Chloroplast DNA haplotype diversity and postglacial recolonization of Hagenia abyssinica (Bruce) J.F. Gmel. in Ethiopia

We investigated genetic variation of 273 individuals from 25 populations of the monotypic species Hagenia abyssinica (Rosaceae) from the highlands of Ethiopia at three chloroplast microsatellite loci. The objectives were to infer the factors that shaped the genetic structure and to reconstruct the recolonization history of the species. Six haplotypes that were phylogenetically grouped into two lineages were identified. Homology of the three loci to the respective regions of the chloroplast genome was confirmed by sequencing. The chloroplast haplotypes found in Hagenia showed a clear pattern of congruence between their geographical distribution and genealogical relationships. A very low haplotype diversity within populations (h _S = 0.079, v _S = 0.058) and a very high population differentiation (G _ST = 0.899, N _ST = 0.926) was observed, reflecting very low mixing between recolonizing lineages. Restricted gene flow through seeds, rare long-distance dispersal, contiguous range expansion and mutation shaped the genetic structure of Hagenia. Fossil pollen records suggested that the trend of postglacial recolonization of Hagenia was first in the south and latter went to the north in Ethiopia.     

Mitochondrial and nuclear markers reveal a lack of genetic structure in the entocommensal nemertean Malacobdella arrokeana in the Patagonian gulfs

Malacobdella arrokeana is an entocommensal nemertean exclusively found in the bivalve geoduck Panopea abbreviata, and it is the only representative of the genus in the southern hemisphere. To characterize its genetic diversity, population structure and recent demographic history, we conducted the first genetic survey on this species, using sequence data for the cytochrome oxidase I gene (COI), 16S rRNA (16S) and the internal transcribed spacer (ITS2). Only four different ITS2 genotypes were found in the whole sample, and the two main haplotypes identified in the mitochondrial dataset were present among all localities with a diversity ranging from 0.583 to 0.939. Nucleotide diversity was low (π = 0.001–0.002). No significant genetic structure was detected between populations, and mismatch distribution patterns and neutrality tests results are consistent with a population in expansion or under selection. Analysis of molecular variance (AMOVA) revealed that the largest level of variance observed was due to intrapopulation variation (100, 100 and 94.39 % for 16S, COI and ITS2, respectively). F _st values were also non-significant. The observed lack of population structure is likely due to high levels of genetic connectivity in combination with the lack or permeability of biogeographic barriers and episodes of habitat modification.     

Demographic History and Population Structure of Blackfin Flounder (Glyptocephalus stelleri) in Japan Revealed by Mitochondrial Control Region Sequences

The demographic history and population genetic structure of the blackfin flounder (Glyptocephalus stelleri) along coastal regions of Japan were investigated. Genetic variation in DNA sequences was examined from the first hypervariable region of the mitochondrial DNA control region. A high level of haplotypic diversity (h = 0.99 ± 0.004) was detected, indicating a high level of intrapopulation genetic diversity. The starburst structure of the minimum spanning tree suggested a very recent origin for most haplotypes. The demographic history of G. stelleri was examined using neutrality tests and mismatch distribution analysis, which also indicated a Pleistocene population expansion at about 124,100–413,400 years ago. Hierarchical molecular variance analysis and conventional population Fst comparisons revealed no significant genetic differentiation throughout the range examined.     

Geographic variation in relict populations: genetics and phenotype of bush-cricket Pholidoptera frivaldskyi (Orthoptera) in Carpathians

A decreasing population size is often causing species extinction, however, relict species persisting in small-sized populations counter this. We analysed spatial genetic variation and past changes in population size at the maternally-inherited mitochondrial DNA level to clarify the origin of all recently known isolated populations of Pholidoptera frivaldskyi occurring in the range of Carpathian Mountains. Along with that we analysed also morphological variation as some phenotypic traits can retain useful information on population genetic structure. We found a relatively low genetic diversity within isolated populations as 778 bp COI gene sequences revealed only 13 unique haplotypes (n = 173 individuals from 10 populations). The spatial analysis of molecular variance identified three geographically homogenous genetic clusters (one in Slovakia and two in Romania) with a high level of differentiation among them, suggesting restricted gene flow, whilst Bayesian skyline simulation reconstructed a negative demographic change through evolutionary time. Inferred genetic pattern clearly coincides with differences in males’ colour phenotype as the extent of pigmentation on the lateral pronotum varied significantly among genetic lineages. We suggest that geographical variation in the species populations has relict-like character and their isolated occurrence is not a result of recent introduction events. Identification of ‘evolutionary units’ may help in the conservation and management of this rare insect species.     

Distribution and polymorphism of Mariner-like elements in the Bambusoideae subfamily

Picea omorika (Pan?.) Purk. is a relict from the Arcto-Tertiary flora with its entire current natural range confined to an area of only 10,000 km² within the Balkans, a region well known as a Quaternary refugium. We have amplified the second intron of the mitochondrial NADH dehydrogenase subunit1 gene in 200 trees originating from ten natural populations to assess the phylogeographic structure and history of this conifer. Five haplotypes harbouring different numbers of 34-bp minisatellites were detected, revealing haplotypic richness of 3.007 and gene diversities H _S = 0.075 and H _T = 0.225. More interestingly, despite the very small distribution range of P. omorika and its dispersal by wind, non-random distribution of haplotypes was observed, resulting in an unexpectedly high estimate of population differentiation (G _ST = 0.668), and 56.8% of molecular variation assigned to variation among populations. Those findings suggest substantial isolation of populations and their partitioning into two gene pools characterized by different history and levels of genetic diversity, and very limited seed flow in this species (Nm = 0.25). They support the hypothesised early arrival of P. omorika in the Balkan region, and residence within this refugium during several ice ages at least. We demonstrate that the assessment of genetic diversity and structuring are not straightforward in species confined to refugial regions, and that past microvicariance might bias formal phylogeographic (G _ST = N _ST = 0.668) and isolation-by-distance analysis (r = 0.028, P > 0.05).     

Conservation genetics of the endangered terrestrial orchid Liparis japonica in Northeast China based on AFLP markers

Levels of genetic diversity and population genetic structure of the rare, endangered terrestrial orchid Liparis japonica were examined for eight natural populations (n = 185) in Northeast China using six AFLP primer pairs, where this species has experienced severe habitat loss and fragmentation. Based on 406 DNA bands, a high level of genetic diversity was found at the species level with the PPB of 85.47 %, while the genetic diversity at the population level was low (PPB = 47.48 %). A significantly high degree of population differentiation was found with 42.69 % variation existed among populations as measured by AMOVA, indicating potential restricted gene flow. The genetic distances between populations were independent of the corresponding geographic distances, and the genetic relationship of individuals had no significant correlation with their spatial distribution. The restricted gene flow might be impacted by reduced population size, habitat destruction and fragmentation. The results in this study suggested that habitat protection and keeping a stable environment are critical for the conservation of L. japonica species.     

Molecular Phylogeography and Evolutionary History of the Estuarine Copepod, Acartia Tonsa, on the Northwest Atlantic Coast

Coastal estuaries are useful model systems to study the ecological and evolutionary responses of organisms to highly variable, discontinuous habitats. For this study, the molecular population genetic diversity of the planktonic calanoid copepod Acartia tonsa (Dana, 1849) was described based on DNA sequence variation for a 183 base-pair region of the mitochondrial 16S rRNA gene. Samples of A. tonsa were collected from four estuaries on the Atlantic coast of the USA during 1993 and 1994, one estuary on the Gulf of Mexico coast in 1994, and one site on the Pacific coast of the USA in 1994. Dispersal of A. tonsa was shown to be restricted, with significant population genetic structuring between different estuaries. For all but the closely-adjacent MA and RI samples, frequencies of haplotypes and/or length polymorphisms within one haplotype (caused by insertion/deletion mutations) revealed highly significant genetic differentiation and geographic isolation. Mt16S haplotypes of A. tonsa from Atlantic and Gulf of Mexico estuaries were assorted among four deeply-diverged clades. Haplotypes within each clade differed by <2%, while differences among clades of 10% to 14% approached those between described Acartia species (e.g., 19% to 28% among A. clausi, A. hudsonica, and A. longiremis). Atlantic and Pacific coast samples identified as A. tonsa had no haplotypes in common and genetic differences between haplotypes ranged from 18% to 29%; phylogenetic analysis supported the separation of Pacific coast A. tonsa as a distinct species. We hypothesize that the observed patterns of molecular genetic diversity and structure of A. tonsa resulted from responses to historical climatic variation, including episodic range compression and displacement, and alteration of NW Atlantic coastal and estuarine environments.     

Mitochondrial DNA Sequence Variation of the Swallowtail Butterfly, Papilio xuthus, and the Cabbage Butterfly, Pieris rapae

We analyzed a portion of mitochondrial COI gene sequences (658 bp) to investigate the genetic diversity and geographic variation of the swallowtail butterfly, Papilio xuthus L. (Lepidoptera: Papilionidae), and the cabbage butterfly, Pieris rapae L. (Lepidoptera: Pieridae). Papilio xuthus showed a moderate level of sequence divergence (0.91% at maximum) in 15 haplotypes, whereas Pi. rapae showed a moderate to high level of sequence divergence (1.67% at maximum) in 30 haplotypes, compared with other relevant studies. Analyses of population genetic structure showed that most populations are not genetically differentiated in both species. The distribution pattern of both species appears to be consistent with category IV of the phylogeographic pattern sensu Avise: a phylogenetic continuity, an absence of regional isolation of mtDNA clones, and extensive distribution of close clones. The observed pattern of genetic diversity and geographic variation of the two butterfly species seem to reflect the abundant habitats, abundant host plants, and flying abilities in connection with the lack of historical biogeographic barriers.     

Genetic structure in the paleoendemic and endangered Petagnaea gussonei (Spreng.) Rauschert (Saniculoideae, Apiaceae) and implications for its conservation

Our investigation aims to understand the genetic structure and evolutionary history of Petagnaea gussonei, an ancient and endangered species belonging to the Saniculoideae subfamily (Apiaceae). It is paleoendemic to Sicily, with a small number of populations in the Nebrodi Mountains. A total of seven chloroplast microsatellite repeat loci and 12 AFLP primer combinations were used to screen 115 individuals corresponding to 17 populations. The ratio of seed to pollen flow was also calculated using the modified Ennos equation. A relatively high level of genetic diversity was detected with AFLPs (e.g., 0.045 < H < 0.278), and a moderate variation was also found using cpSSRs (0 < Hk < 0.667). Two different haplotypes (B and W) were identified, with five populations being monomorphic for haplotype B. There was no genetic differentiation on the basis of haplotypic frequency (G _ST) and similarity (R _ST), and no phylogeographic structure was detected among the populations. AFLP values also confirmed that the populations are not very genetically differentiated. The principal component analysis based on pairwise genetic differences showed three groupings without a geographical correlation. The AMOVA analysis indicates that the amount of variation is higher within populations (82 %) than among populations (18 %). Results of the pollen flow/seed flow ratio indicated positive values for each population, indicating that gene flow by seed is not more efficient than by pollen. Instead, the total pollen/seed flow for all population presents a negative value, suggesting that pollen dispersal does not appear to be more effective over the long range for gene flow than seed dispersal. This differentiation level supports the hypothesis that the fragmentation and isolation of the residual populations is in progress. This phenomenon is due not only to post-ice age climate changes, but also to direct and indirect anthropic actions.     

Mitochondrial DNA Diversity of Honey Bees (Apis mellifera) from Unmanaged Colonies and Swarms in the United States

To study the genetic diversity of honey bees (Apis mellifera L.) from unmanaged colonies in the United States, we sequenced a portion of the mitochondrial DNA COI–COII region. From the 530 to 1,230 bp amplicon, we observed 23 haplotypes from 247 samples collected from 12 states, representing three of the four A. mellifera lineages known to have been imported into the United States (C, M, and O). Six of the 13 C lineage haplotypes were not found in previous queen breeder studies in the United States. The O lineage accounted for 9% of unmanaged colonies which have not yet been reported in queen breeder studies. The M lineage accounted for a larger portion of unmanaged samples (7%) than queen breeder samples (3%). Based on our mitochondrial DNA data, the genetic diversity of unmanaged honey bees in the United States differs significantly from that of queen breeder populations (p < 0.00001). The detection of genetically distinct maternal lineages of unmanaged honey bees suggests that these haplotypes may have existed outside the managed honey bee population for a long period.     

Strong population genetic structure and its implications for the conservation and management of the endangered Itasenpara bitterling

To infer the population genetic structure and genetic diversity of Itasenpara bitterling (Acheilognathus longipinnis), a cyprinid species endemic to Japan and distributed in only three specific regions, we investigated mitochondrial DNA variation. The distribution of the haplotypes among the three regions showed distinct geographic structure, and no common haplotypes were observed among regions. Analysis of molecular variance revealed a significant proportion of the genetic variance was partitioned among regions (93.1 %, P < 0.001), and pairwise estimates of D_A and Φ_ST between regions also revealed strong population structure. Given the strong genetic structure and low genetic diversity within regions, we strongly suggest that each region should be treated as a separate unit in any conservation program and any inter-regional translocations should be avoided.     

Mitochondrial DNA Diversity of Orchid Bee Euglossa fimbriata (Hymenoptera: Apidae) Populations Assessed by PCR-RFLP

Euglossa fimbriata is a euglossine species widely distributed in Brazil and occurring primarily in Atlantic Forest remnants. In this study, the genetic mitochondrial structure of E. fimbriata from six Atlantic Forest fragments was studied by RFLP analysis of three PCR-amplified mtDNA gene segments (16S, COI-COII, and cyt b). Ten composite haplotypes were identified, six of which were exclusive and represented singleton mitotypes. Low haplotype diversity (0.085–0.289) and nucleotide diversity (0.000–0.002) were detected within samples. AMOVA partitioned 91.13% of the overall genetic variation within samples and 8.87% (?_st = 0.089; P < 0.05) among samples. Pairwise comparisons indicated high levels of differentiation among some pairs of samples (?_st = 0.161–0.218; P < 0.05). These high levels indicate that these populations of E. fimbriata, despite their highly fragmented landscape, apparently have not suffered loss of genetic variation, suggesting that this particular population is not currently endangered.     

Population stock structure of leatherback turtles (Dermochelys coriacea) in the Atlantic revealed using mtDNA and microsatellite markers

This study presents a comprehensive genetic analysis of stock structure for leatherback turtles (Dermochelys coriacea), combining 17 microsatellite loci and 763 bp of the mtDNA control region. Recently discovered eastern Atlantic nesting populations of this critically endangered species were absent in a previous survey that found little ocean-wide mtDNA variation. We added rookeries in West Africa and Brazil and generated longer sequences for previously analyzed samples. A total of 1,417 individuals were sampled from nine nesting sites in the Atlantic and SW Indian Ocean. We detected additional mtDNA variation with the longer sequences, identifying ten polymorphic sites that resolved a total of ten haplotypes, including three new variants of haplotypes previously described by shorter sequences. Population differentiation was substantial between all but two adjacent rookery pairs, and F _ST values ranged from 0.034 to 0.676 and 0.004 to 0.205 for mtDNA and microsatellite data respectively, suggesting that male-mediated gene flow is not as widespread as previously assumed. We detected weak (F _ST = 0.008 and 0.006) but significant differentiation with microsatellites between the two population pairs that were indistinguishable with mtDNA data. POWSIM analysis showed that our mtDNA marker had very low statistical power to detect weak structure (F _ST < 0.005), while our microsatellite marker array had high power. We conclude that the weak differentiation detected with microsatellites reflects a fine scale level of demographic independence that warrants recognition, and that all nine of the nesting colonies should be considered as demographically independent populations for conservation. Our findings illustrate the importance of evaluating the power of specific genetic markers to detect structure in order to correctly identify the appropriate population units to conserve.     

Distribution,prevalence and host specificity of avian malaria parasites across the breeding range of the migratory lark sparrow (Chondestes grammacus)

The lark sparrow (Chondestes grammacus) is a ground-nesting passerine that breeds across much of the central North American steppe and sand barrens. Through genotyping and sequencing of avian malaria parasites we examined levels of malaria prevalence and determined the distribution of Haemoproteus and Plasmodium lineages across the breeding range of the lark sparrow. Analysis of 365 birds collected from five breeding locations revealed relatively high levels of malaria prevalence in adults (80 %) and juveniles (46 %), with infections being primarily of Haemoproteus (91 % of sequenced samples). Levels of genetic diversity and genetic structure of malaria parasites with respect to the avian host populations revealed distinct patterns for Haemoproteus and Plasmodium, most likely as a result of their distinct life histories, host specificity, and transmission vectors. With the exception of one common Haemoproteus haplotype detected in all populations, all other haplotypes were either population-specific or shared by two to three populations. A hierarchical analysis of molecular variance of Haemoproteus sequences revealed that 15–18 % of the genetic variation can be explained by differences among host populations/locations (p < 0.001). In contrast to the regional patterns of genetic differentiation detected for the lark sparrow populations, Haemoproteus parasites showed high levels of population-specific variation and no significant differences among regions, which suggests that the population dynamics of the parasites may be driven by evolutionary processes operating at small spatial scales (e.g., at the level of host populations). These results highlight the potential effects of host population structure on the demographic and evolutionary dynamics of parasites.     

Comparative Analysis of Genetic Diversity and Population Structure of Sipunculus nudus as Revealed by Mitochondrial COI Sequences

Genetic diversity and population structure of Sipunculus nudus were evaluated using a 652 base pair fragment of the mitochondrial cytochrome oxidase I gene. The populations were collected from Beihai, Sanya, and Xiamen. A total of 71 polymorphic sites defined 16 distinct haplotypes. The mean haplotype diversity and nucleotide diversity of the three populations were 0.9354 ± 0.0168 and 0.0035 ± 0.0018, respectively. Analysis at the intrapopulation level showed that the Beihai population had the greatest haplotype and nucleotide diversity, followed by the Xiamen and Sanya populations. Analysis of molecular variance showed significant genetic differentiation among the three populations (Fst = 0.0796, P < 0.05). The present results revealed that S. nudus populations had a high level of genetic diversity and distinct population structures.     

Genetic Variation of Sclerotinia sclerotiorum from Multiple Crops in the North Central United States

Sclerotinia sclerotiorum is an important pathogen of numerous crops in the North Central region of the United States. The objective of this study was to examine the genetic diversity of 145 isolates of the pathogen from multiple hosts in the region. Mycelial compatibility groups (MCG) and microsatellite haplotypes were determined and analyzed for standard estimates of population genetic diversity and the importance of host and distance for genetic variation was examined. MCG tests indicated there were 49 different MCGs in the population and 52 unique microsatellite haplotypes were identified. There was an association between MCG and haplotype such that isolates belonging to the same MCG either shared identical haplotypes or differed at no more than 2 of the 12 polymorphic loci. For the majority of isolates, there was a one-to-one correspondence between MCG and haplotype. Eleven MCGs shared haplotypes. A single haplotype was found to be prevalent throughout the region. The majority of genetic variation in the isolate collection was found within rather than among host crops, suggesting little genetic divergence of S. sclerotiorum among hosts. There was only weak evidence of isolation by distance. Pairwise population comparisons among isolates from canola, dry bean, soybean and sunflower suggested that gene flow between host-populations is more common for some crops than others. Analysis of linkage disequilibrium in the isolates from the four major crops indicated primarily clonal reproduction, but also evidence of genetic recombination for isolates from canola and sunflower. Accordingly, genetic diversity was highest for populations from canola and sunflower. Distribution of microsatellite haplotypes across the study region strongly suggest that specific haplotypes of S. sclerotiorum are often found on multiple crops, movement of individual haplotypes among crops is common and host identity is not a barrier to gene flow for S. sclerotiorum in the north central United States.     

Pattern of genetic variation of yellow catfish Pelteobagrus fulvidraco Richardso in Huaihe river and the Yangtze river revealed using mitochondrial DNA control region sequences

Genetic variability and population genetic structure of the yellow catfish Pelteobagrus fulvidraco Richardso in the Huaihe river and the Yangtze river was examined with a 810-bp of the mitochondrial DNA control region. A total of 70 haplotypes were identified from 145 samples, which were characterized with high haplotype diversity (h = 0.9832 ± 0.0041) but low nucleotide diversity (π = 0.0415 ± 0.0201). The analysis of molecular variance and phylogenetic reconstructions detected significant geographic structure between Huaihe river and Yangtze with F_ST = 0.1183 (P = 0.0000). Neighbor-joining (NJ) phylogenetic analyses identified two distinct clades (bootstrap support 99 %). The medium joining network drawn using the complete data set was reticulated and also distinctly split the 70 haplotypes into two groups corresponding to those of the NJ tree. Departures from neutrality were not significant for the Huaihe river and the Yangtze river Pelteobagrus fulvidraco, concordant with the observed multimodal mismatch distributions (P > 0.05), which suggested that the effective size of this species has been large and stable for a long period. The question about the existence of significant genetic differentiation for Pelteobagrus fulvidraco in the Yangtze river and Huaihe river basins remains to be further studied with molecular nuclear markers and larger sample sizes from throughout the river basins.     

Population structure and genetic analysis of narrow-clawed crayfish (Astacus leptodactylus) populations in Turkey

The genetic differentiation among Turkish populations of the narrow-clawed crayfish was investigated using a partial sequence of cytochrome oxidase subunit I gene (585 bp) of 183 specimens from 17 different crayfish populations. Median joining network and all phylogenetic analyses disclosed a strong haplotype structure with three prominent clades diverged by a range between 20 and 50 mutations and substantial inter-group pairwise sequence divergence (5.19–6.95 %), suggesting the presence of three distinct clades within the Anatolian populations of Astacus leptodactylus. The divergence times among the three clades of Turkish A. leptodactylus are estimated to be 4.96–3.70 Mya using a molecular clock of 1.4 % sequence divergence per million years, pointing to a lower Pliocene separation. The high level of genetic variability (H _d  = 95.8 %, π = 4.17 %) and numerous private haplotypes suggest the presence of refugial populations in Anatolia unaffected by Pleistocene habitat restrictions. The pattern of genetic variation among Turkish A. leptodactylus populations, therefore, suggests that the unrevealed intraspecific genetic structure is independent of geographic tendency and congruent with the previously reported geographic distribution and number of subspecies (A. l. leptodactylus and A. l. salinus) of A. leptodactylus.     

Chloroplast DNA-based genetic diversity and phylogeography of Pyrus betulaefolia (Rosaceae) in Northern China

Pyrus betulaefolia Bunge, considered as an intermediate between oriental and occidental pear groups, is one of the most important wild pear species. The number of its populations is decreasing because of habitat destruction, fragmentation, and continuous exploitation, so protection and conservation measures are urgently needed. Assessment of its genetic diversity and phylogeography are imperative for its efficient conservation. Two chloroplast DNA intergenic fragments were used to detect genetic diversity and phylogeography of 320 individuals from 18 wild P. betulaefolia populations. Haplotype variation, genetic differentiation, and historical events of the populations were estimated. The results showed that P. betulaefolia populations sampled in northern China contained a high level of genetic diversity (H _T?=?0.826). A significant isolation-by-distance value (r?=?0.587, P?<?0.001, 1,000 permutations) among all 18 populations indicated a correlation between genetic divergence and geographic distance. Four population groups were identified in a neighbor-joining tree based on the genetic distance. Analyses of molecular variation showed that the genetic variation mainly existed among population groups, representing 64.61 % of the total variation. Phylogeographic analyses indicated that the populations of P. betulaefolia experienced a scenario of rapid range expansion, which probably occurred between 608,000 and 204,580 years ago. Meanwhile, both the restricted gene flow with isolation by distance and allopatric fragmentation were crucial processes responsible for shaping the genetic patterns of P. betulaefolia. The occurrence of specific haplotypes might be ascribed to an ancestral introgression or joint retention of an ancestral polymorphism with other Pyrus species at the northern edge of the distribution of P. betulaefolia. Three populations displaying a high level of haplotype diversity and unique haplotypes were assumed to be relict populations of Quaternary glaciation and should have conservation priority. Three additional large populations should also be preferentially protected by building natural preservation zones.