scholarly journals Phylogenomics of parasitic and non-parasitic lice (Insecta: Psocodea): Combining sequence data and Exploring compositional bias solutions in Next Generation Datasets

2020 ◽  
Author(s):  
Robert S de Moya ◽  
Kazunori Yoshizawa ◽  
Kimberly K O Walden ◽  
Andrew D Sweet ◽  
Christopher H Dietrich ◽  
...  
Keyword(s):  
Sequence Data ◽  
Compositional Bias ◽  
Phylogenomic Analysis ◽  
Data Set ◽  
Genomic Changes ◽  
Insect Order ◽  
Codon Positions ◽  
Phylogenomic Analyses ◽  
Ordinal Level ◽  
Likelihood Mapping

Abstract The insect order Psocodea is a diverse lineage comprising both parasitic (Phthiraptera) and non-parasitic members (Psocoptera). The extreme age and ecological diversity of the group may be associated with major genomic changes, such as base compositional biases expected to affect phylogenetic inference. Divergent morphology between parasitic and non-parasitic members has also obscured the origins of parasitism within the order. We conducted a phylogenomic analysis on the order Psocodea utilizing both transcriptome and genome sequencing to obtain a data set of 2,370 orthologous genes. All phylogenomic analyses, including both concatenated and coalescent methods suggest a single origin of parasitism within the order Psocodea, resolving conflicting results from previous studies. This phylogeny allows us to propose a stable ordinal level classification scheme that retains significant taxonomic names present in historical scientific literature and reflects the evolution of the group as a whole. A dating analysis, with internal nodes calibrated by fossil evidence, suggests an origin of parasitism that predates the K-Pg boundary. Nucleotide compositional biases are detected in third and first codon positions and result in the anomalous placement of the Amphientometae as sister to Psocomorpha when all nucleotide sites are analyzed. Likelihood-mapping and quartet sampling methods demonstrate that base compositional biases can also have an effect on quartet-based methods.

scholarly journals Comprehensive phylogenomic analyses re-write the evolution of parasitism within cynipoid wasps

2020 ◽  
Vol 20 (1) ◽  
Author(s):  
Bonnie B. Blaimer ◽  
Dietrich Gotzek ◽  
Seán G. Brady ◽  
Matthew L. Buffington
Keyword(s):  
Life Histories ◽  
Sister Group ◽  
Dominant Strategy ◽  
Comparative Genomic ◽  
Life Strategy ◽  
Gall Wasp ◽  
Data Set ◽  
Insect Order ◽  
Plant Feeding ◽  
Phylogenomic Analyses

Abstract Background Parasitoidism, a specialized life strategy in which a parasite eventually kills its host, is frequently found within the insect order Hymenoptera (wasps, ants and bees). A parasitoid lifestyle is one of two dominant life strategies within the hymenopteran superfamily Cynipoidea, with the other being an unusual plant-feeding behavior known as galling. Less commonly, cynipoid wasps exhibit inquilinism, a strategy where some species have adapted to usurp other species’ galls instead of inducing their own. Using a phylogenomic data set of ultraconserved elements from nearly all lineages of Cynipoidea, we here generate a robust phylogenetic framework and timescale to understand cynipoid systematics and the evolution of these life histories. Results Our reconstructed evolutionary history for Cynipoidea differs considerably from previous hypotheses. Rooting our analyses with non-cynipoid outgroups, the Paraulacini, a group of inquilines, emerged as sister-group to the rest of Cynipoidea, rendering the gall wasp family Cynipidae paraphyletic. The families Ibaliidae and Liopteridae, long considered archaic and early-branching parasitoid lineages, were found nested well within the Cynipoidea as sister-group to the parasitoid Figitidae. Cynipoidea originated in the early Jurassic around 190 Ma. Either inquilinism or parasitoidism is suggested as the ancestral and dominant strategy throughout the early evolution of cynipoids, depending on whether a simple (three states: parasitoidism, inquilinism and galling) or more complex (seven states: parasitoidism, inquilinism and galling split by host use) model is employed. Conclusions Our study has significant impact on understanding cynipoid evolution and highlights the importance of adequate outgroup sampling. We discuss the evolutionary timescale of the superfamily in relation to their insect hosts and host plants, and outline how phytophagous galling behavior may have evolved from entomophagous, parasitoid cynipoids. Our study has established the framework for further physiological and comparative genomic work between gall-making, inquiline and parasitoid lineages, which could also have significant implications for the evolution of diverse life histories in other Hymenoptera.

scholarly journals Phylogenomic analysis of the Chilean clade ofLiolaemuslizards (Squamata: Liolaemidae) based on sequence capture data

PeerJ ◽  
2017 ◽  
Vol 5 ◽  
pp. e3941 ◽  
Author(s):  
Alejandra Panzera ◽  
Adam D. Leaché ◽  
Guillermo D’Elía ◽  
Pedro F. Victoriano
Keyword(s):  
Incomplete Lineage Sorting ◽  
Phylogenetic Analyses ◽  
Strong Support ◽  
Taxon Sampling ◽  
Phylogenomic Analysis ◽  
Molecular Systematic ◽  
Data Set ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
Phylogenomic Analyses

The genusLiolaemusis one of the most ecologically diverse and species-rich genera of lizards worldwide. It currently includes more than 250 recognized species, which have been subject to many ecological and evolutionary studies. Nevertheless,Liolaemuslizards have a complex taxonomic history, mainly due to the incongruence between morphological and genetic data, incomplete taxon sampling, incomplete lineage sorting and hybridization. In addition, as many species have restricted and remote distributions, this has hampered their examination and inclusion in molecular systematic studies. The aims of this study are to infer a robust phylogeny for a subsample of lizards representing the Chilean clade (subgenusLiolaemus sensu stricto), and to test the monophyly of several of the major species groups. We use a phylogenomic approach, targeting 541 ultra-conserved elements (UCEs) and 44 protein-coding genes for 16 taxa. We conduct a comparison of phylogenetic analyses using maximum-likelihood and several species tree inference methods. The UCEs provide stronger support for phylogenetic relationships compared to the protein-coding genes; however, the UCEs outnumber the protein-coding genes by 10-fold. On average, the protein-coding genes contain over twice the number of informative sites. Based on our phylogenomic analyses, all the groups sampled are polyphyletic.Liolaemus tenuis tenuisis difficult to place in the phylogeny, because only a few loci (nine) were recovered for this species. Topologies or support values did not change dramatically upon exclusion ofL. t. tenuisfrom analyses, suggesting that missing data did not had a significant impact on phylogenetic inference in this data set. The phylogenomic analyses provide strong support for sister group relationships betweenL. fuscus,L. monticola,L. nigroviridisandL. nitidus, andL. plateiandL. velosoi. Despite our limited taxon sampling, we have provided a reliable starting hypothesis for the relationships among many major groups of the Chilean clade ofLiolaemusthat will help future work aimed at resolving theLiolaemusphylogeny.

scholarly journals Reconstructing the Backbone of the Saccharomycotina Yeast Phylogeny Using Genome-Scale Data

2016 ◽  
Vol 6 (12) ◽  
pp. 3927-3939 ◽  
Author(s):  
Xing-Xing Shen ◽  
Xiaofan Zhou ◽  
Jacek Kominek ◽  
Cletus P Kurtzman ◽  
Chris Todd Hittinger ◽  
...  
Keyword(s):  
Evolutionary Biology ◽  
Sequence Data ◽  
Data Matrix ◽  
Data Sets ◽  
Codon Positions ◽  
Phylogenomic Analyses ◽  
Genome Scale ◽  
Yeast Genomes ◽  
Yeast Phylogeny ◽  
Data Matrices

Abstract Understanding the phylogenetic relationships among the yeasts of the subphylum Saccharomycotina is a prerequisite for understanding the evolution of their metabolisms and ecological lifestyles. In the last two decades, the use of rDNA and multilocus data sets has greatly advanced our understanding of the yeast phylogeny, but many deep relationships remain unsupported. In contrast, phylogenomic analyses have involved relatively few taxa and lineages that were often selected with limited considerations for covering the breadth of yeast biodiversity. Here we used genome sequence data from 86 publicly available yeast genomes representing nine of the 11 known major lineages and 10 nonyeast fungal outgroups to generate a 1233-gene, 96-taxon data matrix. Species phylogenies reconstructed using two different methods (concatenation and coalescence) and two data matrices (amino acids or the first two codon positions) yielded identical and highly supported relationships between the nine major lineages. Aside from the lineage comprised by the family Pichiaceae, all other lineages were monophyletic. Most interrelationships among yeast species were robust across the two methods and data matrices. However, eight of the 93 internodes conflicted between analyses or data sets, including the placements of: the clade defined by species that have reassigned the CUG codon to encode serine, instead of leucine; the clade defined by a whole genome duplication; and the species Ascoidea rubescens. These phylogenomic analyses provide a robust roadmap for future comparative work across the yeast subphylum in the disciplines of taxonomy, molecular genetics, evolutionary biology, ecology, and biotechnology. To further this end, we have also provided a BLAST server to query the 86 Saccharomycotina genomes, which can be found at http://y1000plus.org/blast.

scholarly journals Reconstructing the backbone of the Saccharomycotina yeast phylogeny using genome-scale data

2016 ◽  
Author(s):  
Xing-Xing Shen ◽  
Xiaofan Zhou ◽  
Jacek Kominek ◽  
Cletus P. Kurtzman ◽  
Chris Todd Hittinger ◽  
...  
Keyword(s):  
Evolutionary Biology ◽  
Sequence Data ◽  
Data Matrix ◽  
Data Sets ◽  
Codon Positions ◽  
Phylogenomic Analyses ◽  
Genome Scale ◽  
Yeast Genomes ◽  
Yeast Phylogeny ◽  
Data Matrices

AbstractUnderstanding the phylogenetic relationships among the yeasts of the subphylum Saccharomycotina is a prerequisite for understanding the evolution of their metabolisms and ecological lifestyles. In the last two decades, the use of rDNA and multi-locus data sets has greatly advanced our understanding of the yeast phylogeny, but many deep relationships remain unsupported. In contrast, phylogenomic analyses have involved relatively few taxa and lineages that were often selected with limited considerations for covering the breadth of yeast biodiversity. Here we used genome sequence data from 86 publicly available yeast genomes representing 9 of the 11 major lineages and 10 non-yeast fungal outgroups to generate a 1,233-gene, 96-taxon data matrix. Species phylogenies reconstructed using two different methods (concatenation and coalescence) and two data matrices (amino acids or the first two codon positions) yielded identical and highly supported relationships between the 9 major lineages. Aside from the lineage comprised by the family Pichiaceae, all other lineages were monophyletic. Most interrelationships among yeast species were robust across the two methods and data matrices. However, 8 of the 93 internodes conflicted between analyses or data sets, including the placements of: the clade defined by species that have reassigned the CUG codon to encode serine, instead of leucine; the clade defined by a whole genome duplication; and of Ascoidea rubescens. These phylogenomic analyses provide a robust roadmap for future comparative work across the yeast subphylum in the disciplines of taxonomy, molecular genetics, evolutionary biology, ecology, and biotechnology. To further this end, we have also provided a BLAST server to query the 86 Saccharomycotina genomes, which can be found at http://y1000plus.org/blast.

scholarly journals Genomic analysis reveals hidden biodiversity within colugos, the sister group to primates

2016 ◽  
Vol 2 (8) ◽  
pp. e1600633 ◽  
Author(s):  
Victor C. Mason ◽  
Gang Li ◽  
Patrick Minx ◽  
Jürgen Schmitz ◽  
Gennady Churakov ◽  
...  
Keyword(s):  
Sequence Data ◽  
Draft Genome ◽  
Genomic Analysis ◽  
Sister Group ◽  
Phylogenomic Analysis ◽  
Isolated Populations ◽  
Conservation Units ◽  
Genetic Changes ◽  
Genomic Changes ◽  
Rare Genomic Changes

Colugos are among the most poorly studied mammals despite their centrality to resolving supraordinal primate relationships. Two described species of these gliding mammals are the sole living members of the order Dermoptera, distributed throughout Southeast Asia. We generated a draft genome sequence for a Sunda colugo and a Philippine colugo reference alignment, and used these to identify colugo-specific genetic changes that were enriched in sensory and musculoskeletal-related genes that likely underlie their nocturnal and gliding adaptations. Phylogenomic analysis and catalogs of rare genomic changes overwhelmingly support the contested hypothesis that colugos are the sister group to primates (Primatomorpha), to the exclusion of treeshrews. We captured ~140 kb of orthologous sequence data from colugo museum specimens sampled across their range and identified large genetic differences between many geographically isolated populations that may result in a >300% increase in the number of recognized colugo species. Our results identify conservation units to mitigate future losses of this enigmatic mammalian order.

scholarly journals Spider phylogenomics: untangling the Spider Tree of Life

PeerJ ◽  
2016 ◽  
Vol 4 ◽  
pp. e1719 ◽  
Author(s):  
Nicole L. Garrison ◽  
Juanita Rodriguez ◽  
Ingi Agnarsson ◽  
Jonathan A. Coddington ◽  
Charles E. Griswold ◽  
...  
Keyword(s):  
Sister Group ◽  
Acid Sites ◽  
Molecular Dating ◽  
Phylogenomic Analysis ◽  
Ancestral State ◽  
Data Set ◽  
Key Innovation ◽  
Orb Web ◽  
Phylogenomic Analyses ◽  
High Level

Spiders (Order Araneae) are massively abundant generalist arthropod predators that are found in nearly every ecosystem on the planet and have persisted for over 380 million years. Spiders have long served as evolutionary models for studying complex mating and web spinning behaviors, key innovation and adaptive radiation hypotheses, and have been inspiration for important theories like sexual selection by female choice. Unfortunately, past major attempts to reconstruct spider phylogeny typically employing the “usual suspect” genes have been unable to produce a well-supported phylogenetic framework for the entire order. To further resolve spider evolutionary relationships we have assembled a transcriptome-based data set comprising 70 ingroup spider taxa. Using maximum likelihood and shortcut coalescence-based approaches, we analyze eight data sets, the largest of which contains 3,398 gene regions and 696,652 amino acid sites forming the largest phylogenomic analysis of spider relationships produced to date. Contrary to long held beliefs that the orb web is the crowning achievement of spider evolution, ancestral state reconstructions of web type support a phylogenetically ancient origin of the orb web, and diversification analyses show that the mostly ground-dwelling, web-less RTA clade diversified faster than orb weavers. Consistent with molecular dating estimates we report herein, this may reflect a major increase in biomass of non-flying insects during the Cretaceous Terrestrial Revolution 125–90 million years ago favoring diversification of spiders that feed on cursorial rather than flying prey. Our results also have major implications for our understanding of spider systematics. Phylogenomic analyses corroborate several well-accepted high level groupings: Opisthothele, Mygalomorphae, Atypoidina, Avicularoidea, Theraphosoidina, Araneomorphae, Entelegynae, Araneoidea, the RTA clade, Dionycha and the Lycosoidea. Alternatively, our results challenge the monophyly of Eresoidea, Orbiculariae, and Deinopoidea. The composition of the major paleocribellate and neocribellate clades, the basal divisions of Araneomorphae, appear to be falsified. Traditional Haplogynae is in need of revision, as our findings appear to support the newly conceived concept of Synspermiata. The sister pairing of filistatids with hypochilids implies that some peculiar features of each family may in fact be synapomorphic for the pair. Leptonetids now are seen as a possible sister group to the Entelegynae, illustrating possible intermediates in the evolution of the more complex entelegyne genitalic condition, spinning organs and respiratory organs.

scholarly journals Spider phylogenomics: untangling the Spider Tree of Life

2015 ◽  
Author(s):  
Nicole L Garrison ◽  
Juanita Rodriguez ◽  
Ingi Agnarsson ◽  
Jonathan A Coddington ◽  
Charles E Griswold ◽  
...  
Keyword(s):  
Sister Group ◽  
Acid Sites ◽  
Molecular Dating ◽  
Phylogenomic Analysis ◽  
Ancestral State ◽  
Data Set ◽  
Key Innovation ◽  
Orb Web ◽  
Phylogenomic Analyses ◽  
High Level

Spiders (Order Araneae) are massively abundant generalist arthropod predators that are found in nearly every ecosystem on the planet and have persisted for over 380 million years. Spiders have long served as evolutionary models for studying complex mating and web spinning behaviors, key innovation and adaptive radiation hypotheses, and have been inspiration for important theories like sexual selection by female choice. Unfortunately, past major attempts to reconstruct spider phylogeny typically employing the “usual suspect” genes have been unable to produce a well-supported phylogenetic framework for the entire order. To further resolve spider evolutionary relationships we have assembled a transcriptome-based data set comprising 70 ingroup spider taxa. Using maximum likelihood and shortcut coalescence-based approaches, we analyze eight data sets, the largest of which contains 3,398 gene regions and 696,652 amino acid sites forming the largest phylogenomic analysis of spider relationships produced to date. Contrary to long held beliefs that the orb web is the crowning achievement of spider evolution, ancestral state reconstructions of web type support a phylogenetically ancient origin of the orb web and diversification analyses show that the mostly ground-dwelling, web-less RTA clade diversified faster than orb weavers. Consistent with molecular dating estimates we report herein, this may reflect a major increase in biomass of non-flying insects during the Cretaceous Tertiary Revolution 125-90 million years ago favoring diversification of spiders that feed on cursorial rather than flying prey. Our results also have major implications for our understanding of spider systematics. Phylogenomic analyses corroborate several well-accepted high level groupings: Opisthothele, Mygalomorphae, Atypoidina, Aviculariodea, Theraphosidina, Araneomorphae, Entelygynae, Araneoidea, the RTA – clade, Dionycha and the Lycosoidea. Alternatively, our results challenge the monophyly of Eresoidea, Orbiculariae, and Deinopoidea. The composition of the major Paleocribellate and Neocribellate clades, the basal divisions of Araneomorphae, appear to be falsified. Traditional Haplogynae, and even the new concept of Synspermiata, need revision after the departure of Filistatidae and Leptonetidae from the haplogyne clade. The sister pairing of filistatids with hypochilids, implies that some peculiar features of each family may in fact be synapomorphic for the pair. Leptonetids now are seen as a possible sister group to the Entelegynae, illustrating possible intermediates in the evolution of the more complex entelegyne genitalic condition, spinning organs and respiratory organs.

scholarly journals Spider phylogenomics: untangling the Spider Tree of Life

2015 ◽  
Author(s):  
Nicole L Garrison ◽  
Juanita Rodriguez ◽  
Ingi Agnarsson ◽  
Jonathan A Coddington ◽  
Charles E Griswold ◽  
...  
Keyword(s):  
Sister Group ◽  
Acid Sites ◽  
Molecular Dating ◽  
Phylogenomic Analysis ◽  
Ancestral State ◽  
Data Set ◽  
Key Innovation ◽  
Orb Web ◽  
Phylogenomic Analyses ◽  
High Level

Spiders (Order Araneae) are massively abundant generalist arthropod predators that are found in nearly every ecosystem on the planet and have persisted for over 380 million years. Spiders have long served as evolutionary models for studying complex mating and web spinning behaviors, key innovation and adaptive radiation hypotheses, and have been inspiration for important theories like sexual selection by female choice. Unfortunately, past major attempts to reconstruct spider phylogeny typically employing the “usual suspect” genes have been unable to produce a well-supported phylogenetic framework for the entire order. To further resolve spider evolutionary relationships we have assembled a transcriptome-based data set comprising 70 ingroup spider taxa. Using maximum likelihood and shortcut coalescence-based approaches, we analyze eight data sets, the largest of which contains 3,398 gene regions and 696,652 amino acid sites forming the largest phylogenomic analysis of spider relationships produced to date. Contrary to long held beliefs that the orb web is the crowning achievement of spider evolution, ancestral state reconstructions of web type support a phylogenetically ancient origin of the orb web and diversification analyses show that the mostly ground-dwelling, web-less RTA clade diversified faster than orb weavers. Consistent with molecular dating estimates we report herein, this may reflect a major increase in biomass of non-flying insects during the Cretaceous Tertiary Revolution 125-90 million years ago favoring diversification of spiders that feed on cursorial rather than flying prey. Our results also have major implications for our understanding of spider systematics. Phylogenomic analyses corroborate several well-accepted high level groupings: Opisthothele, Mygalomorphae, Atypoidina, Aviculariodea, Theraphosidina, Araneomorphae, Entelygynae, Araneoidea, the RTA – clade, Dionycha and the Lycosoidea. Alternatively, our results challenge the monophyly of Eresoidea, Orbiculariae, and Deinopoidea. The composition of the major Paleocribellate and Neocribellate clades, the basal divisions of Araneomorphae, appear to be falsified. Traditional Haplogynae, and even the new concept of Synspermiata, need revision after the departure of Filistatidae and Leptonetidae from the haplogyne clade. The sister pairing of filistatids with hypochilids, implies that some peculiar features of each family may in fact be synapomorphic for the pair. Leptonetids now are seen as a possible sister group to the Entelegynae, illustrating possible intermediates in the evolution of the more complex entelegyne genitalic condition, spinning organs and respiratory organs.

scholarly journals A 250 plastome phylogeny of the grass family (Poaceae): topological support under different data partitions

PeerJ ◽  
2018 ◽  
Vol 6 ◽  
pp. e4299 ◽  
Author(s):  
Jeffery M. Saarela ◽  
Sean V. Burke ◽  
William P. Wysocki ◽  
Matthew D. Barrett ◽  
Lynn G. Clark ◽  
...  
Keyword(s):  
High Throughput Sequencing ◽  
Sequence Data ◽  
Phylogenetic Signal ◽  
Purifying Selection ◽  
Bootstrap Support ◽  
Phylogenomic Analysis ◽  
Branch Points ◽  
Protein Coding ◽  
Selective Forces ◽  
Phylogenomic Analyses

The systematics of grasses has advanced through applications of plastome phylogenomics, although studies have been largely limited to subfamilies or other subgroups of Poaceae. Here we present a plastome phylogenomic analysis of 250 complete plastomes (179 genera) sampled from 44 of the 52 tribes of Poaceae. Plastome sequences were determined from high throughput sequencing libraries and the assemblies represent over 28.7 Mbases of sequence data. Phylogenetic signal was characterized in 14 partitions, including (1) complete plastomes; (2) protein coding regions; (3) noncoding regions; and (4) three loci commonly used in single and multi-gene studies of grasses. Each of the four main partitions was further refined, alternatively including or excluding positively selected codons and also the gaps introduced by the alignment. All 76 protein coding plastome loci were found to be predominantly under purifying selection, but specific codons were found to be under positive selection in 65 loci. The loci that have been widely used in multi-gene phylogenetic studies had among the highest proportions of positively selected codons, suggesting caution in the interpretation of these earlier results. Plastome phylogenomic analyses confirmed the backbone topology for Poaceae with maximum bootstrap support (BP). Among the 14 analyses, 82 clades out of 309 resolved were maximally supported in all trees. Analyses of newly sequenced plastomes were in agreement with current classifications. Five of seven partitions in which alignment gaps were removed retrieved Panicoideae as sister to the remaining PACMAD subfamilies. Alternative topologies were recovered in trees from partitions that included alignment gaps. This suggests that ambiguities in aligning these uncertain regions might introduce a false signal. Resolution of these and other critical branch points in the phylogeny of Poaceae will help to better understand the selective forces that drove the radiation of the BOP and PACMAD clades comprising more than 99.9% of grass diversity.

Population Subdivision and Molecular Sequence Variation: Theory and Analysis of Drosophila ananassae Data

Genetics ◽  
2003 ◽  
Vol 165 (3) ◽  
pp. 1385-1395
Author(s):  
Claus Vogl ◽  
Aparup Das ◽  
Mark Beaumont ◽  
Sujata Mohanty ◽  
Wolfgang Stephan
Keyword(s):  
Sequence Data ◽  
Isolation By Distance ◽  
Allele Frequencies ◽  
Drosophila Ananassae ◽  
Population Subdivision ◽  
Variation Theory ◽  
Peripheral Populations ◽  
Molecular Variation ◽  
Data Set ◽  
Evolutionary Forces

Abstract Population subdivision complicates analysis of molecular variation. Even if neutrality is assumed, three evolutionary forces need to be considered: migration, mutation, and drift. Simplification can be achieved by assuming that the process of migration among and drift within subpopulations is occurring fast compared to mutation and drift in the entire population. This allows a two-step approach in the analysis: (i) analysis of population subdivision and (ii) analysis of molecular variation in the migrant pool. We model population subdivision using an infinite island model, where we allow the migration/drift parameter 0398; to vary among populations. Thus, central and peripheral populations can be differentiated. For inference of 0398;, we use a coalescence approach, implemented via a Markov chain Monte Carlo (MCMC) integration method that allows estimation of allele frequencies in the migrant pool. The second step of this approach (analysis of molecular variation in the migrant pool) uses the estimated allele frequencies in the migrant pool for the study of molecular variation. We apply this method to a Drosophila ananassae sequence data set. We find little indication of isolation by distance, but large differences in the migration parameter among populations. The population as a whole seems to be expanding. A population from Bogor (Java, Indonesia) shows the highest variation and seems closest to the species center.

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