect wing venation. Here, we used landmark-based wing geometric morphometrics to investigate the population-level phenotypic variation of the two subspecies of Glossina morsitans, G. m. centralis Machado and G. m. morsitans Westwood that occur in Zambia. Twelve homologous landmarks digitised on the right wings of 720 specimens collected from four and five sites (80 per site with 1:1 sex ratio) within the G. m. centralis and G. m. morsitans range respectively, were subjected to generalised Procrustes analysis to obtain wing centroid size (CS) and wing shape variables. Linear permutation models and redundancy analysis were then used to compare CS and wing shape between male and female G. morsitans, the two subspecies G. m. centralis and G. m. morsitans, the sexes of each subspecies and between sample locations within each subspecies range, respectively. Significant differences in CS and wing shape were observed between G. morsitans sexes, subspecies and sample locations within each subspecies range. A neighbour-joining cladogram derived from the analysis of Procrustes distances showed that tsetse within each subspecies range were highly divergent. We conclude that G. morsitans populations in Zambia exhibit significant population-level variation in fly size and wing shape which suggests high levels of population structuring. The main drivers of this structuring could be random genetic drift in G. m. centralis demes and local adaptation to environmental conditions in G. m. morsitans populations. We therefore recommend molecular studies to estimate the levels of gene flow between these populations and identify possible barriers to genetic flow.

Comparison of organelle genomes between endangered mangrove plant Dolichandrone spathacea to terrestrial relative provides insights into its origin and adaptative evolution.

Dolichandrone spathacea is a mangrove associate with high medicinal and ecological values. However, due to the dual-pressure of climate change and human activities, D. spathacea has become endangered in China. Moreover, misidentification between D. spathacea and its terrestrial relative D. cauda-felina poses further challenges to field protection and proper medicinal usage of D. spathacea. Thus, to address these problems, we sequenced and assembled mitochondrial (mt) and chloroplast (cp) genomes for both D. spathacea and D. cauda-felina. Comparative analysis revealed apparently different size and scaffold number between the two mt genomes, but a high similarity between the cp genomes. Eight regions with high sequence divergence were identified between the two cp genomes, which might be used for developing candidate DNA markers for distinguishing the two species. The splitting between D. spathacea and D. cauda-felina was inferred to occur at ~6.8 - 7.7 million years ago (Mya), which may be driven by the environment fluctuations in late Miocene. In the cp genome, 12 genes related to the expression of photosynthesis-associated proteins were detected with signatures of positive selection, which may contribute to the origin and evolutionary adaptation of Dolichandrone mangrove species. These new findings do not only enrich organelle genomic resources of Dolichandrone species, but also provide important genetic clues for improving the conservation and proper usage of endangered mangrove associate D. spathacea.

Chickadees sing different songs in sympatry versus allopatry.

Character displacement theory predicts that closely-related co-occurring species should diverge in relevant traits to reduce costly interspecific interactions such as competition or hybridization. While many studies document character shifts in sympatry, few provide corresponding evidence that these shifts are driven by the costs of co-occurrence. Black-capped (Poecile atricapillus) and mountain chickadees (P. gambeli) are closely-related, ecologically similar, and broadly distributed songbirds with both allopatric and sympatric populations. In sympatry, both species appear to suffer costs of their co-occurrence: 1) both species are in worse body condition compared to allopatry and 2) hybridization sometimes yields sterile offspring. Here, we explored character displacement in the songs of black-capped and mountain chickadees by characterizing variation in male songs from sympatric and allopatric populations. We found that mountain chickadees sing differently in sympatry versus allopatry. Specifically, they produced more notes per song, were more likely to include an extra introductory note, and produced a smaller glissando in their first notes compared to all other populations. Combined with previous research on social dominance and maladaptive hybridization between black-capped and mountain chickadees, we posit that differences in sympatric mountain chickadee song are population-wide shifts to reduce aggression from dominant black-capped chickadees and/or prevent maladaptive hybridization.

Human leukocyte antigen evolutionary divergence as a novel risk factor for donor selection in acute lymphoblastic leukemia patients undergoing haploidentical hematopoietic stem cell transplantation.

Introduction: The human leukocyte antigen (HLA) evolutionary divergence (HED) reflects immunopeptidome diversity and has been shown to predict the response of tumors to immunotherapy. Its impact on allogeneic hematopoietic stem cell transplantation (HSCT) is controversial in different studies. Methods: In this study, we retrospectively analyzed the clinical impact of class I and II HED in 225 acute lymphoblastic leukemia patients undergoing HSCT from related haploidentical donors. The HED for recipient, donor, and donor-recipient pair was calculated based on Grantham distance, which accounts for variations in the composition, polarity, and volume of each amino acid within the peptide-binding groove of two HLA alleles. The median value of HED scores was used as a cut-off to stratify patients with high or low HED. Results: The class I HED for recipient (R_HEDclass I) showed the strongest association with cumulative incidence of relapse (12.2 vs. 25.0%, P = 0.00814) but not with acute graft-versus-host disease. The patients with high class II HED for donor-recipient (D/R_HEDclass II) showed a significantly higher cumulative incidence of severe aGVHD than those with low D/R_HEDclass II (24.0% vs. 6.1%, P = 0.0027). Multivariate analysis indicated that a high D/R_HEDclass II was an independent risk factor for the development of severe aGVHD (P = 0.007), and a high R_HEDclass I had a more than two-fold reduced risk of relapse (P = 0.028). However, there was no discernible difference in overall survival (OS) or disease-free survival (DFS) for patients with high or low HED, which was inconsistent with the previous investigation. Discussion: While the observation are limited by the presented single center retrospective cohort, the results show that HED has poor prognostic value in OS or DFS, as well as the associations with relapse and aGVHD. In haploidentical setting, class II HED for donor-recipient pair (D/R_HEDclass II) is an independent and novel risk factor for finding the best haploidentical donor, which could potentially influence clinical practice if verified in larger cohorts.

Multivariate analysis of phenotypic diversity elite bread wheat (Triticum aestivum L.) genotypes from ICARDA in Ethiopia.

Wheat is an important crop for food security, providing a source of protein and energy for the growing population in Ethiopia. However, both biotic and abiotic factors limit national wheat productivity. The availability of genetically diverse wheat genotypes is crucial for developing new wheat varieties that are both high-yielding and resilient to stress. Therefore, this field trial aimed to assess phenotypic variation and relationship among ICARDA-derived bread wheat genotypes using multivariate analysis techniques. The trial was conducted at three locations: Enewari, Wogere, and Kulumsa using an alpha lattice design with two replications during the main cropping seasons of 2022 and 2023. Phenotypic data on eight agronomic traits and the severity of yellow rust were collected and R programming was used for data analysis. Individual and combined location data analysis of variance showed significant differences (p ≤ 0.05) among genotypes for most of the studied traits. The highest heritability and genetic advance as a percentage of the mean were observed in days to heading (90.8, 21.29), plant height (72.4, 28.6), seeds per spike (61.7, 28), thousand kernel weight (61.9, 12), and area under the disease progress curve (67, 39.8), suggesting a predominance of additive gene action. Grain yield showed a strong positive correlation with days to maturity, plant height, spike length, spikelet per spike, and thousand kernel weight for each location. Dendrogram and phylogenetic tree methods were used to group genotypes into four genetically distinct clusters. Cluster II and III had the greatest inter-cluster distance, indicating higher diversity among their genotypes. This study identified new candidate genotypes with superior agronomic performance, high grain yield traits, and robust resistance to yellow rust, making them valuable for both current and future wheat breeding programs. Additionally, the comprehensive dataset produced in this study could facilitate the identification of genetic variations influencing desirable traits through genome-wide association analysis.

A comparison of basal and activity-dependent exon splicing in cortical-patterned neurons of human and mouse origin.

Rodent studies have shown that alternative splicing in neurons plays important roles in development and maturity, and is regulatable by signals such as electrical activity. However, rodent-human similarities are less well explored. We compared basal and activity-dependent exon splicing in cortical-patterned human ESC-derived neurons with that in cortical mouse ESC-derived neurons, primary mouse cortical neurons at two developmental stages, and mouse hippocampal neurons, focussing on conserved orthologous exons. Both basal exon inclusion levels and activity-dependent changes in splicing showed human-mouse correlation. Conserved activity regulated exons are enriched in RBFOX, SAM68, NOVA and PTBP targets, and centered on cytoskeletal organization, mRNA processing, and synaptic signaling genes. However, human-mouse correlations were weaker than inter-mouse comparisons of neurons from different brain regions, developmental stages and origin (ESC vs. primary), suggestive of some inter-species divergence. The set of genes where activity-dependent splicing was observed only in human neurons were dominated by those involved in lipid biosynthesis, signaling and trafficking. Study of human exon splicing in mouse Tc1 neurons carrying human chromosome-21 showed that neuronal basal exon inclusion was influenced by cis-acting sequences, although may not be sufficient to confer activity-responsiveness in an allospecific environment. Overall, these comparisons suggest that neuronal alternative splicing should be confirmed in a human-relevant system even when exon structure is evolutionarily conserved.

Fine-scale genetic structure and phenotypic divergence of a passerine bird population inhabiting a continuous Mediterranean woodland.

Genetic differentiation between populations inhabiting ecologically different habitats might appear because of limited dispersal and gene flow, which may lead to patterns of phenotypic divergence and local adaptation. In this study, we use dispersal, genotypic (24 microsatellite loci) and phenotypic (body size and clutch size) data to analyse patterns of genetic structuring and phenotypic divergence in a blue tit (Cyanistes caeruleus) population inhabiting a continuous and heterogeneous woodland along a valley. The two slopes of the valley differ in their forest formations and environmental conditions. Findings showed that most blue tits reproduced within their natal slope. Accordingly, microsatellite analyses revealed that populations of blue tits established in the two slopes show subtle genetic differentiation. The two genetic populations diverged in clutch size, exceeding the level of differentiation expected based on genetic drift, hence suggesting divergent selection (or other processes promoting divergence) on this life-history trait. Our findings reveal that restricted dispersal and spatial heterogeneity may lead to genetic differentiation among bird populations at a surprisingly small scale. In this respect, it is worth highlighting that such differentiation occurs for an organism with high dispersal capacity and within a continuous woodland. Moreover, we show that small-scale ecological differences, together with limited gene flow, can result in selection favouring different phenotypes even within the same continuum population.

Variation of chin morphology and mandibular incisor length in different facial divergence patterns: New insights from CBCT records.

AIM: Evaluate constitutional differences in chin morphology and volume, and mandibular tooth size, between different facial divergence patterns. MATERIALS AND METHODS: The sample consisted of 284 pretreatment cone beam computed tomography (CBCT) images of growing and non-growing patients who were stratified into 4 groups based on mandibular plane inclination to cranial base (SN) angle. Linear and angular measurements were made on the lateral CBCT images: mandibular lateral incisor crown (I-C) total (I-A) lengths, the distances between point D (centre of symphysis) and both incisor apex (D-A) and menton (D-Me) and between cemento-enamel junction and menton (CEJ-Me); chin width at the level of the central incisor apex (CWA) and point D (CWD); and the angles of the anterior and posterior symphyseal slopes. The volume of the symphysis was measured using a specialized 3D imaging software. Group differences and associations between parameters were gauged through the three-way ANOVA analysis. RESULTS: I-C, I-A, D-A, D-Me and CEJ-Me were greater in the hyperdivergent group (p < .001). CWA and CWD were wider in the hypodivergent group (p = .003). Volume of the chin and inter-slope angles were similar in all groups (p > .05). The anterior slope angle decreased with hyperdivegence (p < .005) in opposite pattern to the posterior slope angle (p < .005). CONCLUSIONS: Shape differences in mandibular symphysis were observed between opposite divergence patterns. Mandibular incisors were longer with hyperdivergence and shorter with hypodivergence. However, chin volumes were similar across divergence groups. These findings underline the role of genetic and environmental factors that impact facial growth.

Adaptive evolution of pancreatic ribonuclease gene (RNase1) in Cetartiodactyla.

Pancreatic ribonuclease (RNase1), a digestive enzyme produced by the pancreas, is associated with the functional adaptation of dietary habits and is regarded as an attractive model system for studies of molecular evolution. In this study, we identified 218 functional genes and 48 pseudogenes from 114 species that span all four Cetartiodactyla lineages: two herbivorous lineages (Ruminantia and Tylopoda) and two non-herbivorous lineages (Cetancodonta and Suoidea). Multiple RNase1 genes were detected in all species of the two herbivorous lineages, and phylogenetic and genomic location analyses demonstrated that independent gene duplication events occurred in Ruminantia and Tylopoda. In Ruminantia, the gene duplication events occurred in the ancestral branches of the lineage in the Middle Eocene, a time of increasing climatic seasonality during which Ruminantia rapidly radiated. In contrast, only a single RNase1 gene was observed in the species of the two non-herbivorous lineages (Cetancodonta and Suoidea), suggesting that the previous Cetacea-specific loss hypothesis should be rejected. Moreover, the duplicated genes of RNase1 in the two herbivorous lineages (Ruminantia and Tylopoda) may have undergone functional divergence. In combination with the temporal coincidence between gene replication and the enhanced climatic seasonality during the Middle Eocene, this functional divergence suggests that RNase1 gene duplication was beneficial for Ruminantia to use the limited quantities of sparse fibrous vegetation and adapt to seasonal changes in climate. In summary, the findings indicate a complex and intriguing evolutionary pattern of RNase1 in Cetartiodactyla and demonstrate the molecular mechanisms by which organisms adapt to the environment.

Earthworm (Oligochaeta, Lumbricidae) intraspecific genetic variation and polyploidy.

Earthworms are known for their intricate systematics and a diverse range of reproduction modes, including outcrossing, self-fertilization, parthenogenesis, and some other modes, which can occasionally coexist in a single species. Moreover, they exhibit considerable intraspecific karyotype diversity, with ploidy levels varying from di- to decaploid, as well as high genetic variation. In some cases, a single species may exhibit significant morphological variation, contain several races of different ploidy, and harbor multiple genetic lineages that display significant divergence in both nuclear and mitochondrial DNA. However, the relationship between ploidy races and genetic lineages in earthworms remains largely unexplored. To address this question, we conducted a comprehensive review of available data on earthworm genetic diversity and karyotypes. Our analysis revealed that in many cases, a single genetic lineage appears to encompass populations with different ploidy levels, indicating recent polyploidization. On the other hand, some other cases like Octolasion tyrtaeum and Dendrobaena schmidti/D. tellermanica demonstrate pronounced genetic boundaries between ploidy races, implying that they diverged long ago. Certain cases like the Eisenia nordenskioldi complex represent a complex picture with ancient divergence between lineages and both ancient and recent polyploidization. The comparison of phylogenetic and cytological data suggests that some ploidy races have arisen independently multiple times, which supports the early findings by T.S. Vsevolodova-Perel and T.V. Malinina. The key to such a complex picture is probably the plasticity of reproductive modes in earthworms, which encompass diverse modes of sexual and asexual reproduction; also, it has been demonstrated that even high-ploidy forms can retain amphimixis.

Establishing recipiency in divergent L2 contexts of classroom interaction: A conversation analysis.

Establishing recipiency, an indispensable ingredient and manifestation of sustaining intersubjectivity, constitutes the continuous monitoring of an ongoing turn in an interaction. The present study intended to describe how interactants attending a freshman common course in an Ethiopian university elicit and display recipiency in instances of Divergent L2 contexts exhibiting DIUs. Naturally occurring video-recorded classroom interactions of the purposively selected interactants have been analyzed in light of the Conversation Analytic framework to show how interactants elicit and display recipiency. By deploying reactive tokens, incipient speakers negotiate their rights to shape and reshape trajectories of an ongoing thereby displaying recipiency. This contributes to a better understanding of how interactures, in this case the establishment of intersubjectivity and L2 contexts, interplay and unfold in moments of DIUs. Also, viewing interactants as incipient speakers, and thereby articulating turns in view of recipients is a condition for sustaining intersubjectivity through active engagement. This requires upholding unwavering belief about recipients' stake in an interactional exchange. Practically, being attentive to recipients' states in the different trajectories of interactional development, especially, in moments of divergent L2 contexts that exhibit DIUs, would be illuminating. This is because the use of resources to elicit and display recipiency and thereby consider incipient speakers' levels of recipiency, on the part of floor-holding speaker, would enhance possibilities for intersubjectivity.

A new discovery of cryptic species in barred sand burrower Limnichthys fasciatus (Pisces: Creediidae) from the western Pacific, with evolutionary perspectives of anti-equatorial species.

Although the barred sand burrower, Limnichthys fasciatus, is widely distributed throughout the western Pacific, including Japan, Taiwan, and Australia, its morphology and genetics are poorly known. We discovered four cryptic species of Limnichthys from the western Pacific based on mtDNA cytochrome c oxidase subunit I (COI) and 16S ribosomal RNA (rRNA) sequences. Genetic distances showed remarkably large differences (12.7%-24.3% in COI and 7.9%-19.6% in 16S rRNA) between true L. fasciatus (type locality: southeastern Australia) and the others. A relaxed clock model with optimized selected substitution models showed that their deep divergence began in the middle Miocene epoch and subsequently diverged into the current cryptic species in the Plio-Pleistocene. A eurythermal common ancestor may have evolved independently in each region due to geographical events and paleoclimatic fluctuations, which made it possible for L. fasciatus complex to be an anti-equatorial species. Despite their deep genetic divergence, they showed marked phenotypic similarity, suggesting that they have experienced similar selective pressures related to their specific behavior.

Genetically- and environmentally-dependent processes drive interspecific and intraspecific divergence in the Chinese relict endemic genus Dipteronia.

China is a hotspot of relict plant species that were once widespread throughout the Northern Hemisphere. Recent research has demonstrated that the occurrence of long-term stable refugia in the mountainous regions of central and south-western China allowed their persistence through the late Neogene climate fluctuations. One of these relict lineages is Dipteronia, an oligotypic tree genus with a fossil record extending to the Paleocene. Here, we investigated the genetic variability, demographic dynamics and diversification patterns of the two currently recognized Dipteronia species (D ipteronia sinensis and D . dyeriana). Molecular data were obtained from 45 populations of Dipteronia by genotyping three cpDNA regions, two single copy nuclear genes and 15 simple sequence repeat loci. The genetic study was combined with niche comparison analyses on the environmental space, ecological niche modeling, and landscape connectivity analysis. We found that the two Dipteronia species have highly diverged both in genetic and ecological terms. Despite the incipient speciation processes that can be observed in D. sinensis, the occurrence of long-term stable refugia and, particularly, a dispersal corridor along Daba Shan-west Qinling, likely ensured its genetic and ecological integrity to date. Our study will not only help us to understand how populations of Dipteronia species responded to the tectonic and climatic changes of the Cenozoic, but also provide insight into how Arcto-Tertiary relict plants in East Asia survived, evolved, and diversified.

Long genetic and social isolation in Neanderthals before their extinction.

Neanderthal genomes have been recovered from sites across Eurasia, painting an increasingly complex picture of their populations' structure that mostly indicates that late European Neanderthals belonged to a single metapopulation with no significant evidence of population structure. Here, we report the discovery of a late Neanderthal individual, nicknamed "Thorin," from Grotte Mandrin in Mediterranean France, and his genome. These dentognathic fossils, including a rare example of distomolars, are associated with a rich archeological record of Neanderthal final technological traditions in this region ∼50-42 thousand years ago. Thorin's genome reveals a relatively early divergence of ∼105 ka with other late Neanderthals. Thorin belonged to a population with a small group size that showed no genetic introgression with other known late European Neanderthals, revealing some 50 ka of genetic isolation of his lineage despite them living in neighboring regions. These results have important implications for resolving competing hypotheses about causes of the disappearance of the Neanderthals.

The mitochondrial genome of the critically endangered enigmatic Kazakhstani endemic Selevinia betpakdalaensis (Rodentia: Gliridae) and its phylogenetic relationships with other dormouse species.

Dormice (family Gliridae) are an ancient group of rodents. It was fully dominant in the Oligocene and Early Miocene, and its current diversity is represented by a few extant species. A Kazakhstani endemic, the desert dormouse Selevinia betpakdalaensis is one of the most enigmatic dormouse species. Lack of genetic data has not allowed Selevinia to be included in previous molecular phylogenetic analyses. In the current study, we report the first genetic data on S. betpakdalaensis as well as mitochondrial genomes of Myomimus roachi and Glirulus japonicus (retrieved from museum specimens) and a mitogenome of Graphiurus murinus (assembled from SRA data). The assembled mitochondrial genomes were combined with available mitochondrial data from GenBank to reconstruct the mitochondrial phylogeny of Gliridae. Taking into account a distortion of the phylogeny as a result of an analysis of the saturated third codon position, we obtained for the first time a resolved phylogeny of the family. The first split within Gliridae was estimated as an average of 34.6 Mya, whereas divergence time of subfamilies Graphiurinae and Glirinae was assessed at 32.67 Mya. The phylogenetic analysis confirmed the relationship (previously shown based on cranial and mandibular morphology) between Selevinia and the Myomimus.

Evaluation of Incisor Position in a Sample of Orthodontic Patients.

BACKGROUND: To achieve a successful result, the orthodontist must use a systematic approach to plan the orthodontic treatment. Defining the correct position of the upper and lower incisors and evaluating their relationship with intermaxillary discrepancy and facial divergence have been recognized as the starting point for the diagnostic decision regarding extractions and anchorage requirements. The aim of our study was to analyze the relationship between intermaxillary discrepancy (ANPg^), mandibular inclination (SN^GoGn), lip incompetence, and the positioning of the upper and lower incisors (UIPs and LIPs) in a group of orthodontic patients. This retrospective study included 290 lateral cephalograms in 122 males (42.1%) and 168 females (57.9%) aged 8 to 53 years (median 14; interquartile range IQR 12-17). Data were analyzed by means of one-way Analysis of Variance (ANOVA) and linear regression analysis. RESULTS: This study showed a statistically significant increase in LIP values in patients with lip incompetence (p < 0.001). Moreover, the distribution of LIPs in groups with various SN^GoGn and ANPg^ angles was significantly different (p < 0.001). The regression analysis also showed a positive association between the LIP and SN^GoGn and between the LIP and ANPg^. CONCLUSION: The LIP presented a statistically significant difference in patients with and without lip incompetence, which varied significantly in subjects with different sagittal malocclusions and vertical face patterns.

Genetic Diversity and Divergence between Southern Japonica and Northern Japonica Rice Varieties in China.

Given the notable ecological and breeding disparities between southern and northern rice regions, delving into the genetic diversity and divergence between southern and northern japonica rice contributes to enhancing the genetic pool for japonica rice breeding. In this study, we analyzed 90 southern and 51 northern japonica rice varieties, focusing on nucleotide diversity (Pi), agronomic trait variations, population structure, genetic divergence, and a neutral test. For genetic diversity, the results demonstrated higher Pi in northern japonica rice varieties (NJRVs) on Chr2, Chr5, Chr6, Chr8, and Chr10, whereas in southern japonica rice varieties (SJRVs) on Chr7 and Chr9. In addition, SJRVs exhibited higher grain width and thickness, whereas NJRVs featured a higher grain aspect ratio, filled grain number, and grain number per panicle. Regarding genetic divergence, geographic differentiation existed between NJRVs and SJRVs, with Chr5 exhibiting numerous higher genetic differentiation windows, including cloned grain shape-controlling genes RGA1 and SFD5, stemming from intensified selection pressure on SJRVs. In summary, SJRVs and NJRVs exhibited diversity differences and genetic differentiation. Hence, it was suggested to conduct genetic introgression between NJRVs and SJRVs to broaden the genetic basis of the local japonica rice germplasm. By exploiting their heterotic advantage, new japonica rice cultivars with superior comprehensive traits could be developed.

Reticulate evolution: Detection and utility in the phylogenomics era.

Phylogenomics has enriched our understanding that the Tree of Life can have network-like or reticulate structures among some taxa and genes. Two non-vertical modes of evolution - hybridization/introgression and horizontal gene transfer - deviate from a strictly bifurcating tree model, causing non-treelike patterns. However, these reticulate processes can produce similar patterns to incomplete lineage sorting or recombination, potentially leading to ambiguity. Here, we present a brief overview of a phylogenomic workflow for inferring organismal histories and compare methods for distinguishing modes of reticulate evolution. We discuss how the timing of coalescent events can help disentangle introgression from incomplete lineage sorting and how horizontal gene transfer events can help determine the relative timing of speciation events. In doing so, we identify pitfalls of certain methods and discuss how to extend their utility across the Tree of Life. Workflows, methods, and future directions discussed herein underscore the need to embrace reticulate evolutionary patterns for understanding the timing and rates of evolutionary events, providing a clearer view of life's history.

The role of mate competition in speciation and divergence: a systematic review.

Competition for mates can play a critical role in determining reproductive success, shaping phenotypic variation within populations, and influencing divergence. Yet, studies of the role of sexual selection in divergence and speciation have focused disproportionately on mate choice. Here, we synthesize the literature on how mate competition may contribute to speciation and integrate concepts from work on sexual selection within populations - mating systems, ecology, and mate choice. Using this synthesis, we generate testable predictions for how mate competition may contribute to divergence. Then, we identify the extent of existing support for these predictions in the literature with a systematic review of the consequences of mate competition for population divergence across a range of evolutionary, ecological, and geographic contexts. We broadly evaluate current evidence, identify gaps in available data and hypotheses that need testing, and outline promising directions for future work. A major finding is that mate competition may commonly facilitate further divergence after initial divergence has occurred, e.g., upon secondary contact and between allopatric populations. Importantly, current hypotheses for how mate competition contributes to divergence do not fully explain observed patterns. While results from many studies fit predictions of negative frequency dependent selection, agonistic character displacement, and ecological selection, results from ~30% studies did not fit existing conceptual models. This review identifies future research aims for scenarios in which mate competition is likely important but has been understudied, including how ecological context and interactions between mate choice and mate competition can facilitate or hinder divergence and speciation.

Epi-Clock: A sensitive platform to help understand pathogenic disease outbreaks and facilitate the response to future outbreaks of concern.

To predict potential epidemic outbreaks, we tested our strategy, Epi-Clock, which applies the novel ZHU algorithm to different SARS-CoV-2 datasets before outbreaks to search for significant mutational accumulation patterns correlated with outbreak events. Surprisingly, some inter-species genetic distances in Coronaviridae may represent intermediate states of different species or subspecies in the evolutionary history of Coronaviridae. The insertions and deletions in whole-genome sequences between different hosts were separately associated with important roles in host transmission and shifts in Coronaviridae. Furthermore, we believe that non-nucleosomal DNA may play a dominant role in the divergence of different lineages of SARS-CoV-2 in different regions of the world owing to the lack of nucleosome protection. We suggest that strong selective variation among different lineages of SARS-CoV-2 is required to produce strong codon usage bias, which appears in B.1.640.2 and B.1.617.2 (Delta). Notably, we found that an increasing number of other types of substitutions, such as those resulting from the hitchhiking effect, accumulated, especially in the pre-breakout phase, although some of the previous substitutions were replaced by other dominant genotypes. From most validations, we could accurately predict the potential pre-phase of outbreaks with a median interval of 5 days.