Phylogeographic Variation Research Articles

Homogeneous Nuclear Background for Mitochondrial Cline in Northern Range ofNotochthamalus scabrosus

A mitochondrial cline along the Chilean coast in the barnacle Notochthamalus scabrosus suggests a species history of transient allopatry and secondary contact. However, previous studies of nuclear sequence divergence suggested population genetic homogeneity across northern and central Chile. Here, we collect single-nucleotide polymorphism data from pooled population samples sequenced with restriction site−associated DNA sequencing procedures, confirm these data with the use of a GoldenGate array, and identify a discordance between population genetic patterns in the nuclear and mitochondrial genomes. This discordance was noted in previous work on this species, but here it is confirmed that the nuclear genome exhibits only slight phylogeographic variation across 3000 km of coastline, in the presence of a strong and statistically significant mitochondrial cline. There are nevertheless markers (approximately 5% of nuclear single-nucleotide polymorphisms) exhibiting cytonuclear disequilibrium relative to mitotype. Although these data confirm our previous explorations of this species, it is likely that some of the nuclear genomic diversity of this species has yet to be explored, as comparison with other barnacle phylogeography studies suggest that a divergence of similar magnitude should be found in the nuclear genome somewhere else in the species range.

Significant population genetic structuring but a lack of phylogeographic structuring in the endemic Tasmanian tree frog (Litoria burrowsae)

Conservation of frogs is of global concern, owing to declines resulting from habitat destruction, global climate change, and disease. Knowledge of genetic variation in frog species is therefore desirable for the identification of management units. Here we surveyed mitochondrial DNA sequence variation in the Tasmanian endemic hylid frog Litoria burrowsae, which is infected by chytrid fungus, Batrachochytrium dendrobatidis, and may be declining. Neither phylogeographic structure nor deep phylogenetic divergence was detected in the species, although its populations were highly differentiated with respect to haplotype frequencies. The low-haplotype diversity in L. burrowsae suggests a recent bottleneck in the species, and population genetic structuring may reflect isolation by distance as well as founder effects associated with range expansion. Three putative management units were identified that require verification based on nuclear DNA variation and adaptation to local environments.

Climate-Driven Reshuffling of Species and Genes: Potential Conservation Roles for Species Translocations and Recombinant Hybrid Genotypes.

Comprising 50%–75% of the world’s fauna, insects are a prominent part of biodiversity in communities and ecosystems globally. Biodiversity across all levels of biological classifications is fundamentally based on genetic diversity. However, the integration of genomics and phylogenetics into conservation management may not be as rapid as climate change. The genetics of hybrid introgression as a source of novel variation for ecological divergence and evolutionary speciation (and resilience) may generate adaptive potential and diversity fast enough to respond to locally-altered environmental conditions. Major plant and herbivore hybrid zones with associated communities deserve conservation consideration. This review addresses functional genetics across multi-trophic-level interactions including “invasive species” in various ecosystems as they may become disrupted in different ways by rapid climate change. “Invasive genes” (into new species and populations) need to be recognized for their positive creative potential and addressed in conservation programs. “Genetic rescue” via hybrid translocations may provide needed adaptive flexibility for rapid adaptation to environmental change. While concerns persist for some conservationists, this review emphasizes the positive aspects of hybrids and hybridization. Specific implications of natural genetic introgression are addressed with a few examples from butterflies, including transgressive phenotypes and climate-driven homoploid recombinant hybrid speciation. Some specific examples illustrate these points using the swallowtail butterflies (Papilionidae) with their long-term historical data base (phylogeographical diversity changes) and recent (3-decade) climate-driven temporal and genetic divergence in recombinant homoploid hybrids and relatively recent hybrid speciation of Papilio appalachiensis in North America. Climate-induced “reshuffling” (recombinations) of species composition, genotypes, and genomes may become increasingly ecologically and evolutionarily predictable, but future conservation management programs are more likely to remain constrained by human behavior than by lack of academic knowledge.

Phylogeographic Diversity of Pathogenic and Non-Pathogenic Hantaviruses in Slovenia

Slovenia is a very diverse country from a natural geography point of view, with many different habitats within a relatively small area, in addition to major geological and climatic differences. It is therefore not surprising that several small mammal species have been confirmed to harbour hantaviruses: A. flavicollis (Dobrava virus), A. agrarius (Dobrava virus–Kurkino), M. glareolus (Puumala virus), S. areanus (Seewis virus), M. agrestis, M. arvalis and M. subterraneus (Tula virus). Three of the viruses, namely the Dobrava, Dobrava–Kurkino and Puumala viruses, cause disease in humans, with significant differences in the severity of symptoms. Due to changes in haemorrhagic fever with renal syndrome cases (HFRS) epidemiology, a detailed study on phylogenetic diversity and molecular epidemiology of pathogenic and non-pathogenic hantaviruses circulating in ecologically diverse endemic regions was performed. The study presents one of the largest collections of hantavirus L, M and S sequences obtained from hosts and patients within a single country. Several genetic lineages were determined for each hantavirus species, with higher diversity among non-pathogenic compared to pathogenic viruses. For pathogenic hantaviruses, a significant geographic clustering of human- and rodent-derived sequences was confirmed. Several geographic and ecological factors were recognized as influencing and limiting the formation of endemic areas.

Cryptic genetic diversity and complex phylogeography of the boreal North American scorpion, Paruroctonus boreus (Vaejovidae)

Diverse studies in western North America have revealed the role of topography for dynamically shaping genetic diversity within species though vicariance, dispersal and range expansion. We examined patterns of phylogeographical diversity in the widespread but poorly studied North American vaejovid scorpion, Paruroctonus boreus Girard 1854. We used mitochondrial sequence data and parsimony, likelihood, and Bayesian inference to reconstruct phylogenetic relationships across the distributional range of P. boreus, focusing on intermontane western North America. Additionally, we developed a species distribution model to predict its present and historical distributions during the Last Glacial Maximum and the Last Interglacial Maximum. Our results documented complex phylogeographic relationships within P. boreus, with multiple, well-supported crown clades that are either geographically-circumscribed or widespread and separated by short, poorly supported internodes. We also observed subtle variation in predicted habitat suitability, especially at the northern, eastern and southern edges of the predicted distributional range under past climatic conditions. The complex phylogenetic relationships of P. boreus suggests that historical isolation and expansion of populations may have occurred. Variation in the predicted distributional range over time may implicate past climatic fluctuations in generating the patterns of genetic diversity observed in P. boreus. These findings highlight both the potential for cryptic biodiversity in widespread North American scorpion species and the importance of phylogeographical studies for understanding the factors responsible for generating the biodiversity of western North America.

Cleaning up the biogeography of Labroides dimidiatus using phylogenetics and morphometrics

Cleaner fishes are some of the most conspicuous organisms on coral reefs due to their behaviour and prominent body pattern, consisting of a lateral stripe and blue/yellow colouration. All obligate cleaner fishes share this body stripe pattern, which is an important signal for attracting client fishes. However, variability in the cleaning signal of the cleaner fish Labroides dimidiatus has been documented across its range. Here, we investigate the geographic distribution of cleaner signal polymorphisms in L. dimidiatus and contrast this to phylogeographic variation in mitochondrial (mt) DNA. We used samples from 12 sites for genetic analyses, encompassing much of L. dimidiatus’ range from the Red Sea to Fiji. We obtained morphometric measures of the cleaner signal body stripe width from individuals among six of the sites and qualitatively grouped tail stripe shape. mtDNA control region sequences were used for phylogenetic and population genetic analyses. We found that body stripe width was significantly correlated with tail stripe shape and geographical location, with Indian Ocean populations differing in morphology from western Pacific populations. L. dimidiatus haplotypes formed two reciprocally monophyletic clades, although in contrast to morphology, Japanese cleaner fish fell within the same clade as Indian Ocean cleaner fish and both clade types were sympatric in Papua New Guinea. An additional novel finding of our research was that the inclusion of two closely related cleaner fish species, Labroides pectoralis and Labroides bicolor, in the phylogenetic analysis rendered L. dimidiatus polyphyletic. Overall, the findings suggest the diversity within L. dimidiatus is underestimated.

Molecular characterization and phylogeny of whipworm nematodes inferred from DNA sequences of cox1 mtDNA and 18S rDNA

A molecular phylogenetic hypothesis is presented for the genus Trichuris based on sequence data from the mitochondrial cytochrome c oxidase 1 (cox1) and ribosomal 18S genes. The taxa consisted of different described species and several host-associated isolates (undescribed taxa) of Trichuris collected from hosts from Spain. Sequence data from mitochondrial cox1 (partial gene) and nuclear 18S near-complete gene were analyzed by maximum likelihood and Bayesian inference methods, as separate and combined datasets, to evaluate phylogenetic relationships among taxa. Phylogenetic results based on 18S ribosomal DNA (rDNA) were robust for relationships among species; cox1 sequences delimited species and revealed phylogeographic variation, but most relationships among Trichuris species were poorly resolved by mitochondrial sequences. The phylogenetic hypotheses for both genes strongly supported monophyly of Trichuris, and distinct genetic lineages corresponding to described species or nematodes associated with certain hosts were recognized based on cox1 sequences. Phylogenetic reconstructions based on concatenated sequences of the two loci, cox1 (mitochondrial DNA (mtDNA)) and 18S rDNA, were congruent with the overall topology inferred from 18S and previously published results based on internal transcribed spacer sequences. Our results demonstrate that the 18S rDNA and cox1 mtDNA genes provide resolution at different levels, but together resolve relationships among geographic populations and species in the genus Trichuris.

The phylogeographical and population genetic approach to the investigation of the genetic diversity patterns in self-incompatible clonal and polyploidLinnaea borealissubsp.borealis

Surveys of genetic diversity patterns of self-incompatible clonal polyploid plant species are still scarcer than those of diploid plant species. Therefore, I studied the phylogeographical history of Linnaea borealis subsp. borealis to shed light on the colonization history of this clonal self-incompatible polyploid plant in Eurasia using selected regions of plastid DNA and genetic diversity patterns of 22 populations of this species employing AFLP markers. I also addressed the question of whether the genetic diversity patterns in L. borealis subsp. borealis in Eurasia are similar to those of earlier published studies of clonal self-incompatible diploid or polyploid plants. This survey revealed that the shallow phylogeographical history (six plastid haplotypes forming one haplogroup, 100% bootstrap support) and moderate genome-wide diversity estimated using AFLP markers (Fragpoly = 10.8–38.9%, I = 0.060–0.180, FST = 0.289) were general characteristics of L. borealis subsp. borealis in its Eurasian range. The sampling strategy, in most cases at 1–2-m or even 3–5-m intervals, showed that a balance between vegetative and sexual reproduction and limited pollen dispersal among compatible mates can be important for genetic diversity patterns in populations of this taxon. Despite the fact that one-half of the investigated populations were strongly isolated, they still preserved similar levels of genetic diversity across the geographical range. I found no support for the hypothesis that a bottleneck and/or inbreeding had accompanied habitat fragmentation as factors shaping genetic diversity. © 2013 The Linnean Society of London, Botanical Journal of the Linnean Society, 2013, 173, 64–76.

Evolutionary Drivers of Diversification and Distribution of a Southern Temperate Stream Fish Assemblage: Testing the Role of Historical Isolation and Spatial Range Expansion

This study used phylogenetic analyses of mitochondrial cytochrome b sequences to investigate genetic diversity within three broadly co-distributed freshwater fish genera (Galaxias, Pseudobarbus and Sandelia) to shed some light on the processes that promoted lineage diversification and shaped geographical distribution patterns. A total of 205 sequences of Galaxias, 177 sequences of Pseudobarbus and 98 sequences of Sandelia from 146 localities across nine river systems in the south-western Cape Floristic Region (South Africa) were used. The data were analysed using phylogenetic and haplotype network methods and divergence times for the clades retrieved were estimated using *BEAST. Nine extremely divergent (3.5–25.3%) lineages were found within Galaxias. Similarly, deep phylogeographic divergence was evident within Pseudobarbus, with four markedly distinct (3.8–10.0%) phylogroups identified. Sandelia had two deeply divergent (5.5–5.9%) lineages, but seven minor lineages with strong geographical congruence were also identified. The Miocene-Pliocene major sea-level transgression and the resultant isolation of populations in upland refugia appear to have driven widespread allopatric divergence within the three genera. Subsequent coalescence of rivers during the Pleistocene major sea-level regression as well as intermittent drainage connections during wet periods are proposed to have facilitated range expansion of lineages that currently occur across isolated river systems. The high degree of genetic differentiation recovered from the present and previous studies suggest that freshwater fish diversity within the south-western CFR may be vastly underestimated, and taxonomic revisions are required.

Latitude drives diversification in Madagascar's endemic dry forest rodentEliurus myoxinus(subfamily Nesomyinae)

Numerous hypotheses have been proposed for the historical processes governing the rich endemism of Madagas- car's biodiversity. The 'watershed model' suggests that drier climates in the recent geological past have resulted in the contraction of forests around major watersheds, thereby defining areas of endemism. We test whether this hypothesis explains phylogeographical patterns in a dry forest-dependent rodent, Eliurus myoxinus, an endemic species widely distributed through western Madagascar. We sequenced the mitochondrial cytochrome b locus and nuclear introns of the β-fibrinogen and the growth hormone receptor genes for E. myoxinus. Using a parametric bootstrapping approach, we tested whether the mitochondrial gene tree data fit expectations of local differentiation given the watershed model. We additionally estimated population differentiation and historical demographic parameters, and reconstructed the spatial history of E. myoxinus to highlight spatial and temporal patterns of differentiation. The data do not support the watershed model as a clear explanation for the genetic patterns of diversity within extant E. myoxinus populations. We find striking patterns of latitudinal genetic structure within western Madagascar, and indicate possible roles for environmental and ecological gradients along this axis in generating phylogeographical diversity. © 2013 The Linnean Society of London, Biological Journal of the Linnean Society, 2013, 110, 500-517.

Development of microsatellite loci for Cyclocarya paliurus (Juglandaceae), a monotypic species in subtropical China.

• Premise of the study: Microsatellite loci were developed for a monotypic species endemic to subtropical China, Cyclocarya paliurus, to help infer the evolutionary histories of ancient monotypic genera in subtropical China.• Methods and Results: Using the Fast Isolation by AFLP of Sequences COntaining repeats (FIASCO) protocol, 28 primer sets were identified in two wild populations. All loci were polymorphic, with the number of alleles per locus ranging from two to eight. The expected and observed heterozygosities ranged from 0.153 to 0.802 and from 0 to 0.750, respectively. The transferability of the 28 primer pairs was tested on Juglans regia, Pterocarya stenoptera, and Platycarya strobilacea. Twenty-one (75.0%), 22 (78.6%), and 15 (53.6%) markers were successfully amplified in J. regia, P. stenoptera, and P. strobilacea, respectively.• Conclusions: These loci will be useful for in-depth analysis of genetic diversity and phylogeographical variation throughout the distribution range of C. paliurus.

Cryptic species and phylogeographical structure in the tree Cedrela odorata L. throughout the Neotropics

AbstractAimThe origins of much Neotropical biodiversity remain a topic of debate, with both palaeogeographical and more recent climatic drivers playing a role in diversification both among and within species. Here we use a combination of molecular data to assess genetic variation within and among species in the Neotropical tree genus Cedrela, with a focus on Cedrela odorata, to test hypotheses on the drivers of diversification, to place known ecotypic variation in context and to detect intraspecific phylogeographical structure.LocationCentral and South America, Cuba, Cayman Islands, Trinidad and Guadeloupe.MethodsSamples were collected from the field, existing collections and herbaria from across the geographical range, including a total of 528 individuals from 72 sites. A phylogenetic framework was constructed using internal transcribed spacer (ITS) sequence data (intergenic spacers plus flanking 18S and 26S regions), and genetic structure was analysed using a combination of chloroplast DNA sequences (trnC–ycf6, trnH–psbA) and chloroplast and nuclear microsatellite (single sequence repeat, SSR) loci. Phylogenetic reconstruction was undertaken using a combination of Bayesian and parsimony‐based approaches; divergence times were estimated for major nodes. Geographical structure in chloroplast SSR data was analysed using SAMOVA, while that in nuclear SSR data was assessed using a combination of Bayesian clustering and principal coordinates analysis.ResultsITS sequence data supported phylogenetic distinctiveness of four morphologically cryptic species within C. odorata. Chloroplast sequence and microsatellite data showed geographical structuring both among and within species, suggesting the influence of climatic and geographical drivers. Intraspecific genetic divergence was also present in nuclear microsatellite data, suggesting contemporary gene flow limitation across sea and mountain barriers.Main conclusionsThe data support diversification of the genus Cedrela in South America with subsequent recolonization into Central America prior to the formation of the Isthmus of Panama. At least four morphologically cryptic taxa were evident within C. odorata and within‐species phylogeographical divergence across the Andes and within Central America was present, the latter suggestive of Pleistocene climatic influence. Previously recognized ecotypes in Central America should be elevated to species level. The new molecular data support the recent reclassification and will support the monitoring of exploitation in the genus.

Chromosome painting in silico in a bacterial species reveals fine population structure.

Identifying population structure forms an important basis for genetic and evolutionary studies. Most current methods to identify population structure have limitations in analyzing haplotypes and recombination across the genome. Recently, a method of chromosome painting in silico has been developed to overcome these shortcomings and has been applied to multiple human genome sequences. This method detects the genome-wide transfer of DNA sequence chunks through homologous recombination. Here, we apply it to the frequently recombining bacterial species Helicobacter pylori that has infected Homo sapiens since their birth in Africa and shows wide phylogeographic divergence. Multiple complete genome sequences were analyzed including sequences from Okinawa, Japan, that we recently sequenced. The newer method revealed a finer population structure than revealed by a previous method that examines only MLST housekeeping genes or a phylogenetic network analysis of the core genome. Novel subgroups were found in Europe, Amerind, and East Asia groups. Examination of genetic flux showed some singleton strains to be hybrids of subgroups and revealed evident signs of population admixture in Africa, Europe, and parts of Asia. We expect this approach to further our understanding of intraspecific bacterial evolution by revealing population structure at a finer scale.

Genetic variability of the tokay gecko based on mitochondrial and nuclear DNA

With largely allopatric distribution, the black tokay and the red tokay are two distinct morphs of the subspecies Gekko gecko gecko. In consideration of their different morphological characteristics, the taxonomic status of G. g. gecko is disputed. Through detailed morphological comparison, it has been proposed that the black tokay should be elevated to species ranking, but without strong genetic evidence. In order to further investigate the taxonomic status of the tokay gecko (G. gecko), we used one mitochondrial marker (ND2) and three nuclear markers (RAG1, c-mos, and ITS2) to explore the phylogenetic and taxonomic relationship of the tokay gecko. Our results revealed a deep phylogeographical divergence in tokay gecko and at the same time provided us with the evidence of possible introgressive hybridization or/and incomplete lineage sorting between the black tokay and the red tokay. The elevation of the black tokay to species level is also supported by our results. However, due to limited sampling and genetic data, this elevation should be further corroborated by more genetic evidence.

Phylogeographic Diversity of the Winter Moths Operophtera brumata and O. bruceata (Lepidoptera: Geometridae) in Europe and North America

Abstract The European winter moth, Operophtera brumata (L.), an invasive forest defoliator, is undergoing a rapid range expansion in northeastern North America. The source of this invasion, and phylogeographic diversity throughout its native range, has not been explored. To do this, we used samples from a pheromone-baited trap survey of O. brumata collected across its native range in Europe, and invasive range in North America. Traps in North America also attract a congeneric species, the Bruce spanworm O. bruceata (Hulst), and the western Bruce spanworm O. b. occidentalis (Hulst). From this sampling, we sequenced two regions of the cytochrome c oxidase subunit I mitochondrial gene; one region corresponds to the DNA ‘barcode’ region, the other is a nonoverlapping section. We used these sequences, in combination with sequence data from a recent survey of the Geometridae in western North America, for phylogenetic and phylogeographic analyses to characterize genetic divergence and variation for O. brumata in North America and Europe, and O. bruceata and O. b. occidentalis in North America. We found O. brumata mtDNA diversity to be dominated by a single widespread, and common haplotype. In contrast, O. bruceata shows high haplotype diversity that is evenly distributed throughout North America. Phylogeographic patterns indicate an introduction of O. brumata in British Columbia likely originated from Germany, and suggest the invasive population in northeastern North America may have its origins in the United Kingdom, and/or Germany. We found uncorrected pairwise sequence divergence between Operophtera species to be ≈7%. O. b. occidentalis is ≈ 5% divergent from O. bruceata, has a restricted range in the Pacific Northwest, and has unique morphological characters. Together these lines of evidence suggest O. b. occidentalis may be deserving of species status. Additionally, a single morphologically unique Operophtera specimen, similar to O. bruceata, was collected in southern Arizona, far outside the known range of O. bruceata. This suggests that North America may contain further, unsampled, Operophtera diversity.

THE INFLUENCE OF POLLINATOR PHYLOGEOGRAPHY AND MATE PREFERENCE ON FLORAL DIVERGENCE IN A SEXUALLY DECEPTIVE DAISY

Divergent mate preferences and subsequent genetic differentiation between populations has been demonstrated, but its effects on interspecific interactions are unknown. Associated species exploiting these mate preferences, for example, may diverge to match local preferences. We explore this idea in the sexually deceptive, fly-mimicking daisy, Gorteria diffusa, by testing for association between genetic structure in the fly pollinator (a proxy for mate preference divergence) and geographic divergence in floral form. If genetic structure in flies influences interactions with G. diffusa, we expect phylogeographically distinct flies to be associated with different floral forms. Flies associated with forms exploiting only feeding behavior often belonged to several phylogeographic clades, whereas flies associated with forms exploiting male-mating behavior always belonged to distinct clades, indicating the possibility of pollinator-mediated floral divergence through phylogeographic variation in mating preferences of male flies. We tested this hypothesis with reciprocal presentations using male flies from distinct clades associated with separate floral forms. Results show that males from all clades exhibit similar preferences, making pollinator driven divergence through geographic variation in mate preference unlikely. Males, however, showed evidence of learned resistance to deceptive traits, suggesting antagonistic interactions between plants and pollinators may drive deceptive floral trait evolution in G. diffusa.

The role of continental shelf width in determining freshwater phylogeographic patterns in south‐eastern Australian pygmy perches (Teleostei: Percichthyidae)

Biogeographic patterns displayed by obligate freshwater organisms are intimately related to the nature and extent of connectivity between suitable habitats. Two of the more significant barriers to freshwater connections are seawater and major drainage divides. South-eastern Australia provides a contrast between these barriers as it has discrete areas that are likely influenced to a greater or lesser extent by each barrier type. We use continental shelf width as a proxy for the potential degree of river coalescence during low sea levels. Our specific hypothesis is that the degree of phylogeographic divergence between coastal river basins should correspond to the continental shelf width of each region. This predicts that genetic divergences between river basins should be lowest in regions with a wider continental shelf and that regions with similar continental shelf width should have similar genetic divergences. Pygmy perches (Nannoperca australis and Nannoperca 'flindersi') in south-eastern Australia provide an ideal opportunity to test these biogeographic hypotheses. Phylogeographic patterns were examined based on range-wide sampling of 82 populations for cytochrome b and 23 polymorphic allozyme loci. Our results recovered only limited support for our continental shelf width hypothesis, although patterns within Bass clade were largely congruent with reconstructed low sea-level drainage patterns. In addition, we identified several instances of drainage divide crossings, typically associated with low elevational differences. Our results demonstrate high levels of genetic heterogeneity with important conservation implications, especially for declining populations in the Murray-Darling Basin and a highly restricted disjunct population in Ansons River, Tasmania.

Phylogeographical patterns shed light on evolutionary process in South America

The South American continent is composed of several biogeographical regions harbouring the highest biodiversity on the globe, encompassing five of the world's biodiversity 'hot spots'. Nonetheless, the patterns and processes responsible for shaping its astonishing species diversity are largely unknown. Here, we present a review of current South American phylogeographical knowledge based on published articles on this topic. An appraisal of the literature reveals emerging phylogeographical patterns in the biota of South America. The striking phylogeographical divergence observed among organism lineages in South American studies is suggestive of high levels of undocumented species diversity. The interplay between Pleistocene climatic oscillations and Pliocene/Miocene orogenic events has contributed to shaping the current diversity and distribution of modern lineages in both the tropical and temperate regions of South America. Although older divergence times were observed for a range of species, most herpetofauna underwent an intraspecific lineage split much earlier than other organisms. The geographical ranges of species associated with forest habitats were reduced mainly during glacial cycles, whereas species associated with open vegetation domains have shown variable responses to climatic oscillations. The results suggest a highly complex mosaic of phylogeographical patterns in South America. We suggest future research directions to promote a better understanding of the origin and maintenance of the South American biota.

The Phylogeography of Y-Chromosome Haplogroup H1a1a-M82 Reveals the Likely Indian Origin of the European Romani Populations

Linguistic and genetic studies on Roma populations inhabited in Europe have unequivocally traced these populations to the Indian subcontinent. However, the exact parental population group and time of the out-of-India dispersal have remained disputed. In the absence of archaeological records and with only scanty historical documentation of the Roma, comparative linguistic studies were the first to identify their Indian origin. Recently, molecular studies on the basis of disease-causing mutations and haploid DNA markers (i.e. mtDNA and Y-chromosome) supported the linguistic view. The presence of Indian-specific Y-chromosome haplogroup H1a1a-M82 and mtDNA haplogroups M5a1, M18 and M35b among Roma has corroborated that their South Asian origins and later admixture with Near Eastern and European populations. However, previous studies have left unanswered questions about the exact parental population groups in South Asia. Here we present a detailed phylogeographical study of Y-chromosomal haplogroup H1a1a-M82 in a data set of more than 10,000 global samples to discern a more precise ancestral source of European Romani populations. The phylogeographical patterns and diversity estimates indicate an early origin of this haplogroup in the Indian subcontinent and its further expansion to other regions. Tellingly, the short tandem repeat (STR) based network of H1a1a-M82 lineages displayed the closest connection of Romani haplotypes with the traditional scheduled caste and scheduled tribe population groups of northwestern India.

A geographic mosaic of evolutionary lineages within the insular endemic newt Euproctus montanus

Islands are hotspots of biodiversity, with a disproportionately high fraction of endemic lineages, often of ancient origin. Nevertheless, intra-island phylogeographies are surprisingly scarce, leading to a scanty knowledge about the microevolutionary processes induced on island populations by Plio-Pleistocene climatic oscillations, and the manner in which these processes contributed to shape their current genetic diversity. We investigated the phylogeography, historical demography and species distribution models of the Corsican endemic newt Euproctus montanus (north-western Mediterranean). As for many island endemics, the continuous distribution of E. montanus throughout its range has hitherto been considered as evidence for a single large population, a belief that also guided the species' categorization for conservation purposes. Instead, we found a geographic mosaic of ancient evolutionary lineages, with five main clades of likely Pliocene origin (2.6-5.8 My), all but one restricted to northern Corsica. Moreover, the copresence between main lineages in the same population was limited to a single case. As also suggested by growing literature on intra-island phylogeographic variation, it seems that the extensive use of simplifying assumption on the population structure and historical demography of island populations--both in theoretical and applicative studies--should be carefully reconsidered, a claim that is well exemplified by the case presented here.