that K = 3 was the best geneticstructure model, as also reported by Baldoni et al. ( 2009 ) and Sarri et al. ( 2006 ). Second, on the basis of this geneticstructure, most acces- sions clearly clustered according to their geographic origin. Numerous genetic studies have reported genetic differen- tiation between western and eastern Mediterranean areas (Besnard et al. 2002 , 2007 ; Breton et al. 2006 ; Sarri et al. 2006 ). Furthermore, Mediterranean cultivars analysed by RAPD markers showed relative differentiation among Spanish and Italian varieties (Besnard et al. 2001a ), and a clear distinction between Spanish varieties and those from Greece and Turkey (Owen et al. 2005 ). Such a geneticstructure indicates a correlation between the genetic dif- ferentiation of olive trees and their geographic distribution. Despite this geneticstructure, we observed dominance of the eastern maternal lineage (95% of E1 vs. only 5% of western maternal lineages E2 and E3). As previously shown in Mediterranean wild and domesticated olives (Besnard et al. 2002 , 2007 ; Breton et al. 2006 ), all eastern Mediterranean accessions carried E1, whereas lineages E2 and E3 were only observed in the western Mediterranean Basin, but with a relatively low frequency in cultivars (16%; Besnard et al. 2001a ). These cpDNA lineages again confirm that cultivated olive has been selected from dif- ferent gene pools from both eastern and western regions of the Mediterranean Basin (Besnard et al. 2001c ).
The invading potential of B. tabaci is very high, as shown by its worldwide distribution (Frohlich et al., 1999; De Barro, 2006; Boykin et al., 2007). The geneticstructure we observed beyond the northern limit of outdoor develop- ment of this species in this study suggested that its dispersal could not result solely from natural migration in a favourable environment, as we did not detect isolation by distance patterns. Instead, we detected large gene flow between sites, which is inconsistent with the local genetic differentiation we would expect if genetic drift was exerted on isolated glasshouses. This limited genetic differentiation, therefore, is likely the result of stochastic long-distance movement related to intense human trade activity. This is further supported by 100% nucleotide identity of CO1 sequences between B. tabaci individuals on different continents. Ornamental trades are known to have contributed to group B spreading (Brown et al., 1995b). Likewise, plantlet trade can act as a
Regarding ECB, our results confirm that populations are split into two genetically differentiated groups that differ by host-plant use, the maize race and the mugwort– hop race. Indeed, the groups of ECB samples collected on maize and hop showed the common and significantly different genetic patterns characterizing the ECB maize race and hop–mugwort race, respectively (Bourguet et al., 2000b; Martel et al., 2003; Thomas et al., 2003; Bontemps et al., 2004; Malausa et al., 2005). Furthermore, our results reveal no evidence suggesting the existence of any addi- tional host race. Indeed, samples collected on pepper, sun- flower, sorghum, and cocklebur are genetically distinct from the mugwort–hop race but not significantly different from the maize race: the most parsimonious conclusion is that they consisted mostly – if not entirely – of members of the maize race. This conclusion was reinforced by our results on the sex pheromone produced by females origi- nating from pepper and cocklebur. Indeed, in France, the two ECB host races are known to differ, among other traits, by the sex pheromone produced by females and recognized by males. The maize race and the mugwort–hop race use the so-called Z and E pheromone type, respectively (Tho- mas et al., 2003; Bontemps et al., 2004; Pélozuelo et al., 2004). Hence, in agreement with the population geneticstructure, all females emerging from pepper and cocklebur produced exclusively the Z pheromone type.
To date, population geneticstructure has been analyzed in only a few whitefly species, and little is known about population geneticstructure in T. vaporariorum. The re- lated Bemisia tabaci species complex, particularly Mediter- ranean B. tabaci (Med), is characterized by high genetic diversity and differentiation of populations, as indicated by both mitochondrial and microsatellite markers [31,32] (ex- cept in recently introduced populations in Taiwan and France [33,34]). Populations of B. tabaci (Med) in Greece separated by just a few kilometers show population geneticstructure, possibly due to separate founder events or an older population history in this country . Unlike the B. tabaci species complex, T. vaporariorum populations have low genetic diversity in mitochondrial genes [36,37]. Recent findings indicate that sequences of three mitochondrial genes and composition of endosymbiont communities from populations sampled from different continents show little variation (Kapantaidaki et al., unpubl.). Analysis of a few nuclear genes (allozymes) in T. vaporariorum popula- tions from greenhouses in South Korea revealed their sub- division possibly due to restricted gene flow by natural geographic barriers . However, studies of population geneticstructure in T. vaporariorum with other, more polymorphic genetic markers, allowing description of more recent evolutionary processes, have not been performed until now. Recent findings of variation in phenotypic re- sponses, particularly diverse responses to insecticide treat- ments among geographically close populations, suggest differentiation and low gene flow among invaded green- houses .
needed to devise efficient, locally adapted and sustainable strategies for the management and control of these vector populations. It is interesting to note that recent investiga- tions of the population geneticstructure of An. moucheti sampled in the same localities as presented here (at least in Cameroon and the DRC) did not detect such high level of population differentiation within and across the forest block [53,66]. Combined analysis of genetic and ecologi- cal data in a comparative framework should reveal fur- ther insights into the population biology and demographic history of these neglected malaria vectors, and provide relevant information for their control. Recent advances in theoretical population genetics and the rap- idly evolving field of spatial genetics [e.g., ] together with the development and democratization of high throughput sequencing technologies provide the neces- sary tools for such endeavor in non model species. Figure 5 Haplotype networks for COII (above) and ND4 (below)
Dispersal is among the most diﬃcult problems to study empirically in the sea because of the impracticality of direct observations of larval stages. Besides plankton net surveys and/or otolith analysis, which provided sig- niﬁcant results on dispersal (Leis and Miller 1976; Jones et al. 1999; Swearer et al. 1999), natural genetic markers have also produced signiﬁcant results (reviews in Smith et al. 1990; Bohonak 1999). As early as 1975, Ehrlich suggested that assessment of allozymic variation among geographically remote populations of reef ﬁsh is the optimal approach for testing dispersal and migration capabilities of larvae. Allozyme electrophoresis has be- come a powerful technique to demonstrate genetic variation and has been widely used in coral reef ﬁsh surveys (Planes 2002). Analyses of geneticstructure of coral reef ﬁsh populations were initiated in 1982 in Japan (Bell et al. 1982) and in 1984 in Hawaii (Shaklee 1984; Shaklee and Samollow 1984); both looked at al- lozyme variations. With the exception of a remote oce- anic population, these ﬁrst studies undertaken in the Paciﬁc did not reveal signiﬁcant genetic diﬀerentiation among populations. The straightforward conclusion and general belief during that period was that coral reef ﬁsh populations exchanged genes through the pelagic stage at rates suﬃcient to homogenize the geneticstructure over broad geographical ranges. Since the early 1980s several other studies have been undertaken on coral reef ﬁsh and provided divergent outcomes, ranging from panmixis over large areas to local and regional diﬀer- entiation (Ehrlich 1975; Bell et al. 1982; Waples 1987; Lacson et al. 1989; Lacson 1992; Planes 1993; Planes et al. 1993, 1997; Doherty et al. 1994, 1995). The origin of such discrepancies is probably manifold.
Genetic diversity, geneticstructure and diet of ancient and contemporary red deer (Cervus
elaphus L.) from north-eastern France
Annik Schnitzler 1 * , Jose´ Granado 2 , Olivier Putelat 3 , Rose-Marie Arbogast 4 , Dorothe´e Drucker 5 , Anna Eberhard 6 , Anja Schmutz 6 , Yuri Klaefiger 6 , Ge´rard Lang 7 , Walter Salzburger 6 , Joerg Schibler 2 , Angela Schlumbaum 2 , Herve´ Bocherens 5,8 1 LIEC UMR 7360, University of Lorraine - UFR Sci FA, Campus Bridoux, Metz, France, 2 Integrative Prehistoric and Archaeological Science (IPAS), University of Basel, Basel, Switzerland, 3 Arche´ologie Alsace, Se´lestat & UMR 7041 ArScan - Arche´ologies environnementales - Maison de l’Arche´ologie et de l’Ethnologie, Nanterre, France, 4 CNRS UMR 7044 – ARCHIMEDE - Misha, Strasbourg, France, 5 Senckenberg Center for Human Evolution and Palaeoenvironment (HEP), University of Tu¨bingen, Tu¨bingen, Germany, 6 Zoological Institute, University of Basel, Basel, Switzerland, 7 26 A rue principale, Gries, France, 8 Dept of Geosciences (Biogeology), University of Tu¨bingen, Tu¨bingen, Germany
2003 ; Delarze 2012 ). The taxon appears to be currently restricted to north facing calcareous screes of the alpine zone (Thlaspion rotundifolii). Although such habitat is usually not disturbed by human activities, this stenothermic plant requires high-elevation, cold screes on calcareous and such habitats are becoming rare among mid-elevation summits of the Western Prealps. Vulnerable to future climate changes, the majority of population present between 50 and 800 indi- viduals, and largest ones include up to 10,000 individuals. As all members of the sect. Meconella, P. occidentale is per- ennial with leaves in basal rosettes, but presents no means of vegetative propagation (Kadereit 1990 ). Individual plants are outcrossing and often start to flower 1 year after germina- tion, with an average generation time estimated at ca. 8 years supporting high seed production (Nordal et al. 1997 ; B. Clémant, personal observations). The present study aims at describing the distribution of genetic variation among extant populations of the endemic P. occidentale to understand how such a taxon persisted in face of past climate changes. More specifically, it characterizes a comprehensive sample of P. occidentale, as well as closely related outgroups selected based on earlier literature, to delineate its native distribu- tion and address the phylogeography of remnant populations using genome-wide double digest Restriction-site Associ- ated DNA (ddRAD) sequencing. Such historical insights on the geneticstructure within this endemic taxon are used to set conservation priorities.
3 4 m for bidimensional populations or 4 m apart for linear populations, and the genotypes of mother plants at each node were so determined. The geneticstructure in the populations was obvious: alternative alleles at each locus were clustered in opposite parts of the populations, creating a patch structure mainly composed of homozygote individuals. The Wahlund effects could be another explanation of the observed frequent heterozygote deficiency. However for this study, in each pop- ulation, all pod-bearing plants were sampled during a complete flowering period. This sampling procedure, combined with the fact that the mean seed germination rate within a year was 78% and that 4% of the germinating seeds reach maturity in the same year allowed us to discard the hypothesis concerning Walhund effects. The four insignificant inbreeding coefficients obtained in the studied populations probably had no biological significance, but might have resulted from the method of sam- pling.
Diversity and geneticstructure in selfing populations in the absence of selection
Selfing populations are characterized by a peculiar structure in which some multilocus genotypes reach a high frequency in the population while others are rare (Fig 1). Allard (1975) argued that this structure is a consequence of the combination of selfing and selection favoring locally adapted genotypes. However, genetic drift is expected to strongly affect selfing populations and it is unclear whether genetic drift alone could be responsible for the stochastic increase of one or a few genotypes in the population. Moreover, we lack analytical predictions for multilocus diversity under predominant selfing.
Because pollen flow is expected to be sharply reduced when distance increases , local gene exchanges should mainly take place within populations, including between wild and domesticated plants when both are mixed or in close proximity. Accordingly, strong genetic differentiation should take place among populations. The existence of spatial geneticstructure and its scale of organization is a reflection of gene flow in space and time in relation to the spatial distribution and the colonization history of populations. A spatial geneticstructure was found for proximate wild cowpea popula- tions up to 100 km, which reflects a decreased probabil- ity to observe related individuals as the distances between populations increase. This suggests genetic exchanges among populations; however, our results do not directly shed light on the patterns of occurrence of gene flow in space and time. Gene flow via pollen in cowpea is likely to occur up to few km with a very low probability of long distance pollen dispersal, and, in any cases, pollen movement is unlikely at distances over 10 km . On the other hand, seed flow through inges- tion by grazing mammals could involve much longer distances, though the percentage of seed survival through grazing mammal gut does not exceed a few per cent (Pasquet, unpublished observations). Wild cowpea is expected to express high levels of genetic differenti- ation and low levels of within-population genetic diver- sity. In this study, high genetic differentiation was observed at several spatial levels.
classes and were no more present at the higher distance classes. In this population, the isolation by distance pattern seemed to be restricted to a lower spatial scale. Nevertheless, those results indicated that, on average, spatially close ramets were more likely to be genetically related than ramets that were separated by a larger distances. These results highlighted a spatial geneticstructure at very short distance that resulted from a combination of limited gene flow and a low level of clonality. However, correlograms obtained at the genet level were also significant, and no significant difference appeared with the ramet level in the two populations, indicating that clonality did not have a major impact on the spatial geneticstructure at the small scale. Nonrandom gene dispersal is thus the key factor in establishing the internal spatial geneticstructure observed. Although gene movement in seed plants involves both pollen and seed, a variety of arguments and empirical data indicate that the development of spatial geneticstructure within populations is more strongly influenced by seed dispersal than pollen dispersal (Fenster, 1991a; Nason and Hamrick, 1997; Kalisz et al., 2001; Chung et al., 2004). The shape of the regression between the relationship coefficient and the logarithm of the distance obtained for the spatial autocorrelation (genet level, small scale) was found to be concave (k . 0 for cubic regression), suggesting that seed dispersal was more restricted than pollen dispersal (Heuertz et al., 2003; Vekemans and Hardy, 2004). Beattie and Lyons (1975) found that the mean distance of dispersal obtained by capsule explosion of diverse Viola species ranged from 0.8 to 2.1 m. In addition, Viola seeds are known to be dispersed by ants. Studies on seed dispersal by ants show that the distance of transport is very limited. For example, in a review, Gomez and Espadaler (1998) found a mean distance of 0.87 m for northern hemispheric myrme- cochorous species, and for Viola species, some authors reported that the dispersal distance probably does not exceed 2–3 m (Beattie and Lyons, 1975; Oostermeijer, 1989; Ohkawara and Higashu, 1994). Thus, the spatial structure observed at the small scale was probably due to limited seed dispersal by means of capsule explosion and possible ant transport. According to Sokal (1979) and based on correlo- grams, patch size of genetically linked individuals (genets) observed at the small spatial scale can be estimated to be ;1 m. This distance corresponds well to the two distances of seed dispersion (capsule explosion and ant transport).
We also detected significantly more family relationships within the already know grapevine kin groups of i) Gouais [15,34,35], ii) Savagnin and Cabernet franc , iii) Chasselas and Muscat, and iv) Pinot and Riesling , and found traces of existence of two additional groups, each composed by a mix of several families, such as the W-12.6 and W-12.7 groups, comprising family-related table grapes with muscat flavor released by modern breeding. The interaction of geneticstructure and family relationship is known to be difficult to resolve, and 20 microsatellite loci are probably not sufficient to avoid false positives, despite the large number of alleles. Nevertheless, our family relationship analysis, seen as a tentative to understand large scale population patterns and not to precisely detect each single family pair, provided a coherent global picture. This analysis was also coherent with a more specific paper by Lacombe et al. in 2012  who explored direct parentage using an exclusion probabilities algorithm, with a slightly different sample, thus explaining minor differences.
Although the banded murex Hexaplex trunculus (Linnaeus, 1758) has no dispersal stage, it is widely distributed in a relatively broad range of habitats. These features make it a particularly suitable model to reconstruct the history of the fragmentation of its geographical range. We investigated its geneticstructure from the eastern Mediterranean to the Atlantic coast, by sequencing a nuclear intron (i29) and a mitochondrial marker (cox1). We found strong genetic differentiation between all population pairs, congruent with the absence of a dispersing larval stage. A deep phylo- geographical break separated two parapatric lineages, a western lineage (I) and an eastern one (II). The two lineages were separated by a vicariance event dated to the Pliocene by both markers, analysed independently. They co-occur in southern Italy and in the Siculo-Tunisian straight, where some individuals display recombined genotypes (lineage I for one marker, lineage II for the other), suggesting that introgression occurred in sympatric populations. We were unable to determine whether the vicariance was across the STS or located further east across the Peloponnese Arc, but the presence of lineage I in the northern Adriatic is more parsimoniously explained by a more eastern vicariance. Lineage I displayed a stronger signal of demographic expansion than lineage II, and its expansion was estimated to be more recent. This result, which has been reported in other marine species, suggests less drastic conditions for the eastern (and possibly also the central) Mediterranean benthos than for western populations during past climatic oscil- lations. The parapatric distribution still observed today suggests that human exploitation of this snail, which dates back to Antiquity, did not result in efficient introductions among basins, although present-day introductions were recently reported in the Bay of Biscay.
characterized by low read depth and high levels of missing data (Korneliussen et al., 2014; Meisner & Albrechsten, 2018; Klonoski et al., 2019).
Most importantly, however, the strong population geneticstructure reported herein at the landscape scale unambiguously shows that these data are suitable for testing the proposed hypotheses. In particular, a persisting signal of IBD was consis- tently reported beyond the range of short-distance dispersal (> 1 km). This contrasts with a recent meta-analysis of fine-scale spatial genetic structures in bryophytes, which reported the decay of the IBD pattern beyond that range in 30–50% of the datasets investi- gated (Vanderpoorten et al., 2019). We interpret the differences between the present and previous studies on IBD in bryophytes in terms of statistical power of the tests, since previous studies were based on haplotypic or SNP variation at a few loci. This interpre- tation is supported by our sub-sampling analysis of three datasets, which revealed that, for a similar number of polymorphic markers as in Vanderpoorten et al. (2019), we observed significantly higher standard deviations of the IBD slopes between pairs of individuals located at > 1 km from each other in the randomly subsampled data matrices than in the full matrices, with a corresponding decay of the significance of the IBD signal beyond 1 km.
Finally, we used a Bayesian approach to analyze the subset of five populations (74 individuals) with the Structure software, varying K from 1 to 10. The posterior probability of the data, lnPr(X|K), reached a maximum for K = 6, and the posterior probability of K was also the highest (P = 0.999) for this value (Fig. 5A). The computation of the increase of likelihood (delta[LnPr(X|K)]; Fig. 5B), showed that the gain of explanatory power of the model when adding a new cluster to the analysis was the highest at K changing from 6 to 7, and then became null or negative. The frequencies of isolates in the six clusters (Fig. 5C) were significantly different according to their region and plant of origin (χ 2 = 46.5, P = 0.0002, df = 18; Table 5). The major trend seemed to be a geographical structure opposing isolates from the Cap Bon and the North region. Indeed, clusters 2 and 3 encompassed exclusively isolates sampled in the Cab Bon area (7/7 from strawberries in cluster 2, 7 from strawberries, and 4 from faba beans in cluster 3), whereas clusters 5 and 6 comprised respectively 8/8 and 5/7 isolates sampled on grapevine from the Grand Tunis region (Table 5). The two other clusters represented a mixing of isolates from the different regions and plants. However, since all isolates from grapevine were sampled in the Nord and Grand Tunis regions, and all isolates from strawberry and faba beans in the Centre and Cap Bon regions, it was impossible again to truly separate geographic from host plant effects. We performed the same analysis to the restricted sample of 63 isolates from strawberries and faba beans from Cap Bon and Centre regions. The posterior probability of the data and associate indicators all peaked for K = 4 (Fig. 6A and B), but the probability of ancestry of isolates in each cluster (Fig. 6C) was not significantly associated with host plant or geographic origin
Natural populations of U. guianensis have declined dramatically in recent times because of
strong anthropic pressure brought about mainly by deforestation and indiscriminate extrac- tion of the bark for the commercial production of phytotherapeutic preparations [ 7 , 8 ]. In this context, studies on the genetic and chemical variability of medicinal plants are particularly important since they enable the selection of elite individuals that would be of interest to the pharmaceutical industry [ 9 ]. Furthermore, in the field of species conservation, molecular markers such as sequence-related amplified polymorphism (SRAP) are very useful for the identification of genetically distinct individuals with biotechnological potential [ 10 , 11 ]. The SRAP technique is based on five forward and six reverse primers that can be combined ran- domly for the amplification of a large number of open reading frames. Moreover, the SRAP method is reliable, reproducible and does not require prior knowledge of the genome [ 12 ].
Pittet et al Phylogeography of Papaver occidentale
Table S1: Sampling of 136 individuals of the Papaver alpinum complex included here, with name codes as the three first letters of field populations. Coordinates as easternness (E) and northernness (N) in the Swiss Coordinate System. The 112 samples confirmed as native individuals of P. occidentale based on STRUCTURE analyses are indicated as such (Nat), whereas introduced samples (Int) and those genetically pertaining to outgroups P. sendtneri and P. tatricum (Out) are indicated. The mean read depth (DP) and proportion of SNPs with missing data (%NAs) are shown for each sample