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The speciation continuum is the process by which genetic groups diverge until they reach reproductive isolation. It has become common in the literature to show that this process is gradual and flickering, with possibly many instances of secondary contact and introgression after divergence has started. The level of divergence might vary among genomic regions due to, among others, the different forces and roles of selection played by the shared regions. Through hybrid capture, we sequenced ca. 4,000 nuclear regions in populations of six species of wax palms, five of which form a monophyletic group (genus Ceroxylon, Arecaceae: Ceroxyloideae). We show that in this group, the different populations show varying degrees of introgressive hybridization, and two of them are backcrosses of the other three 'pure' species. This is particularly interesting because these three species are dioecious, have a shared main pollinator, and have slightly overlapping reproductive seasons but highly divergent morphologies. Our work supports shows wax palms diverge under positive and background selection in allopatry, and hybridize due to secondary contact and inefficient reproductive barriers, which sustain genetic diversity. Introgressed regions are generally not under positive selection. Peripheral populations are backcrosses of other species; thus, introgressive hybridization is likely modulated by demographic effects rather than selective pressures. In general, these species might function as an 'evolutionary syngameon' where expanding, peripheral, small, and isolated populations maintain diversity by crossing with available individuals of other wax palms. In the Andean context, species can benefit from gained variation from a second taxon or the enhancement of population sizes by recreating a common genetic pool.

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The application of the sterile insect technique (SIT) requires the adaptation of insects to mass-rearing conditions. It is generally accepted that this adaptation may include a reduction in genetic diversity and an associated loss of desirable characteristics for the effective performance of sterile insects in the field. Here, we compare the genetic diversity of two mass-reared strains of the Mexican fruit fly, Anastrepha ludens, and a wild (WIL) population collected near Tapachula, Mexico, using seven DNA microsatellites as molecular genetic markers. The mass-reared strains were a bisexual laboratory strain (LAB) with approximately 130 generations under mass-rearing and a genetic sexing strain, Tapachula-7 (TA7), also under mass-rearing for 100 generations. Our results revealed an overall low level of genetic differentiation (approximately 15%) among the three strains, with the LAB and WIL populations being genetically most similar and TA7 most genetically differentiated. Although there were some differences in allele frequencies between strains, our results show that overall, the adaptation to mass-rearing conditions did not reduce genetic variability compared to the wild sample in terms of heterozygosity or allelic richness, nor did it appear to alter the level of inbreeding with respect to the wild populations. These results are contrary to the general idea that mass-rearing always results in a reduction in genetic diversity. Overall, our findings can contribute to a better understanding of the impact that adaptation to mass-rearing conditions may have on the genetic make-up of strains.

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BACKGROUND AND AIMS: Grasses of the Festuca genus have complex phylogenetic relations due to morphological similarities among species and interspecific hybridization processes. Within Patagonian fescues, information concerning phylogenetic relationships is very scarce. In Festuca pallescens, a widely distributed species, the high phenotypic variability and the occurrence of interspecific hybridization preclude a clear identification of the populations. Given the relevance of natural rangelands for livestock production and their high degradation due to climate change, conservation actions are needed and knowledge about genetic variation is required. METHODS: To unravel the intraspecific phylogenetic relations and to detect genetic differences, we studied 21 populations of the species along its natural geographical distribution by coupling both molecular [internal transcribed spacer (ITS) and trnL-F markers] and morpho-anatomical analyses. Bayesian inference, maximum likelihood and maximum parsimony methods were applied to assemble a phylogenetic tree, including other native species. The morphological data set was analysed by discriminant and cluster analyses. KEY RESULTS: The combined information of the Bayesian tree (ITS marker), the geographical distribution of haplotype variants (trnL-F marker) and the morpho-anatomical traits, distinguished populations located at the margins of the distribution. Some of the variants detected were shared with other sympatric species of fescues. CONCLUSIONS: These results suggest the occurrence of hybridization processes between species of the genus at peripheral sites characterized by suboptimal conditions, which might be key to the survival of these populations.

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This study aimed to assess the genetic differentiation and relationship among five sea cucumber species from the Red Sea in Egypt, namely Holothuria atra, H. impatiens, H. leucospilota, Actinopyga crassa and A. mauritiana, using Inter Simple Sequence Repeated (ISSR) and Start Codon Targeted (SCoT) markers. A collection of 100 specimens, with 20 individuals per species, was gathered for the analysis. With ten ISSR primers, 135 amplified bands were detected, including 11 distinct species-specific bands, indicating high-level polymorphism among species. Using ten SCoT primers, 151 amplicons were generated, including 30 species-specific bands, with 52% polymorphic bands indicating high-level polymorphism among species. The degree of genetic similarity (GS) among the different genotypes of species was calculated based on ISSR bands analysis, which ranged from 93% between H. atra and H. impatiens to 86% between H. atra and A. crassa. The highest genetic similarity was observed between H. atra and H. impatiens (90%), while the lowest was identified between A. crassa and A. mauritiana (75%) using SCoT bands. Notably, the ISSR and SCoT-based DNA analysis revealed similar genetic relationships between H. atra and H. impatiens compared to other sea cucumber species studied. This study provides new insights into the genetic diversity and relationship among sea cucumber species in the Red Sea, which could have implications for their conservation and management.

Este estudo teve como objetivo avaliar a diferenciação genética e a relação entre cinco espécies de pepinos-do-mar do Mar Vermelho no Egito, quais sejam, Holothuria atra, Holothuria impatiens, Holothuria leucospilota, Actinopyga crassa e Actinopyga mauritiana, usando marcadores Inter Simple Sequence Repeated (ISSR) e Start Codon Targeted (SCoT). Uma coleção de 100 espécimes, com 20 indivíduos por espécie, foi reunida para análise. Com 10 primers ISSR, 135 bandas amplificadas foram detectadas, incluindo 11 bandas específicas de espécies distintas, indicando polimorfismo de alto nível entre as espécies. Usando 10 primers SCoT, 151 amplicons foram gerados, incluindo 30 bandas específicas da espécie, com 52% de bandas polimórficas indicando polimorfismo de alto nível entre as espécies. O grau de similaridade genética (GS) entre os diferentes genótipos das espécies foi calculado com base na análise das bandas ISSR, que variou de 93% entre H. atra e H. impatiens a 86% entre H. atra e A. crassa. A maior similaridade genética foi observada entre H. atra e H. impatiens (90%), enquanto a menor foi identificada entre A. crassa e A. mauritiana (75%) usando bandas SCoT. Notavelmente, a análise de DNA baseada em ISSR e SCoT revelou relações genéticas semelhantes entre H. atra e H. impatiens em comparação com outras espécies de pepino-do-mar estudadas. Este estudo fornece novas informações sobre a diversidade genética e a relação entre as espécies de pepino-do-mar no Mar Vermelho, o que pode ter implicações para sua conservação e manejo.

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Despite a century of genetic analysis, the evolutionary processes that have generated the patterns of exceptional genetic and phenotypic variation in the model organism Drosophila melanogaster remains poorly understood. In particular, how genetic variation is partitioned within its putative ancestral range in Southern Africa remains unresolved. Here, we study patterns of population genetic structure, admixture, and the spatial structuring of candidate incompatibility alleles across a global sample, including 223 new accessions, predominantly from remote regions in Southern Africa. We identify nine major ancestries, six that primarily occur in Africa and one that has not been previously described. We find evidence for both contemporary and historical admixture between ancestries, with admixture rates varying both within and between continents. For example, while previous work has highlighted an admixture zone between broadly defined African and European ancestries in the Caribbean and southeastern USA, we identify West African ancestry as the most likely African contributor. Moreover, loci showing the strongest signal of introgression between West Africa and the Caribbean/southeastern USA include several genes relating to neurological development and male courtship behavior, in line with previous work showing shared mating behaviors between these regions. Finally, while we hypothesized that potential incompatibility loci may contribute to population genetic structure across the range of D. melanogaster; these loci are, on average, not highly differentiated between ancestries. This work contributes to our understanding of the evolutionary history of a key model system, and provides insight into the partitioning of diversity across its range.

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The grasshopper Ommexecha virens Serville has low dispersion capacity, and it is regarded as a specialist, only being found in sandy, dry environments with high incidence of sunlight. Considering these aspects, we evaluated the diversity and genetic structure of O. virens natural populations using ISSR (Inter Simple Sequence Repeat) markers. The data pointed to low expected heterozygosity for some populations (HE = 0.06-0.09), probably a consequence of positive inbreeding, which is typical of species showing low or null dispersion indices. Moreover, significant genetic differentiation was observed (FST = 0.50 and GST = 0.51), as well as low number of migrants (Nm = 0.47), indicating that the populations are genetically differentiated. This is likely related to the limitation in dispersing and fragmentation of suitable environment localities colonized by O. virens. The populations of O. virens were structured in three genetic groups associated to different landscapes, revealing the presence of a secondary contact zone, possibly arisen from isolation followed by genetic divergence among populations and subsequent gene flow of divergent individuals of O. virens. At last, we found positive isolation by distance (IBD; r: 0.427; P: 0.025) which is an important factor, since it may be adding to the emergence of reproductive barriers among individuals of O. virens that have been experiencing isolation.

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The freshwater stingray Paratrygon aiereba have coloration, osteological and morphometric variations that could suggest the existence of more than one species in Colombia. In order to evaluate the phylogeography, population structure and genetic diversity for P. aiereba distributed in the Amazon and Orinoco basins, we amplified Cytochrome oxidase subunit 1 (COI) partial region of mitochondrial DNA (mtDNA) in 50 samples from eight different sub-basins. Our results suggest three phylogroups and a vicariance event occurred 43 million years ago proposing how Paratrygon diverged into the basins. A high population structure (ΦST = 0.692; p < 0.005) and a value of (K) of 3 were defined. A high genetic diversity within phylogroups was found: Phylogroup A (h = 0.64; π% = 2.48), Phylogroup B (h = 0.552; π% = 1.67), and Phylogroup C (h = 0.49; π% = 0.73). These results should be considered in local management plans, conservation programs and reclassification in at least Amazon and Orinoco.

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The whole mitochondrial genome of Lateolabrax maculatus (Cuvier, 1828) was used to investigate the reasons for the observed patterns of genetic differentiation among 12 populations in northern and southern China. The haplotype diversity and nucleotide diversity of L. maculatus were 0.998 and 0.00169, respectively. Pairwise FST values between populations ranged from 0.001 to 0.429, correlating positively with geographic distance. Genetic structure analysis and haplotype network analysis indicated that these populations were split into two groups, in agreement with geographic segregation and environment. Tajimas D values, Fus Fs tests and Bayesian skyline plot (BSP) indicated that a demographic expansion event may have occurred in the history of L. maculatus. Through selection pressure analysis, we found evidence of significant negative selection at the ATP6, ND3, Cytb, COX3, COX2 and COX1 genes. In our hypotheses, this study implied that demographic events and selection of local environmental conditions, including temperature, are responsible for population divergence. These findings are a step forward toward the understanding of the genetic basis of differentiation and adaptation, as well as conservation of L. maculatus.(AU)

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Tacuarembó is a department located in northeastern Uruguay, whose population is the result of several migration waves from Europe and Near East, as well as Africans and Afro-descents mostly from Brazil; these waves settled with the territory's various Native ethnic groups (Charrúa, Minuán, and Guaraní). In the past, this population has been the focus of genetic studies showing this trihybrid origin, with greater contributions of Natives and Africans than in other Uruguayan regions. In this study we analyzed eight Alu insertions (A25, ACE, APOA1, B65, D1, F13B, PV92, TPA25) to provide valuable information for ancestrality and genetic differentiation and to compare with both previous studies on the Tacuarembó population and Alu frequencies in other Uruguayan populations. The European contribution to Alu and classical markers was almost equal to that of a previous study using 22 classical markers (63% vs. 65%), while African contribution was higher (30% vs. 15%), and Native American contribution shows an important difference in Alu: 7% versus 20%. We found no significant differences in genetic differentiation between Tacuarembó and Montevideo but significant differences between Tacuarembó and Basque descendants from Trinidad. Our results support previous findings obtained with classical markers that demonstrate the trihybrid composition of the Tacuarembó population, correlated with historical records. Thus, Alu insertions provide interesting information in light of the admixture process in the Uruguayan population.

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Our knowledge of the diversity of potato cyst nematodes in their native areas still remains patchy and should be improved. A previous study based on 42 Peruvian Globodera pallida populations revealed a clear south to north phylogeographic pattern, with five well-supported clades and maximum diversity observed in the south of Peru. In order to investigate this phylogeographic pattern more closely, we genotyped a larger collection of Peruvian populations using both cathepsin L gene sequence data and a new set of 13 microsatellite loci. Using different genetic analyses (STRUCTURE, DAPC), we consistently obtained the same results that led to similar conclusions: the presence of a larger genetic diversity than previously known suggesting the presence of cryptic species in the south of Peru. These investigations also allowed us to clarify the geographic borders of the previously described G. pallida genetic clades and to update our knowledge of the genetic structure of this species in its native area, with the presence of additional clades. A distance-based redundancy analysis (dbRDA) was also carried to understand whether there was a correlation between the population genetic differentiation and environmental conditions. This analysis showed that genetic distances observed between G. pallida populations are explained firstly by geographic distances, but also by climatic and soil conditions. This work could lead to a revision of the taxonomy that may have strong implications for risk assessment and management, especially on a quarantine species.

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The whole mitochondrial genome of Lateolabrax maculatus (Cuvier, 1828) was used to investigate the reasons for the observed patterns of genetic differentiation among 12 populations in northern and southern China. The haplotype diversity and nucleotide diversity of L. maculatus were 0.998 and 0.00169, respectively. Pairwise FST values between populations ranged from 0.001 to 0.429, correlating positively with geographic distance. Genetic structure analysis and haplotype network analysis indicated that these populations were split into two groups, in agreement with geographic segregation and environment. Tajima’s D values, Fu’s Fs tests and Bayesian skyline plot (BSP) indicated that a demographic expansion event may have occurred in the history of L. maculatus. Through selection pressure analysis, we found evidence of significant negative selection at the ATP6, ND3, Cytb, COX3, COX2 and COX1 genes. In our hypotheses, this study implied that demographic events and selection of local environmental conditions, including temperature, are responsible for population divergence. These findings are a step forward toward the understanding of the genetic basis of differentiation and adaptation, as well as conservation of L. maculatus.

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Climatic fluctuations during the Pleistocene influenced the geographical distribution of plant species across the southern region of California. Following an integrative approach, we combined genetic data analysis with Environmental Niche Models (ENMs) to assess the historical range expansion of Yucca schidigera, a long-lived desert perennial native of the Baja California Peninsula. We genotyped 240 individuals with seven nuclear microsatellite to investigate genetic diversity distribution across 13 populations. Indeed, we used Environmental Niche Models to examine the changes on the distribution of suitable climatic conditions for this species during the LIG (~120 ka), LGM (~22 ka) and Mid Holocene (~6 ka). We detected high genetic diversity across Y. schidigera populations (AR = 9.94 ± 0.38 SE; Hexp = 0.791 ± 0.011 SE) with genetic variation decreasing significantly with latitude (allelic richness: R 2 = 0.38, P = 0.023; expected heterocigosity: R2 = 0.32, P = 0.042). We observed low, but significant genetic differentiation (FST = 0.0678; P < 0.001) which was consistent with the parapatric distribution of the three genetic groupings detected by the Bayesian clustering algorithm. The ENMs suggest that suitable habitat for this species increased since the LGM. Our results support a range expansion of Y. schidigera across northwestern Baja California during the late Quaternary. Genetic data suggest that colonization of the current distribution followed a southward directionality as suitable climatic conditions became widely available in this region. High genetic variation across our sample suggests large historic effective population sizes for this section of the geographical range.

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The species Melipona rufiventris Lepeletier, 1836 is a Brazilian native stingless bee that is part of a species complex known as the 'rufiventris group', making it difficult to distinguish between the different species. Populations in this group are facing a severe decline, leading to the risk of local extinction, and therefore, their conservation should be treated as a major concern. This study describes the first set of tri- and tetranucleotide microsatellite markers, using next-generation sequencing technology for use in the identification of genetic diversity and population structure in the 'rufiventris group'. A total of 16 microsatellite loci displayed polymorphism. Analysis of the whole data set (n = 50) detected 63 alleles in all loci, ranging from 2 to 7 with a mean of 3.9 alleles/locus. A genetic diversity analysis revealed high values for population differentiation estimates (FST = 0.252, RST = 0.317, and DEST = 0.284) between the Atlantic Forest, Cerrado, and Caatinga biomes. An additional evidence for genetic divergence among populations was also found in the 'rufiventris group'; these should be treated as separate conservation units or even as separate species. These microsatellite markers have demonstrated a strong potential for assessing population discrimination in this threatened stingless bee group.

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Patterns of genetic variation among populations can reveal the evolutionary history of species. Pinworm parasites are highly host specific and form strong co-evolutionary associations with their primate hosts. Here, we describe the genetic variation observed in four Trypanoxyuris species infecting different howler and spider monkey subspecies in Central America to determine if historical dispersal processes and speciation in the host could explain the genetic patterns observed in the parasites. Mitochondrial (cox1) and ribosomal (28S) DNA were analysed to assess genetic divergence and phylogenetic history of these parasites. Sequences of the 28S gene were identical within pinworms species regardless of host subspecies. However, phylogenetic analyses, haplotype relationships and genetic divergence with cox1 showed differentiation between pinworm populations according to host subspecies in three of the four Trypanoxyuris species analysed. Haplotype separation between host subspecies was not observed in Trypanoxyuris minutus, nor in Trypanoxyuris atelis from Ateles geoffoyi vellerosus and Ateles geoffoyi yucatanensis. Levels of genetic diversity and divergence in these parasites relate with such estimates reported for their hosts. This study shows how genetic patterns uncovered in parasitic organisms can reflect the host phylogenetic and biogeographic histories.

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This study evaluated the genetic structure of wild populations of the endangered primate, Leontopithecus chrysomelas. We tested the assumption that populations of L. chrysomelas, given their larger population size and a higher degree of habitat continuity, would have higher genetic diversity and less genetic structuring than other lion tamarins. We used 11 microsatellites and 122 hair samples from different locations to assess their genetic diversity and genetic structure, and to make inferences about the isolation by distance. The overall expected heterozygosity (0.51 ± 0.03) and the average number of alleles (3.6 ± 0.2) were relatively low, as is the case in other endangered lion tamarins. Genetic clustering analyses indicated two main clusters, whereas the statistical analyses based on genotype similarities and Fst suggested further substructure. A Mantel test showed that only 34% of this genetic differentiation was explained by the linear distance. In addition to linear distance, structural differences in the landscape, physical barriers and behavioural factors may be causing significant genetic structuring. Overall, this study suggests that these populations have a relatively low genetic diversity and a relatively high population genetic structure, putting in question whether the presence of agroforest systems (known locally as cabruca) is enough to fully re-establish functional landscape connectivity.

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Previous studies of population genetic structure in Dissostichus eleginoides have shown that oceanographic and geographic discontinuities drive in this species population differentiation. Studies have focused on the genetics of D. eleginoides in the Southern Ocean; however, there is little knowledge of their genetic variation along the South American continental shelf. In this study, we used a panel of six microsatellites to test whether D. eleginoides shows population genetic structuring in this region. We hypothesized that this species would show zero or very limited genetic structuring due to the habitat continuity along the South American shelf from Peru in the Pacific Ocean to the Falkland Islands in the Atlantic Ocean. We used Bayesian and traditional analyses to evaluate population genetic structure, and we estimated the number of putative migrants and effective population size. Consistent with our predictions, our results showed no significant genetic structuring among populations of the South American continental shelf but supported two significant and well-defined genetic clusters of D. eleginoides between regions (South American continental shelf and South Georgia clusters). Genetic connectivity between these two clusters was 11.3% of putative migrants from the South American cluster to the South Georgia Island and 0.7% in the opposite direction. Effective population size was higher in locations from the South American continental shelf as compared with the South Georgia Island. Overall, our results support that the continuity of the deep-sea habitat along the continental shelf and the biological features of the study species are plausible drivers of intraspecific population genetic structuring across the distribution of D. eleginoides on the South American continental shelf.

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Prodiplosis longifila is reported as a pest of a wide range of species cultivated in America, including citrus, solanaceous species and asparagus. This species has different behavioural traits that are primarily centred on the oviposition habit and the feeding of larvae, which can change depending on the host. However, scarce information is available on population studies and the natural history of this insect, and uncertainty exists about the taxonomic identity and the geographic distribution of this species. The main objective was to perform a phylogenetic and genetic study of P. longifila populations and to define whether the North American and South American populations belong to the same species or whether a differentiation process had occurred due to geographic distance. A second objective was to determine whether this species showed genetic differentiation by host specialization in South America. The phylogenetic and population analyses based on DNA barcodes (cytochrome oxidase I gene) and a region of the ribosomal DNA (ITS2) revealed divergent clades attributable to geographic distance and host specificity. The North American and South American P. longifila insects were confirmed to be genetically distinct, and the genetic distances exceeded the values expected for intraspecific variation. In South America, the population analysis of P. longifila from tomato, sweet pepper (Solanaceae), Tahiti lime and key lime (Rutaceae) hosts evidenced high genetic differentiation between populations associated with different hosts and an absence of gene flow between these groups, suggesting the corresponding formation of cryptic species.

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India is a country bestowed enormously with stingless bees, but genetic information about them is extremely minimal. This study focused to tap the geographic allocation, genetic variability, and differentiation among Tetragonula species complexes from natural and semi-urban habitats. Genetic analyses were assessed among 36 contrasting genotypes utilizing 20 ISSR primers. The dual combination exquisitely and productively amplified 245 DNA fragments at the loci, of which 240 bands were polymorphic (97.95%). Low to moderate level of genetic differentiation was detected from different estimators (Ht 0.29, G' STest 0.16, D est 0.072, F ST 0.14, and Nm 2.68). Hierarchical clustering analysis aided to partition the individual genotypes into its respective five species group formed, aided by substantial bootstrap support values, but differing under morphological identification. It also provided valuable insight into the moderate eco-genetic diversity (H 0.39) prevailing from geographically scattered inhabitants. Potential exploitation of hyper-variable ISSR marker turned out fairly as a promising technique for finding valid polymorphisms and infers relevant variations. This baseline information enhances our understanding of the genetic status of the indigenous species from the country.

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Abstract Evolutionary analyses have been widely used for evaluation of genetic diversity of natural populations and correlate these data to the fitness of the species, especially in the case of threatened species. Calydorea crocoides occurs in a restricted area at altitudes from 800 to 1500 m in southern Brazil and is considered endangered. A study assessing genetic diversity, cytogenetic features and ecological niche was performed aiming to characterize C. crocoides by multidisciplinary approaches. Molecular data highlighted that most of the total variation (76%; p < 0.001) was found within populations and the parameters of genetic diversity were high at the species level (PPB = 98.97%; I = 0.4319; h = 0.2821). Gene flow (Nm) was estimated in 0.97 individuals per generation. Cytogenetically, C. crocoides presents a bimodal karyotype and low asymmetry. DAPI banding pattern was uniform, but the CMA-signal evidenced a pericentric inversion in the population ESC688. The species presents high pollen viability and two different morphologies of pollen grains. Our data showed high levels of polymorphism maintained in this species that could ensure conservationist practices in which the main goal is to preserve the evolutionary potential of the species through the maintenance of genetic diversity.

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Despite its population, geographic size, and emerging economic importance, disproportionately little genome-scale research exists into genetic factors that predispose Brazilians to disease, or the population genetics of risk. After identification of suitable proxy populations and careful analysis of tri-continental admixture in 1,538 North-Eastern Brazilians to estimate individual ancestry and ancestral allele frequencies, we computed 400,000 genome-wide locus-specific branch length (LSBL) Fst statistics of Brazilian Amerindian ancestry compared to European and African; and a similar set of differentiation statistics for their Amerindian component compared with the closest Asian 1000 Genomes population (surprisingly, Bengalis in Bangladesh). After ranking SNPs by these statistics, we identified the top 10 highly differentiated SNPs in five genome regions in the LSBL tests of Brazilian Amerindian ancestry compared to European and African; and the top 10 SNPs in eight regions comparing their Amerindian component to the closest Asian 1000 Genomes population. We found SNPs within or proximal to the genes CIITA (rs6498115), SMC6 (rs1834619), and KLHL29 (rs2288697) were most differentiated in the Amerindian-specific branch, while SNPs in the genes ADAMTS9 (rs7631391), DOCK2 (rs77594147), SLC28A1 (rs28649017), ARHGAP5 (rs7151991), and CIITA (rs45601437) were most highly differentiated in the Asian comparison. These genes are known to influence immune function, metabolic and anthropometry traits, and embryonic development. These analyses have identified candidate genes for selection within Amerindian ancestry, and by comparison of the two analyses, those for which the differentiation may have arisen during the migration from Asia to the Americas.

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