Genetic diversity among Neoleucopis (Diptera: Chamaemyiidae) associated with Marchalina hellenica (Hemiptera: Marchalinidae) in Greece and Italy (Ischia)

Aceria tosichella (the wheat curl mite, WCM) is a global pest of wheat and other cereals, causing losses by direct damage, as well as the transmission of plant viruses. The mite is considered to have an unusually wide host range for an eriophyoid species. The present study tested the commonly held assumption that WCM is a single, highly polyphagous species by assessing the host range of genetically distinct lineages of WCM occurring in Poland on different host plants. Genotyping was performed by analyzing nucleotide sequence data from fragments of the mitochondrial cytochrome c oxidase subunit I (COI) and the nuclear D2 region of 28S rDNA. Mean between-lineage distance estimated using COI data was found to be one order of magnitude greater than the within-clade lineage and, in some cases, comparable to distances between WCM lineages and a congeneric outgroup species. Host acceptance was tested by quantifying population growth for different WCM mitochondrial (mt)DNA lineages when transferred from source host plants to test plants. These experiments revealed significant differences in host colonization ability between mtDNA lineages, ranging from highly polyphagous to more host-specific. The present study reveals that WCM is composed of several discrete genetic lineages with divergent host-acceptance and specificity traits. Genetic variation for host acceptance within A. tosichella s.l. may act as a reproductive barrier between these lineages, most of which had narrow host ranges. Two lineages appear to have high pest potential on cereals, whereas several others appear to specialize on wild grass species. We conclude that WCM is not a homogeneous species comprising polyphagous panmictic populations rather it is a complex of genetically distinct lineages with variable host ranges and therefore variable pest potential. © 2013 The Linnean Society of London, Biological Journal of the Linnean Society, 2013, 109, 165–180. ADDITIONAL KEYWORDS: 28S rDNA D2 – DNA barcoding – acceptance – specificity – mtDNA COI – species complex.

Several geographically distinct mitochondrial DNA (mtDNA) lineages of the big brown bat (Eptesicus fuscus) have been documented in North America. Individuals from 2 of these lineages, an eastern and a western form, co-occur within maternity colonies in Colorado. The discovery of 2 divergent mtDNA lineages in sympatry prompted a set of questions regarding possible biological differences between haplotypes. We captured big brown bats at maternity roosts in Colorado and recorded data on body size, pelage color, litter size, roosting and overwintering behaviors, and local distributions. Wing biopsies were collected for genetic analysis. The ND2 region of the mtDNA molecule was used to determine lineage of the bats. In addition, nuclear DNA (nDNA) intron 1 of the b-globin gene was used to determine if mtDNA lineages are hybridizing. Eastern and western mtDNA lineages differed by 10.3% sequence divergence and examination of genetic data suggests recent population expansion for both lineages. Differences in distribution occur along the Colorado Front Range, with an increasing proportion of western haplotypes farther south. Results from nDNA analyses demonstrated hybridization between the 2 lineages. Additionally, no outstanding distinctiveness was found between the mtDNA lineages in natural history characters examined. We speculate that historical climate changes separated this species into isolated eastern and western populations, and that secondary contact with subsequent interbreeding was facilitated by European settlement.

A growing interest across Europe is emerging to maintain the genetic integrity of honey bee populations and subspecies. In this study we combined different approaches to obtain an over-time distribution map of the main Apis mellifera mitochondrial DNA (mtDNA) lineages in the North of Italy. mtDNA was analysed from individual honey bees and from honey. Honey is a source of environmental DNA (eDNA), which also contains traces of the DNA of the honey bees that have produced it. A total of about 1,600 honey samples produced in the North of Italy over four years (2018-2021) where analysed to detect the A, C1, C2 and M mtDNA lineages. The obtained results will be useful to design conservation strategies of A. mellifera genetic resources in Italy. We demonstrated that eDNA from honey can be exploited to design a cost-effective population genetic study in A. mellifera.

Prehistoric Europe experienced a marked cultural and economic shift around 4000 years ago, when the established Neolithic agriculture-based economy was replaced by herding-pastoralist industry. In recent years new data about the genetic structure of human communities living during this transition period began to emerge. At the same time, the genetic identities of the Eneolithic and Early Bronze Age (EBA) inhabitants from a prehistoric cultural crossroad in western North Pontic steppe region remain understudied. This report presents results of the investigation of maternal genetic lineages of individuals buried in kurgans constructed during the Eneolithic-EBA transition in the western part of the North Pontic Region (NPR). Mitochondrial DNA (mtDNA) lineages from the interments belonging to the Eneolithic as well as the EBA cultures such as Yamna (Pit Grave), Catacomb and Babino (Mnogovalikovaya or KMK) were examined. In the 12 successfully haplotyped specimens, 75% of mtDNA lineages consisted of west Eurasian haplogroup U and its U4 and U5 sublineages. Furthermore, we identified a subgroup of east Eurasian haplogroup C in two representatives of the Yamna culture in one of the studied kurgans. Our results indicate the persistence of Mesolithic hunter-gatherer mtDNA lineages in western NPR through the EBA, as well as suggesting a mtDNA lineage continuum connecting the western NPR inhabitants of the Early Metal Ages to the North Pontic Neolithic population groups.

A hybrid zone between two Brachionus plicatilis rotifer mitochondrial DNA (mtDNA) lineages was recently described in the Iberian Peninsula between a pond (Santed 2) and a lake (Gallocanta). The patterns of mitochondrial and nuclear genetic variation observed suggested that gene flow is mainly male-mediated from the lake to the pond. Here we test two hypotheses: (a) that male-mediated gene flow occurs through assortative mating between individuals from these ponds, (b) that behavioural isolation occurs between the two mtDNA lineages. We isolated, reared and genotyped rotifer clones from resting eggs collected in the sediments of these and two other distant ponds. We devised a quick, inexpensive RFLP method to discriminate between B. plicatilis and its sibling species B. ‘Manjavaeas’ and between both mtDNA B. plicatilis lineages. Behavioural no-choice tests using new-born, virgin males and females were performed between five clones. B. ‘Manjavacas’ and B. plicatilis were reproductively isolated. B. plicatilis clones did not show evidence of reproductive isolation, regardless of their mtDNA lineage, except Santed 2 males, which discriminated strongly against Gallocanta females. These results could help to explain the discrepancies between mitochondrial and nuclear genetic variation reported in the two populations.

Summary1. We determined whether two sympatric mitochondrial DNA (mtDNA) lineages of freshwater shrimp (Decapoda: Atyidae: Paratya australiensis) represent biological species and if they had concerted or independent population responses to hydrographic factors in small streams (the Granite Creeks) in southeastern Australia.2. Allozyme data indicated the presence of two gene pools at sites where the P. australiensis lineages were co‐occurring and the gene pools were statistically assigned with high probability to each respective lineage. This indicated that these mtDNA lineages in P. australiensis were reproductively isolated and thus biological species.3. Populations of both lineages were genetically homogeneous among lowland sites within streams, but were isolated by steep stream gradients among upland sites and for lowland–upland site comparisons. However, the magnitude of differentiation was markedly different between the two lineages. Allozyme diversity also differed between the two lineages, suggesting that they have different effective population sizes. Thus, differences in the magnitude of genetic divergence among populations were probably because of different life‐history characteristics, including dispersal ability and population size.4. Genetic population structure was mostly temporally stable, despite the extreme effects of drought during the first year and substantial stream‐flow during the second. However, stable isotope analyses revealed greater local movement in both lineages during the second year, as greater hydrological connectivity provided more opportunities for dispersal. Thus, although lowland populations within streams were genetically homogeneous, stable isotope data indicated that connections may be sporadic and result from accumulated small‐scale movements among refugial pools.5. Both lineages were therefore found to have similar small‐scale population responses to the unstable habitats of the Granite Creeks. Results highlight the importance of refugia for the capacity of biota to recover from drought and the need for multiple restored patches to reinstate natural population processes (e.g. resilience, recolonization) in degraded systems.

Connectivity between golden eagle (Aquila chrysaetos) populations is poorly understood. Field studies exploring natal dispersal suggest that this raptor is a philopatric species, but with the ability to roam far. However, little is known about the population structure of the species in Europe. Our study is based on 14 microsatellite loci and is complemented by new and previously published mitochondrial control region DNA data. The present dataset includes 121 eagles from Scotland, Norway, Finland, Estonia, the Mediterranean and Alpine regions. Our sampling focused on the Alpine and Mediterranean populations because both mitochondrial DNA (mtDNA) lineages found in golden eagles, the Holarctic and the Mediterranean, are known to co-occur there. Cluster analyses of nuclear DNA support a shallow split into northern and southern populations in Europe, similar to the distribution of the two mtDNA lineages, with the Holarctic lineage occurring in the north and the Mediterranean lineage predominating in the south. Additionally, Scotland shows significant differentiation and low relative migration levels that indicate isolation from the mainland populations. Alpine and Mediterranean golden eagles do not show nuclear structure corresponding to divergent mtDNA lineages. This indicates that the presence of northern Holarctic mitochondrial haplotypes in the Alps and the Mediterranean is attributable to past admixture rather than recent long-distance dispersal.

Simple SummaryAssessing the status of multiple highly divergent mitochondrial DNA (mtDNA) lineages and delimiting the evolutionarily significant units (ESUs) are the foundation of forecasting the influence of climate change on intraspecific genetic variation. In this study, we employed AFLP to investigate the genetic structure of Ammodytes personatus and compared the genetic variation of A. personatus in different ocean current systems. The incongruence between nuclear clades and previous mitochondrial lineages suggested that A. personatus is indeed composed of at least two genetically divergent cryptic species. Our results demonstrate that intra-species diversity should be taken into account to assess the influence of climate change on species. This study also highlights the value of the natural physical setting created by warm and cold ocean currents in eliciting a correlation between temperature and species distribution. In future studies, the exact range of temperature in both groups must be assessed with a sufficient number of samples to predict the influences of global climate change on both groups.The use of molecular techniques in biodiversity research increasingly results in the recognition of multiple divergent mitochondrial DNA (mtDNA) lineages below the morphospecies level. However, the overlapping distribution of multiple divergent lineages raises the question of whether some of these lineages are in fact cryptic species. Assessing the status of these divergent lineages, delimiting evolutionarily significant units (ESUs), and identifying the dominant evolutionary and ecological drivers are critical components of successful wildlife conservation and management strategies. Amplified fragment length polymorphism (AFLP) markers were applied to characterize the phylogeography pattern of a cold water species, the Japanese sand lance Ammodytes personatus, in warm and cold ocean currents. A total of 211 individuals sampled from 12 populations through the species’ range, including samples from Kuroshio Current, Oyashio Current, Tsushima Current, and Yellow Sea, were analyzed. The Bayesian assignment probability test and Neighbor joining (NJ) analysis divided these populations into two genetically and geographically distinct clades (northern and southern clades) characterized by different sea surface temperatures. The incongruence between nuclear clades and previous mitochondrial lineages suggested that A. personatus is indeed composed of at least two genetically divergent cryptic species. Pleistocene glaciation isolation after secondary contact, local thermal adaptation, and isolation by distance may explain the observed geographic pattern of two cryptic species and genetic structure within clades.

Species of Haemoproteus (Haemosporida: Haemoproteidae), avian haemosporidians, have traditionally been described based on morphology of their gametocytes and on limited experimental information on their vertebrate host specificity. We investigated to what extent the morphological species are represented by monophyletic groups based on DNA sequence data using 2 different fragment lengths of the cytochrome b (cyt. b) gene. Phylogenetic reconstructions of obtained cyt. b lineages from 6 morphospecies of Haemoproteus showed that all lineages formed monophyletic clusters matching the morphospecies. Comparing our data with a recently published study showed that this is not always the case; the morphospecies H. belopolskyi consists of 2 distinct clusters of lineages that apparently have converged in morphology. However, the overall broad congruence between the molecular and morphological clustering of lineages will facilitate the integration of the knowledge obtained by traditional and molecular parasitology. Mean between morphospecies variation was 10-fold higher than the within species variation (5.5% vs. 0.54%), suggesting that Haemoproteus lineages with a genetic differentiation >5% are expected to be morphologically differentiated in most cases. When investigate the utility of 2 different fragment sizes of the cyt. b gene, the partial, 479-bp, cyt. b protocol picked up all mitochondrial (mt)DNA lineages that are found when using the full cyt. b gene, 1073 bp, suggesting that this protocol is sufficient for identification of most mtDNA lineages. All of the mtDNA lineages were associated with unique alleles when amplification was possible at a nuclear locus, strengthening the hypothesis that the designation of lineages based on mtDNA is largely genome-wide representative. We, therefore, propose the use of a cyt. b fragment of this length as a standard gene fragment for a DNA bar-coding system for avian Haemoproteus species.

Restriction fragment length polymorphism analysis of mitochondrial DNA (mtDNA) was used to examine the genetic structure among field voles (Microtus agrestis) from southern and central Sweden. A total of 57 haplotypes was identified in 158 voles from 60 localities. Overall mtDNA diversity was high, but both haplotype and nucleotide diversity exhibited pronounced geographic heterogeneity. Phylogenetic analyses revealed a shallow tree with seven primary mtDNA lineages separated by sequence divergences ranging from 0.6% to 1.0%. The geographic structure of mtDNA diversity and lineage distribution was complex but strongly structured and deviated significantly from an equilibrium situation. The extensive mtDNA diversity observed and the recent biogeographic history of the region suggests that the shallow mtDNA structure in the field vole cannot be explained solely by stochastic lineage sorting in situ or isolation by distance. Instead, the data suggest that the genetic imprints of historical demographic conditions and vicariant geographic events have been preserved and to a large extent determine the contemporary geographic distribution of mtDNA variation. A plausible historical scenario involves differentiation of mtDNA lineages in local populations in glacial refugia, a moving postglacial population structure, and bottlenecks and expansions of mtDNA lineages during the postglacial recolonization of Sweden. By combining the mtDNA data with an analysis of Y-chromosome variation, a specific population unit was identified in southwestern Sweden. This population, defined by a unique mtDNA lineage and fixation of a Y-chromosome variant, probably originated in a population bottleneck in southern Sweden about 12,000 to 13,000 calendar years ago.

Geological forces and long‐term climate changes can have profound effects on species. Such effects may be manifested in the pattern and magnitude of genealogical diversity, as revealed by mitochondrial DNA (mtDNA) lineages. The relative importance of the different forces on a regional biota must be evaluated along with a good understanding of geological and climatological history. The peninsula of Baja California of north‐western Mexico is one area where both geology and climate have affected the historical biogeography of the regional biota. Molecular studies based on the genealogical relationships among mtDNA lineages have contributed greatly towards elucidating the historical biogeography of Baja California. Perhaps most noticeably, numerous concordant breaks in mtDNA genealogies half‐way along the peninsula suggest a vicariant history in which the mid‐peninsula was temporarily submerged. This vicariant explanation has recently been criticized, as no conclusive geological evidence exists for a continuous submergence of the mid‐peninsula. As an alternative, a scenario based on climatological factors has been suggested. Here we discuss the validity of the hypothesized mid‐peninsular vicariance event and the climate‐based alternative in explaining the concordant genealogical breaks. We argue that, despite the significant changes in climate brought about by the glacial cycles throughout the Quaternary, a vicariant history involving a mid‐peninsular seaway remains the most parsimonious explanation of the observed patterns in mtDNA genealogies.

The immigration of diverse ethnic groups over the past centuries from surrounding countries into Thailand left footprints in the genetic composition of Thai mitochondrial DNA (mtDNA) lineages. The entire mtDNA control region (1,122 bp) was typed in 190 unrelated male volunteers from the northern Thailand province of Chiang Mai following highest quality standards. For a more precise haplogroup classification, selected single nucleotide polymorphisms from the mtDNA coding region were genotyped. We found several new, so far undescribed mtDNA lineages. Quasi-median networks were constructed for visualisation of character conflicts. The data were put into population-genetic relationships with other Southeast Asian populations. Although the frequencies of the Thai haplogroups were characteristic for Southeast Asia in terms of haplotype composition and genetic structure, the Thai population was significantly different from other Southeast Asian populations. This necessitates establishing regional databases, especially for forensic applications. The population data have been submitted to the EMPOP database (www.empop.org) and will be available on publication.

The late Pleistocene and early Holocene population history of Southeast Asia is not well-known. Our study provides new data on mitochondrial DNA (mtDNA) lineages of the aboriginal inhabitants of the Malay Peninsula, and through an extensive comparison to the known mtDNA diversity in Southeast and East Asia, provides some new insights into the origins and historical geography of certain mtDNA lineages in the region. We extracted DNA from hair samples (dating back 100 years) preserved in the Duckworth Collection and belonging to two Peninsular Malaysian individuals identified as "Negrito." Ancient DNA was analyzed by sequencing hypervariable region I (HVS-I) of the mtDNA control region and the mtDNA region V length polymorphism. The results show that the maternal lineages of these individuals belong to a recently defined haplogroup B sub-branch called B4c2. A comparison of mitochondrial haplotypes and haplogroups with those of 10,349 East Asian individuals indicates their very restricted geographical distribution (southwestern China, Southeast Asia Peninsula, and Indonesia). Recalculation of the B4c2 age across all of East Asia ( approximately 13,000 years) and in different subregions/populations suggests its rapid diffusion in Southeast Asia between the end of the Last Glacial Maximum and the Neolithic expansion of the Holocene.

The topology of the network of western Eurasian mitochondrial DNA (mtDNA) lineage clusters in the context of their expansion and spread in this geographic area is analysed. Special attention is devoted to the inner nods of the reconstructed median network tree, ancestral to mtDNA lineage clusters H and V, to the Caucasus and Trans-Caucasus area populations and to the problem of timing of the expansion of the Caucasoid-specific mtDNA lineage clusters in western Europeversusin the Trans-Caucasus. It appears on several examples that typical for Western Europe mtDNA lineage clusters exhibit significantly earlier expansion in the Trans-Caucasus area. Furthermore, the lineage cluster, radiating from the pre-HV node, is significantly more frequent and divergent in the Trans-Caucasus populations than it is in Europe. Meanwhile, a comparison of the Central Asian and the Trans-Caucasus area populations shows that the former have a significant share of eastern Asian-specific mtDNA lineages, which are almost absent in the latter. Finally, a picture starts to emerge, revealing an ancient Indian—Trans-Caucasian—European continuum of a significant proportion of human maternal lineage clusters, dating back to the period between the Upper and Lower Pleniglacials.KeywordsBefore PresentRFLP TypingLineage ClusterEuropean HaplogroupDemic DiffusionThese keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

The analysis of contact zones between lineages that were previously isolated in allopatry can lead to important insights on evolutionary processes such as selection and adaptation. In this paper we conducted a comparative demographic study of two mitochondrial DNA (mtDNA) lineages of the lizard Lacerta vivipara in the western Pyrénées to provide detail on the dynamics of their contact zone. By surveying haplogroup frequency across the contact area, we revealed the existence of a stable and very narrow contact zone between two parapatric lineages, which we infer to demonstrate a role for selection in the maintenance of this contact zone. We suggest these two lineages evolved in allopatry after retreating to different refugia during the Pleistocene glaciations, and subsequently came into secondary contact after the last glacial maximum. Although haplogroup frequencies were stable over time, we found significant age and environment (temperature) dependent survival differences between mtDNA haplogroups in one contact population sampled yearly from 2002 to 2009. Therefore, temperature‐induced demographic differences between the two mtDNA lineages may be responsible for the stability of this narrow contact zone. This is one of the first demographic studies conducted under natural conditions indicating the possibility of selection on mtDNA.