What is the “modified” CTAB protocol? Characterizing modifications to the CTAB DNA extraction protocol

Applications in Plant Sciences, Год журнала: 2023, Номер 11(3)

Опубликована: Май 1, 2023

Cetyltrimethylammonium bromide (CTAB)-based methods are widely used to isolate DNA from plant tissues, but the unique chemical composition of secondary metabolites among species has necessitated optimization. Research articles often cite a "modified" CTAB protocol without explicitly stating how had been altered, creating non-reproducible studies. Furthermore, various modifications that have applied not rigorously reviewed and doing so could reveal optimization strategies across study systems. We surveyed literature for modified protocols isolation DNA. found every stage modified, we summarized those provide recommendations extraction Future genomic studies will rely on optimized protocols. Our review used, as well here, better standardize extractions, allowing repeatable transparent

Язык: Английский

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When will a changing climate outpace adaptive evolution?

Wiley Interdisciplinary Reviews Climate Change, Год журнала: 2023, Номер 14(6)

Опубликована: Июнь 28, 2023

Abstract Decades of research have illuminated the underlying ingredients that determine scope evolutionary responses to climate change. The field biology therefore stands ready take what it has learned about influences upon rate adaptive evolution—such as population demography, generation time, and standing genetic variation—and apply assess if how populations can evolve fast enough “keep pace” with Here, our review highlights contribute still needs learn provide more mechanistic predictions winners losers We begin by developing broad for contemporary evolution change based on theory. then discuss methods assessing climate‐driven evolution, including quantitative studies, experimental space‐for‐time substitutions. After providing this mechanism‐focused overview both evidence specifically, evolving keep pace change, we next consider factors limit actual responses. In context, dual role phenotypic plasticity in facilitating but also impeding Finally, detail a deeper consideration constraints improve forecasts inform conservation management decisions. This article is categorized under: Climate, Ecology, Conservation > Observed Ecological Changes Extinction Risk Assessing Impacts Climate Change Evaluating Future

Язык: Английский

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A trait‐based approach to determining principles of plant biogeography

American Journal of Botany, Год журнала: 2023, Номер 110(2)

Опубликована: Янв. 17, 2023

Lineage-specific traits determine how plants interact with their surrounding environment. Unrelated species may evolve similar phenotypic characteristics to tolerate, persist in, and invade environments certain characteristics, resulting in some becoming relatively more common types of habitats. Analyses these general patterns geographical trait distribution have led the proposal principles explain diversify space over time. Trait-environment correlation analyses quantify what extent unrelated lineages evolutionary responses a given type habitat. In this synthesis, I give short historical overview on trait-environment analyses, from key observations classic naturalists modern approaches using evolution models, large phylogenies, massive data sets distributions. discuss limitations approaches, including need for realistic lack tropical areas, necessary focus scoring that goes beyond macromorphology. Overcoming will allow field explore new questions related lability niche better identify generalities exceptions

Язык: Английский

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Trait‐based species richness: ecology and macroevolution

Biological reviews/Biological reviews of the Cambridge Philosophical Society, Год журнала: 2023, Номер 98(4), С. 1365 - 1387

Опубликована: Апрель 4, 2023

ABSTRACT Understanding the origins of species richness patterns is a fundamental goal in ecology and evolutionary biology. Much research has focused on explaining two kinds patterns: ( i ) spatial (e.g. latitudinal diversity gradient), ii clade‐based predominance angiosperm among plants). Here, I highlight third kind pattern: trait‐based number with each state character, such as diet or body size). Trait‐based are relevant to many topics evolution, from ecosystem function adaptive radiation paradox sex. Although studies have described particular patterns, these remain far less understood, not been emphasised general category patterns. describe conceptual framework for how arise compared other A systematic review suggests that most often explained by when originates within group (i.e. older states generally higher richness), differences transition rates faster diversification certain states. This latter result contrasts widespread emphasis species‐richness research. show recent actually potentially confounding causes Finally, plethora unanswered questions related

Язык: Английский

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Phylogenomics and biogeography of Guadua: Insights into a neotropical woody bamboo genus

American Journal of Botany, Год журнала: 2025, Номер unknown

Опубликована: Март 24, 2025

Abstract Premise The genus Guadua includes some of the largest bamboo species in neotropics, with certain significant economic importance and used since pre‐Hispanic times to build houses using traditional bajareque technique. are distributed from Mexico South America. potential monophyly this has been suggested based on plastid markers limited sampling. Here we included more nuclear data study morphological classification reconstruct its ancestral area distribution. Methods Samples were collected for 16 taxa (13 species) use single nucleotide polymorphisms (SNPs) derived restriction‐site associated DNA sequencing (RADSeq) construct a phylogenetic hypothesis maximum likelihood coalescent methods. We estimated divergence RelTime method reconstructed geographic areas S‐DEC analysis. Results SNP supported existence two distinct clades, Amplexifolia Angustifolia. origin was as approximately 10.47 million years ago Mesoamerica. biogeographic distribution can likely be explained by combination dispersal vicariant events. Conclusions Our sheds new light relationships within evolutionary history biogeography, enhancing our understanding diversification across various regions.

Язык: Английский

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Chromosomal inversions from an initial ecotypic divergence drive a gradual repeated radiation of Galápagos beetles

Science Advances, Год журнала: 2024, Номер 10(22)

Опубликована: Май 31, 2024

Island faunas exhibit some of the most iconic examples where similar forms repeatedly evolve within different islands. Yet, whether these deterministic evolutionary trajectories islands are driven by an initial, singular divergence and subsequent exchange individuals adaptive genetic variation between remains unclear. Here, we study a gradual, repeated evolution low-dispersive highland ecotypes from dispersive lowland ecotype

Язык: Английский

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Caught in the Act: Incipient Speciation at the Southern limit of Viburnum in the Central Andes

Systematic Biology, Год журнала: 2024, Номер unknown

Опубликована: Июнь 4, 2024

A fundamental objective of evolutionary biology is to understand the origin independently evolving species. Phylogenetic studies species radiations rarely are able document ongoing speciation; instead, modes speciation, entailing geographic separation and/or ecological differentiation, posited retrospectively. The Oreinotinus clade Viburnum has radiated recently from north south through cloud forests Mexico and Central America Andes. Our analyses support a hypothesis incipient speciation in at southern edge its range, central Peru northern Argentina. Although several infraspecific taxa have been recognized this area, multiple lines evidence analytical approaches (including phylogenetic relationships, genetic structure, leaf morphology, climatic envelopes) favor recognition just single species, V. seemenii. We show that what previously as seemenii f. minor occupied drier Tucuman-Bolivian forest region Samaipata Bolivia Salta Plants these populations form well-supported with distinctive signature they evolved smaller, narrower leaves. interpret beginning within-species divergence process elsewhere neotropics resulted repeatedly particular set ecomorphs. Specifically, small, glabrous, entire ecomorph four other montane areas endemism. As predicted based on our ecomorphs Chiapas, Mexico, experience generally conditions, large diurnal temperature fluctuations. In portion range seemenii, characterized by wetter we also may be initial differentiation larger, pubescent, toothy emergence thus appears driven adaptation subtly different conditions separate regions, opposed parapatric along elevational gradients suggested distributions parts neotropics.

Язык: Английский

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Patterns and repeatability of multi‐ecotype assemblages of sympatric salmonids

Global Ecology and Biogeography, Год журнала: 2023, Номер 32(12), С. 2257 - 2270

Опубликована: Окт. 4, 2023

Abstract Aim High repeatability among assemblages of closely related but ecologically distinct ecotypes implies predictability in evolution and assembly communities. The conditions under which ecotype form predictably, the reasons, have been little investigated. Here, we test whether declines as number builds. Location Postglacial lakes with a circumboreal distribution. Time Period Data were extracted from studies published between 1982 2019. Major Taxa Studied Ecotype two Salmonid genera – Salvelinus Coregonus . Fish postglacial commonly occur pairs ecotypes, typically pelagic littoral/benthic form, , contain multiple sympatric ecotypes. Methods We used meta‐analysis to empirically assess how varies across seven examined use broad niche categories well underlying phenotypic traits. Results Within multi‐ecotype did not break down addition third or fourth ecotype. However, was largely absent independent Repeatability trait frequency distributions both genera, yet associations means evident, especially Main Conclusions These results show that can vary greatly lineages; need builds; high may result despite marked differences distribution means. findings only affirm presence repeatable early stages divergence fishes at global scale, also highlight variability taxa

Язык: Английский

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Evolutionary origins of the eastern North American–Mesoamerican floristic disjunction: Current status and future prospects

American Journal of Botany, Год журнала: 2023, Номер 110(3)

Опубликована: Фев. 16, 2023

Biogeographic disjunction patterns, where multiple taxa are shared between isolated geographic areas, represent excellent systems for investigating the historical assembly of modern biotas and fundamental biological processes such as speciation, diversification, niche evolution, evolutionary responses to climate change. Studies on plant genera disjunct across northern hemisphere, particularly eastern North America (ENA) Asia (EAS), have yielded tremendous insight geologic history rich temperate floras. However, one most prevalent patterns involving ENA forests has been largely overlooked: that cloud Mesoamerica (MAM), with examples including Acer saccharum, Liquidambar styraciflua, Cercis canadensis, Fagus grandifolia, Epifagus virginiana. Despite remarkable nature this pattern, which recognized over 75 years, there few recent efforts empirically examine its ecological origins. Here I synthesize previous systematic, paleobotanical, phylogenetic, phylogeographic studies establish what is known about pattern provide a roadmap future research. argue evolution fossil record Mexican flora more broadly, represents key missing piece in broader puzzle hemisphere biogeography. also suggest ENA-MAM an system examining questions how traits life strategies mediate change predicting broadleaf will respond ongoing climatic pressures Anthropocene.

Язык: Английский

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Geogenomic Predictors of Genetree Heterogeneity Explain Phylogeographic and Introgression History: A Case Study in an Amazonian Bird (Thamnophilus aethiops)

Systematic Biology, Год журнала: 2023, Номер 73(1), С. 36 - 52

Опубликована: Окт. 6, 2023

Abstract Can knowledge about genome architecture inform biogeographic and phylogenetic inference? Selection, drift, recombination, gene flow interact to produce a genomic landscape of divergence wherein patterns differentiation genealogy vary nonrandomly across the genomes diverging populations. For instance, genealogical that arise due should be more likely occur on smaller chromosomes, which experience high whereas those tracking histories geographic isolation (reduced caused by barrier) larger sex chromosomes. In Amazonia, populations many bird species diverge introgress rivers, resulting in reticulated signals. Herein, we used reduced representation data disentangle evolutionary history 4 an Amazonian antbird, Thamnophilus aethiops, whose was associated with dynamic evolution Madeira River Basin. Specifically, evaluate whether large river capture event ca. 200 Ka, gave rise genealogies making spatially explicit predictions based processes. We first estimated chromosome-level phylogenies recovered 2 primary topologies genome. The topology (T1) most consistent population for Z-chromosome. second (T2), upon secondary contact. To support these topologies, trained convolutional neural network classify our into alternative diversification models estimate demographic parameters. best-fit model concordant T1 included between non-sister taxa. Finally, modeled levels introgression as functions chromosome length found chromosomes experienced higher flow. Given (1) genetrees supporting T2 were (2) lower (and especially Z-chromosome), argue represents rivers contact barrier loss. Our results suggest significant portion heterogeneity arises extrinsic processes such interacting intrinsic architecture. Future phylogeographic studies would benefit from accounting processes, different parts reveal contrasting, albeit complementary histories, all are relevant disentangling intricate geogenomic mechanisms biotic diversification. [Amazonia; biogeography; modeling; flow; tree; architecture; geogenomics; introgression; linked selection; network; phylogenomic; phylogeography; reproductive isolation; speciation; tree.]

Язык: Английский

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