Empirical Performance of Tree-Based Inference of Phylogenetic Networks

Phylogenetic networks extend the phylogenetic tree structure and allow for modeling vertical and horizontal evolution in a single framework. Statistical inference of phylogenetic networks is prohibitive and currently limited to small networks. An approach that could significantly improve phylogenetic network space exploration is based on first inferring an evolutionary tree of the species under consideration, and then augmenting the tree into a network by adding a set of "horizontal" edges to better fit the data. In this paper, we study the performance of such an approach on networks generated under a birth-hybridization model and explore its feasibility as an alternative to approaches that search the phylogenetic network space directly (without relying on a fixed underlying tree). We find that the concatenation method does poorly at obtaining a "backbone" tree that could be augmented into the correct network, whereas the popular species tree inference method ASTRAL does significantly better at such a task. We then evaluated the tree-to-network augmentation phase under the minimizing deep coalescence and pseudo-likelihood criteria. We find that even though this is a much faster approach than the direct search of the network space, the accuracy is much poorer, even when the backbone tree is a good starting tree. Our results show that tree-based inference of phylogenetic networks could yield very poor results. As exploration of the network space directly in search of maximum likelihood estimates or a representative sample of the posterior is very expensive, significant improvements to the computational complexity of phylogenetic network inference are imperative if analyses of large data sets are to be performed. We show that a recently developed divide-and-conquer approach significantly outperforms tree-based inference in terms of accuracy, albeit still at a higher computational cost

Molecular phylogeny, phylogeography and population genetics of the red seaweed genus <i>Asparagopsis</i>

The red seaweed genus Asparagopsis Montagne (Bonnemaisoniales) was studied with respect to its taxonomy, phylogeny, phylogeography and population genetics. The representatives of this genus, A. armata Harvey and A. taxiformis (Delile) Trevisan, are notorious invaders. Both species occur worldwide and show disjunct distribution patterns. Such patterns may result from recent jump-dispersal or from fragmentation of once panglobally distributed species. First, a phylogeographic approach was deployed in order to delineate the taxonomic units in local scale and to assess if European populations of each of the species originated from a single introduction or multiple cryptic ones. Results showed that the two species recognized A. armata and A. taxiformis are also genetically distinct. Asparagopsis armata was found to consist of a single species worldwide, whereas A. taxiformis constituted three and probably four morphologically cryptic but genetically distinct lineages. At times, lineages were encountered in sympatry and two of them were detected in the Mediterranean Sea. In order to confirm distinction between lineages and to assess invasive potential and colonization mechanisms of the species along the western Italian coast, eight nuclear micro satellite markers were identified against the invasive lineage 2 of A. taxiformis. The markers cross-hybridised only with lineages I and 2. Moreover, it was demonstrated that carpogonia present on many female thalli can affect microsatellite reading patterns because of external (male) allelic contribution. Even after removal of the carpogonia, gametophyte thalli exhibited multiple allelic patterns, which is indicative for polyploidy. The markers were then used to assess genetic structure and diversity within and among Mediterranean populations of A. taxiformis lineages 1 and 2. Analyses based on statistics developed for polyploid species showed that the lineage l-population (HAW) was distinct from Mediterranean lineage 2 populations. A geographically distant Californian lineage 2· population was genetically distinct from the Mediterranean ones as well. The Mediterranean lineage 2-samples showed panmixia. High genotypic diversity, high gene flow, and low differentiation encountered amongst these populations probably are due to a recent invasion of this lineage into the basin

Molecular phylogeny, phylogeography and population genetics of the red seaweed genus <i>Asparagopsis</i>

The red seaweed genus Asparagopsis Montagne (Bonnemaisoniales) was studied with respect to its taxonomy, phylogeny, phylogeography and population genetics. The representatives of this genus, A. armata Harvey and A. taxiformis (Delile) Trevisan, are notorious invaders. Both species occur worldwide and show disjunct distribution patterns. Such patterns may result from recent jump-dispersal or from fragmentation of once panglobally distributed species. First, a phylogeographic approach was deployed in order to delineate the taxonomic units in local scale and to assess if European populations of each of the species originated from a single introduction or multiple cryptic ones. Results showed that the two species recognized A. armata and A. taxiformis are also genetically distinct. Asparagopsis armata was found to consist of a single species worldwide, whereas A. taxiformis constituted three and probably four morphologically cryptic but genetically distinct lineages. At times, lineages were encountered in sympatry and two of them were detected in the Mediterranean Sea. In order to confirm distinction between lineages and to assess invasive potential and colonization mechanisms of the species along the western Italian coast, eight nuclear micro satellite markers were identified against the invasive lineage 2 of A. taxiformis. The markers cross-hybridised only with lineages I and 2. Moreover, it was demonstrated that carpogonia present on many female thalli can affect microsatellite reading patterns because of external (male) allelic contribution. Even after removal of the carpogonia, gametophyte thalli exhibited multiple allelic patterns, which is indicative for polyploidy. The markers were then used to assess genetic structure and diversity within and among Mediterranean populations of A. taxiformis lineages 1 and 2. Analyses based on statistics developed for polyploid species showed that the lineage l-population (HAW) was distinct from Mediterranean lineage 2 populations. A geographically distant Californian lineage 2· population was genetically distinct from the Mediterranean ones as well. The Mediterranean lineage 2-samples showed panmixia. High genotypic diversity, high gene flow, and low differentiation encountered amongst these populations probably are due to a recent invasion of this lineage into the basin

Multiple mitochondrial introgression events and heteroplasmy in trypanosoma cruzi revealed by Maxicircle MLST and next generation sequencing

Background Mitochondrial DNA is a valuable taxonomic marker due to its relatively fast rate of evolution. In Trypanosoma cruzi, the causative agent of Chagas disease, the mitochondrial genome has a unique structural organization consisting of 20–50 maxicircles (∼20 kb) and thousands of minicircles (0.5–10 kb). T. cruzi is an early diverging protist displaying remarkable genetic heterogeneity and is recognized as a complex of six discrete typing units (DTUs). The majority of infected humans are asymptomatic for life while 30–35% develop potentially fatal cardiac and/or digestive syndromes. However, the relationship between specific clinical outcomes and T. cruzi genotype remains elusive. The availability of whole genome sequences has driven advances in high resolution genotyping techniques and re-invigorated interest in exploring the diversity present within the various DTUs. Methodology/Principal Findings To describe intra-DTU diversity, we developed a highly resolutive maxicircle multilocus sequence typing (mtMLST) scheme based on ten gene fragments. A panel of 32 TcI isolates was genotyped using the mtMLST scheme, GPI, mini-exon and 25 microsatellite loci. Comparison of nuclear and mitochondrial data revealed clearly incongruent phylogenetic histories among different geographical populations as well as major DTUs. In parallel, we exploited read depth data, generated by Illumina sequencing of the maxicircle genome from the TcI reference strain Sylvio X10/1, to provide the first evidence of mitochondrial heteroplasmy (heterogeneous mitochondrial genomes in an individual cell) in T. cruzi. Conclusions/Significance mtMLST provides a powerful approach to genotyping at the sub-DTU level. This strategy will facilitate attempts to resolve phenotypic variation in T. cruzi and to address epidemiologically important hypotheses in conjunction with intensive spatio-temporal sampling. The observations of both general and specific incidences of nuclear-mitochondrial phylogenetic incongruence indicate that genetic recombination is geographically widespread and continues to influence the natural population structure of TcI, a conclusion which challenges the traditional paradigm of clonality in T. cruzi

DGEN: A Test Statistic for Detection of General Introgression Scenarios

When two species hybridize, one outcome is the integration of genetic material from one species into the genome of the other, a process known as introgression. Detecting introgression in genomic data is a very important question in evolutionary biology. However, given that hybridization occurs between closely related species, a complicating factor for introgression detection is the presence of incomplete lineage sorting, or ILS. The D-statistic, famously referred to as the "ABBA-BABA" test, was proposed for introgression detection in the presence of ILS in data sets that consist of four genomes. More recently, D_FOIL - a set of statistics - was introduced to extend the D-statistic to data sets of five genomes. The major contribution of this paper is demonstrating that the invariants underlying both the D-statistic and D_FOIL can be derived automatically from the probability mass functions of gene tree topologies under the null species tree model and alternative phylogenetic network model. Computational requirements aside, this automatic derivation provides a way to generalize these statistics to data sets of any size and with any scenarios of introgression. We demonstrate the accuracy of the general statistic, which we call D_GEN, on simulated data sets with varying rates of introgression, and apply it to an empirical data set of mosquito genomes. We have implemented D_GEN and made it available, both as a graphical user interface tool and as a command-line tool, as part of the freely available, open-source software package ALPHA (https://github.com/chilleo/ALPHA)

Introgression of mitochondrial DNA among Myodes voles: consequences for energetics?

Background Introgression of mitochondrial DNA (mtDNA) is among the most frequently described cases of reticulate evolution. The tendency of mtDNA to cross interspecific barriers is somewhat counter-intuitive considering the key function of enzymes that it encodes in the oxidative-phosphorylation process, which could give rise to hybrid dysfunction. How mtDNA reticulation affects the evolution of metabolic functions is, however, uncertain. Here we investigated how morpho-physiological traits vary in natural populations of a common rodent (the bank vole, Myodes glareolus) and whether this variation could be associated with mtDNA introgression. First, we confirmed that M. glareolus harbour mtDNA introgressed from M. rutilus by analyzing mtDNA (cytochrome b, 954 bp) and nuclear DNA (four markers; 2333 bp in total) sequence variation and reconstructing loci phylogenies among six natural populations in Finland. We then studied geographic variation in body size and basal metabolic rate (BMR) among the populations of M. glareolus and tested its relationship with mtDNA type. Results Myodes glareolus and its arctic neighbour, M. rutilus, are reciprocally monophyletic at the analyzed nuclear DNA loci. In contrast, the two northernmost populations of M. glareolus have a fixed mitotype that is shared with M. rutilus, likely due to introgressive hybridization. The analyses of phenotypic traits revealed that the body mass and whole-body, but not mass corrected, BMR are significantly reduced in M. glareolus females from northern Finland that also have the introgressed mitotype. Restricting the analysis to the single population where the mitotypes coexist, the association of mtDNA type with whole-body BMR remained but those with mass corrected BMR and body mass did not. Mitochondrial sequence variation in the introgressed haplotypes is compatible with demographic growth of the populations, but may also be a result of positive selection. Conclusion Our results show that the phenotypic traits vary markedly along the north-south axis of populations of M. glareolus. This variation may be related to adaptation to local environments and coincides with the gradient of genome reticulation between M. glareolus and M. rutilus, which was assessed by mtDNA introgression. Introgression of mtDNA may have affected morpho-physiological traits but do not show strong effects on either body mass or basal metabolic rate alone. We discuss the causes and biological meaning of our results and the means to clarify these questions in future research.peerReviewe

Implementing large genomic single nucleotide polymorphism data sets in phylogenetic network reconstructions: A case study of particularly rapid radiations of cichlid fish

The Midas cichlids of the Amphilophus citrinellus spp. species complex from Nicaragua (13 species) are an extraordinary example of adaptive and rapid radiation (⁠37K SNPs from 19 ingroup lineages) and present estimated phylogenetic networks for this extremely young and fast-evolving radiation of cichlid fish. We demonstrate that the MSNC is more appropriate than the multispecies coalescent alone for the analysis of this rapid radiation.Fil: Olave, Melisa. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Mendoza. Instituto Argentino de Investigaciones de las Zonas Áridas. Provincia de Mendoza. Instituto Argentino de Investigaciones de las Zonas Áridas. Universidad Nacional de Cuyo. Instituto Argentino de Investigaciones de las Zonas Áridas; Argentina. University of Konstanz; AlemaniaFil: Meyer, Axel. University Of Konstanz; Alemani

Genetic analyses suggest separate introductions of the pine pathogen Lecanosticta acicola into Europe

Lecanosticta acicola is a heterothallic ascomycete that causes brown spot needle blight on native and nonnative Pinus spp. in many regions of the world. In this study we investigated the origin of European L. acicola populations and estimated the level of random mating of the pathogen in affected areas. Part of the elongation factor 1-α gene was sequenced, 11 microsatellite regions were screened, and the mating type idiomorphs were determined for 201 isolates of L. acicola collected from three continents and 17 host species. The isolates from Mexico and Guatemala were unique, highly diverse and could represent cryptic species of Lecanosticta. The isolates from East Asia formed a uniform and discrete group. Two distinct populations were identified in both North America and Europe. Approximate Bayesian computation analyses strongly suggest independent introductions of two populations from North America into Europe. Microsatellite data and mating type distributions indicated random recombination in the populations of North America and Europe. Its intercontinental introduction can most likely be explained as a consequence of the movement of infected plant material. In contrast, the spread of L. acicola within Europe appears to be primarily due to conidial dispersion and probably also ascospore dissemination.The project was supported financially by COST CZ LD12031 (DIAROD), the FPS COST Action FP1102 (DIAROD), Project indicators of trees vitality Reg. No. CZ.1.07/2.3.00/20.0265 co-financed by the European Social Fund and the state budget of the Czech Republic, the Scholarship Foundation of the Republic of Austria (OeAD-GmbH, Austria) for J. Janoušek. The research was supported with funding from the Austrian Science Fund FWF and the European Union Seventh Framework Programme FP7 2007–2013 (KBBE 2009-3) under grant agreement 245268 ISEFOR.http://apsjournals.apsnet.org/loi/phytohj2017Forestry and Agricultural Biotechnology Institute (FABI)Genetic