Phylogeographic Patterns Research Articles

Phylogeography of the small grass yellow Eurema brigitta (Stoll, 1780) (Lepidoptera: Pieridae) unveils the existence of distinct taxa within the Palaeotropics

AbstractEurema brigitta (Stoll, 1780) is one of the few butterfly species distributed in most of the Old World tropics. In 2017, we documented its occurrence in Socotra, a UNESCO World Heritage Site. Now, we clarify the origin of this specimen and further describe a phylogeographic pattern of this species by comparing Afrotropical, Malagasy and Oriental‐Australian populations using the mitochondrial cytochrome c oxidase subunit I marker. We found a deep split between the Afrotropical and Oriental‐Australian populations of this taxon, which are separated by the Indian Ocean and dry eremic habitats on the northern coasts. A less deep but significant split also exists between E. b. brigitta (Stoll, 1780) from mainland Africa and E. b. pulchella (Boisduval, 1833) from Madagascar and surrounding islands. The individual from Socotra clearly originates from Africa. In addition, in accordance with the genetic pattern and the known morphological evidence, we propose to transfer the Oriental‐Australian populations into a separate species, Eurema drona (Horsfield, 1829) reinst. stat.

Biogeography and evolutionary history of Puntius sensu lato (Teleostei: Cyprinidae) in Sri Lanka

Sri Lanka’s biota is derived largely from Southeast Asian lineages which immigrated via India following its early-Eocene contact with Laurasia. The island is now separated from southeastern India by the 30 km wide Palk Strait which, during sea-level low-stands, was bridged by the 140 km-wide Palk Isthmus. Consequently, biotic ingress and egress were mediated largely by the climate of the isthmus. Because of their dependence on perennial aquatic habitats, freshwater fish are useful models for biogeographic studies. Here we investigate the timing and dynamics of the colonization of—and diversification on—Sri Lanka by a group of four closely-related genera of cyprinid fishes (Puntius sensu lato). We construct a molecular phylogeny based on two mitochondrial and two nuclear gene markers, conduct divergence timing analyses and ancestral-range estimations to infer historical biogeography, and use haplotype networks to discern phylogeographic patterns. The origin of Puntius s.l. is dated to ~ 20 Ma. The source of diversification of Puntius s.l. is Sri Lanka-Peninsular India. Species confined to perhumid rainforests show strong phylogeographic structure, while habitat generalists show little or no such structure. Ancestral range estimations for Plesiopuntius bimaculatus and Puntius dorsalis support an ‘Out of Sri Lanka’ scenario. Sri Lankan Puntius s.l. derive from multiple migrations across the Palk Isthmus between the early Miocene and the late Pleistocene. Species dependent on an aseasonal climate survived aridification in rainforest refugia in the island’s perhumid southwest and went on to recolonize the island and even southern India when pluvial conditions resumed. Our results support an historical extinction of Sri Lanka’s montane aquatic fauna, followed by a recent partial recolonization of the highlands, showing also that headwater stream capture facilitated dispersal across basin boundaries.

River drainage rearrangements and the phylogeographic pattern of the annual fish Austrolebias arachan (Cyprinodontiformes, Rivulidae)

AbstractPalaeogeographical and climatic processes are among the main factors affecting biological diversity and distribution patterns. In freshwater systems, major dispersal processes are caused by river drainage rearrangements where the direction of flow of a stream changes, allowing range expansions and connection of previously isolated communities. In the Neotropical region, this process has been known to connect part of the southwestern Amazon basin with La Plata basin during the formation of the Bolivian Orocline, and La Plata basin with Atlantic coastal basins since the split from Africa. Several species of annual fishes of the genus Austrolebias are known to inhabit seasonal ponds both in the Rio Negro basin (southern tip of Brazilian shield, Lower Uruguay ecoregion), and the headwaters of rivers draining into the Merín lagoon (coastal drainages, Laguna dos Patos ecoregion). The aim of this article was to analyse the phylogeographic pattern of Austrolebias arachan in the context of putative river rearrangements. Two hypotheses were tested: (a) the spatial configuration of river basins determines the genetic structure and distribution of this species, and (b) coastal drainages captured sections of upland shield river drainages. We analysed a fragment of the mitochondrial cytochrome b gene and a fragment of a nuclear intron locus. Results support the prediction of the first hypothesis: geographic variation within A. arachan is structured according to geography. The second hypothesis was in part confirmed: the migration analyses showed that Rio Negro basin populations could have acted as a source for Laguna Merin basin. However, migration estimates also support gene flow in the opposite direction. The cytochrome b haplotype network configuration and its phylogenetic pattern suggests at least two independent events of capture, with divergence time estimated at the onset of Pleistocene glacial cycles.

Revealing biogeographic patterns in genetic diversity of native and invasive plants and their association with soil community diversity in the Chinese coast

Within‐species genetic diversity is shaped by multiple evolutionary forces within the confines of geography, and has cascading effects on the biodiversity of other taxa and levels. Invasive species are often initially limited in genetic diversity but still respond rapidly to their new range, possibly through ‘pre‐adapted' genotypes or multiple sources of genetic diversity, but little is known about how their genetic structure differs from that of native species and how it alters the genetic‐species diversity relationship. Here, we selected a widespread native species Phragmites australis and its co‐occurring invasive competitor Spartina alterniflora as our model plant species. We investigated the genetic structure of P. australis using two chloroplast fragments and ten nuclear microsatellites in 13 populations along the Chinese coastal wetlands. We discovered a distinct geographical differentiation, showing that the northern and southern populations harbored unique genotypes. We also found a significant increase in genetic diversity (allelic richness and expected heterozygosity) from south to north. Combined with previous studies of S. alterniflora, the Mantel tests revealed a significant correlation of genetic distances between P. australis and S. alterniflora even when controlling for geographic distance, suggesting that the invasive species S. alterniflora might exhibit a phylogeographic pattern similar to that of the native species to some extent. Furthermore, our results suggest that the S. alterniflora invasion has altered the relationship between the genetic diversity of the dominant native plant and the associated species richness of soil nematodes. The reason for the alteration of genetic‐species diversity relationship might be that the biological invasion weakens the environmental impact on both levels of biodiversity. Our findings contribute to understanding the latitudinal patterns of intraspecific genetic diversity in widespread species. This work on the genetic diversity analysis of native species also provides significant implications for the invasion stage and ecological consequences of biological invasions.

Limited congruence in phylogeographic patterns observed for riverine predacious beetles sharing distribution along the mountain rivers

Riverine predacious beetles (RPB) (Carabidae, Staphylinidae) are highly diverse and numerous elements of riverine ecosystems. Their historical and contemporary distribution and diversity are highly dependent on natural flow regimes and topography of watercourses. Despite broad knowledge of their ecology, data on population genetic diversity and connectivity are lacking. This study aimed to fill this gap in order to solve two principal hypotheses assuming (i) congruence of phylogeographic patterns observed for RPB indicating that they share a common history and the ecological adaptations to the dynamic environment, (ii) genetic structuration of populations according to river basins. The Carpathian populations of four ground beetles and three rove beetles were examined using cytochrome oxidase and arginine kinase sequencing. There are substantial differences in RPB demographic history and current genetic diversity. Star-like phylogeny of Bembidion and complex haplotype networks of Paederus/Paederidus, with some haplotypes being drainage-specific and others found in distant populations, indicate a general lack of isolation by distance. Signs of recent demographic expansion were detected for most RPB with the latest population collapse for some rove beetles. To some extent, migration of examined species has to be limited by watersheds. Observed phylogeographic patterns are essential for correctly understanding RPB meta-population functioning.

Phylogeography and genetic diversity of the Japanese mud shrimp Upogebiamajor (Crustacea, Decapoda, Upogebiidae): Natural or anthropogenic dispersal?

Upogebiamajor (De Haan, 1841) is known for forming huge burrows in sandy, intertidal areas that can extend to depths of over 2 m. Despite its widespread distribution in East Asia and Russia, the genetic relatedness of its regional populations remains uncertain, likely owing to difficulties in specimen collection. Therefore, to appraise the phylogeographic patterns, genetic diversity, and morphological variety of U.major, the mitochondrial DNA of specimens collected from Japan, Korea and China were subjected to molecular phylogenetic analyses of COI genes, alongside morphological assessment. As a result, we discovered four principal groups; of these, Group 1 consisted predominantly of Japanese specimens, while Groups 3 and 4 were interpreted as having originated from the continent. Group 2 exhibited genetic segregation from both continental and Japanese descent. Group 1 mostly comprising Japanese specimens implies that the planktonic larvae of U.major were disseminated north and south by ocean currents encompassing the Japanese archipelago. In contrast, individuals probably originating from the continent were discovered in Lake Notoro, Hokkaido and Matsukawa-ura, Fukushima in northeastern Japan, indicating possible introduction from the continent through ocean currents or unintentional introduction with other organisms imported. Additionally, one of the specimens collected from Matsukawa-ura exhibited significant genetic and morphological differences from other specimens, suggesting the possibility of being a subspecies. The outcomes of this study not only offer valuable insights into the origins of distribution of U.major but also introduce a novel challenge of assessing the coexistence of two routes: natural and anthropogenic dispersion.

On the conservation of white-clawed crayfish in the Iberian Peninsula: Unraveling its genetic diversity and structure, and origin.

European crayfish species are a clear example of the drastic decline that freshwater species are experiencing. In particular, the native species of the Iberian Peninsula, the white clawed-crayfish (WCC) Austropotamobius pallipes, is listed as "endangered" by the IUCN and included in Annex II of the EU Habitat Directive and requires especially attention. Currently, implemented conservation management strategies require a better understanding of the genetic diversity and phylogeographic patterns, as well as of its evolutionary history. For this purpose, we have generated the largest datasets of two informative ribosomal mitochondrial DNA regions, i.e., cytochrome oxidase subunit I and 16S, from selected populations of the WCC covering its geographical distribution. These datasets allowed us to analyze in detail the (i) genetic diversity and structure of WCC populations, and (ii) divergence times for Iberian populations by testing three evolutionary scenarios with different mtDNA substitution rates (low, intermediate, and high rates). The results indicate high levels of haplotype diversity and a complex geographical structure for WCC in the Iberian Peninsula. The diversity found includes new unique haplotypes from the Iberian Peninsula and reveals that most of the WCC genetic variability is concentrated in the northern and central-eastern regions. Despite the fact that molecular dating analyses provided divergence times that were not statistically supported, the proposed scenarios were congruent with previous studies, which related the origin of these populations with paleogeographic events during the Pleistocene, which suggests an Iberian origin for these WCC. All results generated in this study, indicate that the alternative hypothesis of an introduced origin of the Iberian WCC is highly improbable. The result of this study, therefore, has allowed us to better understand of the genetic diversity, structure patterns, and evolutionary history of the WCC in the Iberian Peninsula, which is crucial for the management and conservation needs of this endangered species.

Phylogeographical evidence for historical long-distance dispersal in the flightless stick insect Ramulus mikado.

Exploring how organisms overcome geographical barriers to dispersal is a fundamental question in biology. Passive long-distance dispersal events, although infrequent and unpredictable, have a considerable impact on species range expansions. Despite limited active dispersal capabilities, many stick insect species have vast geographical ranges, indicating that passive long-distance dispersal is vital for their distribution. A potential mode of passive dispersal in stick insects is via the egg stage within avian digestive tracts, as suggested by experimental evidence. However, detecting such events under natural conditions is challenging due to their rarity. Therefore, to indirectly assess the potential of historical avian-mediated dispersal, we examined the population genetic structure of the flightless stick insect Ramulus mikado across Japan, based on a multifaceted molecular approach [cytochrome oxidase subunit I (COI) haplotypes, nuclear simple sequence repeat markers and genome-wide single nucleotide polymorphisms]. Subsequently, we identified unique phylogeographic patterns, including the discovery of identical COI genotypes spanning considerable distances, which substantiates the notion of passive long-distance genotypic dispersal. Overall, all the molecular data revealed the low and mostly non-significant genetic differentiation among populations, with identical or very similar genotypes across distant populations. We propose that long-distance dispersal facilitated by birds is the plausible explanation for the unique phylogeographic pattern observed in this flightless stick insect.

The holocentric chromosome microevolution: From phylogeographic patterns to genomic associations with environmental gradients.

Geographic isolation and chromosome evolution are two of the major drivers of diversification in eukaryotes in general, and specifically, in plants. On one hand, range shifts induced by Pleistocene glacial oscillations deeply shaped the evolutionary trajectories of species in the Northern Hemisphere. On the other hand, karyotype variability within species or species complexes may have adaptive potential as different karyotypes may represent different recombination rates and linkage groups that may be associated with locally adapted genes or supergenes. Organisms with holocentric chromosomes are ideal to study the link between local adaptation and chromosome evolution, due to their high cytogenetic variability, especially when it seems to be related to environmental variation. Here, we integrate the study of the phylogeography, chromosomal evolution and ecological requirements of a plant species complex distributed in the Western Euro-Mediterranean region (Carex gr. laevigata, Cyperaceae). We aim to clarify the relative influence of these factors on population differentiation and ultimately on speciation. We obtained a well-resolved RADseq phylogeny that sheds light on the phylogeographic patterns of molecular and chromosome number variation, which are compatible with south-to-north postglacial migration. In addition, landscape genomics analyses identified candidate loci for local adaptation, and also strong significant associations between the karyotype and the environment. We conclude that karyotype distribution in C. gr. laevigata has been constrained by both range shift dynamics and local adaptation. Our study demonstrates that chromosome evolution may be responsible, at least partially, for microevolutionary patterns of population differentiation and adaptation in Carex.

Divergence in Elymus sibiricus is related to geography and climate oscillation: A new look from pan‐chloroplast genome data

AbstractQuaternary glacial climate oscillation and geographical isolation have significantly influenced the geographic distribution pattern and lineage evolution history of species. However, understanding how these factors specifically impact the genealogical structure of dominant Gramineous species in the Qinghai–Tibet Plateau (QTP) remains a subject of investigation. Elymus sibiricus L. (Gramineae), indigenous to the QTP and widely distributed in Eurasia, exhibits remarkable environmental adaptation and phenotypic diversity, making it an ideal candidate for phylogeographic studies. Based on the analysis of 175 complete chloroplast genome sequences, our results indicated that the ancestors of E. sibiricus originated from the QTP and underwent a complex migration history. After the speciation of E. sibiricus, several geo‐groups exhibited independent differentiation, showing minimal gene flow among them. The current phylogeographic patterns of E. sibiricus are a result of frequent climate alternations and the cold climate during the Quaternary glacial, as well as the presence of several geographical barriers that have restricted the gene flow among different geo‐groups. Our research has revealed for the first time that E. sibiricus has a multilineage origin, and its maternal donors are not limited to a single species. Furthermore, the high quality and mapping depth of the variant file provided reliable data for analyzing the patterns based on raw sequencing data. These findings enhance our understanding of the relationship between plant differentiation and climatic and geographical factors of Eurasia.

Phylogeography, hybrid zones and contemporary species boundaries in the south-eastern Australian smooth frogs (Anura: Myobatrachidae: Geocrinia)

Paleo-climatic fluctuations have driven episodic changes in species distributions, providing opportunities for populations to diverge in isolation and hybridise following secondary contact. Studies of phylogeographic diversity and patterns of gene flow across hybrid zones can provide insight into contemporary species boundaries and help to inform taxonomic and conservation inferences. Here we explore geographic diversity within the acoustically divergent yet morphologically conserved south-eastern Australian smooth frog complex and assess gene flow across a narrow hybrid zone using mitochondrial nucleotide sequences and nuclear genome-wide single nucleotide polymorphisms. Our analyses reveal the presence of an evolutionarily distinct taxon restricted to the Otway Plains and Ranges, Victoria, which forms a narrow (9–30 km wide), spatiotemporally stable (>50 years) hybrid zone with Geocrinia laevis, which we describe herein as a new species.

Phylogeography of Ara militaris (Military Macaw): Implications for Conservation

The Military Macaw (Ara militaris) is an endangered bird species with disjunct geographic distribution across the Neotropics, consisting of three recognized subspecies: One in Mexico (A. m. mexicanus) and two in South America (A. m. militaris and A. m. bolivianus). However, due to the limited phenotypic differentiation between these allopatric taxa, their taxonomic status has been the subject of debate. In this study, we explored mitochondrial DNA (mtDNA) variability to determine the phylogeographical pattern through phylogenetic and ecological modelling analyses. We also aimed to describe the evolutionary relationships of twelve A. militaris populations. We identified 41 haplotypes in the 300 bp region of the Cytochrome b (Cyt-b) gene of the mtDNA and low nucleotide diversity. The observed phylogeographic structure suggests the existence of two clades: One composed of A. m. militaris and A. m. bolivianus and another consisting solely of A. m. mexicanus. The A. m. mexicanus clade further divides into two recognized subclades: Sierra Madre Oriental and northeastern portion of the Sierra Madre Occidental. Ecological analyses revealed that the niche similarity between these lineages was lower than expected by chance. Additionally, results from low cross-prediction tests indicated that the two lineages have inhabited different environmental spaces since the Late Pleistocene. This divergence may be associated with a steep ecological gradient and contemporary geographical barrier. Based on our results, we suggest that at least the A. m. mexicanus has a divergent evolutionary history; therefore, it should be considered as a different evolutionarily significant and management unit. We recommend that future conservation strategies in Mexico incorporate effective protection measures, including habitat preservation and the reduction of illegal trade, to ensure the preservation of viable populations.

Acknowledging more biodiversity without more species

Delimiting and naming biodiversity is a vital step toward wildlife conservation and research. However, species delimitation must be consistent across biota so that the limited resources available for nature protection can be spent effectively and objectively. To date, newly discovered lineages typically are either left undescribed and thus remain unprotected or are being erroneously proposed as new species despite mixed evidence for completed speciation, in turn contributing to the emerging problem of taxonomic inflation. Inspired by recent conceptual and methodological progress, we propose a standardized workflow for species delimitation that combines phylogenetic and hybrid zone analyses of genomic datasets (“genomic taxonomy”), in which phylogeographic lineages that do not freely admix are ranked as species, while those that have remained fully genetically compatible are ranked as subspecies. In both cases, we encourage their formal taxonomic naming, diagnosis, and description to promote social awareness toward biodiversity. The use of loci throughout the genome overcomes the unreliability of widely used barcoding genes when phylogeographic patterns are complex, while the evaluation of divergence and reproductive isolation unifies the long-opposed concepts of lineage species and biological species. We suggest that a shift in conservation assessments from a single level (species) toward a two-level hierarchy (species and subspecies) will lead to a more balanced perception of biodiversity in which both intraspecific and interspecific diversity are valued and more adequately protected.

Palaeoclimatic niche modelling reveals the phylogeographic history of the South African shrew Myosorex varius and the colonisation route of the genus Myosorex (Mammalia, Soricidae) from East Africa

Myosorex varius is a South African generalist shrew, which has been found to consist of several genetic clades across its range. A northern clade inhabits the more mesic, summer-rainfall areas of grassland and savannah in the east of South Africa. A southern clade occupies areas of fynbos in the south, and can be further divided into a western subclade occupying winter-rainfall areas and an eastern subclade occupying areas with aseasonal rainfall. Non-South-African members of the African genus Myosorex primarily are limited to isolated montane habitats along the East African Rift System. Here, we used palaeoclimatic niche modelling to examine the effects of Pliocene and Pleistocene climate change on the distributions of M. varius, its clades and the genus as a whole. Results indicate that repeated cycles of range expansion during glacial periods and fragmentation during interglacials are responsible for current phylogeographic patterns within M. varius. Based on their close alignment with rainfall zones and lack of genetic mixing despite areas of contact, it is likely that these (sub)clades are locally adapted to their respective areas. Earlier climatic fluctuations allowed the genus to ‘island hop’ south from East Africa along the East African Rift System, expanding in range during cooler periods and retreating to montane refugia during warmer periods. Areas currently occupied by Myosorex species largely correspond with predicted montane refugia that have allowed them to survive previous warm periods.

Population Structure and Phylogeography of Marine Gastropods Monodonta labio and M. confusa (Trochidae) along the Northwestern Pacific Coast

The genetic structure and demographic history of marine organisms are influenced by biological and ecological features, oceanic currents, and the paleo-geological effects of sea-level fluctuations. In this study, we used mitochondrial COI + 16S gene analysis to investigate the phylogeographic pattern and demography of Monodonta labio and M. confusa in Taiwan, the Ryukyu Islands, Japan, mainland China, and Korea. Our genetic analysis identified two major lineages that were not evident from the distribution patterns of different populations. The Taiwan Strait, which acted as a land bridge during Pleistocene glaciations, and the lack of strong dispersal barriers to gene flow between ocean basins after glaciations shaped the phylogeographic pattern. The genetic differentiation in the Ryukyu Islands was influenced by the specialist-generalist variation hypothesis and the Kuroshio Current. Bayesian skyline plot analyses suggested that the effective population size of M. labio and M. confusa rapidly increased approximately 0.1 and 0.075 million years ago, respectively. Our approximate Bayesian computation analysis suggested that all M. labio and M. confusa populations experienced a decline in population size following a recent population expansion and constant size, respectively. Our study provides a baseline for future investigations of the biogeographical patterns of marine gastropods in the Northwest Pacific and offers valuable insights for the management, sustainable resource utilization, and conservation of this species.

Demographic processes, refugia and dispersal routes during the Pleistocene in a sigmodontine rodent assemblage from the South American Pampas

Abstract The Pampas of South America represents one of the most extended subtropical–temperate grasslands in the world. This ecoregion was influenced by Pleistocene climate oscillations. The sigmodontine rodent assemblage inhabiting this region is a good model system to analyse the impact of these climate changes on evolutionary histories. We performed a comparative phylogeographical study on seven species to evaluate the concordance of phylogeographical patterns among them, to assess if they experienced congruent and synchronous demographic changes, and posit putative centres of origin and dispersal routes. Four species (Calomys musculinus, Oligoryzomys flavescens, Oxymycterus nasutus and Oligoryzomys nigripes) showed evidence of demographic expansion. In the first three, population increases started during Marine Isotope Stage 5 (MIS 5) while in Ol. nigripes, the rise started during MIS 7; this rise would have continued to the present in all cases. Necromys lasiurus, Scapteromys tumidus and Scapteromys aquaticus did not show a pattern of expansion. Four centres of origin were identified; in general, populations sharing the same putative refugium followed common dispersal routes. Our results indicate that the Pampas offered relatively stable habitats over time, mainly in areas associated with watercourses or coastlines, suggesting that recent Pleistocene climate oscillations have had a moderate impact on this ecoregion compared to other regions of South America.

Unique Haplotypes of <i>Artemia salina</i> (Crustacea, Branchiopoda, Anostraca) in Hypersaline Lake Sasyk-Sivash (Crimea)

The genetic structure of the population of the Artemia salina (L., 1758) species from the hypersaline lake Sasyk-Sivash was studied on the basis of a fragment of the gene of the first subunit of cytochrome oxidase c (COI) of mitochondrial DNA. The phylogeny reconstruction was performed using all available nucleotide sequences of this gene for the salina species in the GenBank (NCBI) international database. Genealogical connections between COI haplotypes have been established and phylogeographic patterns have been revealed. Common haplotypes have been noted in Western Mediterranean populations, which may be a consequence of their location in a single migration corridor of birds, which, as is known, contribute to the passive spread of dormant stages of artemia. Geographically isolated groups of populations from Libya, Tunisia, Egypt, Cyprus and Crimea are characterized by unique haplotypes that are not currently found in other Mediterranean populations. It is suggested that unique haplotypes may be endemic to geographically remote regions.

Population genomics of diarrheagenic Escherichia coli uncovers high connectivity between urban and rural communities in Ecuador.

Human movement may be an important driver of transmission dynamics for enteric pathogens but has largely been underappreciated except for international 'travelers' diarrhea or cholera. Phylodynamic methods, which combine genomic and epidemiological data, are used to examine rates and dynamics of disease matching underlying evolutionary history and biogeographic distributions, but these methods often are not applied to enteric bacterial pathogens. We used phylodynamics to explore the phylogeographic and evolutionary patterns of diarrheagenic E. coli in northern Ecuador to investigate the role of human travel in the geographic distribution of strains across the country. Using whole genome sequences of diarrheagenic E. coli isolates, we built a core genome phylogeny, reconstructed discrete ancestral states across urban and rural sites, and estimated migration rates between E. coli populations. We found minimal structuring based on site locations, urban vs. rural locality, pathotype, or clinical status. Ancestral states of phylogenomic nodes and tips were inferred to have 51% urban ancestry and 49% rural ancestry. Lack of structuring by location or pathotype E. coli isolates imply highly connected communities and extensive sharing of genomic characteristics across isolates. Using an approximate structured coalescent model, we estimated rates of migration among circulating isolates were 6.7 times larger for urban towards rural populations compared to rural towards urban populations. This suggests increased inferred migration rates of diarrheagenic E. coli from urban populations towards rural populations. Our results indicate that investments in water and sanitation prevention in urban areas could limit the spread of enteric bacterial pathogens among rural populations.

Genomic analyses indicate the North American Ap-ha variant of the tick-vectored bacterium Anaplasma phagocytophilum was introduced from Europe

BackgroundAnaplasma phagocytophilum is a tick-vectored, obligately intracellular bacterium that infects a diversity of vertebrate hosts. In North America, the Ap-ha variant of A. phagocytophilum can cause dangerous infections in humans, whereas symptomatic human infections in Europe are rare. Conversely, the European host-generalist ecotype of A. phagocytophilum frequently causes illness in domestic ruminants while no comparable infections have been recorded from North America. Despite these differences in pathogenicity, the Ap-ha variant is closely aligned phylogenetically with the European host-generalist ecotype. Furthermore, North American populations of A. phagocytophilum are less genetically diverse than those in Europe. Taken together, these observations suggest that the North American Ap-ha variant may represent an introduced population of this bacterium.Methods Data from publicly available whole genomes of A. phagocytophilum were used to compare phylogeographic patterns and the extent of genetic divergence between the North American Ap-ha variant and the European host-generalist ecotype.ResultsThe results confirm that North American Ap-ha samples are phylogenetically nested within the diversity of the European host-generalist ecotype, and that Ap-ha likely radiated within the last 100 years. As expected, the Ap-ha variant also exhibited relatively low genetic diversity levels compared to the European host-generalist ecotype. Finally, North American Ap-ha harbored significantly more derived alleles than the European host-generalist A. phagocytophilum population.ConclusionsCollectively, these results support the hypothesis that the Ap-ha variant was recently introduced to North America from Europe and underwent a strong genetic bottleneck during this process (i.e. a ‘founder event’). Adaptation to novel vectors may have also played a role in shaping genetic diversity and divergence patterns in these pathogenic bacteria. These findings have implications for future studies aimed at understanding evolutionary patterns and pathogenicity variation within A. phagocytophilum.Graphical

Phylogeography of Limia vittata (Cyprinodontiformes: Poeciliidae): geographical distribution of mitochondrial haplotypes is comparable to other Cuban poeciliids

Abstract The genus Limia is endemic to the Greater Antilles with a single species in Cuba, Limia vittata, widespread in lowland ecosystems. The limited data available regarding its population structure suggest that its levels of intraspecific divergence are lower compared to other Cuban poeciliids. Furthermore, little is known about the dispersal pathways and demographic changes experienced by present-day populations. By analysing two mitochondrial markers and testing scenarios of dispersal and vicariance, we provide insights into the evolutionary history of L. vittata. Here, we show that this species is formed by three genetically differentiated and geographically delimited groups of populations. We also found moderate intraspecific divergence and a mtDNA pattern of high haplotype diversity and low nucleotide diversity which is consistent with a rapid demographic expansion. Our Bayesian analysis recovered dispersal from eastern to western Cuba as the most likely scenario explaining the current distribution of this species. Limia vittata exhibited a distinct regional distribution of haplogroups that corresponds to major core landmasses within Cuba, along with a signature of rapid population expansion during relatively recent palaeoclimatic changes that occurred during the formation of the archipelago. Similar phylogeographic patterns have been identified in other freshwater and terrestrial taxa on the island.