Deep Learning and Likelihood Approaches for Viral Phylogeography Converge on the Same Answers Whether the Inference Model Is Right or Wrong

Analysis of phylogenetic trees has become an essential tool in epidemiology. Likelihood-based methods fit models to phylogenies to draw inferences about the phylodynamics and history of viral transmission. However, these methods are often computationally expensive, which limits the complexity and realism of phylodynamic models and makes them ill-suited for informing policy decisions in real-time during rapidly developing outbreaks. Likelihood-free methods using deep learning are pushing the boundaries of inference beyond these constraints. In this paper, we extend, compare, and contrast a recently developed deep learning method for likelihood-free inference from trees. We trained multiple deep neural networks using phylogenies from simulated outbreaks that spread among 5 locations and found they achieve close to the same levels of accuracy as Bayesian inference under the true simulation model. We compared robustness to model misspecification of a trained neural network to that of a Bayesian method. We found that both models had comparable performance, converging on similar biases. We also implemented a method of uncertainty quantification called conformalized quantile regression that we demonstrate has similar patterns of sensitivity to model misspecification as Bayesian highest posterior density (HPD) and greatly overlap with HPDs, but have lower precision (more conservative). Finally, we trained and tested a neural network against phylogeographic data from a recent study of the SARS-Cov-2 pandemic in Europe and obtained similar estimates of region-specific epidemiological parameters and the location of the common ancestor in Europe. Along with being as accurate and robust as likelihood-based methods, our trained neural networks are on average over 3 orders of magnitude faster after training. Our results support the notion that neural networks can be trained with simulated data to accurately mimic the good and bad statistical properties of the likelihood functions of generative phylogenetic models.

Detection of Ghost Introgression Requires Exploiting Topological and Branch Length Information

In recent years, the study of hybridization and introgression has made significant progress, with ghost introgression-the transfer of genetic material from extinct or unsampled lineages to extant species-emerging as a key area for research. Accurately identifying ghost introgression, however, presents a challenge. To address this issue, we focused on simple cases involving 3 species with a known phylogenetic tree. Using mathematical analyses and simulations, we evaluated the performance of popular phylogenetic methods, including HyDe and PhyloNet/MPL, and the full-likelihood method, Bayesian Phylogenetics and Phylogeography (BPP), in detecting ghost introgression. Our findings suggest that heuristic approaches relying on site-pattern counts or gene-tree topologies struggle to differentiate ghost introgression from introgression between sampled non-sister species, frequently leading to incorrect identification of donor and recipient species. The full-likelihood method BPP uses multilocus sequence alignments directly-hence taking into account both gene-tree topologies and branch lengths, by contrast, is capable of detecting ghost introgression in phylogenomic datasets. We analyzed a real-world phylogenomic dataset of 14 species of Jaltomata (Solanaceae) to showcase the potential of full-likelihood methods for accurate inference of introgression.

Complex Patterns of Diversification in the Gray Zone of Speciation: Model-Based Approaches Applied to Patagonian Liolaemid Lizards (Squamata: Liolaemus kingii clade)

In this study we detangled the evolutionary history of the Patagonian lizard clade Liolaemus kingii, coupling dense geographic sampling and novel computational analytical approaches. We analyzed nuclear and mitochondrial data (restriction site-associated DNA sequencing and cytochrome b) to hypothesize and evaluate species limits, phylogenetic relationships, and demographic histories. We complemented these analyses with posterior predictive simulations to assess the fit of the genomic data to the multispecies coalescent model. We also employed a novel approach to time-calibrate a phylogenetic network. Our results show several instances of mito-nuclear discordance and consistent support for a reticulated history, supporting the view that the complex evolutionary history of the kingii clade is characterized by extensive gene flow and rapid diversification events. We discuss our findings in the contexts of the "gray zone" of speciation, phylogeographic patterns in the Patagonian region, and taxonomic outcomes. [Model adequacy; multispecies coalescent; multispecies network coalescent; phylogenomics; species delimitation.].

Dispersal direction of Malaysian Fasciola gigantica from neighboring southeast Asian countries inferred using mitochondrial DNA analysis

Fasciola gigantica and hybrid Fasciola flukes, responsible for the disease fasciolosis, are found in Southeast Asian countries. In the present study, we performed molecular species identification of Fasciola flukes distributed in Terengganu, Malaysia using multiplex PCR for phosphoenolpyruvate carboxykinase (pepck) and PCR-restriction fragment length polymorphism (RFLP) for DNA polymerase delta (pold). Simultaneously, phylogenetic analysis based on mitochondrial NADH dehydrogenase subunit 1 (nad1) was performed for the first time on Malaysian Fasciola flukes to infer the dispersal direction among neighboring countries. A total of 40 flukes used in this study were identified as F. gigantica. Eight nad1 haplotypes were identified in the F. gigantica population of Terengganu. Median-joining network analysis revealed that the Malaysian population was related to those obtained from bordering countries such as Thailand and Indonesia. However, genetic differentiation was detected using population genetics analyses. Nevertheless, the nucleotide diversity (π) value suggested that F. gigantica with the predominant haplotypes was introduced into Malaysia from Thailand and Indonesia. The dispersal direction suggested by population genetics in the present study may not be fully reliable since Fasciola flukes were collected from a single location in one state of Malaysia. Further studies analyzing more samples from many locations are required to validate the dispersal direction proposed herein.

Phylogeography and phylogeny of Rhinoviruses collected from Severe Acute Respiratory Infection (SARI) cases over successive epidemic periods in Tunisia

Rhinoviruses (RV) are a major cause of Severe Acute Respiratory Infection (SARI) in children, with high genotypic diversity in different regions. However, RV type diversity remains unknown in several regions of the world. In this study, the genetic variability of the frequently circulating RV types in Northern Tunisia was investigated, using phylogenetic and phylogeographic analyses with a specific focus on the most frequent RV types: RV-A101 and RV-C45. This study concerned 13 RV types frequently circulating in Northern Tunisia. They were obtained from respiratory samples collected in 271 pediatric SARI cases, between September 2015 and November 2017. A total of 37 RV VP4-VP2 sequences, selected among a total of 49 generated sequences, was compared to 359 sequences from different regions of the world. Evolutionary analysis of RV-A101 and RV-C45 showed high genetic relationship between different Tunisian strains and Malaysian strains. RV-A101 and C45 progenitor viruses’ dates were estimated in 1981 and 1995, respectively. Since the early 2000s, the two types had a wide spread throughout the world. Phylogenetic analyses of other frequently circulating strains showed significant homology of Tunisian strains from the same epidemic period, in contrast with earlier strains. The genetic relatedness of RV-A101 and RV-C45 might result from an introduction of viruses from different clades followed by local dissemination rather than a local persistence of an endemic clades along seasons. International traffic may play a key role in the spread of RV-A101, RV-C45, and other RVs.

Relax, Keep Walking - A Practical Guide to Continuous Phylogeographic Inference with BEAST

Spatially explicit phylogeographic analyses can be performed with an inference framework that employs relaxed random walks to reconstruct phylogenetic dispersal histories in continuous space. This core model was first implemented 10 years ago and has opened up new opportunities in the field of phylodynamics, allowing researchers to map and analyze the spatial dissemination of rapidly evolving pathogens. We here provide a detailed and step-by-step guide on how to set up, run, and interpret continuous phylogeographic analyses using the programs BEAUti, BEAST, Tracer, and TreeAnnotator.

An Epidemiological Analysis of SARS-CoV-2 Genomic Sequences from Different Regions of India

The number of Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) cases is increasing in India. This study looks upon the geographic distribution of the virus clades and variants circulating in different parts of India between January and August 2020. The NPS/OPS from representative positive cases from different states and union territories in India were collected every month through the VRDLs in the country and analyzed using next-generation sequencing. Epidemiological analysis of the 689 SARS-CoV-2 clinical samples revealed GH and GR to be the predominant clades circulating in different states in India. The northern part of India largely reported the ‘GH’ clade, whereas the southern part reported the ‘GR’, with a few exceptions. These sequences also revealed the presence of single independent mutations—E484Q and N440K—from Maharashtra (first observed in March 2020) and Southern Indian States (first observed in May 2020), respectively. Furthermore, this study indicates that the SARS-CoV-2 variant (VOC, VUI, variant of high consequence and double mutant) was not observed during the early phase of virus transmission (January–August). This increased number of variations observed within a short timeframe across the globe suggests virus evolution, which can be a step towards enhanced host adaptation.

Genetic evidence for the association between COVID-19 epidemic severity and timing of non-pharmaceutical interventions

Unprecedented public health interventions including travel restrictions and national lockdowns have been implemented to stem the COVID-19 epidemic, but the effectiveness of non-pharmaceutical interventions is still debated. We carried out a phylogenetic analysis of more than 29,000 publicly available whole genome SARS-CoV-2 sequences from 57 locations to estimate the time that the epidemic originated in different places. These estimates were examined in relation to the dates of the most stringent interventions in each location as well as to the number of cumulative COVID-19 deaths and phylodynamic estimates of epidemic size. Here we report that the time elapsed between epidemic origin and maximum intervention is associated with different measures of epidemic severity and explains 11% of the variance in reported deaths one month after the most stringent intervention. Locations where strong non-pharmaceutical interventions were implemented earlier experienced much less severe COVID-19 morbidity and mortality during the period of study.

Potential mammalian species for investigating the past connections between Amazonia and the Atlantic Forest

Much evidence suggests that Amazonia and the Atlantic Forest were connected through at least three dispersion routes in the past: the Eastern route, the central route, and the Western route. However, few studies have assessed the use of these routes based on multiple species. Here we present a compilation of mammal species that potentially have dispersed between the two forest regions and which may serve to investigate these connections. We evaluate the present-day geographic distributions of mammals occurring in both Amazonia and the Atlantic Forest and the likely connective routes between these forests. We classified the species per habitat occupancy (strict forest specialists, species that prefer forest habitat, or generalists) and compiled the genetic data available for each species. We found 127 mammalian species presently occurring in both Amazonia and the Atlantic Forest for which, substantial genetic data was available. Hence, highlighting their potential for phylogeographic studies investigating the past connections between the two forests. Differently from what was previously proposed, the present-day geographic distribution of mammal species found in both Amazonia and the Atlantic Forest points to more species in the eastern portion of the dry diagonal (and adjoining forested habitats). The Central route was associated with the second most species. Although it remains to be seen how this present-day geography reflects the paleo dispersal routes, our results show the potential of using mammal species to investigate and bring new insights about the past connections between Amazonia and the Atlantic Forest.

Phylogeography and morphological evolution of Pseudechiniscus (Heterotardigrada: Echiniscidae)

Tardigrades constitute a micrometazoan phylum usually considered as taxonomically challenging and therefore difficult for biogeographic analyses. The genus Pseudechiniscus, the second most speciose member of the family Echiniscidae, is commonly regarded as a particularly difficult taxon for studying due to its rarity and homogenous sculpturing of the dorsal plates. Recently, wide geographic ranges for some representatives of this genus and a new hypothesis on the subgeneric classification have been suggested. In order to test these hypotheses, we sequenced 65 Pseudechiniscus populations extracted from samples collected in 19 countries distributed on 5 continents, representing the Neotropical, Afrotropical, Holarctic, and Oriental realms. The deep subdivision of the genus into the cosmopolitan suillus-facettalis clade and the mostly tropical-Gondwanan novaezeelandiae clade is demonstrated. Meridioniscus subgen. nov. is erected to accommodate the species belonging to the novaezeelandiae lineage characterised by dactyloid cephalic papillae that are typical for the great majority of echiniscids (in contrast to pseudohemispherical papillae in the suillus-facettalis clade, corresponding to the subgenus Pseudechiniscus). Moreover, the evolution of morphological traits (striae between dorsal pillars, projections on the pseudosegmental plate IV', ventral sculpturing pattern) crucial in the Pseudechiniscus taxonomy is reconstructed. Furthermore, broad distributions are emphasised as characteristic of some taxa. Finally, the Malay Archipelago and Indochina are argued to be the place of origin and extensive radiation of Pseudechiniscus.

Sampling bias and model choice in continuous phylogeography: Getting lost on a random walk

Phylogeographic inference allows reconstruction of past geographical spread of pathogens or living organisms by integrating genetic and geographic data. A popular model in continuous phylogeography—with location data provided in the form of latitude and longitude coordinates—describes spread as a Brownian motion (Brownian Motion Phylogeography, BMP) in continuous space and time, akin to similar models of continuous trait evolution. Here, we show that reconstructions using this model can be strongly affected by sampling biases, such as the lack of sampling from certain areas. As an attempt to reduce the effects of sampling bias on BMP, we consider the addition of sequence-free samples from under-sampled areas. While this approach alleviates the effects of sampling bias, in most scenarios this will not be a viable option due to the need for prior knowledge of an outbreak’s spatial distribution. We therefore consider an alternative model, the spatial Λ-Fleming-Viot process (ΛFV), which has recently gained popularity in population genetics. Despite the ΛFV’s robustness to sampling biases, we find that the different assumptions of the ΛFV and BMP models result in different applicabilities, with the ΛFV being more appropriate for scenarios of endemic spread, and BMP being more appropriate for recent outbreaks or colonizations.

Phylogeography studies past location and migration using information from current geographic locations of genetic sequences. For example, phylogeography can be used to reconstruct the history of geographical spread of an outbreak using the genetic sequences of the pathogen collected at different times and locations. Here, we investigate the effects of different model assumptions on phylogeographic inference. In particular, we examine the effects of the strategy used to collect samples. We show that sample collection biases can have a strong impact on the quality of phylogeographic reconstruction: geographically biased sampling scheme can be very detrimental for popular continuous phylogeography models. We consider different ways to counter these effects, from utilising alternative phylogeographic models, to the inclusion of partially informative samples (known cases without genetic sequences). While these strategies do alleviate the effects of sampling biases, they also lead to considerable additional computational burden. We also investigate the intrinsic differences of different phylogeographic models, and their effects on reconstructed patterns in different scenarios.

Going back to the roots: Evaluating Bayesian phylogeographic models with discrete trait uncertainty

Phylogeography is a popular way to analyze virus sequences annotated with discrete, epidemiologically-relevant, trait data. For applied public health surveillance, a key quantity of interest is often the state at the root of the inferred phylogeny. In epidemiological terms, this represents the geographic origin of the observed outbreak. Since determining the origin of an outbreak is often critical for public health intervention, it is prudent to understand how well phylogeographic models perform this root state classification task under various analytical scenarios. Specifically, we investigate how discrete state space and sequence data set influence the root state classification accuracy. We performed phylogeographic inference on several simulated DNA data sets while i) increasing the number of sequences and ii) increasing the total number of possible discrete trait values. We show that phylogeographic models tend to perform best at intermediate sequence data set sizes. Further, we demonstrate that a popular metric used for evaluation of phylogeographic models, the Kullback-Leibler (KL) divergence, both increases with discrete state space and data set sizes. Further, by modeling phylogeographic root state classification accuracy using logistic regression, we show that KL is not supported as a predictor of model accuracy, indicating its limited utility for assessing phylogeographic model performance on empirical data. These results suggest that relying solely on the KL metric may lead to artificially inflated support for models with finer discretization schemes and larger data set sizes. These results will be important for public health practitioners seeking to use phylogeographic models for applied infectious disease surveillance.

Phylogeography and Antigenic Diversity of Low-Pathogenic Avian Influenza H13 and H16 Viruses

Low-pathogenic avian influenza viruses (LPAIVs) are genetically highly variable and have diversified into multiple evolutionary lineages that are primarily associated with wild-bird reservoirs. Antigenic variation has been described for mammalian influenza viruses and for highly pathogenic avian influenza viruses that circulate in poultry, but much less is known about antigenic variation of LPAIVs. In this study, we focused on H13 and H16 LPAIVs that circulate globally in gulls. We investigated the evolutionary history and intercontinental gene flow based on the hemagglutinin (HA) gene and used representative viruses from genetically distinct lineages to determine their antigenic properties by hemagglutination inhibition assays. For H13, at least three distinct genetic clades were evident, while for H16, at least two distinct genetic clades were evident. Twenty and ten events of intercontinental gene flow were identified for H13 and H16 viruses, respectively. At least two antigenic variants of H13 and at least one antigenic variant of H16 were identified. Amino acid positions in the HA protein that may be involved in the antigenic variation were inferred, and some of the positions were located near the receptor binding site of the HA protein, as they are in the HA protein of mammalian influenza A viruses. These findings suggest independent circulation of H13 and H16 subtypes in gull populations, as antigenic patterns do not overlap, and they contribute to the understanding of the genetic and antigenic variation of LPAIVs naturally circulating in wild birds.IMPORTANCE Wild birds play a major role in the epidemiology of low-pathogenic avian influenza viruses (LPAIVs), which are occasionally transmitted-directly or indirectly-from them to other species, including domestic animals, wild mammals, and humans, where they can cause subclinical to fatal disease. Despite a multitude of genetic studies, the antigenic variation of LPAIVs in wild birds is poorly understood. Here, we investigated the evolutionary history, intercontinental gene flow, and antigenic variation among H13 and H16 LPAIVs. The circulation of subtypes H13 and H16 seems to be maintained by a narrower host range, in particular gulls, than the majority of LPAIV subtypes and may therefore serve as a model for evolution and epidemiology of H1 to H12 LPAIVs in wild birds. The findings suggest that H13 and H16 LPAIVs circulate independently of each other and emphasize the need to investigate within-clade antigenic variation of LPAIVs in wild birds.

Bat coronavirus phylogeography in the Western Indian Ocean

Bats provide key ecosystem services such as crop pest regulation, pollination, seed dispersal, and soil fertilization. Bats are also major hosts for biological agents responsible for zoonoses, such as coronaviruses (CoVs). The islands of the Western Indian Ocean are identified as a major biodiversity hotspot, with more than 50 bat species. In this study, we tested 1,013 bats belonging to 36 species from Mozambique, Madagascar, Mauritius, Mayotte, Reunion Island and Seychelles, based on molecular screening and partial sequencing of the RNA-dependent RNA polymerase gene. In total, 88 bats (8.7%) tested positive for coronaviruses, with higher prevalence in Mozambican bats (20.5% ± 4.9%) as compared to those sampled on islands (4.5% ± 1.5%). Phylogenetic analyses revealed a large diversity of α- and β-CoVs and a strong signal of co-evolution between CoVs and their bat host species, with limited evidence for host-switching, except for bat species sharing day roost sites. These results highlight that strong variation between islands does exist and is associated with the composition of the bat species community on each island. Future studies should investigate whether CoVs detected in these bats have a potential for spillover in other hosts.

First insight into phylogeography of Mycobacterium bovis and M. caprae from cattle in Bulgaria

Bovine tuberculosis (bTB) represents a significant economic burden to the agriculture. In spite of decades of the control program, Mycobacterium bovis infection levels in cattle in Bulgaria continued to rise over recent years. In order to gain a better understanding of the M. bovis diversity, we used spoligotyping for strain differentiation and the data were compared to the international databases Mbovis.org and SITVIT2 for shared type and clade assignment. Study sample included 30 M. tuberculosis complex isolates from cattle originating from different regions of Bulgaria. The isolates were subdivided by spoligotyping into 4 spoligotypes: 2 types shared by 20 and 8 isolates and 2 singletons. SITVIT2-defined types SIT645 and SIT647 belonged to the common and classical bovine ecotype M. bovis (9 isolates) while types SIT120 and SIT339 belonged to the M. caprae ecotype (21 isolates). A certain phylogeographic gradient of the spoligotypes and clades at the within-country level was observed: M. caprae was prevalent in the central/southwestern, while classical M. bovis in the northeastern Bulgaria. Whereas all four types have global or European circulation, neither was described in the neighboring Balkan countries. M. caprae isolates identified in this study mostly belong to the Central/Eastern European cluster. In summary, this study provided a first insight into phylogeography of M. bovis in Bulgaria and described, for the first time, M. caprae as an important infectious agent of bTB in this country.

The Unique Lipidomic Signatures of Saccharina latissima Can Be Used to Pinpoint Their Geographic Origin

The aquaculture of macroalgae for human consumption and other high-end applications is experiencing unprecedented development in European countries, with the brown algae Saccharina latissima being the flag species. However, environmental conditions in open sea culture sites are often unique, which may impact the biochemical composition of cultured macroalgae. The present study compared the elemental compositions (CHNS), fatty acid profiles, and lipidomes of S. latissima originating from three distinct locations (France, Norway, and the United Kingdom). Significant differences were found in the elemental composition, with Norwegian samples displaying twice the lipid content of the others, and significantly less protein (2.6%, while French and UK samples contained 6.3% and 9.1%, respectively). The fatty acid profiles also differed considerably, with UK samples displaying a lower content of n-3 fatty acids (21.6%), resulting in a higher n-6/n-3 ratio. Regarding the lipidomic profile, samples from France were enriched in lyso lipids, while those from Norway displayed a particular signature of phosphatidylglycerol, phosphatidylinositol, and phosphatidylcholine. Samples from the UK featured higher levels of phosphatidylethanolamine and, in general, a lower content of galactolipids. These differences highlight the influence of site-specific environmental conditions in the shaping of macroalgae biochemical phenotypes and nutritional value. It is also important to highlight that differences recorded in the lipidome of S. latissima make it possible to pinpoint specific lipid species that are likely to represent origin biomarkers. This finding is relevant for future applications in the field of geographic origin traceability and food control.

Genome Resolved Biogeography of Mamiellales

Among marine phytoplankton, Mamiellales encompass several species from the genera Micromonas, Ostreococcus and Bathycoccus, which are important contributors to primary production. Previous studies based on single gene markers described their wide geographical distribution but led to discussion because of the uneven taxonomic resolution of the method. Here, we leverage genome sequences for six Mamiellales species, two from each genus Micromonas, Ostreococcus and Bathycoccus, to investigate their distribution across 133 stations sampled during the Tara Oceans expedition. Our study confirms the cosmopolitan distribution of Mamiellales and further suggests non-random distribution of species, with two triplets of co-occurring genomes associated with different temperatures: Ostreococcuslucimarinus, Bathycoccusprasinos and Micromonaspusilla were found in colder waters, whereas Ostreococcus spp. RCC809, Bathycoccus spp. TOSAG39-1 and Micromonascommoda were more abundant in warmer conditions. We also report the distribution of the two candidate mating-types of Ostreococcus for which the frequency of sexual reproduction was previously assumed to be very low. Indeed, both mating types were systematically detected together in agreement with either frequent sexual reproduction or the high prevalence of a diploid stage. Altogether, these analyses provide novel insights into Mamiellales' biogeography and raise novel testable hypotheses about their life cycle and ecology.

Genome-wide profiles indicate wolf population connectivity within the eastern Carpathian Mountains

The Carpathian Mountains provide critical wildlife habitat in central Europe, and previous genome-wide studies have found western Carpathian Mountain wolves (Canis lupus) to be a separate population. Whereas differentiation to the north may be explained by a lowland-mountain transition and habitat fragmentation, the eastern Carpathian Mountains extending through Romania appear to offer continuous wildlife habitat southward. Our objective was to assess gene flow patterns and population connectivity among wolves in Romania, western Ukraine, and the Republic of Moldova. We sought to determine if the Carpathian Mountain region is best described by a north-south gradient in genetic profiles, or whether Romanian wolves show population structure with northern individuals clustering with western Ukraine. We genotyped 48 individuals with 170 000 single nucleotide polymorphism markers, and successful profiles from Romania (n = 27) and Moldova (n = 2) were merged with existing data from western Ukraine (n = 10). Expected heterozygosity was 0.234 (SE 0.001) for Romania and 0.229 (SE 0.001) for western Ukraine, whereas observed heterozygosity values were 0.230 (SE 0.001) versus 0.231 (SE 0.001). Population structure analyses with a maximum likelihood method supported K = 1 population, followed by K = 2 where Romania formed one cluster, and western Ukraine and Moldova formed another. Principal component analysis results were broadly consistent with K = 2. Pairwise F_ST between western Ukraine and Romania was 0.042 (p = 0.001). Our findings indicated weak population differentiation, and future research may clarify whether the spatial distribution of genetic diversity in the region is associated with environmental and ecological factors such as terrain ruggedness and the distribution of prey species.

The First Complete Genome Sequences of Hepatitis C Virus Subtype 2b from Latin America: Molecular Characterization and Phylogeographic Analysis

The hepatitis C virus (HCV) has remarkable genetic diversity and exists as eight genotypes (1 to 8) with distinct geographic distributions. No complete genome sequence of HCV subtype 2b (HCV-2b) is available from Latin American countries, and the factors underlying its emergence and spread within the continent remain unknown. The present study was conducted to determine the first full-length genomic sequences of HCV-2b isolates from Latin America and reconstruct the spatial and temporal diversification of this subtype in Brazil. Nearly complete HCV-2b genomes isolated from two Brazilian patients were obtained by direct sequencing of long PCR fragments and analyzed together with reference sequences using the Bayesian coalescent and phylogeographic framework approaches. The two HCV-2b genomes were 9318 nucleotides (nt) in length (nt 37-9354). Interestingly, the long RT-PCR technique was able to detect co-circulation of viral variants that contained an in-frame deletion of 2022 nt encompassing E1, E2, and p7 proteins. Spatiotemporal reconstruction analyses suggest that HCV-2b had a single introduction in Brazil during the early 1980s, displaying an epidemic history characterized by a low and virtually constant population size until the present time. These results coincide with epidemiological data in Brazil and may explain the low national prevalence of this subtype.

Phylodynamic and transmission pattern of rabies virus in China and its neighboring countries

Rabies is a fatal disease caused by infection with rabies virus (RABV), and human rabies is still a critical public-health concern in China. Although there have been some phylogenetic studies about RABV transmission patterns, with the accumulation of more rabies sequences in recent years, there is an urgent need to update and clarify the spatial and temporal patterns of RABV circulating in China on a national scale. In this study, we collected all available RABV nucleoprotein gene sequences from China and its neighboring countries and performed comparative analysis. We identified six significant subclades of RABV circulating in China and found that each of them has a specific geographical distribution, reflecting possible physical barriers to gene flow. The phylogeographic analysis revealed minimal viral movement among different geographical locations. An analysis using Bayesian coalescent methods indicated that the current RABV strains in China may come from a common ancestor about 400 years ago, and currently, China is amid the second event of increasing RABV population since the 1950s, but the population has decreased gradually. We did not detect any evidence of recombination in the sequence dataset, nor did we find any evidence for positive selection during the expansion of RABV. Overall, geographic location and neutral genetic drift may be the main factors in shaping the phylogeography of RABV transmission in China.

Vagrant birds as a dispersal vector in transoceanic range expansion of vascular plants

Birds are thought to be important vectors underlying the disjunct distribution patterns of some terrestrial biota. Here, we investigate the role of birds in the colonisation by Ochetophila trinervis (Rhamnaceae), a vascular plant from the southern Andes, of sub-Antarctic Marion Island. The location of O. trinervis on the island far from human activities, in combination with a reconstruction of island visitors' travel history, precludes an anthropogenic introduction. Notably, three bird species occurring in the southern Andes inland have been observed as vagrants on Marion Island, with the barn swallow Hirundo rustica as the most common one. This vagrant displays long-distance migratory behaviour, eats seeds when insects are in short supply, and has started breeding in South America since the 1980s. Since naturalised O. trinervis has never been found outside the southern Andes and its diaspores are incapable of surviving in seawater or dispersing by wind, a natural avian dispersal event from the Andes to Marion Island, a distance of >7500 km, remains the only probable explanation. Although one self-incompatible shrub seems doomed to remain solitary, its mere establishment on a Southern Ocean island demonstrates the potential of vagrancy as a driver of extreme long-distance dispersal of terrestrial biota.

Phylogeography of the Assassin Bug Sphedanolestes impressicollis in East Asia Inferred From Mitochondrial and Nuclear Gene Sequences

The assassin bug, Sphedanolestes impressicollis (Hemiptera: Reduviidae), is widely distributed in East Asia. It is an ideal model for evaluating the effects of climatic fluctuation and geographical events on the distribution patterns of East Asian reduviids. Here, we used two mitochondrial genes and one nuclear gene to investigate the phylogeographic pattern of the assassin bug based on comprehensive sampling in China, Japan, South Korea, Vietnam, and Laos. High levels of genetic differentiation were detected among the geographic populations classified into the northern and southern groups. A significant correlation was detected between genetic and geographical distances. The East China Sea land bridge served as a “dispersal corridor” during Pleistocene glaciation. The estimated divergence time indicated that the northern group may have separated from the eastern Chinese populations when the sea level rapidly rose during the “Ryukyu Coral Sea Stage” and the East China Sea land bridge was completely submerged. Demographic history and ecological niche modeling suggested that appropriate climatic conditions may have accounted for the rapid spread across the Korean Peninsula and Japan during the late Pleistocene. Our study underscores the pivotal roles of the Pleistocene sea level changes and climatic fluctuations in determining the distribution patterns of East Asian reduviids.

Phylogeography and conservation genetics of the endangered Tugarinovia mongolica (Asteraceae) from Inner Mongolia, Northwest China

Tugarinovia (Family Asteraceae) is a monotypic genus. It’s sole species, Tugarinovia mongolica Iljin, is distributed in the northern part of Inner Mongolia, with one additional variety, Tugarinovia mongolica var ovatifolia, which is distributed in the southern part of Inner Mongolia. The species has a limited geographical range and declining populations. To understand the phylogeographic structure of T. mongolica, we sequenced two chloroplast DNA regions (psbA-trnH and psbK-psbI) from 219 individuals of 16 populations, and investigated the genetic variation and phylogeographic patterns of T. mongolica. The results identified a total of 17 (H1-H17) chloroplast haplotypes. There were no haplotypes shared between the northern (T. mongolica) and southern groups (T. mongolica var. ovatifolia), and they formed two distinct lineages. The regional split was also supported by AMOVA and BEAST analyses. AMOVA showed the main variation that occurred between the two geographic groups. The time of divergence of the two groups can be dated to the early Pleistocene epoch, when climate fluctuations most likely resulted in the allopatric divergence of T. mongolica. The formation of the desert blocked genetic flow and enhanced the divergence of the northern and southern groups. Our results indicate that the genetic differences between T. mongolica and T. mongolica var. ovatifolia are consistent with previously proposed morphological differences. We speculate that the dry, cold climate and the expansion of the desert during the Quaternary resulted in the currently observed distribution of extant populations of T. mongolica. In the northern group, the populations Chuanjinsumu, Wuliji and Yingen displayed the highest genetic diversity and should be given priority protection. The southern group showed a higher genetic drift (F_ST = 1, G_ST = 1), and the inbreeding load (H_S = 0) required protection for each population. Our results propose that the protection of T. mongolica should be implemented through in situ and ex situ conservation practices to increase the effective population size and genetic diversity.

Bi-directional Recurrent Neural Network Models for Geographic Location Extraction in Biomedical Literature

Phylogeography research involving virus spread and tree reconstruction relies on accurate geographic locations of infected hosts. Insufficient level of geographic information in nucleotide sequence repositories such as GenBank motivates the use of natural language processing methods for extracting geographic location names (toponyms) in the scientific article associated with the sequence, and disambiguating the locations to their co-ordinates. In this paper, we present an extensive study of multiple recurrent neural network architectures for the task of extracting geographic locations and their effective contribution to the disambiguation task using population heuristics. The methods presented in this paper achieve a strict detection F1 score of 0.94, disambiguation accuracy of 91% and an overall resolution F1 score of 0.88 that are significantly higher than previously developed methods, improving our capability to find the location of infected hosts and enrich metadata information.

Phylogeny, character evolution and spatiotemporal diversification of the species-rich and world-wide distributed tribe Rubieae (Rubiaceae)

The Rubiaceae tribe Rubieae has a world-wide distribution with up to 1,000 species. These collectively exhibit an enormous ecological and morphological diversity, making Rubieae an excellent group for macro- and microevolutionary studies. Previous molecular phylogenetic analyses used only a limited sampling within the tribe or missed lineages crucial for understanding character evolution in this group. Here, we analyze sequences from two plastid spacer regions as well as morphological and biogeographic data from an extensive and evenly distributed sampling to establish a sound phylogenetic framework. This framework serves as a basis for our investigation of the evolution of important morphological characters and the biogeographic history of the Rubieae. The tribe includes three major clades, the Kelloggiinae Clade (Kelloggia), the Rubiinae Clade (Didymaea, Rubia) and the most species-rich Galiinae Clade (Asperula, Callipeltis, Crucianella, Cruciata, Galium, Mericarpaea, Phuopsis, Sherardia, Valantia). Within the Galiinae Clade, the largest genera Galium and Asperula are para- and polyphyletic, respectively. Smaller clades, however, usually correspond to currently recognized taxa (small genera or sections within genera), which may be used as starting points for a refined classification in this clade. Life-form (perennial versus annual), flower shape (long versus short corolla tube) and fruit characters (dry versus fleshy, with or without uncinate hairs) are highly homoplasious and have changed multiple times independently. Inference on the evolution of leaf whorls, a characteristic feature of the tribe, is sensitive to model choice. Multi-parted leaf whorls appear to have originated from opposite leaves with two small interpetiolar stipules that are subsequently enlarged and increased in number. Early diversification of Rubieae probably started during the Miocene in western Eurasia. Disjunctions between the Old and the New World possibly are due to connections via a North Atlantic land bridge. Diversification of the Galiineae Clade started later in the Miocene, probably in the Mediterranean, from where lineages reached, often multiple times, Africa, eastern Asia and further on the Americas and Australia.

LASER server: ancestry tracing with genotypes or sequence reads

Summary

To enable direct comparison of ancestry background in different studies, we developed LASER to estimate individual ancestry by placing either sezquenced or genotyped samples in a common ancestry space, regardless of the sequencing strategy or genotyping array used to characterize each sample. Here we describe the LASER server to facilitate application of the method to a wide range of genetic studies. The server provides genetic ancestry estimation for different geographic regions and user-friendly interactive visualization of the results.

Availability and Implementation

The LASER server is freely accessible at http://laser.sph.umich.edu/

Supplementary information

Supplementary data are available at Bioinformatics online.

Phylogeography of Daphnia magna Straus (Crustacea: Cladocera) in Northern Eurasia: Evidence for a deep longitudinal split between mitochondrial lineages

Species with a large geographic distributions present a challenge for phylogeographic studies due to logistic difficulties of obtaining adequate sampling. For instance, in most species with a Holarctic distribution, the majority of studies has concentrated on the European or North American part of the distribution, with the Eastern Palearctic region being notably understudied. Here, we study the phylogeography of the freshwater cladoceran Daphnia magna Straus, 1820 (Crustacea: Cladocera), based on partial mitochondrial COI sequences and using specimens from populations spread longitudinally from westernmost Europe to easternmost Asia, with many samples from previously strongly understudied regions in Siberia and Eastern Asia. The results confirm the previously suspected deep split between Eastern and Western mitochondrial haplotype super-clades. We find a narrow contact zone between these two super-clades in the eastern part of Western Siberia, with proven co-occurrence in a single lake in the Novosibirsk region. However, at present there is no evidence suggesting that the two mitochondrial super-clades represent cryptic species. Rather, they may be explained by secondary contact after expansion from different refugia. Interestingly, Central Siberia has previously been found to be an important contact zone also in other cladoceran species, and may thus be a crucial area for understanding the Eurasian phylogeography of freshwater invertebrates. Together, our study provides an unprecedented complete, while still not global, picture of the phylogeography of this important model species.

Use of airborne lidar data to improve plant species richness and diversity monitoring in lowland and mountain forests

We explored the potential of airborne laser scanner (ALS) data to improve Bayesian models linking biodiversity indicators of the understory vegetation to environmental factors. Biodiversity was studied at plot level and models were built to investigate species abundance for the most abundant plants found on each study site, and for ecological group richness based on light preference. The usual abiotic explanatory factors related to climate, topography and soil properties were used in the models. ALS data, available for two contrasting study sites, were used to provide biotic factors related to forest structure, which was assumed to be a key driver of understory biodiversity. Several ALS variables were found to have significant effects on biodiversity indicators. However, the responses of biodiversity indicators to forest structure variables, as revealed by the Bayesian model outputs, were shown to be dependent on the abiotic environmental conditions characterizing the study areas. Lower responses were observed on the lowland site than on the mountainous site. In the latter, shade-tolerant and heliophilous species richness was impacted by vegetation structure indicators linked to light penetration through the canopy. However, to reveal the full effects of forest structure on biodiversity indicators, forest structure would need to be measured over much wider areas than the plot we assessed. It seems obvious that the forest structure surrounding the field plots can impact biodiversity indicators measured at plot level. Various scales were found to be relevant depending on: the biodiversity indicators that were modelled, and the ALS variable. Finally, our results underline the utility of lidar data in abundance and richness models to characterize forest structure with variables that are difficult to measure in the field, either due to their nature or to the size of the area they relate to.

Introduction to the human gut microbiota

The human gastrointestinal (GI) tract harbours a complex and dynamic population of microorganisms, the gut microbiota, which exert a marked influence on the host during homeostasis and disease. Multiple factors contribute to the establishment of the human gut microbiota during infancy. Diet is considered as one of the main drivers in shaping the gut microbiota across the life time. Intestinal bacteria play a crucial role in maintaining immune and metabolic homeostasis and protecting against pathogens. Altered gut bacterial composition (dysbiosis) has been associated with the pathogenesis of many inflammatory diseases and infections. The interpretation of these studies relies on a better understanding of inter-individual variations, heterogeneity of bacterial communities along and across the GI tract, functional redundancy and the need to distinguish cause from effect in states of dysbiosis. This review summarises our current understanding of the development and composition of the human GI microbiota, and its impact on gut integrity and host health, underlying the need for mechanistic studies focusing on host-microbe interactions.

Diversification of the rainfrog Pristimantis ornatissimus in the lowlands and Andean foothills of Ecuador

Geographic barriers and elevational gradients have long been recognized as important in species diversification. Here, we illustrate an example where both mechanisms have shaped the genetic structure of the Neotropical rainfrog, Pristimantis ornatissimus, which has also resulted in speciation. This species was thought to be a single evolutionary lineage distributed throughout the Ecuadorian Chocó and the adjacent foothills of the Andes. Based on recent sampling of P. ornatissimus sensu lato, we provide molecular and morphological evidence that support the validity of a new species, which we name Pristimantis ecuadorensis sp. nov. The sister species are elevational replacements of each other; the distribution of Pristimantis ornatissimus sensu stricto is limited to the Ecuadorian Chocó ecoregion (< 1100 m), whereas the new species has only been found at Andean localities between 1450–1480 m. Given the results of the Multiple Matrix Regression with Randomization analysis, the genetic difference between P. ecuadorensis and P. ornatissimus is not explained by geographic distance nor environment, although environmental variables at a finer scale need to be tested. Therefore this speciation event might be the byproduct of stochastic historic extinction of connected populations or biogeographic events caused by barriers to dispersal such as rivers. Within P. ornatissimus sensu stricto, morphological patterns and genetic structure seem to be related to geographic isolation (e.g., rivers). Finally, we provide an updated phylogeny for the genus, including the new species, as well as other Ecuadorian Pristimantis.

A novel recombinant variant of latent membrane protein 1 from Epstein Barr virus in Argentina denotes phylogeographical association

Epstein Barr virus (EBV) infection in Argentina occurs at an early age and occasionally develops infectious mononucleosis (IM). EBV is also related with lymphomas. LMP1, the viral oncoprotein is polymorphic and is used to define viral variants.

Novel probabilistic models of spatial genetic ancestry with applications to stratification correction in genome-wide association studies

Motivation

Genetic variation in human populations is influenced by geographic ancestry due to spatial locality in historical mating and migration patterns. Spatial population structure in genetic datasets has been traditionally analyzed using either model-free algorithms, such as principal components analysis (PCA) and multidimensional scaling, or using explicit spatial probabilistic models of allele frequency evolution. We develop a general probabilistic model and an associated inference algorithm that unify the model-based and data-driven approaches to visualizing and inferring population structure. Our spatial inference algorithm can also be effectively applied to the problem of population stratification in genome-wide association studies (GWAS), where hidden population structure can create fictitious associations when population ancestry is correlated with both the genotype and the trait.

Results

Our algorithm Geographic Ancestry Positioning (GAP) relates local genetic distances between samples to their spatial distances, and can be used for visually discerning population structure as well as accurately inferring the spatial origin of individuals on a two-dimensional continuum. On both simulated and several real datasets from diverse human populations, GAP exhibits substantially lower error in reconstructing spatial ancestry coordinates compared to PCA. We also develop an association test that uses the ancestry coordinates inferred by GAP to accurately account for ancestry-induced correlations in GWAS. Based on simulations and analysis of a dataset of 10 metabolic traits measured in a Northern Finland cohort, which is known to exhibit significant population structure, we find that our method has superior power to current approaches.

Availability and Implementation

Our software is available at https://github.com/anand-bhaskar/gap .

Contacts

abhaskar@stanford.edu or ajavanma@usc.edu.

Supplementary information

Supplementary data are available at Bioinformatics online.

Mitogenomic Phylogeny, Diversification, and Biogeography of South American Spiny Rats

Echimyidae is one of the most speciose and ecologically diverse rodent families in the world, occupying a wide range of habitats in the Neotropics. However, a resolved phylogeny at the genus-level is still lacking for these 22 genera of South American spiny rats, including the coypu (Myocastorinae), and 5 genera of West Indian hutias (Capromyidae) relatives. Here, we used Illumina shotgun sequencing to assemble 38 new complete mitogenomes, establishing Echimyidae, and Capromyidae as the first major rodent families to be completely sequenced at the genus-level for their mitochondrial DNA. Combining mitogenomes and nuclear exons, we inferred a robust phylogenetic framework that reveals several newly supported nodes as well as the tempo of the higher level diversification of these rodents. Incorporating the full generic diversity of extant echimyids leads us to propose a new higher level classification of two subfamilies: Euryzygomatomyinae and Echimyinae. Of note, the enigmatic Carterodon displays fast-evolving mitochondrial and nuclear sequences, with a long branch that destabilizes the deepest divergences of the echimyid tree, thereby challenging the sister-group relationship between Capromyidae and Euryzygomatomyinae. Biogeographical analyses involving higher level taxa show that several vicariant and dispersal events impacted the evolutionary history of echimyids. The diversification history of Echimyidae seems to have been influenced by two major historical factors, namely (1) recurrent connections between Atlantic and Amazonian Forests and (2) the Northern uplift of the Andes.

Bayesian phylogeography of influenza A/H3N2 for the 2014-15 season in the United States using three frameworks of ancestral state reconstruction

Ancestral state reconstructions in Bayesian phylogeography of virus pandemics have been improved by utilizing a Bayesian stochastic search variable selection (BSSVS) framework. Recently, this framework has been extended to model the transition rate matrix between discrete states as a generalized linear model (GLM) of genetic, geographic, demographic, and environmental predictors of interest to the virus and incorporating BSSVS to estimate the posterior inclusion probabilities of each predictor. Although the latter appears to enhance the biological validity of ancestral state reconstruction, there has yet to be a comparison of phylogenies created by the two methods. In this paper, we compare these two methods, while also using a primitive method without BSSVS, and highlight the differences in phylogenies created by each. We test six coalescent priors and six random sequence samples of H3N2 influenza during the 2014–15 flu season in the U.S. We show that the GLMs yield significantly greater root state posterior probabilities than the two alternative methods under five of the six priors, and significantly greater Kullback-Leibler divergence values than the two alternative methods under all priors. Furthermore, the GLMs strongly implicate temperature and precipitation as driving forces of this flu season and nearly unanimously identified a single root state, which exhibits the most tropical climate during a typical flu season in the U.S. The GLM, however, appears to be highly susceptible to sampling bias compared with the other methods, which casts doubt on whether its reconstructions should be favored over those created by alternate methods. We report that a BSSVS approach with a Poisson prior demonstrates less bias toward sample size under certain conditions than the GLMs or primitive models, and believe that the connection between reconstruction method and sampling bias warrants further investigation.

For the better part of the last decade, epidemiological researchers have employed a Bayesian framework to reconstruct phylogenetic trees and determine the spatiotemporal relationships between clades of viruses. Recently, an extension of this framework has enabled direct assessment of how various demographic, geographic, genetic, and environmental variables play a role in these relationships, but there has yet to be a comparison between the former and the latter. Here, we aim to assess the differences between the two reconstruction techniques, as well as an additional primitive method, using the 2014–15 influenza season in the U.S. as a case study under a variety of population growth scenarios. We highlight how the new method demonstrates significant increases in commonly-reported trends in phylogenies and that the method identifies climate predictors that appear to be consistent with known trends in seasonal trends in influenza. However, we found that this method appears to be the most heavily influenced by the locations at which the viruses were obtained. Our work offers valuable insight for researchers wishing to study the evolutionary history of viruses and also may prove useful in determining the correct method to choose for a given application of virus phylogeography.

Comparative analysis of genetic polymorphisms among Monascus strains by ISSR and RAPD markers

BACKGROUND

The genus Monascus includes several species of fungi valued across Asia for their culinary uses and diverse medicinal properties. In this study, we evaluated the applicability of random amplified polymorphic DNA (RAPD) and inter-simple sequence repeats (ISSR) markers in characterizing the genetic diversity in 41 Monascus strains collected from various regions of Fujian Province, the leading producer of Monascus in China.

RESULTS

Seven screened ISSR primers generated 56 polymorphic bands, of which 93.33% were polymorphic. The genetic similarity coefficients (GSC) of the strains ranged from 0.50 to 1.00. Comparative sequence analysis using seven screened RAPD primers amplified a total of 49 polymorphic bands, of which 81.67% were polymorphic; GSC values ranged from 0.62 to 1.00.

CONCLUSION

Correlation analysis revealed a significant positive correlation in genetic distances assessed using above two markers, which indicated they were suitable for Monascus species characterization. ISSR markers were more suitable for the classification and determination of Monascus species, while RAPD markers appear to be preferable for analyzing the differences among strains within the same species. Our study revealed that Monascus possesses rich genetic diversity, and that the genetic relationships among the selected strains were, to a very limited extent, correlated to their geographical variation. © 2016 Society of Chemical Industry.

Male Circumcision and the Epidemic Emergence of HIV-2 in West Africa

BACKGROUND

Epidemic HIV-2 (groups A and B) emerged in humans circa 1930-40. Its closest ancestors are SIVsmm infecting sooty mangabeys from southwestern Côte d'Ivoire. The earliest large-scale serological surveys of HIV-2 in West Africa (1985-91) show a patchy spread. Côte d'Ivoire and Guinea-Bissau had the highest prevalence rates by then, and phylogeographical analysis suggests they were the earliest epicenters. Wars and parenteral transmission have been hypothesized to have promoted HIV-2 spread. Male circumcision (MC) is known to correlate negatively with HIV-1 prevalence in Africa, but studies examining this issue for HIV-2 are lacking.

METHODS

We reviewed published HIV-2 serosurveys for 30 cities of all West African countries and obtained credible estimates of real prevalence through Bayesian estimation. We estimated past MC rates of 218 West African ethnic groups, based on ethnographic literature and fieldwork. We collected demographic tables specifying the ethnic partition in cities. Uncertainty was incorporated by defining plausible ranges of parameters (e.g. timing of introduction, proportion circumcised). We generated 1,000 sets of past MC rates per city using Latin Hypercube Sampling with different parameter combinations, and explored the correlation between HIV-2 prevalence and estimated MC rate (both logit-transformed) in the 1,000 replicates.

RESULTS AND CONCLUSIONS

Our survey reveals that, in the early 20th century, MC was far less common and geographically more variable than nowadays. HIV-2 prevalence in 1985-91 and MC rates in 1950 were negatively correlated (Spearman rho = -0.546, IQR: -0.553--0.546, p≤0.0021). Guinea-Bissau and Côte d'Ivoire cities had markedly lower MC rates. In addition, MC was uncommon in rural southwestern Côte d'Ivoire in 1930.The differential HIV-2 spread in West Africa correlates with different historical MC rates. We suggest HIV-2 only formed early substantial foci in cities with substantial uncircumcised populations. Lack of MC in rural areas exposed to bushmeat may have had a role in successful HIV-2 emergence.

[Evaluation of PAE and AE for identifying generalized tracks using snakes in Hidalgo, Mexico]

One of the most important concepts in Panbiogeography is the generalized track, which represents an ancestral biota fragmented by geological events that can be recovered through several methods, including Parsimony analysis of endemicity (PAE) and endemicity analysis (EA). PAE has been frequently used to identify generalized tracks, while EA is primarily designed to find areas of endemicity, but has been recently proposed for identifying generalized tracks as well. In this study we evaluated these methods to find generalized tracks using the distribution of the 84 snake species of Hidalgo. PAE found one generalized track from three individual tracks (Agkistrodon taylori, Crotalus totonacus and Pliocercus elapoides), supported by 89 % of Bootstrap, and EA identified two generalized tracks, with endemicity index values of 2.71-2.96 and 2.84-3.09, respectively. Those areas were transformed to generalized tracks. The first generalized track was retrieved from three individual tracks (Micrurus bernadi, Rhadinaea marcellae and R. quinquelineata), and the second was recovered from two individual tracks (Geophis mutitorques and Thamnophis sumichrasti). These generalized tracks can be considered a unique distribution pattern, because they resembled each other and agreed in shape. When comparing both methods, we noted that both are useful for identifying generalized tracks, and although they can be used independently, we suggest their complementary use. Nevertheless, to obtain accurate results, it is useful to consider theoretical bases of both methods, along with an appropriate choice of the size of the area. Results using small-grid size in EA are ideal for searching biogeographical patterns within geopolitical limits. Furthermore, they can be used for conservation proposals at state level where endemic species become irreplaceable, and where losing them would imply the extinction of unique lineages.

Water as Source of Francisella tularensis Infection in Humans, Turkey

Francisella tularensis DNA extractions and isolates from the environment and humans were genetically characterized to elucidate environmental sources that cause human tularemia in Turkey. Extensive genetic diversity consistent with genotypes from human outbreaks was identified in environmental samples and confirmed water as a source of human tularemia in Turkey.

Phylogeography of Influenza A(H3N2) Virus in Peru, 2010-2012

It remains unclear whether lineages of influenza A(H3N2) virus can persist in the tropics and seed temperate areas. We used viral gene sequence data sampled from Peru to test this source-sink model for a Latin American country. Viruses were obtained during 2010-2012 from influenza surveillance cohorts in Cusco, Tumbes, Puerto Maldonado, and Lima. Specimens positive for influenza A(H3N2) virus were randomly selected and underwent hemagglutinin sequencing and phylogeographic analyses. Analysis of 389 hemagglutinin sequences from Peru and 2,192 global sequences demonstrated interseasonal extinction of Peruvian lineages. Extensive mixing occurred with global clades, but some spatial structure was observed at all sites; this structure was weakest in Lima and Puerto Maldonado, indicating that these locations may experience greater viral traffic. The broad diversity and co-circulation of many simultaneous lineages of H3N2 virus in Peru suggests that this country should not be overlooked as a potential source for novel pandemic strains.

Parallel Evolution of Copy-Number Variation across Continents in Drosophila melanogaster

Genetic differentiation across populations that is maintained in the presence of gene flow is a hallmark of spatially varying selection. In Drosophila melanogaster, the latitudinal clines across the eastern coasts of Australia and North America appear to be examples of this type of selection, with recent studies showing that a substantial portion of the D. melanogaster genome exhibits allele frequency differentiation with respect to latitude on both continents. As of yet there has been no genome-wide examination of differentiated copy-number variants (CNVs) in these geographic regions, despite their potential importance for phenotypic variation in Drosophila and other taxa. Here, we present an analysis of geographic variation in CNVs in D. melanogaster. We also present the first genomic analysis of geographic variation for copy-number variation in the sister species, D. simulans, in order to investigate patterns of parallel evolution in these close relatives. In D. melanogaster we find hundreds of CNVs, many of which show parallel patterns of geographic variation on both continents, lending support to the idea that they are influenced by spatially varying selection. These findings support the idea that polymorphic CNVs contribute to local adaptation in D. melanogaster In contrast, we find very few CNVs in D. simulans that are geographically differentiated in parallel on both continents, consistent with earlier work suggesting that clinal patterns are weaker in this species.

Historical Biogeography Using Species Geographical Ranges

Spatial variation in biodiversity is the result of complex interactions between evolutionary history and ecological factors. Methods in historical biogeography combine phylogenetic information with current species locations to infer the evolutionary history of a clade through space and time. A major limitation of most methods for historical biogeographic inference is the requirement of single locations for terminal lineages, reducing contemporary species geographical ranges to a point in two-dimensional space. In reality, geographic ranges usually show complex geographic patterns, irregular shapes, or discontinuities. In this article, we describe a method for phylogeographic analysis using polygonal species geographic ranges of arbitrary complexity. By integrating the geographic diversification process across species ranges, we provide a method to infer the geographic location of ancestors in a Bayesian framework. By modeling migration conditioned on a phylogenetic tree, this approach permits reconstructing the geographic location of ancestors through time. We apply this new method to the diversification of two neotropical bird genera, Trumpeters (Psophia) and Cinclodes ovenbirds. We demonstrate the usefulness of our method (called rase) in phylogeographic reconstruction of species ancestral locations and contrast our results with previous methods that compel researchers to reduce the distribution of species to one point in space. We discuss model extensions to enable a more general, spatially explicit framework for historical biogeographic analysis.

Biogeographic calibrations for the molecular clock

Molecular estimates of evolutionary timescales have an important role in a range of biological studies. Such estimates can be made using methods based on molecular clocks, including models that are able to account for rate variation across lineages. All clock models share a dependence on calibrations, which enable estimates to be given in absolute time units. There are many available methods for incorporating fossil calibrations, but geological and climatic data can also provide useful calibrations for molecular clocks. However, a number of strong assumptions need to be made when using these biogeographic calibrations, leading to wide variation in their reliability and precision. In this review, we describe the nature of biogeographic calibrations and the assumptions that they involve. We present an overview of the different geological and climatic events that can provide informative calibrations, and explain how such temporal information can be incorporated into dating analyses.

New Routes to Phylogeography: A Bayesian Structured Coalescent Approximation

Phylogeographic methods aim to infer migration trends and the history of sampled lineages from genetic data. Applications of phylogeography are broad, and in the context of pathogens include the reconstruction of transmission histories and the origin and emergence of outbreaks. Phylogeographic inference based on bottom-up population genetics models is computationally expensive, and as a result faster alternatives based on the evolution of discrete traits have become popular. In this paper, we show that inference of migration rates and root locations based on discrete trait models is extremely unreliable and sensitive to biased sampling. To address this problem, we introduce BASTA (BAyesian STructured coalescent Approximation), a new approach implemented in BEAST2 that combines the accuracy of methods based on the structured coalescent with the computational efficiency required to handle more than just few populations. We illustrate the potentially severe implications of poor model choice for phylogeographic analyses by investigating the zoonotic transmission of Ebola virus. Whereas the structured coalescent analysis correctly infers that successive human Ebola outbreaks have been seeded by a large unsampled non-human reservoir population, the discrete trait analysis implausibly concludes that undetected human-to-human transmission has allowed the virus to persist over the past four decades. As genomics takes on an increasingly prominent role informing the control and prevention of infectious diseases, it will be vital that phylogeographic inference provides robust insights into transmission history.

When studying infectious diseases it is often important to understand how germs spread from location-to-location, person-to-person, or even one part of the body to another. Using phylogeographic methods, it is possible to recover the history of spread of pathogens (or other organisms) by studying their genetic material. Here we reveal that some popular, fast phylogeographic methods are inaccurate, and we introduce a new more reliable method to address the problem. By comparing different phylogeographic methods based on principled population models and fast alternatives, we found that different approaches can give diametrically opposed results, and we offer concrete examples in the context of the ongoing Ebola outbreak in West Africa and the world-wide outbreaks of Avian Influenza Virus and Tomato Yellow Leaf Curl Virus. We found that the most popular phylogeographic method often produces completely inaccurate conclusions. One of the reasons for its popularity has been its computational speed, which has allowed users to analyse large genetic datasets with complex models. More accurate approaches have until now been considerably slower, and therefore we propose a new method called BASTA that achieves good accuracy in a reasonable time. We are relying more and more on genetic sequencing to learn about the origin and spread of infections, and as this role continues to grow, it will be essential to use accurate phylogeographic methods when designing policies to prevent or curb the spread of disease.

Inferring Population Genetic Structure in Widely and Continuously Distributed Carnivores: The Stone Marten (Martes foina) as a Case Study

The stone marten is a widely distributed mustelid in the Palaearctic region that exhibits variable habitat preferences in different parts of its range. The species is a Holocene immigrant from southwest Asia which, according to fossil remains, followed the expansion of the Neolithic farming cultures into Europe and possibly colonized the Iberian Peninsula during the Early Neolithic (ca. 7,000 years BP). However, the population genetic structure and historical biogeography of this generalist carnivore remains essentially unknown. In this study we have combined mitochondrial DNA (mtDNA) sequencing (621 bp) and microsatellite genotyping (23 polymorphic markers) to infer the population genetic structure of the stone marten within the Iberian Peninsula. The mtDNA data revealed low haplotype and nucleotide diversities and a lack of phylogeographic structure, most likely due to a recent colonization of the Iberian Peninsula by a few mtDNA lineages during the Early Neolithic. The microsatellite data set was analysed with a) spatial and non-spatial Bayesian individual-based clustering (IBC) approaches (STRUCTURE, TESS, BAPS and GENELAND), and b) multivariate methods [discriminant analysis of principal components (DAPC) and spatial principal component analysis (sPCA)]. Additionally, because isolation by distance (IBD) is a common spatial genetic pattern in mobile and continuously distributed species and it may represent a challenge to the performance of the above methods, the microsatellite data set was tested for its presence. Overall, the genetic structure of the stone marten in the Iberian Peninsula was characterized by a NE-SW spatial pattern of IBD, and this may explain the observed disagreement between clustering solutions obtained by the different IBC methods. However, there was significant indication for contemporary genetic structuring, albeit weak, into at least three different subpopulations. The detected subdivision could be attributed to the influence of the rivers Ebro, Tagus and Guadiana, suggesting that main watercourses in the Iberian Peninsula may act as semi-permeable barriers to gene flow in stone martens. To our knowledge, this is the first phylogeographic and population genetic study of the species at a broad regional scale. We also wanted to make the case for the importance and benefits of using and comparing multiple different clustering and multivariate methods in spatial genetic analyses of mobile and continuously distributed species.

Hitting an Unintended Target: Phylogeography of Bombus brasiliensis Lepeletier, 1836 and the First New Brazilian Bumblebee Species in a Century (Hymenoptera: Apidae)

This work tested whether or not populations of Bombus brasiliensis isolated on mountain tops of southeastern Brazil belonged to the same species as populations widespread in lowland areas in the Atlantic coast and westward along the Paraná-river valley. Phylogeographic and population genetic analyses showed that those populations were all conspecific. However, they revealed a previously unrecognized, apparently rare, and potentially endangered species in one of the most threatened biodiversity hotspots of the World, the Brazilian Atlantic Forest. This species is described here as Bombus bahiensis sp. n., and included in a revised key for the identification of the bumblebee species known to occur in Brazil. Phylogenetic analyses based on two mtDNA markers suggest this new species to be sister to B. brasiliensis, from which its workers and queens can be easily distinguished by the lack of a yellow hair-band on the first metasomal tergum. The results presented here are consistent with the hypothesis that B. bahiensis sp. n. may have originated from an ancestral population isolated in an evergreen-forest refuge (the so-called Bahia refuge) during cold, dry periods of the Pleistocene. This refuge is also known as an important area of endemism for several animal taxa, including other bees. Secondary contact between B. bahiensis and B. brasiliensis may be presently prevented by a strip of semi-deciduous forest in a climate zone characterized by relatively long dry seasons. Considering the relatively limited range of this new species and the current anthropic pressure on its environment, attention should be given to its conservation status.

Mapping biodiversity and setting conservation priorities for SE Queensland's rainforests using DNA barcoding

Australian rainforests have been fragmented due to past climatic changes and more recently landscape change as a result of clearing for agriculture and urban spread. The subtropical rainforests of South Eastern Queensland are significantly more fragmented than the tropical World Heritage listed northern rainforests and are subject to much greater human population pressures. The Australian rainforest flora is relatively taxonomically rich at the family level, but less so at the species level. Current methods to assess biodiversity based on species numbers fail to adequately capture this richness at higher taxonomic levels. We developed a DNA barcode library for the SE Queensland rainforest flora to support a methodology for biodiversity assessment that incorporates both taxonomic diversity and phylogenetic relationships. We placed our SE Queensland phylogeny based on a three marker DNA barcode within a larger international rainforest barcode library and used this to calculate phylogenetic diversity (PD). We compared phylo- diversity measures, species composition and richness and ecosystem diversity of the SE Queensland rainforest estate to identify which bio subregions contain the greatest rainforest biodiversity, subregion relationships and their level of protection. We identified areas of highest conservation priority. Diversity was not correlated with rainforest area in SE Queensland subregions but PD was correlated with both the percent of the subregion occupied by rainforest and the diversity of regional ecosystems (RE) present. The patterns of species diversity and phylogenetic diversity suggest a strong influence of historical biogeography. Some subregions contain significantly more PD than expected by chance, consistent with the concept of refugia, while others were significantly phylogenetically clustered, consistent with recent range expansions.

Diversity of Francisella tularensis subsp. holarctica lineages, China

We analyzed 10 isolates of Francisella tularensis subspecies holarctica from China and assigned them to known clades by using canonical single-nucleotide polymorphisms. We found 4 diverse subtypes, including 3 from the most basal lineage, biovar japonica. This result indicates unprecedented levels of diversity from a single region and suggests new models for emergence.

Mapping biodiversity and setting conservation priorities for SE Queensland's rainforests using DNA barcoding

Australian rainforests have been fragmented due to past climatic changes and more recently landscape change as a result of clearing for agriculture and urban spread. The subtropical rainforests of South Eastern Queensland are significantly more fragmented than the tropical World Heritage listed northern rainforests and are subject to much greater human population pressures. The Australian rainforest flora is relatively taxonomically rich at the family level, but less so at the species level. Current methods to assess biodiversity based on species numbers fail to adequately capture this richness at higher taxonomic levels. We developed a DNA barcode library for the SE Queensland rainforest flora to support a methodology for biodiversity assessment that incorporates both taxonomic diversity and phylogenetic relationships. We placed our SE Queensland phylogeny based on a three marker DNA barcode within a larger international rainforest barcode library and used this to calculate phylogenetic diversity (PD). We compared phylo- diversity measures, species composition and richness and ecosystem diversity of the SE Queensland rainforest estate to identify which bio subregions contain the greatest rainforest biodiversity, subregion relationships and their level of protection. We identified areas of highest conservation priority. Diversity was not correlated with rainforest area in SE Queensland subregions but PD was correlated with both the percent of the subregion occupied by rainforest and the diversity of regional ecosystems (RE) present. The patterns of species diversity and phylogenetic diversity suggest a strong influence of historical biogeography. Some subregions contain significantly more PD than expected by chance, consistent with the concept of refugia, while others were significantly phylogenetically clustered, consistent with recent range expansions.

Syndromic Surveillance of Infectious Diseases meets Molecular Epidemiology in a Workflow and Phylogeographic Application

Traditionally, epidemiologists have counted cases and groups of symptoms. Modeling on these data consists of predicting expansion or contraction in the number of cases over time in epidemic curves or compartment models. Geography is considered a variable when these data are presented in choropleth maps. These approaches have significant drawbacks if the cases counted are not accurately diagnosed. For example, most regional public health authorities count influenza like illnesses (ILI). Cases of these diseases are designated as ILI if the patient exhibits fever, respiratory symptoms, and perhaps gastrointestinal symptoms. Several molecular epidemiological studies have shown that there are many pathogens that cause these symptoms and the relative proportions of these pathogens change over time and space. One way to bridge the gap between syndromic and genetic surveillance of infectious diseases is to compare signals of symptoms to pathogens recorded in molecular databases. We present a web-based workflow application that uses chief complaints found in the public Twitter feed as a syndromic surveillance tool and connects outbreak signals in these data to pathogens historically known to circulate in the same area. For the pathogen(s) of interest, we provide Genbank links to metadata and sequences in a workflow for phylogeographic analysis and visualization. The visualizations provide information on the geographic traffic of the spread of the pathogens and places that are hubs for their transport.

Phylogeography of Rhodiola kirilowii (Crassulaceae): a story of Miocene divergence and quaternary expansion

The evolution and current distribution of the Sino-Tibetan flora have been greatly affected by historical geological events, such as the uplift of the Qinghai-Tibetan Plateau (QTP), and Quaternary climatic oscillations. Rhodiola kirilowii, a perennial herb with its distribution ranging from the southeastern QTP and the Hengduan Mountains (HM) to adjacent northern China and central Asia, provides an excellent model to examine and disentangle the effect of both geological orogeny and climatic oscillation on the evolutionary history of species with such distribution patterns. We here conducted a phylogeographic study using sequences of two chloroplast fragments (trnL-F and trnS-G) and internal transcribed spacers in 29 populations of R. kirilowii. A total of 25 plastid haplotypes and 12 ITS ribotypes were found. Molecular clock estimation revealed deep divergence between the central Asian populations and other populations from the HM and northern China; this split occurred ca. 2.84 million year ago. The majority of populations from the mountains of northern China were dominated by a single haplotype or ribotype, while populations of the HM harbored both high genetic diversity and high haplotype diversity. This distribution pattern indicates that HM was either a diversification center or a refugium for R. kirilowii during the Quaternary climatic oscillations. The present distribution of this species on mountains in northern China may have resulted from a rapid glacial population expansion from the HM. This expansion was confirmed by the mismatch distribution analysis and negative Tajima's D and Fu's FS values, and was dated to ca. 168 thousand years ago. High genetic diversity and population differentiation in both plastid and ITS sequences were revealed; these imply restricted gene flow between populations. A distinct isolation-by-distance pattern was suggested by the Mantel test. Our results show that in old lineages, populations may harbour divergent genetic forms that are sufficient to maintain or even increase overall genetic diversity despite fragmentation and low within-population variation.