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119 results for “lineage diversification”
Phylogenomic discordance is driven by wide-spread introgression and incomplete lineage sorting during rapid species diversification within rattlesnakes (Viperidae: Crotalus and Sistrurus)
<p>Phylogenomics allows us to uncover the historical signal of evolutionary processes through time and estimate phylogenetic networks accounting for these signals. Insight from genome-wide data further allows us to pinpoint the contributions to phylogenetic signal from hybridization, introgression, and ancestral polymorphism across the genome. Here, we focus on how these processes have contributed to phylogenetic discordance among rattlesnakes (genera <em>Crotalus</em> and <em>Sistrurus</em>), a group for which there are numerous conflicting phylogenetic hypotheses based on a diverse array of molecular datasets and analytical methods. We address the instability of the rattlesnake phylogeny using genomic data generated from transcriptomes sampled from nearly all known species. These genomic data, analyzed with coalescent and network-based approaches, reveal numerous instances of rapid speciation where individual gene trees conflict with the species tree. Moreover, the evolutionary history of rattlesnakes is dominated by incomplete speciation and frequent hybridization, both of which have likely influenced past interpretations of phylogeny. We present a new framework in which the evolutionary relationships of this group can only be understood in light of genome-wide data and network-based analytical methods. Our data suggest that network radiations, like those seen within the rattlesnakes, can only be understood in a phylogenomic context, necessitating similar approaches in our attempts to understand evolutionary history in other rapidly radiating species.</p> <p>La filogenómica nos permite descubrir la señal histórica de los procesos evolutivos a través del tiempo y estimar redes filogenéticas tomando en cuenta estas señales. El conocimiento de datos genómicos incluso permiten distinguir la contribución de la señal filogenética de la hibridación, introgresión, y de polimorfismos ancestrales a lo largo del genoma. En este trabajo nos enfocamos en como estos procesos han contribuido a la discordancia filogenética entre las serpientes de cascabel, un grupo en el que hay numerosos conflictos en las hipótesis filogenéticas obtenidas de un grupo variado de datos moleculares y métodos analíticos. Nosotros abordamos la inestabilidad de la filogenia de las serpientes de cascabel (generos <em>Crotalus</em> y <em>Sistrurus</em>) usando datos genómicos generados de transcriptomas muestreados en la mayoría de las especies conocidas. Estos datos genómicos, analizados con métodos basados en coalescencia y redes filogenéticas, revelaron numerosos casos de especiación rápida donde los arboles de genes individuales conflictúan con el árbol de especies. Además, la historia evolutiva de las serpientes de cascabel esta dominada por una especiación incompleta y una frecuente hibridación, las cuales probablemente han influenciado interpretaciones pasadas de las filogenias. Nosotros presentamos un nuevo marco en el que las relaciones evolutivas de este grupo solo pueden ser entendidas en base a datos de genomicos y métodos analíticos basados en redes filogenéticas. Nuestros datos sugieren que la radiación en redes filogenéticas, como se ha visto dentro de las serpientes de cascabel, solo puede ser entendida en un contexto filogenómico, necesitando aproximaciones similares en nuestro intento de entender la historia evolutiva en otras especies con radiaciones rápidas.</p>
Data from: Lineage diversification of fringe-toed lizards (Phrynosomatidae: Uma notata complex) in the Colorado Desert: Delimiting species in the presence of gene flow
Multi-locus nuclear DNA data were used to delimit species of fringe-toed lizards of the Uma notata complex, which are specialized for living in wind-blown sand habitats in the deserts of southwestern North America, and to infer whether Quaternary glacial cycles or Tertiary geological events were important in shaping the historical biogeography of this group. We analyzed ten nuclear loci collected using Sanger sequencing and genome-wide sequence and single-nucleotide polymorphism (SNP) data collected using restriction-associated DNA (RAD) sequencing. A combination of species discovery methods (concatenated phylogenies, parametric and non-parametric clustering algorithms) and species validation approaches (coalescent-based species tree/isolation-with-migration models) were used to delimit species, infer phylogenetic relationships, and to estimate effective population sizes, migration rates, and speciation times. Uma notata, U. inornata, U. cowlesi, and an undescribed species from Mohawk Dunes, Arizona (U. sp.) were supported as distinct in the concatenated analyses and by clustering algorithms, and all operational taxonomic units were decisively supported as distinct species by ranking hierarchical nested speciation models with Bayes factors based on coalescent-based species tree methods. However, significant unidirectional gene flow (2NM >1) from U. cowlesi and U. notata into U. rufopunctata was detected under the isolation-with-migration model. Therefore, we conservatively delimit four species-level lineages within this complex (U. inornata, U. notata, U. cowlesi, and U. sp.), treating U. rufopunctata as a hybrid population (U. notata x cowlesi). Both concatenated and coalescent-based estimates of speciation times support the hypotheses that speciation within the complex occurred during the late Pleistocene, and that the geological evolution of the Colorado River delta during this period was an important process shaping the observed phylogeographic patterns.
Data from: Interaction among ploidy, breeding system, and lineage diversification
If particular traits consistently affect rates of speciation and extinction, broad macroevolutionary patterns can be interpreted as consequences of selection at high levels of the biological hierarchy. Identifying traits associated with diversification rates is difficult because of the wide variety of characters under consideration and the statistical challenges of testing for associations from comparative phylogenetic data. Ploidy (diploid vs. polyploid states) and breeding system (self-incompatible vs. self-compatible states) are both thought to be drivers of differential diversification in angiosperms. We fit twenty-nine diversification models to extensive trait and phylogenetic data in Solanaceae and investigate how speciation and extinction rate differences are associated with ploidy, breeding system, and the interaction between these traits. We show that diversification patterns in Solanaceae are better explained by breeding system and an additional unobserved factor, rather than by ploidy. We also find that the most common evolutionary pathway to polyploidy in Solanaceae occurs via direct breakdown of self-incompatibility by whole-genome duplication, rather than indirectly via breakdown followed by polyploidization. Comparing multiple stochastic diversification models that include complex trait interactions alongside hidden states enhances our understanding of the macroevolutionary patterns in plant phylogenies.
Not out of the Mediterranean: Atlantic populations of the gorgonian Paramuricea clavata are a separate sister species under further lineage diversification
<p>The accurate delimitation of species boundaries in non-bilaterian marine taxa is notoriously difficult, with consequences for many studies in ecology and evolution. Anthozoans are a diverse group of key structural organisms worldwide, but the lack of reliable morphological characters and informative genetic markers hampers our ability to understand species diversification. We investigated population differentiation and species limits in Atlantic (Iberian Peninsula) and Mediterranean lineages of the octocoral genus <em>Paramuricea</em> previously identified as <em>P</em>. <em>clavata</em>. We used a diverse set of molecular markers (microsatellites, RNA-seq derived single-copy orthologues [SCO] and <em>mt</em>-<em>mutS</em> [mitochondria]) at 49 locations. Clear segregation of Atlantic and Mediterranean lineages was found with all markers. Species-tree estimations based on SCO strongly supported these two clades as distinct, recently diverged sister species with incomplete lineage sorting, <em>P</em>. cf. <em>grayi</em> and <em>P</em>. <em>clavata</em>, respectively. Furthermore, a second putative (or ongoing) speciation event was detected in the Atlantic between two <em>P</em>. cf. <em>grayi</em> colour morphotypes (yellow and purple) using SCO and supported by microsatellites. While segregating <em>P</em>. cf. <em>grayi</em> lineages showed considerable geographic structure, dominating circalittoral communities in southern (yellow) and western (purple) Portugal, their occurrence in sympatry at some localities suggests a degree of reproductive isolation. Overall, our results show that previous molecular and morphological studies have underestimated species diversity in <em>Paramuricea</em> occurring in the Iberian Peninsula, which has important implications for conservation planning. Finally, our findings validate the usefulness of phylotranscriptomics for resolving evolutionary relationships in octocorals.</p>
Dataset from: Incomplete lineage sorting and reticulate evolution mask species relationships in Brunelliaceae, an Andean family with rapid, recent diversification
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Supplementary materials for: Phylogenomics, lineage diversification rates, and the evolution of diadromy in clupeiformes (anchovies, herrings, sardines, and relatives)
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Data from: Lineage diversification of fringe-toed lizards (Phrynosomatidae: Uma notata complex) in the Colorado Desert: Delimiting species in the presence of gene flow
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Phylogenomic discordance is driven by wide-spread introgression and incomplete lineage sorting during rapid species diversification within rattlesnakes (Viperidae: Crotalus and Sistrurus)
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Data from: Ecological and geographic dimensions of diversification in Piper subgenus Ottonia: a lineage of neotropical rainforest shrubs
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Supplemental data for: Lineage diversification and rampant hybridization among subspecies explain taxonomic confusion in the endemic Hawaiian fern Polypodium pellucidum
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Data from: Diversification of trait combinations in coevolving plants and insect lineages
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Not out of the Mediterranean: Atlantic populations of the gorgonian Paramuricea clavata are a separate sister species under further lineage diversification
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Data from: Interaction among ploidy, breeding system, and lineage diversification
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Pleistocene glacial cycles drove lineage diversification and fusion in the Yosemite toad (Anaxyrus canorus)
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Data from: Species diversification in a lineage of Mexican red oak (Quercus section Lobatae subsection Racemiflorae)—the interplay between distance, habitat, and hybridization
In widespread taxa in which hybridization is suspected of being an important aspect of species biology, the patterns and drivers of lineage diversification are not always clear. Here, we examine the patterns of species diversification in a monophyletic lineage of oaks endemic to western Mexico, a center of global oak diversity. This group of four species inhabits a variety of soil types and exhibits varying patterns of species distribution ranging from widespread to restricted, with the range bisected by the Trans-Mexican Volcanic Belt (TVB). Using chloroplast and nuclear microsatellites, we evaluated genetic diversity, diversification, and genetic group assignment across 49 populations. Chloroplast data identified 29 haplotypes in three distinct lineages, many of these found occurring on opposite sides of the TVB. Individual species were only loosely associated to specific chloroplast haplotypes but the distribution of shared haplotypes supports a one-time wider distribution. One lineage was highly divergent and geographically isolated, likely representing a case of chloroplast capture via hybridization and may indicate a range expansion of Racemiflorae into new territory. Nuclear gene diversity varied little across species and populations; however, differentiation and genetic assignment analysis was strongly structured geographically and tended to cluster with broad soil types. Soil specialist taxa produced homogeneous genetic structure while soil generalists showed varying patterns of mixed ancestry and high levels of admixture. Speciation appears driven by a combination of distance and edaphic factors leading to drift. Hybridization appears to be complementary, occurring most often in non-specific soil environments and in marginal areas, and contributes to a long-scale pattern of gene exchange as species ranges fluctuate with time.
Data from: Pleistocene niche stability and lineage diversification in the subtropical spider Araneus omnicolor (Araneidae)
The influence of Quaternary climate oscillations on the diversification of the South American fauna is being increasingly explored. However, most of these studies have focused on taxa that are endemic to tropical environments, and relatively few have treated organisms restricted to subtropical biomes. Here we used an integrative phylogeographical framework to investigate the effects of these climate events on the ecological niche and genetic patterns of the subtropical orb-weaver spider Araneus omnicolor (Araneidae). We analyzed the mitochondrial (Cytochrome Oxidase I, COI) and nuclear (Internal Transcribed Subunit II, ITS2) DNA of 130 individuals throughout the species' range, and generated distribution models in three different climate scenarios [present, Last Glacial Maximum (LGM), and Last Interglacial Maximum (LIG)]. Additionally, we used an Approximate Bayesian Computation (ABC) approach to compare possible demographic scenarios and select the hypothesis that better explains the genetic patterns of A. omnicolor. We obtained high haplotype diversity but low nucleotide variation among sequences. The population structure and demographic analyses showed discrepancies between markers, suggesting male-biased dispersal in the species. The time-calibrated COI phylogenetic inference showed a recent diversification of lineages (Middle/Late Pleistocene), while the paleoclimate modeling indicated niche stability since ~120 Kya. The ABC results agreed with the niche models, supporting a panmictic population as the most likely historical scenario for the species. These results indicate that A. omnicolor experienced no niche or population reductions during the Late Pleistocene, despite the intense landscape modifications that occurred in the subtropical region, and that other factors beside LGM and LIG climate oscillations might have contributed to the demographic history of this species. This pattern may be related to the high dispersal ability and wide environmental tolerance of A. omnicolor, highlighting the need for more phylogeographical studies with invertebrates and other generalist taxa, in order to understand the effects of Quaternary climate changes on Neotropical biodiversity.
Data from: Pleistocene diversification in an ancient lineage: a role for glacial cycles in the evolutionary history of Dioon Lindl. (Zamiaceae).
Premise of the study: Recent estimates of crown ages for cycad genera (Late Miocene) challenge us to consider what processes have produced the extant diversity of this ancient group in such relatively little time. Pleistocene climate change has driven major shifts in species distributions in Mexico and may have led to speciation in the genus Dioon by forcing populations to migrate up in elevation thereby becoming separated by topography. Methods: We inferred orthologs from transcriptomes of five species and sequenced these in 42 individuals representing all Dioon species. From these data and published plastid sequences we inferred dated species trees and lineage-specific diversification rates. Key results: 84 nuclear orthologs and plastid data confirm four major clades within Dioon, all of Pleistocene age. Gene tree analysis, divergence dates, and an increase in diversification rate support very recent and rapid divergence of extant taxa. Conclusions: This study confirms the Pleistocene age of Dioon species and implicates Pleistocene climate change and established topography in lineage spitting. These results add to our understanding of the cycads as evolutionarily dynamic lineages, not relicts or evolutionary dead ends. We also find that well-supported secondary calibration points can be reliable in the absence of fossils. Our hypothesis of lineage splitting mediated by habitat shifts may be applicable to other taxa that are restricted to elevation specific ecotones.
Data from: Boom and bust: ancient and recent diversification in bichirs (Polypteridae: Actinopterygii), a relictual lineage of ray-finned fishes
Understanding the history that underlies patterns of species richness across the Tree of Life requires an investigation of the mechanisms that not only generate young species-rich clades, but also those that maintain species-poor lineages over long stretches of evolutionary time. However, diversification dynamics that underlie ancient species-poor lineages are often hidden due to a lack of fossil evidence. Using information from the fossil record and time calibrated molecular phylogenies, we investigate the history of lineage diversification in Polypteridae, which is the sister lineage of all other ray-finned fishes (Actinopterygii). Despite originating at least 390 million years (Myr) ago, molecular timetrees support a Neogene origin for the living polypterid species. Our analyses demonstrate polypterids are exceptionally species depauperate with a stem lineage duration that exceeds 380 million years (Ma) and is significantly longer than the stem lineage durations observed in other ray-finned fish lineages. Analyses of the fossil record show an early Late Cretaceous (100.5–83.6 Ma) peak in polypterid genus richness, followed by 60 Ma of low richness. The Neogene species radiation and evidence for high-diversity intervals in the geological past suggest a "boom and bust" pattern of diversification that contrasts with common perceptions of relative evolutionary stasis in so-called "living fossils."
Data from: Timing and number of colonizations but not diversification rates affect diversity patterns in hemosporidian lineages on a remote oceanic archipelago
Parasite diversity on remote oceanic archipelagos is determined by the number and timing of colonizations, and in-situ diversification rate. In this study we compare intra-archipelago diversity of two hemosporidian parasite genera, Plasmodium and Leucocytozoon, infecting birds of the Mascarene archipelago. Despite the generally higher vagility of Plasmodium parasites, we report a much lower diversity of Plasmodium cytochrome-b haplotypes in the archipelago compared to Leucocytozoon. Using phylogenetic data, we find that this difference in diversity is consistent with differences in the timing and the number of colonizations, while rates of diversification do not vary significantly between the two genera. The prominence of immigration history in explaining current diversity patterns highlights the importance of historical contingencies in driving disparate biogeographic patterns in potentially harmful blood parasites infecting island birds.
Data from: Differential divergence in autosomes and sex chromosomes is associated with intra-island diversification at a very small spatial scale in a songbird lineage
<p>Recently diverged taxa showing marked phenotypic and ecological diversity are optimal systems to understand the genetic processes underlying speciation. We used genome-wide markers to investigate the diversification of the Reunion grey white eye (<i>Zosterops borbonicus</i>) on the small volcanic island of Reunion (Mascarene archipelago), where this species complex exhibits four geographic forms that are parapatrically distributed across the island and differ strikingly in plumage colour. One form restricted to the highlands is separated by a steep ecological gradient from three distinct lowland forms which meet at narrow hybrid zones that are not associated with environmental variables. Analyses of genomic variation based on SNP data from genotyping-by-sequencing and pooled RADseq approaches, reveal that signatures of selection associated with elevation can be found at multiple regions across the genome, whereas most loci associated with the lowland forms are located on the Z sex chromosome. We identified <i>TYRP1</i>, a Z-linked colour gene, as a likely candidate locus underlying colour variation among lowland forms. Tests of demographic models revealed that highland and lowland forms diverged in the presence of gene flow, and divergence has progressed as gene flow was restricted by selection at loci across the genome. This system is promising to investigate how natural selection and reproductive isolation shape the genomic landscape of divergence at multiple stages of the speciation process.</p>
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