Genetic Differentiation Research Articles

Global spread, genetic differentiation and selection of barley spot form of net blotch isolates.

Spot form of net blotch, caused by Pyrenophora teres f. maculata, is a significant necrotrophic disease of barley that spread world-wide in the 20th century. Genetic relationships were analysed to determine the diversity, survival and dispersal of a diverse collection of 346 isolates from Australia, Southern Africa, North America, Asia Minor and Europe. The results, based on genome-wide DArTseq data, indicated isolates from Turkey were the most differentiated with regional sub-structuring, together with individuals closely related to geographically distant genotypes. Elsewhere, population subdivision related to country of origin was evident, although low levels of admixturing was found that may represent rare genotypes or migration from unsampled populations. Canadian isolates were the next most diverged and Australian and South African the most closely related. With the exception of Turkish isolates, multiple independent Cyp51A mutation events (which confer insensitivity to demethylation inhibitor fungicides) between countries and within regions was evident, with strong selection for a transposable element insertion at the 3' end of the promoter and counter-selection elsewhere. Individuals from Western Australia shared genomic regions and Cyp51A haplotypes with South African isolates, suggesting a recent common origin.

Occurrence of giant migratory locust Locusta migratoria (Acrididae) on Tsushima Island, Japan

This study focused on the populations of Locusta migratoria (Linnaeus, 1758) on Tsushima Island, Japan, which exhibited the largest mean adult body size when compared to other populations from various climatic regions. Certain individuals, designated as “giant locusts,” displayed exceptionally large sizes, with females and males identified when with head widths surpassing 10.5 mm and 8.0 mm, respectively. The maximum weight recorded for a giant locust was 8.9 g, in contrast to other examined females with the maximum weight ranging from 3.1 to 5.5 g. Notably, giant females exhibited the ability to yield larger egg pods and progeny compared to their counterparts. A positive correlation emerged between body size of adult females and the number of ovarioles. To explore the potential heritability of body size, selection experiments were conducted across two generations. A significant impact of selection on adult body size was apparent at LD 12:12h, whereas this effect was not evident at LD 16:8h. Furthermore, crossing experiments showed that body size at hatching closely resembled that of the female parent or demonstrated dimensions intermediary between the two parents, suggesting a complex genetic basis for the observed body size variations. This study provides no evidence of genetic differentiation between the giant locusts and the other locusts on this island.

Genetic Diversity of Dominant Species Betula pendula in River Valley Forests in the Irtysh River Basin and Sustainable Conservation Measures for the Future

Biodiversity is the basis for the maintenance and functioning of ecosystems. Genetic diversity is at the heart of biodiversity, and therefore an understanding of the current state of plant genetic diversity can contribute to the future provision of sustainable ecological values and services by ecosystems. This study was conducted in the Irtysh River basin (five tributaries) with the dominant species of river valley forests, Betula pendula. Sampling points were set up at approximately 10 km intervals within each tributary using a random sampling method for genetic diversity studies based on chloroplast microsatellite molecular markers. The results indicated that (1) nine alleles were identified in 198 samples. The genetic diversity of Betula pendula was relatively rich in all tributaries (I = 0.216~0.546); genetic diversity was significantly higher in the downstream area of the basin than in the midstream and upstream areas of the basin. Genetic differentiation was at a low level in the tributaries except for the Berezek River, where genetic differentiation was high. (2) Genetic variation was mainly derived from within populations, accounting for 62% of the total genetic variation. The genetic distance was significantly positively correlated with the geographical distance (p < 0.05). The Betula pendula population structure was divided into two major groups. (3) Twelve haplotypes were identified in the basin. The dominant haplotypes in the upper tributaries were H2 and H4, while in the lower tributaries these were H1 and H3. Therefore, this paper suggests the future establishment of a germplasm resource bank for populations of the Berezek River, and the implementation of priority conservation measures for the downstream populations with higher genetic diversity, so as to realize the sustainable ecological value of the valley forests of the Betula pendula.

Population Genetics of Culex tritaeniorhynchus (Diptera: Culicidae) in Türkiye.

Mosquitoes are important vectors of pathogens that can affect humans and animals. Culex tritaeniorhynchus is an important vector of arboviruses such as Japanese encephalitis virus, West Nile virus among various human and animal communities. These diseases are of major public health concern and can have huge economic and health burdens in prevalent countries. Although populations of this important mosquito species have been detected in the Mediterranean and Aegean regions of Türkiye; little is known about its population structure. Our study is to examine the population genetics and genetic composition of Cx. tritaeniorhynchus mosquitoes collected from several localities using cytochrome oxidase subunit I (COI) and the NADH dehydrogenase subunit 5 genes (ND5). This is the first extensive study of Cx. tritaeniorhynchus in the mainland Türkiye with sampling spanning many of provinces. In this study, DNA extraction, amplification of mitochondrial COI and ND5 genes and population genetic analyses were performed on ten geographic populations of Culex tritaeniorhynchus in the Aegean and Mediterranean region of Türkiye. Between 2019 and 2020, 96 samples were collected from 10 geographic populations in the Aegean and Mediterranean regions; they were molecularly analyzed and 139 sequences (50 sequence for COI and 89 sequence for ND5) were used to determine the population structure and genetic diversity. For ND5 gene region, the samples produced 24 haplotypes derived from 15 variable sites and for COI gene region, 43 haplotypes were derived from 17 variable sites. The haplotype for both gene regions was higher than nucleotide diversity. Haplotype phylogeny revealed two groups present in all populations. AMOVA test results show that the geographical populations were the same for all gene regions. Results suggest that Cx. tritaeniorhynchus is a native population in Türkiye, the species is progressing towards speciation and there is no genetic differentiation between provinces and regions. This study provides useful information on the molecular identifcation and genetic diversity of Cx. tritaeniorhynchus; these results are important to improve mosquito control programs.

Mitogenome-based genetic management of captive Great Hornbill in Thailand: Implications for reintroduction

The Great Hornbill (Buceros bicornis) is globally vulnerable due to high rates of deforestation and hunting and are therefore a target for restoration. Captive breeding programs in Thailand maintain many Great Hornbills, however active genetic management of captive hornbills was not incorporated into the species recovery plan. With Great Hornbill reintroductions planned for northern Thailand in the immediate future, lack of genetic profiles and phylogenetic relationships among potential founders might hamper population recovery efforts. We assessed the mitochondrial genome (mitogenome) diversity, genetic structure, and evolutionary history of 97 captive Great Hornbills across five zoos in Thailand. Among the 97 samples, we found 21 haplotypes with a haplotype and nucleotide diversity of h = 0.81336 ± 0.021 and pi = 0.00108 ± 0.00040, respectively. The maintenance of mitogenome diversity and no genetic differentiation between five captive populations (FST = 0.00000–0.09723, p > 0.05) might be a result of frequent founder exchange among facilities. Phylogenetic analysis revealed the existence of a southern clade BBITH13, indicating a genetically distinct southern population. To protect these genetic lineages and maintain adaptability of hornbills that have been reintroduced, breeding facilities that contain unique haplotypes should be given high priority in breeding plans. Our data support the evolutionary value of the captive hornbill population in Thailand and highlight the significance of incorporating active genetic management strategies into the species recovery plan for Great Hornbills.

The International Union for Conservation of Nature Red List does not account for intraspecific diversity

Abstract The International Union for Conservation of Nature (IUCN) Red List identifies threatened and endangered species and is a key instrument in global biodiversity conservation efforts. Our understanding of the structure and value of genetic biodiversity below the species level is rapidly increasing. Nonetheless, the IUCN assessment criteria overlook genetic variation within species. Here, we address this blind spot and discuss the principles of species conservation status classification relative to intraspecific biodiversity. We focus on coastal species, which thrive in heterogeneous environments known to drive genetic differentiation. The focal example species, Atlantic cod and sugar kelp, have contrasting life histories, are ecologically and economically important constituents of the coastal ecosystem, and are currently not classified as threatened in Norway and Canada. We expose important variation in population structure, the presence of ecotypes and genetic-environment covariation, as well as loss of ecotypes that threatens the conservation of these species. Because the genetic makeup of species directly influences their resilience, omitting this information from conservation status assessments can result in loss of adaptive capacity to future stressors, such as climate change. Consequently, recognizing and preserving intraspecific variation emerges as vital for species’ abilities to adapt to and survive in future ocean conditions.

Genetic structure of ten Artemia populations from China: cumulative effects of ancient geological events, climatic changes, and human activities

This study investigated the population genetics and distribution patterns of Artemia populations from ten inland salt lakes in China. A total of 1,274,698 Artemia single nucleotide polymorphisms (SNPs) were identified. The results showed that these populations could be geographically and genetically divided into four distinct groups, and that the Tibetan populations were further divided into two subpopulations with a trend of decreasing genetic diversity from west to east. The Tibetan population had the highest genetic diversity, whereas the Shanxi population had the lowest. There was moderate genetic differentiation between the Tibetan populations and greater genetic differentiation between the Xinjiang and Shanxi populations. IBD (isolation by distance) suggested that geographical isolation contributes to genetic differentiation. In addition, there was some degree of gene flow among the ten populations, with A. sinica showing unidirectional gene flow in all populations in the eastern Nagri region. Species distribution modeling showed that mean annual temperature, temperature seasonality, and annual precipitation were the main environmental factors affecting the distribution of Artemia populations and suitable habitats for Tibetan populations will be further reduced in the future. It is necessary to strengthen the protection of germplasm resources and formulate scientific protocols for the sustainable development and utilization of Artemia resources.

Exploring Genetic Divergence in Cowpea: A Comprehensive Review

Genetic divergence in cowpea (Vigna unguiculata L. Walp) presents a compelling area of study with profound implications for breeding programs, crop improvement strategies, and agricultural sustainability. This abstract encapsulates a comprehensive review of the genetic divergence observed within cowpea populations. By examining the genetic diversity, population structure, and molecular markers employed in cowpea research, this review aims to elucidate the underlying genetic mechanisms driving divergence within the species. The review explores the ecological and geographical factors influencing genetic differentiation, as well as the implications for breeding objectives and germplasm conservation. Furthermore, it discusses the potential applications of genetic divergence analysis in enhancing crop adaptation, resilience, and productivity in diverse agroecological contexts. Through a synthesis of current research findings and emerging trends, this review provides valuable insights into the genetic architecture of cowpea and its implications for sustainable crop improvement strategies.

Combining biometrics and genetics to distinguish two subspecies of the Great Cormorant Phalacrocorax carbo carbo and P. c. sinensis at an inland lake in southeast Norway

Cover photo: Adult Great Cormorant of the subspecies Phalacrocorax carbo sinensis in breeding plumage. Photo: Frode Falkenberg. Great Cormorants Phalacrocorax carbo are now regularly seen in inland watercourses in southeast Norway, after the P. c. sinensis subspecies first established breeding colonies in coastal south Norway in 1996. Although both the sinensis and carbo subspecies occur, the ratio between them is unknown. We tested the accuracy of subspecific identification based on biometrics and genetic analyses in 75 Great Cormorants that drowned in fishing nets in a lake in southeast Norway during the period 2009-2020. Primarily based on the gular pouch angle (GPA), we classified 40 individuals to the carbo subspecies and 35 individuals to the sinensis subspecies. Eight of the carbo individuals and 14 of the sinensis individuals were within the overlapping range of GPA and were therefore classified to subspecies by supplementary measurements (bill depth minimum and bill length). Genetic analyses were based on seven polymorphic microsatellite markers. Assuming one panmictic population, we performed Structure analyses to separate the genotypes into two assumed genetic clusters. The two clusters, carbo and sinensis, could only be separated when adding information about morphological subspecies identities for the carbo, sinensis and carbo/sinensis groups. The sinensis and the carbo/sinensis groups belonged almost entirely to one genetic cluster, whereas the carbo group consisted of individuals with varying proportions of mixed ancestry. Furthermore, we found significant genetic differentiation between the carbo and sinensis groups, and between the carbo and the carbo/sinensis groups, but no significant differentiation between the sinensis and the carbo/sinensis groups. Our results suggest that gene flow is more common from sinensis into carbo than vice-versa, and that the use of GPA < 73° has limitations for the identification of Great Cormorant subspecies in areas where both forms occur. We conclude that the numbers of carbo vs. sinensis individuals in our sample were 32 and 43, respectively.

DNA barcoding, phylogeography and evolutionary dynamics of Chrysichthys auratus

This study embarked on an exploration into the genetic structure and evolutionary history of the Chrysichthys auratus species, leveraging PCR amplification, phylogenetic trees, and haplotype networks. Specific DNA segments were successfully amplified and visualized through electrophoresis. Newly obtained sequences were Bank into GenBank and given accession numbers (OR730807-OR730808-OR730809). The Neighbor-Joining method provided insights into the evolutionary relationships among taxa, further augmented by bootstrap values and the Tamura 3-parameter method. A comprehensive geographical haplotype network showcased pronounced genetic differentiation, especially between remote populations. Nonetheless, shared haplotypes between proximate regions indicated either ancestral genetic connections or ongoing gene flow. Employing the COI-DNA barcodes, an in-depth understanding of intra- and inter-populational genetic diversity was achieved. The study's findings unravel the intricate genetic landscape and evolutionary dynamics of C. auratus, offering novel perspectives into its demographic history across its vast native habitat.

Germplasm evaluation and identification of the population source of hard clam (Mercenaria mercenaria) in China using SSR and COI markers

In aquaculture, good germplasm resources are nearly decisive for its development. The hard clam (Mercenaria mercenaria), a significant marine aquaculture bivalve in China, has flourished quickly since being introduced from North America in 1997. However, for numerous reasons, it has suffered from germplasm deterioration and uncertain origins. To address these issues, seven microsatellite DNA loci (SSRs) and mtCOI were employed to evaluate germplasm and trace the origins of various Chinese populations. The results of these two molecular genetic markers revealed weak genetic differentiation among all Chinese populations, with high genetic diversity observed across most individuals, except for a few outliers. This suggests an alarming situation regarding germplasm resources in China. Based on results of traceability analysis, the most likely areas of origin for the Chinese populations are Chesapeake Bay and the southern region of Cape Hatteras. This study provides a crucial theoretical foundation for the cultivation, conservation, and subsequent introduction of hard clam populations in China, thereby ensuring the sustainable growth of the hard clam breeding sector.

Genetic diversity and phylogeographic patterns of the peacock jewel-damselfly, Rhinocypha fenestrella (Rambur, 1842).

Despite is known to have widespread distribution and the most active species of the family Chlorocyphidae, the molecular data of Rhinocypha fenestrella (Rambur, 1842) are relatively scarce. The present study is the first that examined the genetic diversity and phylogeographic pattern of the peacock jewel-damselfly R. fenestrella by sequencing the cytochrome C oxidase I (cox1) and 16S rRNA gene regions from 147 individuals representing eight populations in Malaysia. A total of 26 and 10 unique haplotypes were revealed by the cox1 and 16S rRNA genes, respectively, and 32 haplotypes were recovered by the concatenated sequences of cox1+16S. Analyses indicated that haplotype AB2 was the most frequent and the most widespread haplotype in Malaysia while haplotype AB1 was suggested as the common ancestor haplotype of the R. fenestrella that may arose from the Negeri Sembilan as discovered from cox1+16S haplotype network analysis. Overall haplotype and nucleotide diversities of the concatenated sequences were Hd = 0.8937 and Pi = 0.0028, respectively, with great genetic differentiation (FST = 0.6387) and low gene flow (Nm = 0.14). Population from Pahang presented the highest genetic diversity (Hd = 0.8889, Pi = 0.0022, Nh = 9), whereas Kedah population demonstrated the lowest diversity (Hd = 0.2842, Pi = 0.0003, Nh = 4). The concatenated sequences of cox1+16S showed genetic divergence ranging from 0.09% to 0.97%, whereas the genetic divergence for cox1 and 16S rRNA genes were 0.16% to 1.63% and 0.01% to 0.75% respectively. This study provides for the first-time insights on the intraspecific genetic diversity, phylogeographic pattern and ancestral haplotype of Rhinocypha fenestrella. The understanding of molecular data especially phylogeographic pattern can enhance the knowledge about insect origin, their diversity, and capability to disperse in particular environments.

Isolation by disturbance: a pattern of genetic structure of the coral Pocillopora grandis in the Gulf of California

Genetic differentiation within species can be influenced by the distance between populations (isolation by distance, IBD) or by differences in the habitats they occupy (isolation by environment, IBE). Understanding the population structure and dynamics that influence genetic diversity within small (<100 km2) multi-use marine protected areas (MPAs) and varying disturbances or protections is relevant to better designing and managing them. Pocillopora grandis communities were studied at 10 different sites in the Gulf of California, Mexico. The comparison between sites inside and outside an MPA or whether the population structure followed IBD or IBE was investigated with the genetic marker HSP70B. Environmental heterogeneity was used to test for IBE, and was measured by comparing the present benthic communities by site and through analysis of satellite images, while distance was used to test for IBD. Mantel tests found that the population of P. grandis did not follow IBD or IBE. Instead, cluster analysis grouped low (no-take zones) and high (crown-of-thorns starfish outbreaks and highly visited by tourists) disturbance sites together with the remaining sites within and outside of the MPA in another cluster (ΦRT = 0.082, p = 0.007). Furthermore, lower genetic diversity was found at sites with low and high disturbance. Our results suggest that instead of IBE or IBD influencing the population structure, the protection and disturbance levels could have a correlation with genetic patterns (i.e. isolation by disturbance, ID). These findings will be valuable for MPAs in terms of efficient management of genetic diversity objectives by considering the appropriate spacing and protections, depending on how vulnerable a species is to disturbance.

The role of historical biogeography in shaping colour morph diversity in the common wall lizard.

The maintenance of polymorphisms often depends on multiple selective forces, but less is known on the role of stochastic or historical processes in maintaining variation. The common wall lizard (Podarcis muralis) is a colour polymorphic species in which local colour morph frequencies are thought to be modulated by natural and sexual selection. Here, we used genome-wide single-nucleotide polymorphism data to investigate the relationships between morph composition and population biogeography at a regional scale, by comparing morph composition with patterns of genetic variation of 54 populations sampled across the Pyrenees. We found that genetic divergence was explained by geographic distance but not by environmental features. Differences in morph composition were associated with genetic and environmental differentiation, as well as differences in sex ratio. Thus, variation in colour morph frequencies could have arisen via historical events and/or differences in the permeability to gene flow, possibly shaped by the complex topography and environment. In agreement with this hypothesis, colour morph diversity was positively correlated with genetic diversity and rates of gene flow and inversely correlated with the likelihood of the occurrence of bottlenecks. Concurrently, we did not find conclusive evidence for selection in the two colour loci. As an illustration of these effects, we observed that populations with higher proportions of the rarer yellow and yellow-orange morphs had higher genetic diversity. Our results suggest that processes involving a decay in overall genetic diversity, such as reduced gene flow and/or bottleneck events have an important role in shaping population-specific morph composition via non-selective processes.

Genetic structure and landscape effects on gene flow in the Neotropical lizard Norops brasiliensis (Squamata: Dactyloidae).

One key research goal of evolutionary biology is to understand the origin and maintenance of genetic variation. In the Cerrado, the South American savanna located primarily in the Central Brazilian Plateau, many hypotheses have been proposed to explain how landscape features (e.g., geographic distance, river barriers, topographic compartmentalization, and historical climatic fluctuations) have promoted genetic structure by mediating gene flow. Here, we asked whether these landscape features have influenced the genetic structure and differentiation in the lizard species Norops brasiliensis (Squamata: Dactyloidae). To achieve our goal, we used a genetic clustering analysis and estimate an effective migration surface to assess genetic structure in the focal species. Optimized isolation-by-resistance models and a simulation-based approach combined with machine learning (convolutional neural network; CNN) were then used to infer current and historical effects on population genetic structure through 12 unique landscape models. We recovered five geographically distributed populations that are separated by regions of lower-than-expected gene flow. The results of the CNN showed that geographic distance is the sole predictor of genetic variation in N. brasiliensis, and that slope, rivers, and historical climate had no discernible influence on gene flow. Our novel CNN approach was accurate (89.5%) in differentiating each landscape model. CNN and other machine learning approaches are still largely unexplored in landscape genetics studies, representing promising avenues for future research with increasingly accessible genomic datasets.

Genetic basis for Rapana venosa with different peristome color based on microsatellite, DNA methylation, and transcriptome analysis

Abstract Rapana venosa, a well-known and economic species mainly distributed in the Asian region, has three distinct color patterns in the peristome: pure orange, pure dark stripes, and part stripes. The present study combined microsatellite, DNA methylation, and transcriptome to assess the genetic basis of three color patterns of R. venosa in the peristome. The different color patterns of R. venosa showed no significant genetic differentiation, and each color group was relatively independent with respect to gene flow. Each color pattern showed a high methylation rate of more than 60%. The full-methylation rates for the three color patterns were 34.47%, 35.67%, and 32.54%, respectively. The Gene Ontology (GO) classification and functional enrichment revealed three ontologies: molecular function, cellular components, and biological processes. The function of translation, ribosomal structure, and biogenesis accounted for the top classification, followed by general function prediction. This study also revealed some functional genes related to color and shell formation, including Scavenger receptor cysteine-rich protein (SRCR), beta-carotene ketolase, tyrosinase proteins, and Lustrin A. These findings suggest that the color polymorphism of R. venosa is possibly attributed to environmental effects. The research is also essential for selecting better germplasm for the breeding of Rapana venosa.

A foundation for comparative genomics and evolutionary studies in Nucella lapillus based on complete mitogenome assembly

The Atlantic dog whelk, Nucella lapillus, is a marine snail that exhibits divergent evolution in response to habitat adaptation, resulting in distinct populations at the phenotypic, genotypic, and karyotypic levels. In this study, we utilized short- and long-read NGS data to perform a de novo assembly of the entire mitochondrial genome of N. lapillus and developed a multiplex PCR protocol to sequence most of its length using ONT sequencing. Our analysis revealed a typical circular configuration of 16,474 bp in length with 13 protein-coding genes, 22 different tRNA genes, 2 of them showing two copies, 2 rRNA genes, and a control region. Long-read sequencing enabled us to identify a 1826 bp perfect inverted repeat within the control region. Comparative analysis of the mitogenomes of related species in the Muricidae family revealed a conserved gene configuration for N. lapillus. We found a low genetic diversity, as well as a moderate genetic differentiation among the studied populations. Interestingly, there was no observed differentiation between the two chromosomal races, suggesting either introgression and permanent incorporation of the mitochondrial DNA haplotype from one of the chromosomal races into the other or a slower evolutionary rate of the mtDNAs with respect to that of the karyotypes. Our study serves as a foundation for comparative genomics and evolutionary investigations in this species.

Integrated meta-analysis and transcriptomics pinpoint genomic loci and novel candidate genes associated with submergence tolerance in rice

BackgroundDue to rising costs, water shortages, and labour shortages, farmers across the globe now prefer a direct seeding approach. However, submergence stress remains a major bottleneck limiting the success of this approach in rice cultivation. The merger of accumulated rice genetic resources provides an opportunity to detect key genomic loci and candidate genes that influence the flooding tolerance of rice.ResultsIn the present study, a whole-genome meta-analysis was conducted on 120 quantitative trait loci (QTL) obtained from 16 independent QTL studies reported from 2004 to 2023. These QTL were confined to 18 meta-QTL (MQTL), and ten MQTL were successfully validated by independent genome-wide association studies from diverse natural populations. The mean confidence interval (CI) of the identified MQTL was 3.44 times narrower than the mean CI of the initial QTL. Moreover, four core MQTL loci with genetic distance less than 2 cM were obtained. By combining differentially expressed genes (DEG) from two transcriptome datasets with 858 candidate genes identified in the core MQTL regions, we found 38 common differentially expressed candidate genes (DECGs). In silico expression analysis of these DECGs led to the identification of 21 genes with high expression in embryo and coleoptile under submerged conditions. These DECGs encode proteins with known functions involved in submergence tolerance including WRKY, F-box, zinc fingers, glycosyltransferase, protein kinase, cytochrome P450, PP2C, hypoxia-responsive family, and DUF domain. By haplotype analysis, the 21 DECGs demonstrated distinct genetic differentiation and substantial genetic distance mainly between indica and japonica subspecies. Further, the MQTL7.1 was successfully validated using flanked marker S2329 on a set of genotypes with phenotypic variation.ConclusionThis study provides a new perspective on understanding the genetic basis of submergence tolerance in rice. The identified MQTL and novel candidate genes lay the foundation for marker-assisted breeding/engineering of flooding-tolerant cultivars conducive to direct seeding.

High levels of genetic variation and differentiation in wild tropical gourds provide a novel resource for cucurbit crop improvement

Social Impact StatementThe genetic variation of crop wild relatives will be key for our survival, as environmental change represents an increasing global threat for agriculture and food security. Cucurbita lundelliana and Cucurbita okeechobeensis subsp. martinezii are wild relatives of cultivated squashes and pumpkins that could be used for crop improvement. A genomic approach was used to characterize genetic resources in these taxa, that is, to identify candidate sites in the genome involved in responses to abiotic stress, and to understand the roles of gene flow and environmental differentiation in their divergence. This study highlights the importance of conserving these two species as phytogenetic resources for crop improvement.Summary Crop wild relatives (CWR) are reservoirs of genetic diversity and they are important for the maintenance of crop evolutionary potential. Mexico is the centre of domestication and diversity for many CWR. The genus Cucurbita originated in America, where at least six independent domestication events took place. Nonetheless, Cucurbita CWR have been seldom studied. In the present study, we test the role of incomplete lineage sorting (ILS) and secondary contact in the divergence of C. okeechobeensis subsp. martinezii and C. lundelliana. Additionally, we seek to understand the role of environmental differentiation in their divergence. We obtained 1,638 single nucleotide polymorphisms (SNPs) for 107 individuals from the most recently diverged wild species in this genus, encompassing 25 localities of C. lundelliana and nine localities of C. okeechobeensis subsp. martinezii in Mexico. We found higher genetic variation in C. lundelliana (HE = 0.227) than in C. okeechobeensis subsp. martinezii (HE = 0.187). Each taxon constitutes a well‐differentiated genetic group, with an area of introgression in Pantanos de Centla. We found candidate loci associated to hydric and thermal stress, which could be valuable for crop improvement. Our study supported a scenario of ILS followed by secondary contact, where divergence was probably driven by Pleistocene climate change. These CWR represent important phytogenetic resources for crop improvement given their high levels of genetic variation and differentiation and their SNPs associated to different climatic variables.

Species delimitation using multiple sources of evidence from the Pinus strobiformis-Pinus ayacahuite Species Complex

Background: The Trans-Mexican Volcanic Belt (TMVB) in central Mexico is characterized by peaks of high altitude and geologic instability. In this zone, Pinus strobiformis and Pinus ayacahuite form a contact zone with Pinus veitchii. The taxonomical circumscription of white pines in Central Mexico has been unstable, especially regarding the status of P. veitchii.
 Questions: What are the species boundaries of the montane Mexican white pines species complex? Is Pinus veitchii a hybrid or an independently evolving lineage?
 Studied species: Pinus strobiformis, Pinus veitchii and Pinus ayacahuite species complex.
 Study site and dates: United States of America and Mexico from 2003 to 2022.
 Methods: We performed multivariate analyses on 10 morphological characters and characterized the climatic niche divergence and the genetic differentiation using SNPs.
 Results: Our results showed that P. veitchii is morphologically similar to P. strobiformis, but does not have intermediate morphological values with P. ayacahuite. The ecological niche differentiation was not significant.  Genetic analyses showed P. veitchii as an independent lineage with evidence of admixture with P. ayacahuite, suggesting a gene flow but not a hybrid origin.
 Conclusions: Two of the three lines of evidence support three independent lineages. Environmental information showed niche conservatism, morphology and genetic structure showed differentiation of all three taxa, with a greater morphological similarity between P. strobiformis and P. veitchii, and genetic analyses recovered evidence of introgression, suggesting a complex demographic history in the Trans Mexican Volcanic Belt.