Isolation and characterization of eight microsatellite loci from the house finch (Carpodacus mexicanus)

I isolated the first set of polymorphic microsatellite markers from the house finch, Carpodacus mexicanus, a well‐studied North American bird species, as part of an effort to compare levels of genetic diversity in introduced and native populations. Here, I describe eight independently assorting microsatellite loci screened for polymorphism using 40 house finches. Polymorphism levels ranged from six to 14 alleles (mean = 10.6), making these markers a powerful tool for paternity and population level analyses of this widely distributed North American species.     

Microsatellite markers for an invasive tetraploid tree,Chinese tallow (Triadica sebifera)

We present six polymorphic microsatellite loci for Chinese tallow tree (Triadica sebifera, Euphorbiaceae), which is native to East Asia and is an aggressive, invasive species in the southeastern USA, particularly along the Coastal Plain. Microsatellite loci were tested for polymorphism across a total of 79 individuals from populations across the native range of China and in introduced populations of the southeastern USA, California, Hawaii, and Australia. Across these samples, we found a high level of polymorphism, suggesting they will be useful for deducting the introduction history of this invasive species.     

Hybridization of invasive <Emphasis Type="Italic">Phragmites australis</Emphasis> with a native subspecies in North America

Interspecific hybridization can lead to the extinction of native populations and increased aggressiveness in hybrid forms relative to their parental lineages. However, interbreeding among subspecies is less often recognized as a serious threat to native species. Phragmites australis offers an excellent opportunity to investigate intraspecific hybridization since both native and introduced lineages occur in North America. Introduced Phragmites is a highly successful estuarine plant invader throughout North America, but native Phragmites populations are declining in the eastern US. Despite range overlaps, hybridization has not yet been detected between the native and introduced lineages in the wild, suggesting that phenological or physiological barriers preclude cross-pollination. We demonstrate, for the first time, that native and introduced populations of Phragmites can hybridize. There is substantial overlap in flowering period between native and introduced populations from the same geographic locations. We manually cross-pollinated native individuals with pollen from introduced Phragmites and recovered viable offspring. We then used microsatellite markers to prove that alleles unique to the pollen parent were transferred to progeny. Our results imply a mechanism for the further decline of native Phragmites in North America and a potential for the formation of aggressive hybrid offspring.     

Nuclear microsatellite DNA markers for New Zealand kiwi (Apteryx spp.)

Kiwi (Apterygidae) is an endemic New Zealand avian family comprising five species whose conservation is actively managed. We present five polymorphic microsatellite DNA loci isolated from North Island brown kiwi (Apteryx mantelli). In addition, we demonstrate cross‐amplification, and in some cases, polymorphism, of these microsatellite DNA loci in four other kiwi species. Therefore, these markers may be broadly applicable to conservation genetic studies within this family.     

Molecular data provide strong evidence of natural hybridization between native and introduced lineages of <Emphasis Type="Italic">Phragmites australis</Emphasis> in North America

Hybridization, both within and between taxa, can be an important evolutionary stimulus for bioinvasions. Novel intra-taxon hybridizations may arise either between formerly allopatric introduced lineages, or between native and introduced lineages. The latter can occur following a cryptic invasion of a non-native lineage, such as the nineteenth century introduction to North America of a European lineage of the common reed Phragmites australis. Previous studies found no evidence of natural hybridization between native and introduced lineages of P. australis, but produced some F₁ hybrids under experimental conditions when the seed parent was native and the pollen parent was introduced. In this study we used microsatellite data to compare genotypes of P. australis along a transect of approximately 2,000 km in eastern North America. Although hybridization appears uncommon, simulations and principle component analysis of genetic data provided strong evidence for natural hybridization at two sites adjacent to Lake Erie in which native and introduced lineages were sympatric. The seed parent was the native lineage in some cases, and the introduced lineage in other cases. There is now the potential for P. australis hybrids to become increasingly invasive, and managers should consider as a priority the removal of introduced stands from sites where they co-exist with native stands.     

Distinct invasion sources of common ragweed <Emphasis Type="Italic">(Ambrosia artemisiifolia)</Emphasis> in Eastern and Western Europe

The common ragweed (Ambrosia artemisiifolia L.; Asteraceae) is a North American native that is invading Eurasia. Besides its economic impact on crop yield, it presents a major health problem because of its highly allergenic pollen. The plant was imported inadvertently to Europe in the eighteenth century and has become invasive in several countries. By analyzing French and North American populations, it was previously shown that French populations were best described as a mixture of native sources and that range expansion in France probably involved sequential bottlenecks. Here, our aim was to determine whether Eastern European populations of A. artemisiifolia originated from the previously established French populations or from independent trans-Atlantic colonization events. We used nuclear microsatellite markers to elucidate the relationships among populations from Eastern and Western Europe in relation to populations from a broad survey across the native North American range. We found that A. artemisiifolia from Eastern Europe did not originate from the earlier established French populations but rather represents multiple independent introductions from other sources, or introductions from a not yet identified highly diverse native population. Eastern European populations show comparable amounts of genetic variability as do previously characterized French and North American populations, but analyses of population structure clearly distinguish the two European groups. This suggests separate introductions in Eastern and Western Europe as well as divergent sources for these two invasions, possibly as a result of distinct rules for trade and exchange for Eastern Europe during most of the twentieth century.     

When invasion increases population genetic structure: a study with <Emphasis Type="Italic">Centaurea diffusa</Emphasis>

Biological invasions offer excellent systems to study the evolutionary processes involved in introductions of species to new ranges. Molecular markers can reveal invasion histories and the effects of introductions on amounts and structuring of genetic variation. We used five polymorphic microsatellite loci to elucidate genetic diversity and population structure between native range and introduced range populations of a prominent North American rangeland weed, Centaurea diffusa (Asteraceae). We found that the total number of alleles and the number of private alleles was slightly higher in the native Eurasian range, and that allelic richness did not differ between the ranges, indicating overall levels of diversity were similar in Eurasia and North America. It therefore seems unlikely that this invasion has been affected by genetic bottlenecks or founder effects. Indeed, results of assignment tests suggest that multiple introductions have contributed to North America’s C. diffusa invasion. Additionally, assignment tests show that both Eurasian and North American sites had a strong pattern of mixed genetic ancestry. This mixed assignment corresponded to a lack of geographic population structure among Eurasian samples. The lack of population structure in the native range conflicts with general expectations and findings to date for invasion genetics, and cautions that even species’ native ranges may show signs of recent ecological upheaval. Despite the mixed assignments, North American samples showed strong population structure, suggesting that the invasion has been characterized by long-range dispersal of genetically distinct propagules across the introduced range.     

Population genetics and symbiont assemblages support opposing invasion scenarios for the red turpentine beetle (Dendroctonus valens)

Exotic forest insects and their symbionts pose an increasing threat to forest health. This is apparently true for the red turpentine beetle (Dendroctonus valens), which was unintentionally introduced to China, where the beetle has killed millions of healthy native pine trees. Previous population genetics studies that used cytochrome oxidase I as a marker concluded that the source of D. valens in China was western North America. In contrast, surveys of fungi associated with D. valens demonstrated that more fungal species are shared between China and eastern North America than between China and western North America, suggesting that the source population of D. valens could be eastern North America. In this study, we used microsatellite markers to determine population structure of D. valens in North America as well as the source population of the beetle in China. The analyses revealed that four genetically distinct populations (herein named the West, Central, Northeast and Mexico) represent the native range of D. valens. Clustering analyses and a simulation‐based approximate Bayesian computation (ABC) approach supported the hypothesis that western North America is the source of the invasive D. valens population. This study provides a demonstration of non‐congruence between patterns inferred by studies on population genetics and symbiont assemblages in an invasive bark beetle.     

Microsatellite isolation from the gall midge Spurgia capitigena (Diptera: Cecidomyiidae), a biological control agent of leafy spurge

Spurgia capitigena is a gall midge that has been released as a biological control agent of leafy spurge (Euphorbia esula), a noxious rangeland weed in North America. We isolated 15 microsatellite loci from S. capitigena with from two to 27 alleles at each locus. These markers will allow us to examine the structure and levels of neutral genetic variation in native and introduced populations.     

Natural range expansion and human-assisted introduction leave different genetic signatures in a hermaphroditic freshwater snail

Colonization events like range expansion or biological invasions can be associated with population bottlenecks. Small population size may lead to loss of genetic diversity due to random genetic drift, to loss of heterozygosity due to increased inbreeding and should leave a signature on the genetic polymorphism and genetic structure of populations. The mating system might additionally influence the outcome of such a process. Here, we compare invasive and native populations of the hermaphroditic freshwater snail Lymnaea stagnalis. In the native range we included populations that were ice-free during the last glaciation period and populations that were glaciated and are located at the edge of the species’ native distribution range. The microsatellite data show substantial loss of genetic variation in the introduced range and no signs of high propagule pressure or admixture. The expressed polymorphism was so low that mating system analysis was not possible. In the native region, all populations display strong levels of differentiation (global F _ST: 0.341) independent of colonization history and exhibit no significant pattern of inbreeding. However, the populations in more recently colonized habitats show diminished genetic diversity. Overall, these results illustrate how dramatic the reduction in genetic diversity can be for hermaphroditic animals and that gene flow in the native range can be surprisingly low despite short distances.     

Isolation and characterization of microsatellite loci in Paspalum notatum Flüggé (Poaceae)

Paspalum notatum is a forage grass recognized as one of the major constituents of the native grasslands in the New World. The knowledge of the genetic diversity and structure of P. notatum populations is fundamental for the conservation and germplasm management of this species. About 11 microsatellite markers were isolated from P. notatum and characterized in 25 accessions. The average number of alleles per locus was 7.9 and the PIC ranged from 0.36 to 0.89. The data demonstrated that the most of markers are suitable to detect polymorphism and to study the genetic diversity in the P. notatum species. Moreover, the transferability of these microsatellite were tested on other three congeneric species.     

First Insights into the Genetic Diversity of the Pinewood Nematode in Its Native Area Using New Polymorphic Microsatellite Loci

The pinewood nematode, Bursaphelenchus xylophilus, native to North America, is the causative agent of pine wilt disease and among the most important invasive forest pests in the East-Asian countries, such as Japan and China. Since 1999, it has been found in Europe in the Iberian Peninsula, where it also causes significant damage. In a previous study, 94 pairs of microsatellite primers have been identified in silico in the pinewood nematode genome. In the present study, specific PCR amplifications and polymorphism tests to validate these loci were performed and 17 microsatellite loci that were suitable for routine analysis of B. xylophilus genetic diversity were selected. The polymorphism of these markers was evaluated on nematodes from four field origins and one laboratory collection strain, all originate from the native area. The number of alleles and the expected heterozygosity varied between 2 and 11 and between 0.039 and 0.777, respectively. First insights into the population genetic structure of B. xylophilus were obtained using clustering and multivariate methods on the genotypes obtained from the field samples. The results showed that the pinewood nematode genetic diversity is spatially structured at the scale of the pine tree and probably at larger scales. The role of dispersal by the insect vector versus human activities in shaping this structure is discussed.     

Microsatellite population genetics of the emerald ash borer (Agrilus planipennis Fairmaire): comparisons between Asian and North American populations

The emerald ash borer (EAB) (Agrilus planipennis Fairmaire) (Coleoptera; Buprestidae), is an invasive wood-boring beetle native to northeast Asia. This species was first detected in Michigan USA in 2002, and is a significant threat to native and ornamental ash tree species (Fraxinus spp.) throughout North America. We characterized seven polymorphic microsatellite markers for EAB and used these to investigate EAB population structure in the early invasive populations within North America and in comparison with Asia. We found 2–9 alleles per microsatellite locus, no evidence of linkage disequilibrium, and no association with known coding sequences, suggesting that these markers are suitable for population genetic analysis. Microsatellite population genetic structure was examined in 48 EAB populations sampled between 2003 and 2008 from five regions, three in the introduced range, Michigan (US) and Ontario and Quebec (Canada) and two Asian regions, China and South Korea, where EAB is native. We found significant genetic variation geographically but not temporally in EAB populations. Bayesian clustering analyses of individual microsatellite genotypes showed strong clustering among multiple North American populations and populations in both China and South Korea. Finally, allelic richness and expected heterozygosity were higher in the native range of EAB, but there was no difference in observed heterozygosity, suggesting a significant loss of alleles upon introduction but no significant change in the distribution of alleles within and among individuals.     

Development of polymorphic microsatellite loci for North American river otters (Lontra canadensis) and amplification in related Mustelids

In order to complement ecological research on native and reintroduced populations of the North American river otter (Lontra canadensis), we developed 10 polymorphic microsatellite loci that would permit us to evaluate population genetic structure and conduct fecal DNA analyses. The number of alleles per locus ranged from 3 to 14 and observed heterozygosity ranged from 0.23 to 0.68. Preliminary screening revealed that primers were polymorphic in a subset of other Mustelids.     

Strong association between polymorphisms in an intronic microsatellite and in the coding sequence of the BoLA-DKB3 gene: implications for micro-satellite stability and PCR-based DRB3 typing

A highly polymorphic microsatellite in the bovine DRB3 gene was characterized by polymerase chain reaction (PCR) analysis and DNA sequencing. A very strong association between expressed DRB3 polymorphism and microsatellite alleles was revealed by PCR analysis of genomic DNA from 116 animals representing three breeds of cattle. The results indicated a low frequency of microsatellite length mutations as the association was consistent over breeds. The DRB3 microsatellite may be utilized in a PCR-based typing method of bovine class II alleles. The microsatellite polymorphism did not distinguish all known DRB3 alleles, but it was shown that this method may be complemented by the use of allele-specific PCR based on the extensive polymorphism in the DRB3 exon 2. The DNA sequences of seven microsatellite alleles, associated with different class II hap-lotypes, were determined. The DRB3 microsatellite is composed of three repeat motifs, a stretch of at least 10 uninterrupted (TG)_n dinucleotides, a long but interrupted stretch of (GA)_n dinucleotides, and a few (CAGA)_n tetranucleotides. There were pronounced sequence differences beween alleles and the results indicated that the evolution of this microsatellite has involved length mutations of the dinucleotide repeats as well as point mutations causing interruptions in the dinucleotide repeats.     

Evidence for multiple introductions of Centaurea stoebe micranthos (spotted knapweed,Asteraceae) to North America

Invasive species’ success may depend strongly on the genetic resources they maintain through the invasion process. We ask how many introductions have occurred in the North American weed Centaurea stoebe micranthos (Asteraceae), and explore whether genetic diversity and population structure have changed as a result of introduction. We surveyed individuals from 15 European native range sites and 11 North American introduced range sites at six polymorphic microsatellite loci. No significant difference existed in the total number of alleles or in the number of private alleles found in each range. Shannon–Weaver diversity of phenotype frequencies was also not significantly different between the ranges, while expected heterozygosity was significantly higher in the invasive range. Population structure was similar between the native range and the invasive range, and isolation by distance was not significant in either range. Traditional assignment methods did not allocate any North American individuals to the sampled European populations, while Bayesian assignment methods grouped individuals into nine genetic clusters, with three of them shared between North America and Europe. Invasive individuals tended to have genetically admixed profiles, while natives tended to assign more strongly to a single cluster. Many North American individuals share assignment with Romania and Bulgaria, suggesting two separate invasions that have undergone gene flow in North America. Samples from three other invasive range sites were genetically distinct, possibly representing three other unique introductions. Multiple introductions and the maintenance of high genetic diversity through the introduction process may be partially responsible for the invasive success of C. stoebe micranthos.     

Inferring the origin of populations introduced from a genetically structured native range by approximate Bayesian computation: case study of the invasive ladybird Harmonia axyridis

Correct identification of the source population of an invasive species is a prerequisite for testing hypotheses concerning the factors responsible for biological invasions. The native area of invasive species may be large, poorly known and/or genetically structured. Because the actual source population may not have been sampled, studies based on molecular markers may generate incorrect conclusions about the origin of introduced populations. In this study, we characterized the genetic structure of the invasive ladybird Harmonia axyridis in its native area using various population genetic statistics and methods. We found that native area of H. axyridis most probably consisted of two geographically distinct genetic clusters located in eastern and western Asia. We then performed approximate Bayesian computation (ABC) analyses on controlled simulated microsatellite data sets to evaluate (i) the risk of selecting incorrect introduction scenarios, including admixture between sources, when the populations of the native area are genetically structured and sampling is incomplete and (ii) the ability of ABC analysis to minimize such risks by explicitly including unsampled populations in the scenarios compared. Finally, we performed additional ABC analyses on real microsatellite data sets to retrace the origin of biocontrol and invasive populations of H. axyridis, taking into account the possibility that the structured native area may have been incompletely sampled. We found that the invasive population in eastern North America, which has served as the bridgehead for worldwide invasion by H. axyridis, was probably formed by an admixture between the eastern and western native clusters. This admixture may have facilitated adaptation of the bridgehead population.     

Global genetic analysis reveals the putative native source of the invasive termite,Reticulitermes flavipes,in France

Biological invasions are recognized as a major threat to both natural and managed ecosystems. Phylogeographic and population genetic analyses can provide information about the geographical origins and patterns of introduction and explain the causes and mechanisms by which introduced species have become successful invaders. Reticulitermes flavipes is a North American subterranean termite that has been introduced into several areas, including France where introduced populations have become invasive. To identify likely source populations in the USA and to compare the genetic diversity of both native and introduced populations, an extensive molecular genetic study was undertaken using the COII region of mtDNA and 15 microsatellite loci. Our results showed that native northern US populations appeared well differentiated from those of the southern part of the US range. Phylogenetic analysis of both mitochondrial and nuclear markers showed that French populations probably originated from southeastern US populations, and more specifically from Louisiana. All of the mtDNA haplotypes shared between the United States and France were found in Louisiana. Compared to native populations in Louisiana, French populations show lower genetic diversity at both mtDNA and microsatellite markers. These findings are discussed along with the invasion routes of R. flavipes as well as the possible mechanisms by which French populations have evolved after their introduction.     

Microsatellite analysis of relationships among North American plums (Prunus sect. Prunocerasus, Rosaceae)

Fifteen microsatellite primer pairs developed in sweet cherry and peach were used to explore genetic relationships among North American plums (Prunus section Prunocerasus). In all, 186 putative alleles were detected with a mean value of 12.4 per locus. The Jaccard coefficient of similarity was calculated between all pairs of accessions and their genetic similarities represented by a UPGMA dendrogram. Despite the apparent closeness among native American plums as evidenced by their ability to hybridize freely and their very similar ITS and trnL-trnF nucleotide sequences, all pairs of accessions among the North American plums shared fewer than half of their alleles. Some of the relationships suggested by the UPGMA dendrogram are congruent with current taxonomic hypotheses, but others are difficult to interpret. Further resolution of relationships among American plums will require molecular markers more variable than ITS yet less variable than microsatellites.     

Genetic variation and biogeography of the disjunct Vitis subg. Vitis (Vitaceae)

Aim Vitis subg. Vitis provides an example of a plant disjunction occurring in the Northern Hemisphere. It shows broad morphological variation but is assumed to be a species complex with limited genetic differentiation. Based on a comprehensive sampling of taxa and polymorphism in both chloroplast and nuclear DNA, we assessed genetic variation within this subgenus. Our aims were to clarify the relationships among species and to examine their historical biogeography. Location Asia, Europe, North America. Methods We analysed a total of 30 species and putative hybrids from subgenus Vitis and examined the infra‐specific variation in some species. Polymorphism in chloroplast DNA was assessed in trnL and trnH–psbA–trnK sequences (c. 2170 bp) and in 15 microsatellite loci. We also obtained nuclear data for size variation at 24 microsatellite loci. Phylogenetic inference was performed with Bayesian analyses. A maximum parsimony network was constructed to depict the evolutionary relationships among haplotypes, and microsatellite data were also subjected to hierarchical clustering analysis using the Ward distance. In addition, we assessed size homoplasy by sequencing both chloroplast and nuclear microsatellite loci. Results Chloroplast polymorphisms resolved subgenus Vitis as a monophyletic group with limited genetic variation. The ancestral haplotypes were found in Eurasia. American taxa all harboured derived haplotypes. Most of them formed a monophyletic group that did not include Vitis californica. The four main haplotypes in Vitis vinifera corresponded to two different origins. Nuclear microsatellites indicated that genetic variation was especially large in North America. Asian species exhibited a lower level of nuclear divergence and the European V. vinifera corresponded to a differentiated nuclear lineage. Main conclusions We obtained some evidence that subgenus Vitis has an Asian origin and then dispersed to Europe and North America. Geographic separation was followed by diversification, presumably during the Pleistocene, resulting in phylogeographic patterns similar to other biota. In contrast to chloroplast DNA, nuclear DNA shows a larger than expected genetic variation. Our molecular data also highlight the need to re‐examine certain aspects of the current subgeneric classification.