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Spurs have played an important role in the radiation of the genus Aquilegia, but little is known about how the spurless state arose in A. ecalcarata. Here we aim to characterize the genetic divergence within A. ecalcarata and gain insights into the origin of this species. A total of 19 populations from A. ecalcarata and 23 populations from three of its closest relatives (Aquilegia kansuensis, Aquilegia rockii and Aquilegia yabeana) were sampled in this study. We sequenced fifteen nuclear gene fragments across the genome and three chloroplast loci to conduct phylogenetic, PCoA and STRUCTURE analyses. Our analyses indicate that A. ecalcarata may not be monophyletic and can be divided into two distinct lineages (A. ecalcarata I and A. ecalcarata II). A. ecalcarata I is genetically close to A. kansuensis, whereas A. ecalcarata II is close to A. rockii. Isolation-with-migration analysis suggested that historical gene flow was low between A. ecalcarata I and A. rockii, as well as between A. ecalcarata II and A. kansuensis. The two distinct lineages of A. ecalcarata show significant divergence in 13 floral traits and also have distinct distributions. In addition, both A. ecalcarata I and II are adapted to a stony environment that differs from that of their closest relatives, indicating a habitat shift may have driven new adaptations. Our findings enrich the understanding of how floral evolution contributes to species diversification.

The study was planned to evaluate the inter, and intra population genetic variation in general protein banding pattern in Oestrus ovis larvae, by using 10% sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS PAGE). The larvae were collected from slaughtered goats head from five different locations (AAS, PN, LA, GM, and BC) of Karachi, Pakistan. The data obtained was subjected to POPGENE (Population Genetic Analysis) software for analysis. The polymorphic loci within populations ranged from 45.45% to 90.91%. Polymorphic loci observed in all populations were 90.91%. The expected heterozygosity observed was 0.181±0.096 in all populations. The chi-square test showed 5 out of 11 loci at H-W equilibrium. The overall fixation index (FST) value was 0.108, showing that the likelihood of subpopulations being differentiated from one another is about 11 percent. The gene flow value (Nm=2.065) was higher, showing that genes flow occurs between populations. The values of genetic identity were greater, and genetic distance was smaller among all the populations. It means that all the populations were more alike and closer to each other. It was concluded that there was no sympatric and parapatric population differentiation observed among all the population of O. ovis. The populations of the five different locations were not genetically and reproductively isolated from each other.

Phytophthora sojae, the causal agent of Phytophthora root and stem rot of soybean, has been managed with single Rps genes since the 1960s but has subsequently adapted to many of these resistance genes, rendering them ineffective. The objective of this study was to examine the pathotype and genetic diversity of P. sojae from soil samples across Illinois, Indiana, Kentucky, and Ohio by assessing which Rps genes were still effective and identifying possible population clusters. There were 218 pathotypes identified from 473 P. sojae isolates with an average of 6.7 out of 15 differential soybean lines exhibiting a susceptible response for each isolate. Genetic characterization of 103 P. sojae isolates from across Illinois, Indiana, Kentucky, and Ohio with 19 simple sequence repeat markers identified 92 multilocus genotypes. There was a moderate level of population differentiation between these four states, with pairwise FSTvalues ranging from 0.026 to 0.246. There were also moderate to high levels of differentiation between fields, with pairwise FSTvalues ranging from 0.071 to 0.537. Additionally, cluster analysis detected the presence of P. sojae population structure across neighboring states. The level of pathotype and genetic diversity, in addition to the identification of population clusters, supports the hypothesis of occasional outcrossing events that allow an increase in diversity and the potential to select for a loss in avirulence to specific resistance genes within regions. The trend of suspected gene flow among neighboring fields is expected to be an ongoing issue with current agricultural practices.

Largely understudied, mesophotic coral ecosystems lie below shallow reefs (at30 m depth) and comprise ecologically distinct communities. Brooding reproductive modes appear to predominate among mesophotic-specialist corals and may limit genetic connectivity among populations. Using reduced representation genomic sequencing, we assessed spatial population genetic structure at 50 m depth in an ecologically important mesophotic-specialist species Agaricia grahamae, among locations in the Southern Caribbean. We also tested for hybridisation with the closely related (but depth-generalist) species Agaricia lamarcki, within their sympatric depth zone (50 m). In contrast to our expectations, no spatial genetic structure was detected between the reefs of Curaçao and Bonaire (~40 km apart) within A. grahamae. However, cryptic taxa were discovered within both taxonomic species, with those in A. lamarcki (incompletely) partitioned by depth and those in A. grahamae occurring sympatrically (at the same depth). Hybrid analyses and demographic modelling identified contemporary and historical gene flow among cryptic taxa, both within and between A. grahamae and A. lamarcki. These results (1) indicate that spatial connectivity and subsequent replenishment may be possible between islands of moderate geographic distances for A. grahamae, an ecologically important mesophotic species, (2) that cryptic taxa occur in the mesophotic zone and environmental selection along shallow to mesophotic depth gradients may drive divergence in depth-generalists such as A. lamarcki, and (3) highlight that gene flow links taxa within this relativity diverse Caribbean genus.

Introgressive hybridization plays a key role in adaptive evolution and species diversification in many groups of species. However, frequent hybridization and gene flow between species makes estimation of the species phylogeny and key population parameters challenging. Here, we show that by accounting for phasing and using full-likelihood analysis methods, introgression histories and population parameters can be estimated reliably from whole-genome sequence data. We employ full-likelihood methods under the multispecies coalescent (MSC) model with and without gene flow to analyze the genomic data from six members of the erato-sara clade of Heliconius butterflies and infer the species phylogeny and cross-species introgression events. The methods naturally accommodate random fluctuations in genealogical history across the genome due to deep coalescence. To avoid heterozygote phasing errors in haploid sequences commonly produced by genome assembly methods, we process and compile unphased diploid sequence alignments and use analytical methods to average over uncertainties in heterozygote phase resolution. There is robust evidence for introgression across the genome, both among distantly related species deep in the phylogeny and between sister species in shallow parts of the tree. We obtain chromosome-specific estimates of key population parameters such as introgression directions, times and probabilities, as well as species divergence times and population sizes for modern and ancestral species. We confirm ancestral gene flow between the sara clade and an ancestral population of H. telesiphe, a likely hybrid speciation origin for H. hecalesia, and gene flow between sister species H. erato and H. himera. Inferred introgression among ancestral species also explains the history of two chromosomal inversions deep in the phylogeny of the group. This study illustrates how a full-likelihood approach based on the multispecies coalescent makes it possible to extract rich historical information of species divergence and gene flow from genomic data.

Pyrenophora tritici-repentis causes tan spot, an important foliar disease of wheat. A collection of P. tritici-repentis isolates from Tunisia, located in one of the main secondary centers of diversification of durum wheat, was tested for phenotypic race classification based on virulence on a host differential set and for the presence of the necrotrophic effector (NE) genes ToxA, ToxB, and toxb by PCR analysis. While races 2, 4, 5, 6, 7, and 8 were identified according to their virulence phenotypes, PCR testing indicated the presence of “atypical” isolates that induced necrosis on the wheat differential ‘Glenlea,’ but lacked the expected ToxA gene, suggesting the involvement of other NEs in the P. tritici-repentis/wheat interaction. Genetic diversity and the P. tritici-repentis population structure were explored further by examining 59 Tunisian isolates and 35 isolates from Algeria, Azerbaijan, Canada, Iran, and Syria using 24 simple sequence repeat markers. Average genetic diversity, overall gene flow, and percentage polymorphic loci were estimated as 0.58, 2.09, and 87%, respectively. Analysis of molecular variance showed that 81% of the genetic variance occurred within populations and 19% occurred between populations. Cluster analysis by the unweighted pair group method indicated that ToxB– isolates grouped together and were distantly related to ToxB+ isolates. Based on Nei’s analysis, the global collection clustered into two distinct groups according to their region of origin. The results suggest that geographic origin and the host specificity imposed by different NEs can lead to differentiation among P. tritici-repentis populations.

Peronospora tabacina is an obligate parasite that causes blue mold of tobacco. The pathogen reproduces primarily by sporangia, whereas the sexual oospores are rarely observed. A collection of 122 isolates of P. tabacina was genotyped using nine microsatellites to assess the population structure of individuals from subpopulations collected from central, southern, and western Europe; the Middle East; Central America; North America; and Australia. Genetic variations among the six subpopulations accounted for ∼8% of the total variation, including moderate levels of genetic differentiation, high gene flow among these subpopulations, and a positive correlation between geographic and genetic distance (r = 0.225; P < 0.001). Evidence of linkage disequilibrium (P < 0.001) showed that populations contained partially clonal subpopulations but that subpopulations from Australia and Mediterranean Europe did not. High genetic variation and population structure among samples could be explained by continuous gene flow across continents via infected transplant exchange and/or long-distance dispersal of sporangia via wind currents. This study analyzed the most numerous P. tabacina collection and allowed conclusions regarding the migration, mutation, and evolutionary history of this obligate biotrophic oomycete. The evidence pointed to the species origin in Australia and identified intracontinental and intercontinental migration patterns of this important pathogen.[Formula: see text] Copyright © 2022 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license .

Rice false smut caused by Ustilaginoidea virens is one of the most devastating fungal diseases of rice panicles worldwide. In this study, two novel molecular markers derived from single nucleotide polymorphism-rich genomic DNA fragments and a previously reported molecular marker were used for analyzing the genetic diversity and population structure of 167 U. virens isolates collected from nine areas in the Sichuan–Chongqing region, China. A total of 62 haplotypes were identified, and a few haplotypes with high frequency were found and distributed in two to three areas, suggesting gene flow among different geographical populations. All isolates were divided into six genetic groups. Groups I and VI were the largest, with 61 and 48 isolates, respectively. The pairwise FST values showed significant genetic differentiation among all compared geographical populations. Analysis of molecular variance showed that intergroup genetic variation accounted for 40.17% of the total genetic variation, while 59.83% of genetic variation came from intragroup genetic variation. The unweighted pair-group method with arithmetic means dendrogram and population structure revealed that the genetic composition of isolates collected from Santai, Nanchong, Yongchuan, and Wansheng dominated by the same genetic subgroup was different from those collected from other areas. In addition, genetic recombination was found in a few isolates. These findings will help to improve the strategies for rice false smut management and resistance breeding, such as evaluating breeding lines with different isolates or haplotypes at different elevations and landforms.

Understanding the relationship between incursions of insect pests and established populations is critical to implementing effective control. Studies of genetic variation can provide powerful tools to examine potential invasion pathways and longevity of individual pest outbreaks. The major fruit fly pest in eastern Australia, Queensland fruit fly Bactrocera tryoni (Froggatt), has been subject to significant long‐term quarantine and population reduction control measures in the major horticulture production areas of southeastern Australia, at the species southern range limit. Previous studies have employed microsatellite markers to estimate gene flow between populations across this region. In this study, we used an independent genetic marker, mitochondrial DNA (mtDNA) sequences, to screen genetic variation in established and adjacent outbreak populations in southeastern Australia. During the study period, favorable environmental conditions resulted in multiple outbreaks, which appeared genetically distinctive and relatively geographically localized, implying minimal dispersal between simultaneous outbreaks. Populations in established regions were found to occur over much larger areas. Screening mtDNA (female) lineages proved to be an effective alternative genetic tool to assist in understanding fruit fly population dynamics and provide another possible molecular method that could now be employed for better understanding of the ecology and evolution of this and other pest species.

Natural Trap Cave (Bighorn Mountains, Wyoming) preserves an abundance of fossil remains from extinct Late Pleistocene fauna and is situated near a past migration route that likely connected populations in Eastern Beringia and the contiguous US—the ice-free corridor between the Cordilleran and Laurentide icesheets. Some palaeontological evidence supports a correspondingly high affinity between fauna recorded in Natural Trap Cave and Eastern Beringia versus elsewhere in the contiguous US, but this hypothesis has not yet been extensively tested using genetic data. In the present study, we analysed 16 horse specimens and one camel specimen from Natural Trap Cave. Of the horse specimens we analysed, we obtained 10 unique and previously unreported mitochondrial haplotypes belonging to two distinct (extinct) genetic clades—two haplotypes corresponded to a caballine horse (Equus sp.) and eight corresponded to the stilt-legged horse (Haringtonhippus francisci). With only one exception, it appears these newly sequenced individuals all shared a common ancestor more recently with Eastern Beringian individuals than with others from the contiguous US. In addition, mitochondrial data from a specimen assigned to Camelops sp. revealed that it shares a closer affinity with specimens from the Yukon Territory than those from Idaho or Nevada, though all appear to belong to a single species (“yesterday''s camel”; Camelops cf. hesternus). Together, these results are consistent with a high level of genetic connectivity between horse and camel populations in the Bighorn Mountains and Eastern Beringia during the Pleistocene. © 2021 Elsevier Ltd and INQUA

The effects of genetic introgression on species boundaries and how they affect species' integrity and persistence over evolutionary time have received increased attention. The increasing availability of genomic data has revealed contrasting patterns of gene flow across genomic regions, which impose challenges to inferences of evolutionary relationships and of patterns of genetic admixture across lineages. By characterizing patterns of variation across thousands of genomic loci in a widespread complex of true toads (Rhinella), we assess the true extent of genetic introgression across species thought to hybridize to extreme degrees based on natural history observations and multilocus analyses. Comprehensive geographic sampling of five large-ranged Neotropical taxa revealed multiple distinct evolutionary lineages that span large geographic areas and, at times, distinct biomes. The inferred major clades and genetic clusters largely correspond to currently recognized taxa; however, we also found evidence of cryptic diversity within taxa. While previous phylogenetic studies revealed extensive mitonuclear discordance, our genetic clustering analyses uncovered several admixed individuals within major genetic groups. Accordingly, historical demographic analyses supported that the evolutionary history of these toads involved cross-taxon gene flow both at ancient and recent times. Lastly, ABBA-BABA tests revealed widespread allele sharing across species boundaries, a pattern that can be confidently attributed to genetic introgression as opposed to incomplete lineage sorting. These results confirm previous assertions that the evolutionary history of Rhinella was characterized by various levels of hybridization even across environmentally heterogeneous regions, posing exciting questions about what factors prevent complete fusion of diverging yet highly interdependent evolutionary lineages.Uma atenção crescente tem sido dada aos efeitos da introgressão genética nos limites das espécies e como eles afetam a integridade e a persistência das espécies ao longo do tempo evolutivo. A crescente disponibilidade de dados genômicos revelou padrões contrastantes de fluxo gênico entre regiões do genoma, o que impõe desafios às inferências de relações evolutivas e de padrões de mistura genética entre linhagens. Com base em padrões de variação em milhares de marcadores genômicos em um complexo amplamente distribuído de sapos (Rhinella), avaliamos a extensão de introgressão genética entre espécies que, acredita-se, hibridizam amplamente com base em observações de história natural e análises multi-locus. Nossa amostragem geográfica abrangente de cinco táxons neotropicais revelou várias linhagens evolutivas distintas que abrangem grandes áreas geográficas e, por vezes, biomas distintos. Os principais clados e grupos genéticos inferidos correspondem em grande parte aos táxons atualmente reconhecidos; no entanto, também encontramos evidência de diversidade críptica. De acordo com estudos filogenéticos anteriores que revelaram extensa discordância mitonuclear, nossas análises de agrupamento genético revelaram vários indivíduos geneticamente misturados. Adicionalmente, análises demográficas históricas sugerem que a história evolutiva desses sapos envolveu fluxo gênico entre táxons tanto em épocas antigas quanto recentes. Por fim, testes ABBA-BABA revelaram amplo compartilhamento de alelos entre espécies, um padrão que pode ser atribuído à introgressão genética ao invés de sorteamento incompleto de alelos entre linhagens. Esses resultados confirmam sugestões anteriores de que a história evolutiva de Rhinella foi caracterizada por vários níveis de hibridização, mesmo entre ambientes distintos, levantando questões sobre quais fatores impedem a fusão completa de linhagens evolutivas divergentes porém altamente interdependentes.

The three-spined stickleback (Gasterosteus aculeatus) has repeatedly and independently adapted to freshwater habitats from standing genetic variation (SGV) following colonization from the sea. However, in the Mediterranean Sea G. aculeatus is believed to have gone extinct, and thus the spread of locally adapted alleles between different freshwater populations via the sea since then has been highly unlikely. This is expected to limit parallel evolution, that is the extent to which phylogenetically related alleles can be shared among independently colonized freshwater populations. Using whole genome and 2b-RAD sequencing data, we compared levels of genetic differentiation and genetic parallelism of 15 Adriatic stickleback populations to 19 Pacific, Atlantic and Caspian populations, where gene flow between freshwater populations across extant marine populations is still possible. Our findings support previous studies suggesting that Adriatic populations are highly differentiated (average F-ST approximate to 0.45), of low genetic diversity and connectivity, and likely to stem from multiple independent colonizations during the Pleistocene. Linkage disequilibrium network analyses in combination with linear mixed models nevertheless revealed several parallel marine-freshwater differentiated genomic regions, although still not to the extent observed elsewhere in the world. We hypothesize that current levels of genetic parallelism in the Adriatic lineages are a relic of freshwater adaptation from SGV prior to the extinction of marine sticklebacks in the Mediterranean that has persisted despite substantial genetic drift experienced by the Adriatic stickleback isolates.

The Lusitanian (Microtus lusitanicus) and the Mediterranean (Microtus duodecimcostatus) pine voles are recently diverged sister species endemic of the Iberian Peninsula that can be identified with ecological and morphological characters, but in areas where the 2 species co-occur, species designation may be difficult. Genetic discrimination between M. lusitanicus and M. duodecimcostatus has not been achieved yet possibly because of their estimated recent split and an evolutionary history that includes inter-species gene flow. Following our previous observations on exons 5-7 of the p53 gene, here we analyze the potential use of the p53 genomic region as a discrimination marker of these species by extending our analyses to several kb upstream and downstream of the p53 gene and characterizing the degree of genetic differentiation in 7 markers within this region. Additionally, we fully sequenced the P53 protein of both species. We observed: (i) generally high differentiation in this region; (ii) M. duodecimcostatus showed in general higher values of nucleotide and haplotype diversities; (iii) the concatenated phylogenetic tree separates the 2 species; (iv) the 2 P53 proteins only differ in 1 amino acid; (v) 4 of the markers, 2 in p53, one in Atp1b2, and another in Wrap53, contain species-specific genetic variation thus allowing a reliable discrimination between specimens from both species, irrespective of sampling location or introgression status. We provide additional data on the putative role of p53 in the evolution of these species and present researchers with a fast and cost-effective resource for M. lusitanicus and M. duodecimcostatus identification.

Post-polyploid diploidization associated with descending dysploidy and interspecific introgression drives plant genome evolution by unclear mechanisms. Raphanus is an economically and ecologically important Brassiceae genus and model system for studying post-polyploidization genome evolution and introgression. Here, we report the de novo sequence assemblies for 11 genomes covering most of the typical sub-species and varieties of domesticated, wild and weedy radishes from East Asia, South Asia, Europe, and America. Divergence among the species, sub-species, and South/East Asian types coincided with Quaternary glaciations. A genus-level pan-genome was constructed with family-based, locus-based, and graph-based methods, and whole-genome comparisons revealed genetic variations ranging from single-nucleotide polymorphisms (SNPs) to inversions and translocations of whole ancestral karyotype (AK) blocks. Extensive gene flow occurred between wild, weedy, and domesticated radishes. High frequencies of genome reshuffling, biased retention, and large-fragment translocation have shaped the genomic diversity. Most variety-specific gene-rich blocks showed large structural variations. Extensive translocation and tandem duplication of dispensable genes were revealed in two large rearrangement-rich islands. Disease resistance genes mostly resided on specific and dispensable loci. Variations causing the loss of function of enzymes modulating gibberellin deactivation were identified and could play an important role in phenotype divergence and adaptive evolution. This study provides new insights into the genomic evolution underlying post-polyploid diploidization and lays the foundation for genetic improvement of radish crops, biological control of weeds, and protection of wild species' germplasms.

Population structure can reveal the diversity, gene flow, and dispersal of a species. This information can be used to make management decisions and reveal fundamental aspects of an organism’s biology. Distinct intrinsic (e.g., biological characteristics) and extrinsic (e.g., geographical and historical events, environment, human pressures) factors can influence population structure, with significant differences among species. However, detection of population structure in migratory lamprey species can be difficult to detect due to their lack of natal homing; this is particularly the case for anadromous lampreys, with their potential for wide dispersal at sea during their parasitic feeding stage. We review phenotypic and genetic markers, as well as the methods that have been used to assess population structure in lampreys, and discuss the relative strengths and limitations of each. Structure has been detected in several anadromous species using some of these methods, even without homing in these species, but we briefly contrast the weak population structure observed in anadromous species with the stronger structure observed in freshwater-resident lamprey species (particularly non-migratory brook lampreys). We relate lamprey population structure to species-specific ecological traits, such as juvenile dispersal tendencies, and provide case studies of six species. Delineation of appropriate management units in migratory lamprey species is important for conservation and management.

The southernmost stock of longfin smelt (Spirinchus thaleichthys) is approaching extirpation in the San Francisco Estuary (SFE); however, patterns of genetic structure, diversity and gene flow which are vital for management are poorly understood in this species. Here, we use genome-wide data to evaluate population structure of longfin smelt across a broad latitudinal scale across estuaries ranging from the SFE to Yakutat Bay and Lake Washington, and fine scale within the Fraser River and the SFE. Results indicate high genetic structure between major estuaries, fine-scale structure within the Fraser River, and low levels of structure within the SFE. Genetic structure was more pronounced between northern estuaries whereas southern estuaries showed shared ancestry and ongoing gene flow, most notably unidirectional northward migration out of the SFE. Furthermore, we detected signatures of local adaptation within the Fraser River and the Skeena River estuaries. Taken together, our results identify broad patterns of genetic diversity in longfin smelt shaped by co-ancestry, unidirectional migration and local adaptation. Results also suggest that the SFE population is genetically distinct from northernmost populations and an important source for maintaining nearby populations., The authors thank Colin Grant (US Fish and Wildlife Service), who made many of the initial inquiries soliciting longfin smelt samples, and Josh Israel (US Bureau of Reclamation), who performed initial genetic analyses. The authors also thank the following individuals and agencies for help collecting samples: Hobbslab and staff -UC Davis; Matt Dekar and staff -US Fish and Wildlife Service; Kathy Hieb, Jennifer Giannetta, Jeremiah Bautista, Aaron Ng, Rebecca Garwood, James Ray, Justin Garwood, and Mike Wallace -California Department of Fish and Wildlife; Laurie Lloyd, Olaf Langness -Washington Department of Fish and Wildlife, Thomas Quinn, University of Washington; Eric Taylor -The University of British Columbia, John Kelson -Fish BiologistConsultant, Smithers, British Columbia; Mayumi Arimitsu -US Geological Survey, Alaska Science Center. Finally, the authors also thank a number of internal reviewers, Genomic Variation Lab Personnel, and other agency biologists who helped this project, including Matthew Campbell, Daphne Gille, Levi Lewis, Andrea Schreier, Josh Israel, and Alisha Goodbla. Funding for this project was generously provided by the California Department of Water Resources, Agreement Number 4600011196.

SummaryStandard models of plant speciation assume strictly dichotomous genealogies in which a species, the ancestor, is replaced by two offspring species. The reality in wind-pollinated trees with long evolutionary histories is more complex: species evolve from other species through isolation when genetic drift exceeds gene flow; lineage mixing can give rise to new species (hybrid taxa such as nothospecies and allopolyploids). The multi-copy, potentially multi-locus 5S rDNA is one of few gene regions conserving signal from dichotomous and reticulate evolutionary processes down to the level of intra-genomic recombination. Therefore, it can provide unique insights into the dynamic speciation processes of lineages that diversified tens of millions of years ago. Here, we provide the first high-throughput sequencing (HTS) of the 5S intergenic spacers (5S-IGS) for a lineage of wind-pollinated subtropical to temperate trees, theFagus crenata – F. sylvaticas.l. lineage, and its distant relativeF. japonica.The observed 4,963 unique 5S-IGS variants reflect a complex history of hybrid origins, lineage sorting, mixing via secondary gene flow, and intra-genomic competition between two or more paralogous-homoeologous 5S rDNA lineages. We show that modern species are genetic mosaics and represent a striking case of ongoing reticulate evolution during the past 55 million years.Significance statementThe evolution of extra-tropical wind-pollinated tree genera involves dynamic speciation processes. High-throughput sequencing of the multi-copy, potentially multi-locus 5S rDNA reveals a complex history of hybrid origins, lineage sorting and mixing, and intra-genomic competition between paralogous-homeologous loci in the core group of Eurasian beech trees (genusFagus) and their distant relative,F. japonica. The modern species are genetic mosaics and represent a striking case of at least 55 million years of ongoing reticulate evolution.

Corydoras is the richest genus of Corydoradinae, and many of its species have not been identified to date. We characterized Corydoras carlae and Corydoras sp. by performing cytogenetic, morphometric, and molecular analyses to facilitate correct identification and species delimitation and contribute an understanding of the evolutionary process of this group of fish. Individuals of C. carlae were collected in the Florido River, a tributary of the Iguassu River upstream of Iguassu Falls, and individuals of Corydoras sp. were collected in the Poco Preto River, a tributary of the Iguassu River downstream of Iguassu Falls. Corydoras sp. presented an extra rDNA 5S marker in an interstitial position on the short arm of one of the chromosomes of the submetacentric pair 15. Mitochondrial (COI) and nuclear (RAG1) sequences were efficient in discriminating C. carlae and Corydoras sp. Both species had exclusive haplotypes, which suggests the absence of gene flow between species. Furthermore, species delimitation analysis (GMYC and ABGD) suggested two MOTUs for Corydoras specimens from the Iguassu River. Differences in morphometric proportions were also observed. Considering the data gathered in this study, C. carlae and Corydoras sp. comprise distinct evolutionary lineages that are probably undergoing a recent speciation process.

Establishing conservation priorities requires an understanding of the diversity within and among taxa. Land snails in the subgenus Monadenia consist of six species, three of which are recognized in Oregon, M. fidelis, M. chaceana and a recently discovered M. infumata found north of its presumed range limits in Northern California. Further, M. fidelis is composed of at least six named subspecies, one of which is a candidate for federal listing, and extensive sampling and expert assessments of shell morphology have uncovered even more distinct forms. Still, it is unknown if these morphological variants are truly distinctive units of diversity or rather reflect environmentally driven plasticity. Here we investigate whether there are multiple, structured units of diversity in Washington, Oregon, and California Monadenia. We used COI, a mitochondrial barcode gene, a ddRAD-based genome-wide SNP dataset, along with expert-assessment of morphology, to better delimit diversity of Monadenia in Oregon and in parts of Washington and California to inform conservation strategies for this group. Morphological analyses confirm the existence of distinctive morphotypes, but genomic data show widespread admixture, even at the species level. Still, we do find limited geographic structuring between samples collected in the northern versus southern portions of the study area and possibly weak structuring between populations in the Coast Ranges compared to the Cascade Mountains. Genetic differentiation was similar among the morphotypes in the north–south grouping, but pairwise estimates of differentiation were much greater among some morphotypes and species. Our finding of admixture and gene flow across Monadenia, even at the species level, complicates assessment of individuated units of diversity critical for establishing conservation prioritization. Further work is still necessary, such as including more Monadenia taxa, in order to evaluate species limits and investigate mechanisms underlying the morphological diversity in this group.

Alpheus lobidens sensu lato is one of the most common groups of snapping shrimps in the Indo-West Pacific. The objective of this study was to investigate the phylogenetic relationships among lineages of A. lobidens s.l. throughout their geographical distribution and identifying possible morphological characteristics that support the lineages from this combined dataset. Molecular data were obtained by analysing 16S rRNA from nine individuals of A. lobidens, three of A. buckupi, one of A. inopinatus and six other Alpheus species. The genetic analyses (mean p-distance and Bayesian Inference) indicate considerable genetic divergence and at least nine lineages within the A. lobidens species complex. The high morphological variability observed in Alpheus spp. and the high rates of interspecific genetic divergence agree with the Marine Ecoregions of the World and ocean currents, which suggests limited gene flow among those lineages, indicating that these could be treated as new species. However, as no informative morphological characters were identified, describing the six new taxa of the complex recognised in this study was unfeasible. Future studies using a higher number of specimens and applying more sensitive methods for detecting structural differences, might help morphologically define the new species that were uncovered herein.

BACKGROUND The invasion of Helicoverpa armigera (Hubner) (Lepidoptera: Noctuidae) into the New World has made it possible for this pest to hybridize with a native American species, H. zea (Boddie), under natural conditions. We investigated the viability and development of hybrids of these two Helicoverpa species. We reared the parental species and evaluated crosses between H. armigera males and H. zea females and vice versa, two intercrosses between hybrids, and eight backcrosses between hybrids and parental species. We estimated the length of immature stages, fecundity, survival, sex ratio, and heterosis. RESULTS Although hybridization occcurred, with heterosis during the development of immatures, reproductive incompatibilities also were observed between the parental species and between hybrids from subsequent crosses. The interspecific crosses between hybrids and backcrosses confirmed the possibility of introgression events and their perpetuation in field populations. The results indicate that hybridization events are favored at high population levels, while at low population levels the 'species identities' will be maintained. CONCLUSIONS The possibility of interspecific gene flow and its perpetuation through successive crosses and backcrosses suggests several recommenations for management. Populations of both species should be maintained at an equilibrium level to reduce the chance of interspecific crosses, which are presumably more likely to occur during pest outbreaks. The existence of hybridization and resistance to different active pesticide ingredients should be monitored. All practices related to managing the resistance of these pests to chemical and biological insecticides should be systematized to reduce the chance of selecting for resistant individuals.

The pomegranate (Punica granatum L.) is an ancient fruit plant which has been consumed for its nutritional value and medicinal properties by mankind. Several studies have been carried out on the genetic variability and cultivar genetic finger printing of this plant species. Some of these studies claimed presence of very low degree of genetic variability in these cultivars, while some others reported a good level of genetic diversity in them. The similar controversy exists about the suitability of different molecular markers for genetic variability studies as well as cultivar discrimination. We therefore carried out the print study to compare the level of genetic variability as revealed by both nuclear (SSRs), and chloroplast genetic regions (trnH-psbA spacer, and matk gene) to reveal the discriminating power of these markers and provide some data on barcoding and mini-barcodes of pomegranate cultivars. We used both experimental data produced in our lab also utilized some published sequencing data from NCBI database. We used different bioinformatic approaches. DAPC analysis revealed that SSR markers are suitable for genetic variability analysis of pomegranate cultivars, but revealed some degree of genetic admixture among pomegranates. Therefore, these markers are suitable for gene flow studies but may not portray exact cultivar assignment. Both trnH-psbA and matK sequences could produce a better cultivar assignment. Barcoding and mini-barcode analyses revealed that pomegranates may be divided in two major genetic groups with some degree of divergence within these two major groups. Data indicates that, pomegranate plants possibly migrated or were introduced from Iran to the other parts of the world and it was accompanied with genetic divergence as discussed in this report.

Okra [Abelmoschus esculentus (L.) Monech.] is an annual herb of the family Malvaceae and has tremendous nutritional and industrial potential. However, the unknown genome size, variation in ploidy level makes it more challenging for okra breeders to enhance their genetic potential. In this context, the genetic analysis of allelic polymorphism and population structure analysis of okra germplasm is pivotal for its genetic improvement. In the present investigation, a total of 96 okra genotypes were undertaken for morpho-genetic diversity analyses using 13 morphological parameters and 65 SSR markers. Out of 65 SSRs, 50 primers were polymorphic and the mean polymorphic information content (PIC) value was 0.38. The polymorphic loci AVRDC OKRA 64 revealed a maximum PIC value of 0.71 and the number of alleles per locus varied from 2 to 7, with an average of 3.34 alleles per locus. The neighbour-joining (N-J) tree grouped the genotypes into three distinct clusters (I-III), of which Cluster I comprised of cultivated species, A. esculentus and A. caillei, while, Cluster II and III consisted of other related wild species. Furthermore, the population structure analysis distinguished the okra genotypes into two distinct genetic groups comprising cultivated (A. esculentus) and wild-type okra. The variability analysis based on 13 agro-morphological traits revealed that the genotype DOV-92 exhibited the highest per se performance for total fruit yield, followed by Pusa Bhindi-5. The PCA (Principal Component Analysis) analysis revealed that the first three components account for more than 50% of the total genetic variation. The present investigation deciphered a high morphological and genetic diversity in cultivated and wild okra germplasm. Thus, it could serve as important genetic resources for okra improvement programmes.

Disentangling the effects of neutral and adaptive processes in maintaining phenotypic variation across environmental gradients is challenging in natural populations. Song sparrows (Melospiza melodia) on the California Channel Islands occupy a pronounced east-west climate gradient within a small spatial scale, providing a unique opportunity to examine the interaction of genetic isolation (reduced gene flow) and the environment (selection) in driving variation. We used reduced representation genomic libraries to infer the role of neutral processes (drift and restricted gene flow) and divergent selection in driving variation in thermoregulatory traits with an emphasis on the mechanisms that maintain bill divergence among islands. Analyses of 22,029 neutral SNPs confirm distinct population structure by island with restricted gene flow and relatively large effective population sizes, suggesting bill differences are probably not a product of genetic drift. Instead, we found strong support for local adaptation using 3294 SNPs in differentiation-based and environmental association analyses coupled with genome-wide association tests. Specifically, we identified several putatively adaptive and candidate loci in or near genes involved in bill development pathways (e.g., BMP, CaM, Wnt), confirming the highly complex and polygenic architecture underlying bill morphology. Furthermore, we found divergence in genes associated with other thermoregulatory traits (i.e., feather structure, plumage colour, and physiology). Collectively, these results suggest strong divergent selection across an island archipelago results in genomic changes in a suite of traits associated with climate adaptation over small spatial scales. Future research should move beyond studying univariate traits to better understand multidimensional responses to complex environmental conditions.

Background In recent years, farmers have complained that the only way to obtain seeds is to select plants that show good performance under local climate conditions in the region. This study aimed to investigate the diversity of rice accessions grown in the region to build a breeding program. Methods and results A total of 62 accessions of rice from farmers and research stations were collected from the Kurdistan region, including short-grain and long-grain types, for molecular genetics and diversity analysis. In this study, 37 polymorphic simple sequence repeat (SSR) markers were selected with several molecular genetics software programs. The results show that these SSR markers are very effective for this investigation, generating a total of 152 observed alleles (Na), 75.166 Effective number of alleles (Ne) and an average of 4.1 and 2.03 alleles per locus, respectively. The average polymorphic information content (PIC) per locus was recorded as 0.404. The research presented here confirms two subpopulations, japonica (C1 and C2) and indica (C3), based on molecular genetics data analysis. Analysis of molecular variance revealed that the 72% variance was due to the variation among populations and 28% within the population. Conclusions Altogether, these results indicate that there is very low gene flow. These results show the importance of the study of genetic diversity and relationships for starting breeding and improvement programs for rice in the Kurdistan region. Supplementary Information The online version contains supplementary material available at 10.1007/s11033-021-06920-x.

Gene flow and reticulation are increasingly recognized as important processes in the diversification of many taxonomic groups. With the increasing ease of collecting genomic data and the development of multispecies coalescent network approaches, such reticulations can be accounted for when inferring phylogeny and diversification. Caribbean Anolis lizards are a classic example of an adaptive radiation in which species have independently radiated on the islands of the Greater Antilles into the same ecomorph classes. Within the Jamaican radiation at least one species, Anolis opalinus, has been documented to be polyphyletic in its mitochondrial DNA, which could be the result of an ancient reticulation event or incomplete lineage sorting (ILS). Here, we generate mtDNA and genotyping-by-sequencing (GBS) data and implement gene tree, species tree, and multispecies coalescent network methods to infer the diversification of this group. Our mtDNA gene tree recovers the same relationships previously inferred for this group, which is strikingly different from the species tree inferred from our GBS data. Posterior predictive simulations suggest that our genomic data violate commonly adopted assumptions of the multispecies coalescent model (MSCM), so we use network approaches to infer phylogenetic relationships. The inferred network topology contains a reticulation event but does not explain the mtDNA polyphyly observed in this group; however, coalescent simulations suggest that the observed mtDNA topology is likely the result of past introgression. How common a signature of gene flow and reticulation is across the radiation of Anolis is unknown; however, the reticulation events that we demonstrate here may have allowed for adaptive evolution, as has been suggested in other, more recent, adaptive radiations. [Adaptive radiation; hybridization; introgression; multispecies network coalescent; posterior predictive simulation.]

Oceanic islands are natural laboratories where evolutionary processes can be studied more readily. In the present work we use nuclear microsatellites to quantitatively assess the roles of hybridization, colonization, gene flow and geographical barriers in four Parolinia spp. endemic to Gran Canaria in connection with known geological events throughout the dynamic geological ontogeny of the island. Our genetic analyses show that these Parolinia spp. share 69% of all alleles detected and display low genetic divergence among populations, suggesting a close genetic relationship and recent differentiation. This close relationship is more evident between Parolinia platypetala and Parolinia ornata, which were included in the same genetic pool in the STRUCTURE analysis, and probably represent the early stages of an incipient speciation process, as suggested by the absence of gene flow barriers between them. NEWHYBRIDS, STRUCTURE and MIGRATE analyses unequivocally suggest frequent past migration and hybridization from P. ornata to P. filifolia, but contemporary migration is low overall. Despite the overall genetic closeness among the Parolinia spp. assessed, microsatellites dispelled doubts regarding the appropriate name/s for two taxonomically conflicting populations. In line with the predictions of the surfing syngameon hypothesis, ancestral hybridization, vicariance and dispersal events linked to the complex ontogeny of the island may have been key factors to shape the current genetic diversity and structure of Parolinia in Gran Canaria.

Understanding of the present-day genetic diversity, population structure, and evolutionary history of tree species can inform resource management and conservation activities, including response to pressures presented by a changing climate. Cercis canadensis (Eastern Redbud) is an economically valuable understory tree species native to the United States (U.S.) that is also important for forest ecosystem and wildlife health. Here, we document and explain the population genetics and evolutionary history of this deciduous tree species across its distributed range. In this study, we used twelve microsatellite markers to investigate 691 wild-type trees sampled at 74 collection sites from 23 Eastern U.S. states. High genetic diversity and limited gene flow were revealed in wild, natural stands of C. canadensis with populations that are explained by two major genetic clusters. These findings indicate that an ancient population bottleneck occurred coinciding with the last glacial maximum (LGM) in North America. The structure in current populations likely originated from an ancient population in the eastern U.S. that survived LGM and then later diverged into two contemporary clusters. Data suggests that populations have expanded since the last glaciation event from one into several post-glacial refugia that now occupy this species’ current geographic range. Our enhanced understanding benchmarks the genetic variation preserved within this species and can direct future efforts in conservation, and resource utilization of adaptively resilient populations that present the greatest genetic and structural diversity.

Phenotypic and genetic divergence are shaped by the homogenizing effects of gene flow and the differentiating processes of genetic drift and local adaptation. Herein, we examined the mechanisms that underlie phenotypic (size and color) and genetic divergence in 35 populations (535 individuals) of the poison frog Epipedobates anthonyi along four elevational gradients (0-1800 m asl) in the Ecuadorian Andes. We found phenotypic divergence in size and color despite relatively low genetic divergence at neutral microsatellite loci. Genetic and phenotypic divergence were both explained by landscape resistance between sites (isolation-by-resistance, IBR), likely due to a cold and dry mountain ridge between the northern and southern elevational transects that limits dispersal and separates two color morphs. Moreover, environmental differences among sites also explained genetic and phenotypic divergence, suggesting isolation-by-environment (IBE). When northern and southern transects were analyzed separately, genetic divergence was predicted either by distance (isolation-by-distance, IBD; northern) or environmental resistance between sites (IBR; southern). In contrast, phenotypic divergence was primarily explained by environmental differences among sites, supporting the IBE hypothesis. These results indicate that although distance and geographic barriers are important drivers of population divergence, environmental variation has a two-fold effect on population divergence. On the one hand, landscape resistance between sites reduces gene flow (IBR), while on the other hand, environmental differences among sites exert divergent selective pressures on phenotypic traits (IBE). Our work highlights the importance of studying both genetic and phenotypic divergence to better understand the processes of population divergence and speciation along ecological gradients.

Surveys of patterns of genetic variation in natural sympatric and allopatric populations of recently diverged species are necessary to understand the processes driving intra- and interspecific diversification. The South American moths Cactoblastis cactorum, Cactoblastis doddi and Cactoblastis bucyrus are specialized in the use of cacti as host plants. These species have partially different geographic ranges and differ in patterns of host plant use. However, there are areas that overlap, particularly, in northwestern Argentina, where they are sympatric. Using a combination of genome-wide SNPs and mitochondrial data we assessed intra and interspecific genetic variation and investigated the relative roles of geography and host plants on genetic divergence. We also searched for genetic footprints of hybridization between species. We identified three well delimited species and detected signs of hybridization in the area of sympatry. Our results supported a hypothetical scenario of allopatric speciation in the generalist C. cactorum and genetic interchange during secondary geographic contact with the pair of specialists C. bucyrus and C. doddi that probably speciated sympatrically. In both cases, adaptation to new host plants probably played an important role in speciation. The results also suggested the interplay of geography and host plant use as drivers of divergence and limiting gene flow at intra and interspecific levels.

Interpreting the formation of genomic variation landscape, especially genomic regions with elevated differentiation (i.e. islands), is fundamental to a better understanding of the genomic consequences of adaptation and speciation. Edaphic islands provide excellent systems for understanding the interplay of gene flow and selection in driving population divergence and speciation. However, discerning the relative contribution of these factors that modify patterns of genomic variation remains difficult. We analysed 132 genomes from five recently divergent species in Primulina genus, with four species distributed in Karst limestone habitats and the fifth one growing in Danxia habitats. We demonstrated that both gene flow and linked selection have contributed to genome-wide variation landscape, where genomic regions with elevated differentiation (i.e., islands) were largely derived by divergent sorting of ancient polymorphism. Specifically, we identified several lineage-specific genomic islands that might have facilitated adaptation of P. suichuanensis to Danxia habitats. Our study is amongst the first cases disentangling evolutionary processes that shape genomic variation of plant specialists, and demonstrates the important role of ancient polymorphism in the formation of genomic islands that potentially mediate adaptation and speciation of endemic plants in special soil habitats.

— Lineage recombination is an important source of genetic and morphological variation in species-rich groups of plants. Tetraploids that are intermediate in morphology and ecology with respect to sympatric diploids are regularly hypothesized to be the products of hybridization. Arctostaphylos mewukka is one such intermediate tetraploid long regarded as the result of hybridization and genome duplication among divergent and geographically overlapping diploids widely distributed across the western slope of the Sierra Nevada. Here we set out to test this hypothesis leveraging the notion that allopolyploids arise repetitively and may show signs of reciprocal organellar exchange among species between maternal and paternal progenitors. We compared nuclear ribosomal and plastid sequence data acquired from samples within and outside this target species complex. Molecular sequence data show striking patterns indicative of widespread reticulation and chloroplast capture events across the genus Arctostaphylos. Results support the notion that outcrossing, long-lived woody plant species such as members of the genus Arctostaphylos can retain a secured morphological identity despite ongoing influence of interspecific gene flow that would otherwise render species boundaries vulnerable to dissolution.

Tobacco rattle virus (TRV) is an important soil-borne virus of potato that is transmitted by stubby-root nematodes. TRV causes corky ringspot, a tuber disease of economic importance to potato production. Utilizing protein-coding regions of the whole genome and a range of computational tools, the genetic diversity, and population structure of TRV isolates from several potato-growing regions (Colorado, Idaho, Indiana, Minnesota, Nebraska, North Dakota, and Washington State) in the USA were determined. Phylogenetic analyses based on RNA2 nucleotide sequences, the coat protein (CP) and nematode transmission (2b) genes, showed geographical clustering of USA isolates with previously known American isolates, while European isolates grouped in a distinct cluster. This was corroborated by the observed genetic differentiation and infrequent gene flow between American and European isolates. Low genetic diversity was revealed among American isolates compared to European isolates. Phylogenetic clustering based on RNA1 genes (RdRp, RdRp-RT, and 1a) were all largely incongruent to that of 1b gene (virus suppressor of RNA silencing). This genetic incongruence suggested the influence of recombination. Furthermore, the RdRp, RdRp-RT, and 1a genes were predicted to be more conserved and under negative selection, while the 1b gene was less constrained. Different evolutionary lineages between TRV RNA1 and RNA2 genomic segments were revealed.

Migration is a widespread phenomenon among many insect species, including herbivorous crop pests. At present, scant information exists on the long-range migration of the polyphagous armyworm, Spodoptera exigua and its underlying climatic determinants (i.e. East Asian or South Asian monsoon circulation). In this study, we employed a population genetics approach to delineate S. exigua migration patterns across multiple Asian countries.Using mitochondrial cytochrome I (COI) and microsatellite markers, low-to-moderate levels of genetic diversity were detected among 101 S. exigua populations collected across China, Pakistan and Vietnam. Haplotype diversity and nucleotide diversity did not differ between years. Two spatially explicit genetic clusters were detected, an eastern and a western clade, with the former comprising populations in the East Asia monsoon area. No genetic differentiation was recorded among armyworm populations in the year-round breeding area, nor among those of the overwintering and nonoverwintering areas. Five of the most widespread mitochondrial haplotypes reflected the extensive gene flow across at a large spatial scale.Low-to-moderate levels of genetic diversity were observed, and evidence was found for genetic clustering in certain geographical areas. Accordingly, our unique insights into S. exigua population genetics and spatiotemporal migration dynamics help to guide applied ecological studies, ecological intensification schemes or (area-wide) pest management campaigns in China and abroad. © 2021 Society of Chemical Industry.

Euschistus heros (Hemiptera: Pentatomidae) has two allopatric strains with a hybrid zone in central Brazil. Asymmetric dispersal and gene flow between these strains of E. heros have been observed, where the South strain (SS) moves more quickly to the northern regions of the country than the North strain (NS) to the southern areas. In addition, SS generally has a bigger body size and presents dark brown coloration, and NS is usually smaller in size and presents light brown coloration. Here, we studied the reproductive behavior and tested for the presence of assortative mating and reproductive barriers between the two allopatric strains of E. heros. Nonrandom mating was observed in the SS strain based on mating choice trials and the reproductive isolation indexes. SS females and males prefer to mate with their co-specific (same strain) partner, while NS insects showed no mating preference. The insect’s pronotum width was positively associated with the mating choice suggesting size-assortative mating in E. heros. Reciprocal crosses between strains yielded similar reproductive outputs when compared with pure strain crosses, suggesting similar fitness of hybrid pure strains. The asymmetric gene flow in the hybridization zone that favors SS seems to be associated with the reproductive behavior of the species, which favors the typical phenotype found in the SS populations.

We provide an example of ecological vicariance among two epilithic, high mountain taxa of mosses. Phylogenetic analyses using plastid (rps4-trnS, atpB-rbcL, trnL-trnF) and nuclear (EST-115, EST-317, ITS region) markers and morphological data revealed the distinctiveness of the neglected Orthotrichum killiasii, here resurrected from the synonymy of Lewinskya speciosa and newly combined in Lewinskya. Furthermore, our data indicate a speciation process within O. killiasii related to the rock type inhabited (silicate vs. carbonate). We translate this into the recognition of two subspecies, corresponding to O. killiasii s.s. and the recently described O. simonyi. The incongruence between nuclear and plastid markers in some accessions and the partial but rare incongruence between ITS ribotypes and the morphological manifestation in phenotypes indicate incomplete lineage sorting with respect to rather recent segregation and possible gene flow between the two entities.

The increasing awareness that hybridization, and resultant gene flow, plays a major role in animal diversification has led to a growing number of studies that have focused on assessing the morphological consequences of this process. Analyses of mammalian hybrids have identified skeletal effects of hybridization, including a suite of anomalous dental and sutural traits on the skull that are present at high frequencies in hybrid populations. These studies have also detected consistent patterns of morphological shape and size differences between hybrids and parental taxa across a wide variety of organisms. However, more research is required to understand the universality of these traits and shape/size differences. Building on these previous studies, a sample of genetically determined canid hybrids was examined, specifically the eastern coyote (Canis latrans var.), a hybrid between coyotes, wolves, and dogs, to test whether this group exhibits a comparable pattern of anomalous nonmetric characters, and to assess differences in craniomandibular shape and size. First, specimens of C. latrans var., C. latrans, and C. lupus were scored for anomalous traits, including supernumerary and rotated teeth, dental crowding, and sutural anomalies. Geometric morphometric analyses were then conducted on a subset of these individuals to explore craniomandibular size and shape variation, as well as allometry. The results are largely consistent with other studies, indicating that the incidence of dental anomalies, dental crowding, and sutural anomalies is significantly higher in hybrids. However, differences are not significant for supernumerary teeth. The exploration of morphometric variation identifies intermediate morphology in the hybrids, and some indication of greater morphological variability in the mandible. When these results are combined with previous studies, they suggest that skeletal signatures of hybridization are common to different mammalian taxa across multiple generations; however, some traits such as supernumerary teeth may be lost after a few generations.

Husk tomato is an annual vegetable crop grown for its fruits in Mexico, where it grows as weedy and wild. Eight races are recognized from wild (Wild and Milpero) and cultivated (Arandas, Manzano, Puebla, Rendidora, Salamanca, and Tamazula) conditions based on morphological and ecological traits. However, few studies have addressed the genetic diversity and divergence of all races. We aimed to (i) assess the genetic diversity and structure of 10 cultivars representing the recognized races of husk tomato and (ii) compare the genetic diversity of the cultivated and wild pools. We identified 270 single nucleotide polymorphisms from 40 samples using multiplex ISSR genotyping by sequencing (MIG-seq). The results showed lower to moderate diversity in each cultivar (HE = 0.082–0.147) and lower to moderate pairwise genetic differentiation (FST = − 0.011 to 0.195) between cultivars. The Bayesian clustering analysis identified three genetic groups (K = 3) with ancestry coefficients (Q = 0.6–0.89) that suggest gene flow among cultivars. Ordination and classification analysis based on genetic distances revealed two main genetic clusters related to fruit traits and geographic regions where cultivars are commercialized, while a third group included the Wild and Milpero. Analysis of molecular variance revealed higher variation within cultivars (80%) than among cultivars (18%). The cultivated pool harbors 96% of the diversity present in the wild (Ht = 0.322 vs. Ht = 0.311) and does not show severe genetic bottlenecks related to the domestication process. Our results suggest that husk tomato domestication, like other Mesoamerican crops, might be diffuse rather than from a single geographic origin.

We conducted genomic characterization based on SNP and SilicoDArT markers on the invasive Himalayan balsam (Impatiens glandulifera) plants originating from native and non-native regions of their distribution. When genetic relationships were explored by PCoA using SNP and SilicoDArT marker data, the first, second, and third principal coordinates explained altogether 37.4% and 31.0% of the variability, respectively. Samples from the UK, Canada, and Pakistan were grouped together, while Indian plants were clearly distinct based on SNP markers but relatively close to the UK-Canada-Pakistan group based on SilicoDArT markers. Constructed trees differentiated individuals into clusters resembling the PCoA patterns. The Bayesian BAPS analysis performed for the SNP data revealed that the individuals were distributed in seven clusters, representing samples from each of the four Finnish populations, India, Pakistan, and the combination of the UK and Canada. Similar clustering was visible in the UPGMA tree. The Indian cluster did not display any ancestral gene flow with the others, while the Pakistani cluster showed ancestral gene flow only with the combined UK and Canada cluster. Furthermore, the latter cluster displayed ancestral gene flow with the Finnish populations varying from 0% to 3.1%. The BAPS analyses conducted for the SilicoDArT data differ slightly: The individuals were distributed in nine clusters, and the Indian cluster exhibited ancestral gene flow with the mixed cluster including Canadian, Pakistani, and UK samples, and one Finnish sample. The AMOVA showed that 45% and 26% of variation was present among the I. glandulifera groups/populations and the rest within them based on SNP and SilicoDArT markers, respectively. The Bayesian BAPS analyses and the gene flow networks were the most informative tools for resolving relationships among native and introduced plants. It is notable that the small sample sizes for non-Finnish plant materials may affect the accuracy of the gene flow and other estimates.

Background In parasitism arm race processes and red queen dynamics between host and parasites reciprocally mold many aspects of their genetics and evolution. We performed a parallel assessment of population genetics and demography of two species of pinworms with different degrees of host specificity (Trypanoxyuris multilabiatus, species-specific; and T. minutus, genus-specific) and their host, the mantled howler monkey (Alouatta palliata), based on mitochondrial DNA sequences and microsatellite loci (these only for the host). Given that pinworms and primates have a close co-evolutionary history, covariation in several genetic aspects of their populations is expected. Results Mitochondrial DNA revealed two genetic clusters (West and East) in both pinworm species and howler monkeys, although population structure and genetic differentiation were stronger in the host, while genetic diversity was higher in pinworms than howler populations. Co-divergence tests showed no congruence between host and parasite phylogenies; nonetheless, a significant correlation was found between both pinworms and A. palliata genetic pairwise distances suggesting that the parasites’ gene flow is mediated by the host dispersal. Moreover, the parasite most infective and the host most susceptible haplotypes were also the most frequent, whereas the less divergent haplotypes tended to be either more infective (for pinworms) or more susceptible (for howlers). Finally, a positive correlation was found between pairwise p-distance of host haplotypes and that of their associated pinworm haplotypes. Conclusion The genetic configuration of pinworm populations appears to be molded by their own demography and life history traits in conjunction with the biology and evolutionary history of their hosts, including host genetic variation, social interactions, dispersal and biogeography. Similarity in patterns of genetic structure, differentiation and diversity is higher between howler monkeys and T. multilabiatus in comparison with T. minutus, highlighting the role of host-specificity in coevolving processes. Trypanoxyuris minutus exhibits genetic specificity towards the most frequent host haplotype as well as geographic specificity. Results suggest signals of potential local adaptation in pinworms and further support the notion of correlated evolution between pinworms and their primate hosts.

Processes of island colonisation have long been of interest to biologists. Colonisation events themselves are rarely observed, but the processes involved may be inferred using genetic approaches. We investigated possible means of island colonisation by common toads (Bufo bufo) in western Scotland (the Isle of Skye and five neighbouring small islands), using evidence derived from nuclear microsatellites and mitochondrial (mt) DNA. Levels of microsatellite allelic richness for populations on Skye were high and comparable to adjacent mainland populations, but lower for populations on small islands. Pairwise measures of genetic distances between populations and a clustering algorithm were both suggestive of frequent gene flow between Skye and the mainland. For small islands the levels of genetic differentiation were higher, implying stronger isolation and no evidence for inbreeding. The distribution of mtDNA haplotypes broadly mirrored the genetic structure revealed by microsatellites. Reconciled with existing palaeoclimatological evidence, since the last glaciation, our findings rule out the possibility that the B. bufo populations stem from glacial refugia, or that recent anthropogenic transfer of toads is responsible for their current distribution. The most parsimonious explanation of our data is that the studied inshore islands have been repeatedly colonised via rafting from the mainland or neighbouring islands. This may give us insights into the processes likely to take place when ice sheets retreat poleward as a result of climate change. It also has implications for the colonisation of both native and invasive non-native species, and hence the biosecurity of island refugia.

Targeted gene flow (TGF) could bolster the adaptive potential of isolated populations threatened by climate change, but could also lead to outbreeding depression. Here, we explore these possibilities by creating mixed- and within-population crosses in a terrestrial-breeding frog species threatened by a drying climate. We reared embryos of the crawling frog (Pseudophryne guentheri) on wet and dry soils and quantified fitness-related traits upon hatching. TGF produced mixed outcomes in hybrids, which depended on crossing direction (origin of gametes from each sex). North-south crosses led to low embryonic survival if eggs were of a southern origin, and high malformation rates when eggs were from a northern population. Conversely, east-west crosses led to one instance of hybrid vigour, evident by increased fitness and desiccation tolerance of hybrid offspring relative to offspring produced from within-population crosses. These contrasting results highlight the need to experimentally evaluate the outcomes of TGF for focal species across generations prior to implementing management actions., Rudin-Bitterli et al. created pure and reciprocal crosses of the Australian crawling frog Pseudophryne guentheri among geographically distant populations to investigate fitness impacts of targeted gene flow in counteracting a drying environment. When reared on wet and dry soils, embryonic survival depended on the origin of gametes from each sex, highlighting the need to experimentally evaluate the outcomes of TGF prior to implementing management actions.

The southeastern United States is home to some of the richest biodiversity in the world. Over the last 200 years, however, rapid industrialization and urbanization have threatened many natural areas, including freshwater habitats. River impoundments have also rapidly altered freshwater habitats, often resulting in species extirpation or extinction. The Coosa River in Alabama experienced one of the largest faunal declines in modern history after impoundment, making it an ideal system for studying how invertebrate species are affected by reservoir creation. One such species, the Rough Hornsnail, Pleurocera foremani, is an endangered freshwater snail in the family Pleuroceridae. We sampled all known localities of P. foremani and used 2bRAD-seq to measure genetic diversity. We assessed riverscape genomic patterns across the current range of P. foremani and measured gene flow within and between impoundments. We also investigated the degree to which P. foremani displays an isolation by distance pattern and conforms to broad hypotheses that have been put forth for population genetics of riverine species like the Mighty Headwater Hypothesis that predicts greater genetic diversity in headwater reaches compared with mainstem populations. Like most other freshwater species, a pattern of isolation by distance was observed in P. foremani. We also found that Coosa River dams are a barrier to gene flow, and genetic fragmentation of P. foremani is likely to increase. However, gene flow appeared common within reservoirs and tributaries. Additionally, we found that spatial genetic structure of P. foremani deviates from what is expected under the Mighty Headwaters Hypothesis, adding to a growing body of research suggesting that the majority of genetic diversity in low-dispersing gastropods is found in mainstem populations.

The European hedgehog (Erinaceus europaeus) is widely distributed in Europe, from Iberia and Italy to Scandinavia, and in New Zealand. They inhabit a wide range of environments, from natural habitats to urban areas. Finland is the northern edge of the current distribution area, which has expanded from Pleistocene refugia in Europe. Finnish hedgehogs are not only found in the suburbs, but also in urban areas such as the capital city, Helsinki. However, the phylogenetic relationships to other populations and the population structure were unknown for the urban hedgehogs in Helsinki. We reconstructed a molecular phylogeny and analyzed the population structure and genetic diversity from samples of 106 hedgehogs collected around Helsinki in 2017–2019, based on partial sequences of the mitochondrial control region and cytochrome b gene as well as 11 microsatellite loci. Our phylogenetic data indicate that the Helsinki population is closely related to the Estonian population. This means that at least part of the Helsinki population originates from Estonia, due to natural expansion from glacial refugia and anthropogenic introduction for vermin control, as shown in previous reports. The microsatellite data indicated that the Helsinki population is genetically homogeneous, with low genetic diversity. This may be due to the absence of effective geographic barriers to gene flow at present, but it is also possible that the subpopulations formed by migration are concealed by the genetic uniformity resulting from founder effect of natural expansion to the northward or artificial introduction. Further study is necessary to evaluate the effect of urban fragmentation in Helsinki.

Humid mountain forests (HMF) in Mexico have been heavily degraded by anthropogenic activities. A key conservation strategy consists of propagating HMF species in forest nurseries for subsequent repopulation in degraded areas. We evaluated genetic diversity in three natural populations (Huitepec, Bazom, and Mitziton) and one nursery population of Styrax magnus Lundell (Styracaceae) in Chiapas, Mexico. We expected a lower genetic diversity in the nursery than in wild populations. Styrax magnus is restricted to the Mexican state of Chiapas, close to the border with Guatemala and is likely to be at risk of extinction due to habitat loss and its low establishment rate. We used ten enzyme loci to determine genetic diversity. Genetic structure was examined by calculating genetic differentiation (Fst) and Nei’s genetic distances (Nei, Am Nat 106:283–292, 1972), in addition a Bayesian analysis was performed. The populations examined showed a moderate (He = 0.31) average genetic diversity. Bazom was the most distant and genetically differentiated population and showed the lowest genetic diversity (He = 0.21). Mitziton was the most diverse population (He = 0.40), whereas the nursery population showed an intermediate diversity (He = 0.30). We found a high level of total genetic differentiation (Fst = 0.48, P

We analyzed the genetic connectivity between mullets (Mugil liza) captured around the protected Natural Monument of Cagarras Islands (MoNa Cagarras) and inside Rodrigo de Freitas Lagoon, using microsatellite markers polymorphisms. Our data revealed the occurrence of 31 shared alleles (from 41 sampled), a high similarity in both allelic frequencies and genetic diversity and lack of differentiation between collection points (FST = 0.000, p > 0.05, STRUCTURE best estimative K = 1), results which, analyzed together, are strongly indicative of panmixia. We conclude that individuals collected inside the Rodrigo de Freitas Lagoon are genetically similar to those individuals collected around MoNa Cagarras. Given the importance of estuaries for the reproduction and development of individuals of M. liza, it is recommended that the Rodrigo de Freitas Lagoon to be managed in order to maintain genetic connectivity and diversity between the two ecosystems.