Complex Phylogeographic Patterns Research Articles

Cryptic diversity and phylogeographic patterns ofDeto echinata(Isopoda: Detonidae) in southern Africa

Recent phylogeographic studies of poorly-dispersing coastal invertebrates in highly biodiverse regions have led to the discovery of high levels of cryptic diversity and complex phylogeographic patterns that suggest isolation, geological, and ecological processes have shaped their biodiversity. Studies of southern African coastal invertebrates have uncovered cryptic diversity for various taxa and phylogeographic patterns that, although sharing some similarities across taxa, do differ. These findings underscore the need for additional studies to better understand the biodiversity levels, distributional patterns, and processes responsible for producing coastal biodiversity in that region. The coastal isopodDeto echinatais of particular interest, as its complex taxonomic history, poor dispersal capabilities, and broad geographic distribution suggest the potential for cryptic diversity. We use mitochondrial and nuclear sequences to characterizeD. echinataindividuals from localities ranging from northern Namibia to Glentana, about 2,500 km along the coastline on the south coast of South Africa. These are used to assess whetherD. echinataharbors cryptic genetic diversity and whether phylogeographic distributional patterns correlate with those previously documented for other coastal isopods in the region. Analysis of mitochondrial and nuclear sequences revealed two deeply-divergent lineages that exhibit a distributional break in the Cape Peninsula region. These findings suggestD. echinatais a cryptic species complex in need of taxonomic revision and highlight the need for further taxonomic and phylogeographic studies of similarly poorly-dispersing coastal invertebrates in southern Africa.

Cryptic speciation shapes the biogeographic history of a northern distributed moss

Abstract Increasing evidence indicates that wide distributed bryophyte taxa with homogeneous morphology may represent separate evolutionary lineages. The evolutionary histories of these cryptic lineages may be related to historical factors, such as the climatic oscillations in the Quaternary. Thus, the post-glacial demographic signatures paired with cryptic speciation may result in complex phylogeographic patterns. This research has two aims: to determine whether the widespread moss Racomitrium lanuginosum represents cryptic molecular taxa across the Northern Hemisphere and to infer the effects of Quaternary glaciations on spatial genetic diversity. We used the internal transcribed spacer (ITS) marker to resolve the phylogeographic history of the species and single nucleotide polymorphisms (genotyping-by-sequencing) to infer the genetic structure and demographic history. Finally, we assessed the historical changes in the distribution range using species distribution models. Racomitrium lanuginosum comprises distinct molecular lineages sympatrically distributed in the Northern Hemisphere. We also uncovered long-distance dispersal from eastern North America to Scandinavia and potential in situ survival in northern Scandinavia. Due to the genetic signatures, the Alaska Peninsula could be considered a glacial refugium. The species experienced post-glacial expansion northwards in the Northern Hemisphere, mainly from the Alaska Peninsula. Our results exemplify the complex phylogeographic history in cold environments and contribute to recognizing evolutionary patterns in the Northern Hemisphere.

DNA barcodes highlight genetic diversity patterns in rodents from lowland desert and Andean areas in Argentina

Rodents are an important component of South America fauna. Their high diversity has motivated researchers to continually review their taxonomy, genetic diversity, species limits, and phylogenetic relationships. Here, we applied DNA-barcodes for assessing the taxonomic and genetic diversity in the two major lineages of South American rodents: caviomorphs and sigmodontines. We analysed 335 COI barcodes in 34morphologically determined species from 39localities along central Andes and arid lands of Argentina. Neighbour-joining and maximum likelihood reconstruction provided clear separation between species. The Barcode Index number and Bayesian Poisson tree processes were used to confirm concordance between sequence clusters and species designations by taxonomy. We found deep divergence within the Phyllotis xanthopygus species complex, with distances up to 13.0% between geographically separated lineages. Minor divergences (3.30% and 2.52%) were found within Abrothrix hirta, and Tympanoctomys barrerae, respectively, with differentiation in their genetic lineages. Also, we documented geographically separated clusters for Akodon spegazzinii and A.oenos with up to 2.3% divergence, but clustering methods failed to distinguish them as different species. Sequence results show a clear barcode gap with a mean intraspecific divergence (0.56%) versus a minimum nearest-neighbour distance averaging (10.1%). Distances between congeneric species varied from 4.1 to 14%, with the exception of two related forms within Euneomys and the sister species Akodon spegazzinii and A.oenos. This study constitutes a substantial contribution to the global barcode reference library. It provides insights into the complex phylogeographic patterns and speciation scenarios in rodents, while highlighting areas that require in-depth taxonomic and integrative research.

Genetic diversity of Leishmania tropica: Unexpectedly complex distribution pattern

In this study, we characterized a collection of clinical samples obtained from Syrian and Turkish patients with cutaneous leishmaniasis using internal transcribed spacer 1 (ITS1) sequences. All obtained sequences belonged to Leishmania tropica. Combining them with those available from GenBank allowed us performing a broad-scale analysis of genetic diversity for this species. We demonstrated that L. tropica has a complex phylogeographic pattern with some haplotypes being widespread across endemic countries and others restricted to particular regions. We hypothesize that at least some of them may be associated with alternative vectors or animal reservoirs.

Contrasting genetic structuring in the closely related basidiomycetes Trichaptum abietinum and Trichaptum fuscoviolaceum (Hymenochaetales)

Trichaptum abietinum and Trichaptum fuscoviolaceum (Hymenochaetales, Basidiomycota) are closely related saprotrophic fungi, widely distributed on coniferous wood in temperate regions worldwide. Three intersterility groups have previously been detected in T. abietinum, while no prezygotic barriers have been proven within T. fuscoviolaceum. The aim of this study was to reveal the phylogeography and genetic relationship between these two closely related species and to explore whether the previously observed intersterility groups in T. abietinum are reflected in the genetic data. We assembled worldwide fruit body collections of both species (N = 314) and generated DNA sequences from three nuclear (ITS2, LSU, IGS) and one mitochondrial rDNA region (mtLSU). The two species are genetically well separated in all analyses. In correspondence with observations from earlier mating studies, our results revealed that T. fuscoviolaceum is genetically more uniform than T. abietinum. Multiple genetic sub-groups exist in T. abietinum that may correspond to the previously observed intersterility groups. However, there is low consistency across the investigated loci in delimiting the different sub-groups, except for a consistent North American group. As for many other widespread fungi, a complex phylogeographic pattern is found in T. abietinum which may have been formed by geographic, as well as multiple genetic intersterility barriers.

Complex phylogeographic patterns in the intertidal goby Chaenogobius annularis around Kyushu Island as a boundary zone of three different seas

Paleoenvironmental changes in marginal seas on the coast of the northwestern Pacific during the Quaternary have caused genetic differentiation and subsequent secondary contacts between populations of coastal organisms in this region. However, little is known about how geographical isolation and the subsequent connection events associated with these multiple marginal seas have shaped the population structure of coastal organisms in the boundary area. The coastal area of Kyushu Island of the Japanese Archipelago, where the East China Sea (ECS), the Sea of Japan (SJ), and the Pacific Ocean (PO) adjoin within a narrow region, would be a suitable field for elucidating the effect of multiple vicariances. Herein, we conducted phylogeographical analyses of the intertidal goby Chaenogobius annularis, focusing on populations around Kyushu Island, using partial mitochondrial (mt) DNA sequences and analysis of 8 microsatellite (ms) DNA loci. We discovered a new lineage distributed along the coast of the ECS distinct from the already-known SJ and PO lineages, which we termed the ECS lineage. This ECS lineage showed remarkable mito-nuclear discordance: mtDNA analyses indicated that the ECS lineage is a highly diverged lineage branched from the PO lineage, whereas msDNA analyses suggested that the ECS lineage is closely related to the SJ lineage. This discordance could have been due to ancient hybridization. In addition, we detected SJ-PO and ECS-SJ hybrid zones on the western Seto Inland Sea and on the northwestern coast of Kyushu, respectively. Such a complex population structure suggests that the secondary contacts after multiple isolation events among marginal seas around Kyushu have a great impact on coastal biodiversity in the area and emphasize the peculiarities of the region.

Phylogeny of the Eurasian Wren Nannus troglodytes (Aves: Passeriformes: Troglodytidae) reveals deep and complex diversification patternsof Ibero-Maghrebian and Cyrenaican populations.

The Mediterranean Basin represents a Global Biodiversity Hotspot where many organisms show high inter- and intraspecific differentiation. Extant phylogeographic patterns of terrestrial circum-Mediterranean faunas were mainly shaped through Pleistocene range shifts and range fragmentations due to retreat into different glacial refugia. Thus, several extant Mediterranean bird species have diversified by surviving glaciations in different hospitable refugia and subsequently expanded their distribution ranges during the Holocene. Such a scenario was also suggested for the Eurasian Wren (Nannus troglodytes) despite the lack of genetic data for most Mediterranean subspecies. Our phylogenetic multi-locus analysis comprised 18 out of 28 currently accepted subspecies of N. troglodytes, including all but one subspecies which are present in the Mediterranean Basin. The resulting phylogenetic reconstruction dated the onset of the entire Holarctic radiation of three Nannus species to the early Pleistocene. In the Eurasian Wren, two North African subspecies represented separate basal lineages from the Maghreb (N. t. kabylorum) and from the Libyan Cyrenaica (N. t. juniperi), being only distantly related to other Mediterranean populations. Although N. troglodytes appeared to be paraphyletic with respect to the Nearctic Winter Wren (N. hiemalis), respective nodes did not receive strong statistical support. In contrast, paraphyly of the Ibero-Maghrebian taxon N. t. kabylorum was strongly supported. Southern Iberian populations of N. t. kabylorum did not clade with Maghrebian populations of the same subspecies but formed a sister clade to a highly diverse European clade (including nominate N. t. troglodytes and eight further taxa). In accordance with a pattern also found in other birds, Eurasian populations were split into a western clade (Europe, Caucasus) and an eastern clade (Central Asia, Sino-Himalayas, East Asia). This complex phylogeographic pattern revealed cryptic diversification in N. troglodytes, especially in the Iberio-Maghrebian region.

Next-generation phylogeography of the cockle Cerastoderma glaucum: Highly heterogeneous genetic differentiation in a lagoon species.

AimCoastal lagoons form an intriguing example of fragmented marine habitats. Restricted gene flow among isolated populations of lagoon species may promote their genetic divergence and may thus provide a first step toward speciation. In the present study, the population genetic structure of the lagoon cockle Cerastoderma glaucum has been investigated to clarify the complex phylogeographic pattern found in previous studies, to localize major genetic breaks, and to discuss their origin and maintenance.LocationThe Atlantic and Mediterranean coasts, including the Baltic, North Sea, and Black Sea.MethodsA total of 204 C. glaucum individuals from 14 populations were genotyped using restriction site‐associated DNA sequencing (RADseq). The genetic diversity, divergence, and structure were analyzed using genome‐wide single nucleotide polymorphisms (SNPs). Phylogenetic relationships were inferred under a coalescent model using svdquartets.ResultsThe RADseq approach allowed inferring phylogeographic relationships with an unprecedented resolution. Three deeply divergent lineages were identified within C. glaucum that are separated by many genetic barriers: one lineage in the Aegean–Black Sea region, one in the Ionian Sea, and the last one widely distributed from the Western Mediterranean to the Baltic Sea. The nested branching pattern displayed on the species tree largely agrees with the likely scenario of C. glaucum postglacial expansion from the Mediterranean to the Baltic Sea.Main conclusionThe genetic differentiations between geographically separated lagoons proved to be strong, highlighting the evolutionary influence of these naturally fragmented habitats. The postglacial expansion created complex patterns of spatial segregation of genetic diversity with allele frequency gradients in many outlier loci, but also discrepancies between the nuclear and mitochondrial genetic markers that probably arose from genetic surfing of mitochondrial variation.

Deep mitochondrial lineage divergence among populations of the southern stingray (Hypanus americanus (Hildebrand & Schroeder, 1928)) throughout the Southeastern United States and Caribbean

Although over half of all known elasmobranchs are batoids, with many species exploited and several of conservation concern, little is known of their population genetic structure and micro-evolutionary history. Here, we used sequence variation in 648 bp of the mitochondrial control region to study the phylogeography of the southern stingray (Hypanus americanus (Hildebrand & Schroeder, 1928)) (previously Dasyatis americana) throughout the Carolinas, Florida, and the Caribbean. Out of 267 individuals sampled from eight locations, 67 haplotypes were identified and analysis of molecular variance revealed a high level of genetic partitioning (ΦST = 0.49; P < 0.00001) that was delineated into three geographic regions: (i) the USA and Belize, (ii) the Bahamas and the West Indies, and (iii) Grand Cayman Islands. Phylogenetic and statistical parsimony analyses identified three divergent lineages that were largely concordant with the population structure. However, the geographic distribution of haplotypes described a complex phylogeographic pattern with numerous haplotypes from the divergent lineages co-occurring at the same sampling site. The strong genetic partitioning detected for the Grand Cayman population suggests that this small and isolated population might warrant individualized conservation management.

Global phylogeography and genetic diversity of the zoonotic tapeworm Echinococcus granulosus sensu stricto genotype G1

Echinococcus granulosus sensu stricto (s.s.) is the major cause of human cystic echinococcosis worldwide and is listed among the most severe parasitic diseases of humans. To date, numerous studies have investigated the genetic diversity and population structure of E. granulosus s.s. in various geographic regions. However, there has been no global study. Recently, using mitochondrial DNA, it was shown that E. granulosus s.s. G1 and G3 are distinct genotypes, but a larger dataset is required to confirm the distinction of these genotypes. The objectives of this study were to: (i) investigate the distinction of genotypes G1 and G3 using a large global dataset; and (ii) analyse the genetic diversity and phylogeography of genotype G1 on a global scale using near-complete mitogenome sequences. For this study, 222 globally distributed E. granulosus s.s. samples were used, of which 212 belonged to genotype G1 and 10 to G3. Using a total sequence length of 11,682 bp, we inferred phylogenetic networks for three datasets: E. granulosus s.s. (n = 222), G1 (n = 212) and human G1 samples (n = 41). In addition, the Bayesian phylogenetic and phylogeographic analyses were performed. The latter yielded several strongly supported diffusion routes of genotype G1 originating from Turkey, Tunisia and Argentina. We conclude that: (i) using a considerably larger dataset than employed previously, E. granulosus s.s. G1 and G3 are indeed distinct mitochondrial genotypes; (ii) the genetic diversity of E. granulosus s.s. G1 is high globally, with lower values in South America; and (iii) the complex phylogeographic patterns emerging from the phylogenetic and geographic analyses suggest that the current distribution of genotype G1 has been shaped by intensive animal trade.

Resolving complex phylogeographic patterns in the Balkan Peninsula using closely related wall-lizard species as a model system

The Balkan Peninsula constitutes a biodiversity hotspot with high levels of species richness and endemism. The complex geological history of the Balkans in conjunction with the climate evolution are hypothesized as the main drivers generating this biodiversity. We investigated the phylogeography, historical demography, and population structure of closely related wall-lizard species from the Balkan Peninsula and southeastern Europe to better understand diversification processes of species with limited dispersal ability, from Late Miocene to the Holocene. We used several analytical methods integrating genome-wide SNPs (ddRADseq), microsatellites, mitochondrial and nuclear DNA data, as well as species distribution modelling. Phylogenomic analysis resulted in a completely resolved species level phylogeny, population level analyses confirmed the existence of at least two cryptic evolutionary lineages and extensive within species genetic structuring. Divergence time estimations indicated that the Messinian Salinity Crisis played a key role in shaping patterns of species divergence, whereas intraspecific genetic structuring was mainly driven by Pliocene tectonic events and Quaternary climatic oscillations. The present work highlights the effectiveness of utilizing multiple methods and data types coupled with extensive geographic sampling to uncover the evolutionary processes that shaped the species over space and time.

Revisiting the genetic diversity and population structure of the critically endangered leatherback turtles in the South-west Atlantic Ocean: insights for species conservation

The worldwide population of the leatherback turtle (Dermochelys coriacea) encompasses seven subpopulations among the Pacific, Atlantic and Indian Oceans. It has experienced declines across parts of its distribution, with the subpopulation of the South-west Atlantic listed as critically endangered by the IUCN Red List. The main threats to this subpopulation include its interaction with fisheries, coastal development, pollution and climate change. In this study, we sequenced mitochondrial DNA from 52 leatherback turtles in Brazil and combined these with published data from other Atlantic Ocean rookeries. The haplotype diversities of the Atlantic population rookeries ranged from 0.112 to 0.533 and are not directly proportional to current rookery sizes. The Brazilian rookery, despite recording low nest numbers per year, had the second-highest haplotype diversity among all Atlantic rookeries (h = 0.532). A mixed-stock analysis revealed that the South American pelagic aggregate is primarily composed of individuals from West Africa (84%), with contributions from the North Atlantic rookeries (14%). Leatherback turtles appear to have a complex phylogeographic pattern, showing evidence of multiple colonization events and a lack of isolation by distance. Our novel dataset, based on DNA sequences of 695 base pairs, will provide baseline data needed to understand population dynamics in the region, building comprehensive population assessments to support and develop management strategies. Having both the only known regular rookery in the South-west Atlantic, and a mixed-origin foraging area for the species along its coast, Brazil has a key role in the conservation of the leatherback turtle.

Complex phylogeographic patterns indicate Central American origin of two widespread Mesoamerican Quercus (Fagaceae) species

The northern Neotropical region is characterized by a heterogeneous geological and climatic history. Recent studies have shown contrasting patterns regarding the role of geographic elements as barriers that could have determined phylogeographic structure in various species. Recently, the phylogeography and biogeography of Quercus species have been studied intensively, and the patterns observed so far suggest contrasting evolutionary histories for Neotropical species in comparison with their Holarctic relatives. The goal of this study was to describe the phylogeographic structure of two Neotropical oak species (Quercus insignis and Quercus sapotifolia) in the context of the geological and palaeoclimatic history of the northern Neotropics. Populations through the distribution range of both species were collected and characterized using nine chloroplast DNA microsatellite loci. Both oak species showed high levels of genetic diversity and strong phylogeographic structure. The distribution of genetic variation in Q. insignis suggested an influence of two major barriers, the Isthmus of Tehuantepec and the Nicaraguan Depression, while Q. sapotifolia exhibited a genetic structure defined by the heterogeneity of the Chortis highlands. The haplotype networks of both species indicated complex histories, suggesting that colonization from the Sierra Madre de Chiapas to central Mexico and from the north of the Nicaraguan Depression to the Costa Rican mountains may have occurred during different stages, and apparently more than one time. In conclusion, the phylogeographic structure of Neotropical oak species seems to be defined by a combination of geological and climatic events.

Digging up the roots of an insular hotspot of genetic diversity: decoupled mito-nuclear histories in the evolution of the Corsican-Sardinian endemic lizard Podarcis tiliguerta

BackgroundMediterranean islands host a disproportionately high level of biodiversity and endemisms. Growing phylogeographic evidence on island endemics has unveiled unexpectedly complex patterns of intra-island diversification, which originated at diverse spatial and temporal scales. We investigated multilocus genetic variation of the Corsican-Sardinian endemic lizard Podarcis tiliguerta with the aim of shedding more light on the evolutionary processes underlying the origin of Mediterranean island biodiversity.ResultsWe analysed DNA sequences of mitochondrial (12S and nd4) and nuclear (acm4 and mc1r) gene fragments in 174 individuals of P. tiliguerta from 81 localities across the full range of the species in a geographic and genealogical framework. We found surprisingly high genetic diversity both at mitochondrial and nuclear loci. Seventeen reciprocally monophyletic allopatric mitochondrial haplogroups were sharply divided into four main mitochondrial lineages (two in Corsica and two in Sardinia) of Miocene origin. In contrast, shallow divergence and shared diversity within and between islands was observed at the nuclear loci. We evaluated alternative biogeographic and evolutionary scenarios to explain such profound discordance in spatial and phylogenetic patterning between mitochondrial and nuclear genomes. While neutral models provided unparsimonious explanations for the observed pattern, the hypothesis of environmental selection driving mitochondrial divergence in the presence of nuclear gene flow is favoured.ConclusionsOur study on the genetic variation of P. tiliguerta reveals surprising levels of diversity underlining a complex phylogeographic pattern with a striking example of mito-nuclear discordance. These findings have profound implications, not only for the taxonomy and conservation of P. tiliguerta. Growing evidence on deep mitochondrial breaks in absence of geographic barriers and of climatic factors associated to genetic variation of Corsican-Sardinian endemics warrants additional investigation on the potential role of environmental selection driving the evolution of diversity hotspots within Mediterranean islands.

Combined hybridization and mitochondrial capture shape complex phylogeographic patterns in hybridogenetic Cataglyphis desert ants

Some species of Cataglyphis desert ants have evolved a hybridogenetic mode of reproduction at the social scale. In hybridogenetic populations, two distinct genetic lineages coexist. Non-reproductive offspring (workers) are hybrids of the two lineages, whereas sexual offspring (males and new queens) are produced by parthenogenesis and belong to the mother queen lineage. How this unusual reproductive system affects phylogeographic patterns and speciation processes remains completely unknown to date. Using one mitochondrial and four nuclear genes, we examined the phylogenetic relationships between three species of Cataglyphis (C. hispanica, C. humeya and C. velox) where complex DNA inheritance through social hybridogenesis may challenge phylogenetic inference. Our results bring two important insights. First, our data confirm a hybridogenetic mode of reproduction across the whole distribution range of the species C. hispanica. In contrast, they do not provide support for hybridogenesis in the populations sampled of C. humeya and C. velox. This suggests that these populations are not hybridogenetic, or that hybridogenesis is too recent to result in reciprocally monophyletic lineages on nuclear genes. Second, due to mitochondrial introgression between lineages (Darras and Aron, 2015), the faster-evolving COI marker is not lineage specific, hence, unsuitable to further investigate the segregation of lineages in the species studied. Different mitochondrial haplotypes occur in each locality sampled, resulting in strongly structured populations. This micro-allopatric structure leads to over-splitting species delimitation on mitochondrial gene, as every locality could potentially be considered a putative species; haploweb analyses of nuclear markers, however, yield species delimitations that are consistent with morphology. Overall, this study highlights how social hybridogenesis varies across species and shapes complex phylogeographic patterns.

Scrophularia arguta, a widespread annual plant in the Canary Islands: a single recent colonization event or a more complex phylogeographic pattern?

Many studies have addressed evolution and phylogeography of plant taxa in oceanic islands, but have primarily focused on endemics because of the assumption that in widespread taxa the absence of morphological differentiation between island and mainland populations is due to recent colonization. In this paper, we studied the phylogeography of Scrophularia arguta, a widespread annual species, in an attempt to determine the number and spatiotemporal origins of dispersal events to Canary Islands. Four different regions, ITS and ETS from nDNA and psbA‐trnH and psbJ‐petA from cpDNA, were used to date divergence events within S. arguta lineages and determine the phylogenetic relationships among populations. A haplotype network was obtained to elucidate the phylogenetic relationships among haplotypes. Our results support an ancient origin of S. arguta (Miocene) with expansion and genetic differentiation in the Pliocene coinciding with the aridification of northern Africa and the formation of the Mediterranean climate. Indeed, results indicate for Canary Islands three different events of colonization, including two ancient events that probably happened in the Pliocene and have originated the genetically most divergent populations into this species and, interestingly, a recent third event of colonization of Gran Canaria from mainland instead from the closest islands (Tenerife or Fuerteventura). In spite of the great genetic divergence among populations, it has not implied any morphological variation. Our work highlights the importance of nonendemic species to the genetic richness and conservation of island flora and the significance of the island populations of widespread taxa in the global biodiversity.

Mitogenome analysis reveals a complex phylogeographic relationship within the wild tiger population of Thailand

We present the first study of the complete mitogenome of wild tigers Panthera tigris in Thailand. Thailand has been recognised as one of the most important countries within the geo- graphic range of P. tigris and is home to 2 subspecies: Indochinese P. t. corbetti in the north and Malayan P. t. jacksoni in the south. We obtained samples from wild tigers in a large forest complex in northern Thailand (Western Forest Complex, WEFCOM) and from locally confiscated individu- als in southern Thailand close to the border with Malaysia. Our results support the occurrence of both Indochinese and Malayan tigers in Thailand and reveal complex phylogeographic patterns of the wild tiger population in Southeast Asia.

Insights to genetic characterization tools for epidemiological tracking of Francisella tularensis in Sweden.

Tularaemia, caused by the bacterium Francisella tularensis, is endemic in Sweden and is poorly understood. The aim of this study was to evaluate the effectiveness of three different genetic typing systems to link a genetic type to the source and place of tularemia infection in Sweden. Canonical single nucleotide polymorphisms (canSNPs), MLVA including five variable number of tandem repeat loci and PmeI-PFGE were tested on 127 F. tularensis positive specimens collected from Swedish case-patients. All three typing methods identified two major genetic groups with near-perfect agreement. Higher genetic resolution was obtained with canSNP and MLVA compared to PFGE; F. tularensis samples were first assigned into ten phylogroups based on canSNPs followed by 33 unique MLVA types. Phylogroups were geographically analysed to reveal complex phylogeographic patterns in Sweden. The extensive phylogenetic diversity found within individual counties posed a challenge to linking specific genetic types with specific geographic locations. Despite this, a single phylogroup (B.22), defined by a SNP marker specific to a lone Swedish sequenced strain, did link genetic type with a likely geographic place. This result suggests that SNP markers, highly specific to a particular reference genome, may be found most frequently among samples recovered from the same location where the reference genome originated. This insight compels us to consider whole-genome sequencing (WGS) as the appropriate tool for effectively linking specific genetic type to geography. Comparing the WGS of an unknown sample to WGS databases of archived Swedish strains maximizes the likelihood of revealing those rare geographically informative SNPs.

Phylogeographic and phenotypic assessment of a basal haplochromine cichlid fish from Lake Chila, Zambia

The basal haplochromine genus Pseudocrenilabrus comprises three valid species, although the current taxonomy most probably underestimates species richness. Previous phylogeographic studies on the P. philander species complex revealed a clear structuring of populations, shaped by river capture events. Here we report the discovery of P. cf. philander in Lake Chila, a small lake south of Lake Tanganyika. We were interested whether discrete morphs, similar to what has been found in Lake Mweru and the Lunzua River, were present in Lake Chila. We evaluated the phenotypic variability of the population in relation to other lacustrine and riverine populations by quantifying colouration and body shape. To place the specimens in a phylogeographic framework, we inferred a phylogeny based on the most variable part of the mitochondrial control region. We found two divergent mtDNA lineages in Lake Chila and tested for population structure and admixture between the lineages using microsatellite data. Our study reveals a complex phylogeographic pattern and demonstrates admixture of distant mtDNA lineages in Lake Chila, producing a hybrid swarm with substantial phenotypic variability. Unlike in Lake Mweru, Pseudocrenilabrus has not diversified further into discrete morphs in Lake Chila, probably because of the long-term instability of the lake and the presumed recency of the admixture event.

Francisella tularensis subsp. tularensis group A.I, United States.

We used whole-genome analysis and subsequent characterization of geographically diverse strains using new genetic signatures to identify distinct subgroups within Francisella tularensis subsp. tularensis group A.I: A.I.3, A.I.8, and A.I.12. These subgroups exhibit complex phylogeographic patterns within North America. The widest distribution was observed for A.I.12, which suggests an adaptive advantage.