The role of hybridization and subsequent introgression has been demonstrated in an increasing number of species. Recently, Fontaine
- NSF-PAR ID:
- Publisher / Repository:
- Date Published:
- Journal Name:
- Molecular Ecology
- Page Range / eLocation ID:
- p. 2361-2372
- Medium: X
- Sponsoring Org:
- National Science Foundation
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Abstract Phylogenomic data from a rapidly increasing number of studies provide new evidence for resolving relationships in recently radiated clades, but they also pose new challenges for inferring evolutionary histories. Most existing methods for reconstructing phylogenetic hypotheses rely solely on algorithms that only consider incomplete lineage sorting (ILS) as a cause of intra- or intergenomic discordance. Here, we utilize a variety of methods, including those to infer phylogenetic networks, to account for both ILS and introgression as a cause for nuclear and cytoplasmic-nuclear discordance using phylogenomic data from the recently radiated flowering plant genus Polemonium (Polemoniaceae), an ecologically diverse genus in Western North America with known and suspected gene flow between species. We find evidence for widespread discordance among nuclear loci that can be explained by both ILS and reticulate evolution in the evolutionary history of Polemonium. Furthermore, the histories of organellar genomes show strong discordance with the inferred species tree from the nuclear genome. Discordance between the nuclear and plastid genome is not completely explained by ILS, and only one case of discordance is explained by detected introgression events. Our results suggest that multiple processes have been involved in the evolutionary history of Polemonium and that the plastid genome does not accurately reflect species relationships. We discuss several potential causes for this cytoplasmic-nuclear discordance, which emerging evidence suggests is more widespread across the Tree of Life than previously thought. [Cyto-nuclear discordance, genomic discordance, phylogenetic networks, plastid capture, Polemoniaceae, Polemonium, reticulations.]more » « less
The tree of life is highly reticulate, with the history of population divergence emerging from populations of gene phylogenies that reflect histories of introgression, lineage sorting and divergence. In this study, we investigate global patterns of oak diversity and test the hypothesis that there are regions of the oak genome that are broadly informative about phylogeny.
We utilize fossil data and restriction‐site associated
DNAsequencing ( RAD‐seq) for 632 individuals representing nearly 250 Quercusspecies to infer a time‐calibrated phylogeny of the world's oaks. We use a reversible‐jump Markov chain Monte Carlo method to reconstruct shifts in lineage diversification rates, accounting for among‐clade sampling biases. We then map the > 20 000 RAD‐seq loci back to an annotated oak genome and investigate genomic distribution of introgression and phylogenetic support across the phylogeny.
Oak lineages have diversified among geographic regions, followed by ecological divergence within regions, in the Americas and Eurasia. Roughly 60% of oak diversity traces back to four clades that experienced increases in net diversification, probably in response to climatic transitions or ecological opportunity.
The strong support for the phylogeny contrasts with high genomic heterogeneity in phylogenetic signal and introgression. Oaks are phylogenomic mosaics, and their diversity may in fact depend on the gene flow that shapes the oak genome.
Premise of the Study
This investigation establishes the first
DNA‐sequence‐based phylogenetic hypothesis of species relationships in the coca family (Erythroxylaceae) and presents its implications for the intrageneric taxonomy and neotropical biogeography of Erythroxylum. We also identify the closest wild relatives and evolutionary relationships of the cultivated coca taxa. Methods
We focused our phylogenomic inference on the largest taxonomic section in the genus
Erythroxylum( ArcherythroxylumO.E.Schulz) using concatenation and gene tree reconciliation methods from hybridization‐based target capture of 427 genes. Key Results
We show that neotropical
Erythroxylumare monophyletic within the paleotropical lineages, yet Archerythroxylumand all of the other taxonomic sections from which we sampled multiple species lack monophyly. We mapped phytogeographic states onto the tree and found some concordance between these regions and clades. The wild species E. gracilipesand E. cataractarumare most closely related to the cultivated E. cocaand E. novogranatense, but relationships within this “coca” clade remain equivocal. Conclusions
Our results point to the difficulty of morphology‐based intrageneric classification in this clade and highlight the importance of integrative taxonomy in future systematic revisions. We can confidently identify
E. gracilipesand E. cataractarumas the closest wild relatives of the coca taxa, but understanding the domestication history of this crop will require more thorough phylogeographic analysis.
The “sexy shrimp”
Thor amboinensisis currently considered a single circumtropical species. However, the tropical oceans are partitioned by hard and soft barriers to dispersal, providing ample opportunity for allopatric speciation. Herein, we test the null hypothesis that T. amboinensisis a single global species, reconstruct its global biogeographical history, and comment on population‐level patterns throughout the Tropical Western Atlantic. Location
Coral reefs in all tropical oceans.
Thor amboinensiswere obtained through field collection and museum holdings. We used one mitochondrial ( COI) and two nuclear (NaK, enolase) gene fragments for global species delimitation and phylogenetic analyses ( n= 83 individuals, 30 sample localities), while phylogeographical reconstruction in the TWAwas based on COIonly ( n= 303 individuals, 10 sample localities). Results
We found evidence for at least five cryptic lineages (9%–22%
COIpairwise sequence divergence): four in the Indo‐West Pacific and one in the Tropical Western Atlantic. Phylogenetic reconstruction revealed that endemic lineages from Japan and the South Central Pacific are more closely related to the Tropical Western Atlantic lineage than to a co‐occurring lineage that is widespread throughout the Indo‐West Pacific. Concatenated and species tree phylogenetic analyses differ in the placement of an endemic Red Sea lineage and suggest alternate dispersal pathways into the Atlantic. Phylogeographical reconstruction throughout the Tropical Western Atlantic reveals little genetic structure over more than 3,000 km. Main conclusions Thor amboinensisis a species complex that has undergone a series of allopatric speciation events and whose members are in secondary contact in the Indo‐West Pacific. Nuclear‐ and mitochondrial‐ gene phylogenies show evidence of introgression between lineages inferred to have been separated more than 20 Ma. Phylogenetic discordance between multi‐locus analyses suggest that T. amboinensisoriginated in the Tethys sea and dispersed into the Atlantic and Indo‐West Pacific through the Tethys seaway or, alternatively, originated in the Indo‐West Pacific and dispersed into the Atlantic around South Africa. Population‐level patterns in the Caribbean indicate extensive gene flow across the region.
The Lesser Sunda Islands are situated between the Sunda and Sahul Shelves, with a linear arrangement that has functioned as a two‐way filter for taxa dispersing between the Asian and Australo‐Papuan biogeographical realms. Distributional patterns of many terrestrial vertebrates suggest a stepping‐stone model of island colonization. Here we investigate the timing and sequence of island colonization in Asian‐origin fanged frogs from the volcanic Sunda Arc islands with the goal of testing the stepping‐stone model of island colonization.
The Indonesian islands of Java, Lombok, Sumbawa, Flores and Lembata.
Taxon Limnonectes dammermaniand L. kadarsani(Family: Dicroglossidae) Methods
DNAwas sequenced from 153 frogs to identify major lineages and to select samples for an exon‐capture experiment. We designed probes to capture sequence data from 974 exonic loci (1,235,981 bp) from 48 frogs including the outgroup species, L. microdiscus. The resulting data were analysed using phylogenetic, population genetic and biogeographical model testing methods. Results
DNAphylogeny finds L. kadarsaniparaphyletic with respect to L. dammermani, with a pectinate topology consistent with the stepping‐stone model. Phylogenomic analyses of 974 exons recovered the two species as monophyletic sister taxa that diverged ~7.6 Ma with no detectable contemporary gene flow, suggesting introgression of the L. dammermanimitochondrion into L. kadarsanion Lombok resulting from an isolated ancient hybridization event ~4 Ma. Within L. kadarsani,the Lombok lineage diverged first while the Sumbawa and Lembata lineages are nested within a Flores assemblage composed of two parapatrically distributed lineages meeting in central Flores. Biogeographical model comparison found strict stepping‐stone dispersal to be less likely than models involving leap‐frog dispersal events. Main conclusions
These results suggest that the currently accepted stepping‐stone model of island colonization might not best explain the current patterns of diversity in the archipelago. The high degree of genetic structure, large divergence times, and absent or low levels of migration between lineages suggests that
L. kadarsanirepresents five distinct species.