Table of Contents
Overview
Definition of Phylogenetics
Phylogenetics is the study of the evolutionary history of life, using genetics to establish relationships between organisms based on empirical data and heritable traits, such as DNA sequences, protein amino acid sequences, and morphological characteristics.[1.1] This process, known as phylogenetic inference, aims to reconstruct the evolutionary history of biological entities, including individuals and groups of organisms.[1.1] The primary output of these studies is the phylogenetic tree, also known as a phylogeny or evolutionary tree, which graphically represents the evolutionary relationships among species or taxa over time.[4.1] This diagram highlights the similarities and differences among species, illustrating their common ancestry and evolutionary pathways.[4.1] Phylogenetic trees, sometimes referred to as cladograms or dendrograms, allow researchers to visualize how different species are related based on genetic and morphological similarities and differences.[6.1] The methodology of phylogenetics has evolved to incorporate various data types, including molecular, archaeological, and historical studies, to construct objective representations of these relationships.[3.1] Consequently, phylogenetics plays a crucial role in understanding the diversity and evolutionary history of life on Earth.[7.1]Importance in Biology
Phylogenetics is essential in biology, offering insights into the evolutionary history and relationships among organisms. It employs various data types, such as morphological, behavioral, and molecular information, to construct phylogenetic trees that depict these relationships.[10.1] Molecular techniques, especially DNA sequencing, provide a vast array of characters for comparison, enhancing the understanding of phylogenetic relationships beyond traditional morphological methods.[8.1] By analyzing genetic differences, primarily in DNA sequences, molecular phylogenetics elucidates evolutionary relationships and processes contributing to species diversity.[9.1] Advancements in DNA sequencing technologies, such as next-generation sequencing (NGS), have transformed phylogenetics by enabling more comprehensive analyses. NGS facilitates the characterization of genomes across various species, providing deeper insights into evolutionary dynamics.[17.1] Despite its potential, NGS adoption in phylogeography and phylogenetics has been slower due to challenges like the focus on non-model organisms and the need for extensive sampling.[18.1] Nonetheless, integrating genomic data has expanded traditional phylogenetics, allowing for modeling multiple sources of heterogeneity in evolutionary signals.[20.1] Combining fossil records with molecular data enhances our understanding of evolutionary relationships by providing insights into extinct biodiversity and dynamics often inaccessible through genetic data alone.[23.1] Tracing phenotypic trait evolution along phylogenetic trees is crucial for revealing the molecular basis of morphological change. Moreover, combining morphological and molecular data in Bayesian relaxed clock analysis allows for joint estimates of tree topology, divergence times, and evolutionary rates, addressing broad evolutionary questions and inferring dynamics of speciation and extinction.[24.1] However, challenges persist in accurately dating fossils, as the incompleteness of the fossil record can lead to underestimating node ages in phylogenetic trees, resulting in discrepancies between fossil evidence and molecular dating estimates.[38.1] The proportion of imprecise-date fossils further impacts the accuracy of fossil age estimates, necessitating careful consideration of these factors in phylogenetic analyses.[37.1]History
Early Speculations and Theories
The study of phylogenetics, which focuses on the evolutionary history of life, has its roots in early speculations and theories about the relationships among organisms. Initially, phylogenetics was concerned with establishing connections between various biological entities, including populations, species, and even genes, through the analysis of genetic and morphological data.[2.1] The field began to take a more scientific approach as researchers sought to construct objective representations of evolutionary relationships. This involved utilizing genetic, molecular, archaeological, and historical studies to explain and predict similarities and differences among organisms.[3.1] The results of these investigations are often depicted as phylogenetic trees, which illustrate ancestral relationships and evolutionary distances based on genetic variations, such as nucleotide substitutions in homologous DNA sequences across different species.[3.1] Thus, the early development of phylogenetics laid the groundwork for a more systematic understanding of evolutionary biology, transitioning from speculative ideas to a rigorous scientific discipline focused on the inference of evolutionary histories.Development of Phylogenetic Methods
The development of phylogenetics has profoundly impacted nearly every branch of biology since its inception around 50 years ago. Initially established to classify organisms based on a set of cladistic rules, this methodology was notably advanced by the German entomologist Willi Hennig in the mid-20th century.[44.1] This foundational approach has evolved into the central paradigm of evolutionary biology, providing a key framework for understanding various disciplines, including genomics, community ecology, epidemiology, and conservation biology.[45.1] Phylogenetics aims to reconstruct the evolutionary history of organisms and classify them based on shared ancestry, leading to the creation of phylogenetic trees, or cladograms, that visually represent these relationships.[44.1] A pivotal moment in phylogenetics occurred in 1977 when Carl Woese and George Fox published a paper that established the tripartite structure of the living world, fundamentally altering our understanding of evolutionary relationships.[49.1] This discovery significantly influenced evolutionary biology by providing a framework for understanding the emergence of life. In the mid-2000s, advancements in next-generation sequencing techniques revolutionized DNA sequencing, dramatically reducing costs and increasing data generation speed.[54.1] Consequently, genome sequencing expanded beyond model organisms, facilitating comparative studies that reveal the genetic basis for phenotypic variation across species.[55.1] Phylogenetic methods and theory have proven powerful in identifying functional genetic variation underlying trait evolution, with statistical comparative approaches expected to become more common as whole genomes populate the tree of life.[55.1] Moreover, next-generation sequencing (NGS) techniques have facilitated the generation of vast amounts of sequence data, enhancing our understanding of evolutionary relationships among species.[54.1] Techniques such as Restriction-site Associated DNA (RAD) sequencing have profoundly impacted phylogeography and phylogenetics, allowing researchers to analyze genetic variation and evolutionary patterns more effectively.[56.1] The development of phylogenetic methods has advanced significantly over the past decade, particularly with new models for estimating dated trees, originally known as the fossilized birth-death (FBD) process. This model has evolved into a family of models enabling researchers to coestimate evolutionary parameters, such as diversification and sampling, alongside divergence times for various applications in paleobiology.[52.1] Furthermore, integrating morphological and molecular data through Bayesian relaxed clock analysis, also known as total-evidence dating, allows for a joint estimate of tree topology, divergence times, and evolutionary rates within a multivariate statistical framework.[53.1] These methodologies provide novel insights into broad evolutionary and deep-time questions and facilitate the inference of speciation and extinction dynamics, as well as variations in species diversification among lineages using time-calibrated phylogenetic trees.[53.1] Additionally, integrating modern and fossil occurrence data enhances our ability to make inferences across multiple taxonomic and phylogenetic scales, strengthening the use of paleontological findings as anchoring points for investigating ongoing ecological and evolutionary processes.[50.1]Recent Advancements
Bioinformatics in Phylogenetics
Recent advancements in bioinformatics have significantly enhanced the field of phylogenetics, particularly through the integration of genomic sequencing and computational methodologies. Phylogenomics, which encompasses a range of theoretical and methodological innovations, has expanded traditional phylogenetics by leveraging the increasing availability of genomic sequencing products and computational power. This approach allows for the modeling of multiple sources of heterogeneity in evolutionary signals, thereby improving the accuracy of phylogenetic inferences.[87.1] The development of computational methods for inferring species trees, particularly those based on the multispecies coalescent (MSC) model, has been a notable advancement. These methods utilize data from multiple genomic regions and, increasingly, whole genomes, which facilitates a more comprehensive understanding of evolutionary relationships.[88.1] Furthermore, Bayesian phylogenetics has emerged as a powerful framework that offers substantial computational savings, accommodating the challenges posed by increased genomic sampling.[86.1] In addition to these theoretical advancements, practical tools have been developed to visualize complex phylogenetic trees and associated data. For instance, iTol and PhyloGeoTool are examples of software that support interactive visualization, making it easier for researchers to analyze large phylogenetic datasets.[85.1] These tools are essential for managing the vast amounts of data generated by modern genomic studies, allowing for more effective exploration of evolutionary relationships.Genomic Sequencing Techniques
Recent advancements in genomic sequencing techniques have significantly transformed the field of phylogenetics, enabling researchers to resolve complex evolutionary relationships that traditional methods often struggle to clarify. Over the last decade, the paradigm of molecular systematics has shifted due to the advent of high-throughput sequencing technologies, which facilitate the reconstruction of evolutionary relationships using genome-scale datasets. This "big data" approach has provided biologists with a new array of tools for analyzing phylogenetic relationships more comprehensively than before.[90.1] One of the key advantages of genomic sequencing is its ability to identify orthologous genes or proteins, which are crucial for accurate phylogenetic analysis. The process involves multiple sequence alignment and the selection of appropriate substitution models and inference methodologies, allowing for a more nuanced understanding of evolutionary dynamics.[91.1] Furthermore, genome analysis can resolve relationships within species by offering new genetic markers for population genetics studies, particularly in pathogens such as those causing anthrax or tuberculosis.[89.1] This additional data from complete genome sequences is essential for separating phylogenetic signals from noise, thereby enhancing the accuracy of evolutionary interpretations.[89.1]In this section:
Applications Of Phylogenetics
Conservation Biology
Phylogenetics plays a crucial role in conservation biology by providing insights into the evolutionary relationships among species, which is essential for effective conservation planning and prioritization. The concept of phylogenetic diversity (PD) has emerged as a significant metric in conservation, quantifying the conservation value of species by summing the phylogenetic branch lengths that connect them. This approach highlights the importance of preserving species that are evolutionarily distinct, as they contribute uniquely to biodiversity.[158.1] Phylogenetic analysis aids in identifying evolutionary relationships among species, which is vital for prioritizing conservation efforts, especially in biodiversity hotspots. By understanding these relationships, conservationists can make informed decisions about which species to prioritize for protection, ensuring that efforts are directed towards those that are most at risk and have significant evolutionary value.[157.1] For instance, phylogenetic considerations can inform strategies for ex situ conservation, helping to prioritize species for germplasm and living collections based on their evolutionary uniqueness.[135.1] Advancements in genetic sequencing technologies have significantly transformed the field of systematics, particularly through the emergence of phylogenomics, which has developed over the past two decades. This discipline relies on genomic datasets rather than solely on morphological characters or a limited number of genetic markers, allowing for a more comprehensive understanding of phylogenetic relationships among taxa.[159.1] The use of phylogenetic tools has notably increased in conservation biology and community ecology, as these tools are essential for identifying centers of diversification and understanding community assembly processes.[156.1] Consequently, this enhanced understanding of evolutionary relationships plays a crucial role in prioritizing conservation efforts, particularly in biodiversity hotspots, thereby contributing to the protection of Earth's evolutionary heritage.[156.1] In practical applications, phylogenetics has been utilized to inform conservation strategies for endangered species by reconstructing their phylogenetic histories and identifying critical genetic loci that can aid in their preservation.[134.1] This approach not only enhances the effectiveness of conservation actions but also supports the development of preemptive measures to protect at-risk species.[157.1] Overall, the application of phylogenetic analysis in conservation biology is essential for maintaining biodiversity and ensuring the survival of species in a rapidly changing environment.Medicine and Public Health
Phylogenetic analysis is a crucial tool in both medicine and public health, with significant applications in forensic science. Its importance was first recognized in Sweden in 1992, where it was used as strong forensic evidence in criminal prosecutions related to HIV _transmission.[129.1] To enhance the accuracy of DNA evidence, phylogenetic analysis should be conducted under strictly controlled conditions and in conjunction with other methods to provide robust forensic evidence.[129.1] This comprehensive approach allows forensic experts to effectively address diverse crime scenes and types of evidence. In assessing epidemiological relationships between viral DNA sequences, phylogenetic analysis is essential. It is crucial to perform this analysis on appropriate local control sequences and to sequence at least two samples to strengthen forensic evidence regarding transmission.[131.1] This method has been applied in various studies, including the exploration of suspected HIV-1 transmission cases, demonstrating its effectiveness.[132.1] In the context of viral diseases, phylogenetic analysis enhances our understanding of viral mutations, which is critical for vaccine development and public health strategies. For instance, investigating structural mutations in the SARS-CoV-2 spike protein has provided insights into the virus's pathogenesis, aiding in the discovery of potential treatments and _vaccine targets.[141.1] Specific variants, such as D614G and E484K, have been identified as threats to immune responses, influencing the design of COVID-19 vaccines and antibody treatments.[142.1] The field of forensic DNA analysis is transforming due to advanced technologies like next-generation sequencing (NGS), rapid DNA analysis, AI-driven workflows, 3D genomics, and mobile DNA platforms, which expand forensic capabilities.[144.1] These innovations provide forensic sciences with tools that enhance accuracy and efficiency.[144.1] As these technologies evolve, they are expected to create added value and potentially lead to a paradigm shift within the _criminal justice system.[146.1] Phylogenetic analysis is also crucial in predicting potential future mutations of viruses such as HIV and Influenza, essential for vaccine design and _public health preparedness. By analyzing genomic data, researchers can reconstruct phylogenetic relationships and simulate mutation rates.[147.1] The seasonal influenza vaccine is designed to protect against predicted circulating viruses, though identifying these poses challenges. Features from phylogenetic trees and computational methods are used to predict future strains.[149.1] The main circulating strains of influenza A include A (H1N1) pdm09 and H3N2, with the HA gene exhibiting the fastest mutation rate.[148.1] To ensure vaccine effectiveness, influenza vaccine strains must be updated annually, involving modeling mutation fitness to forecast virus evolution and select representative strains.[151.1]In this section:
Challenges In Phylogenetic Analysis
Data Accuracy and Reliability
Phylogenetic analysis faces significant challenges regarding data accuracy and reliability, particularly as the volume of molecular sequence data has increased dramatically. The rapid accumulation of such data, driven by advancements in sequencing technologies, has led to a twenty-fold increase in available sequence data over the past decade, which in turn has complicated the reconstruction of evolutionary histories for genes and species.[177.1] This growth has outpaced the development of phylogenetic methods and algorithms, resulting in computational challenges that emerge at various stages of analysis.[177.1] One of the primary issues is the handling of large datasets, which necessitates efficient algorithms and software tools capable of processing vast amounts of data within reasonable timeframes.[175.1] The computational demands associated with analyzing these large datasets can affect the reliability of the resulting phylogenetic trees. Specifically, the two main concerns in reconstructing phylogenetic trees from extensive data matrices are computation time and reliability, as both multiple sequence alignment and phylogenetic inference are notoriously time-consuming processes.[178.1] Furthermore, the computational challenges are compounded by issues such as numerical stability, the scalability of search algorithms, and high memory requirements.[176.1] The accuracy of phylogenetic analyses is significantly influenced by biological factors such as gene duplication and horizontal gene transfer (HGT). HGT, defined as the transfer of DNA sequences between species outside of inheritance, plays a crucial role in prokaryotic evolution and serves as a significant source of genomic novelty, which can lead to phenomena such as antibiotic resistance and the emergence of virulent strains.[171.1] The frequency of HGT events among microorganisms has been highlighted in genomic analyses, indicating that these events can complicate phylogenetic inference.[170.1] Additionally, the intricate history of gene duplication and loss presents further challenges, particularly in deep phylogenies, where the accuracy of phylogenetic signal may vary across different gene families with distinct histories of duplication and loss.[173.1] Therefore, understanding these biological factors is essential for improving the reliability of phylogenetic analyses. To mitigate these challenges, researchers are encouraged to adhere to best practices in phylogenetic analysis. This includes rigorous data quality control measures to verify the accuracy and integrity of sequences, as well as the careful selection of appropriate models of evolution, which can greatly impact the accuracy of the analysis.[179.1] By addressing these issues, researchers can enhance the reliability of phylogenetic trees and improve our understanding of evolutionary relationships among species.Future Directions
Emerging Technologies
Emerging technologies are poised to significantly enhance the field of phylogenetics, particularly through advancements in computational power and the integration of machine learning techniques. Phylogenomics, which encompasses a range of theoretical and methodological innovations, leverages the increasing availability of genomic sequencing and computational resources to model the complexities of evolutionary relationships more effectively.[220.1] This evolution in methodology not only improves the accuracy of phylogenetic analyses but also addresses the challenges posed by heterogeneous signals across different data sources.[82.1] The application of machine learning in phylogenetics has shown considerable promise, particularly in inferring tree topologies and branch lengths, selecting substitution models, and conducting downstream analyses related to introgression and diversification.[227.1] As researchers continue to explore the potential of supervised machine learning approaches, careful consideration of training datasets, network architectures, and data encodings will be essential to accommodate the intricate processes that traditional methods struggle to resolve.[226.1] This integration of machine learning with conventional phylogenetic techniques is expected to enhance both the efficiency and accuracy of phylogenetic tree construction, thereby advancing our understanding of evolutionary processes.[219.1] Moreover, the development of digital data management tools and web-based platforms has facilitated large-scale collaboration among researchers, enabling the creation of comprehensive, openly accessible data repositories.[213.1] These platforms support the integration of bioinformatics and large-scale phylogeny reconstruction, which are crucial for addressing contemporary biodiversity challenges.[214.1] As the field continues to evolve, the demand for skilled researchers adept at harnessing big data and emerging technologies will likely increase, further driving innovation in phylogenetic research.[218.1]Integration with Other Disciplines
The integration of phylogenetic data into conservation planning is increasingly recognized as a vital component for addressing contemporary environmental challenges, particularly in the context of climate change and habitat loss. The main goal of discussions surrounding this integration is to provide a platform for presenting methods that allow for the incorporation of phylogenetic and extinction risk data into conservation strategies.[221.1] Despite the growing appreciation for evolutionary and genetic knowledge in conservation theory, such insights are often underutilized in practical conservation planning and policy.[222.1] The scientific justification for employing phylogenetic diversity (PD) in conservation efforts is supported by its potential to enhance biodiversity preservation and maintain evolutionary potential.[232.1] More than two decades ago, the concept of phylogenetic diversity was proposed as an additional criterion for nature conservation, emphasizing the importance of understanding the evolutionary history of species in conservation assessments.[231.1] This approach aims to prioritize species based on their phylogenetic positions, which reflect their evolutionary legacy and can inform conservation priorities.[232.1] The integration of genomics and phylogenetics into conservation management is a complex process that may not keep pace with the rapid changes brought about by climate change. While this integration has the potential to foster adaptive potential and diversity through mechanisms such as hybrid introgression, which can provide novel variation for ecological divergence and evolutionary speciation, it may not be sufficient to respond quickly to the challenges posed by climate change.[224.1] Furthermore, the projected impacts of climate change are expected to affect not only the evolutionary history encapsulated within species assemblages but also the phylogenetic structure of species communities. This phylogenetic composition plays a crucial role in shaping ecological processes and ecosystem functioning.[225.1] Phylogenetic insights have been recognized as crucial for informing biodiversity conservation priorities, a concept first proposed by Vane-Wright et al. over two decades ago.[231.1] This approach integrates the evolutionary history of organisms into conservation assessments, allowing conservationists to prioritize efforts for endangered species effectively.[232.1] Furthermore, research indicates that plant communities characterized by higher species richness and phylogenetic diversity can enhance the diversity of associated herbivores and their predators through trophic interactions.[233.1] This interconnectedness underscores the importance of phylogenetic diversity in habitat restoration initiatives, although further exploration is needed to understand its effects on other ecological guilds through non-trophic mechanisms.[233.1]In this section:
References
[1] Phylogenetics - Wikipedia — In biology, phylogenetics (/ ˌfaɪloʊdʒəˈnɛtɪks, - lə -/) is the study of the evolutionary history of life using genetics, which is known as phylogenetic inference. It establishes the relationship between organisms with the empirical data and observed heritable traits of DNA sequences, protein amino acid sequences, and morphology. The results are a phylogenetic tree —a
[2] Phylogenetic Inference - Stanford Encyclopedia of Philosophy — Phylogenetics is the study of the evolutionary history and relationships among individuals, groups of organisms (e.g., populations, species, or higher taxa), or other biological entities with evolutionary histories (e.g., genes, biochemicals, or developmental mechanisms). Phylogenetic inference is the task of inferring this history, and as with other problems of inference, there are
[3] Phylogenetics | Evolutionary Relationships & Classification - Britannica — Phylogenetics | Evolutionary Relationships & Classification | Britannica Ask the Chatbot Games & Quizzes History & Society Science & Tech Biographies Animals & Nature Geography & Travel Arts & Culture ProCon Money Videos https://www.britannica.com/science/phylogenetics Article History The field of phylogenetics takes a functional and more scientific turn in its attempts to construct an objective depiction of evolutionary relationships between organisms based on genetic, molecular, archaeological, and historical studies and with the specific purpose of explaining, predicting, and testing similarities and differences between organisms. Ancestral relationships among species are commonly represented as phylogenetic trees (also called cladograms or dendrograms). Taking two homologous DNA sequences in different species, one can estimate evolutionary distance by measuring the number of nucleotide substitutions that have occurred over time.
[4] Phylogenetic tree - Wikipedia — A phylogenetic tree, phylogeny or evolutionary tree is a graphical representation which shows the evolutionary history between a set of species or taxa during a specific time. In other words, it is a branching diagram or a tree showing the evolutionary relationships among various biological species or other entities based upon similarities and differences in their physical or genetic
[6] Phylogenetics - Definition and Examples - Biology Online Dictionary — A phylogenetic tree is a “tree” diagram that shows the hypothetical evolutionary relatedness and history of groups of organisms based on the phylogenies of different biological species. Evolutionary trees are essential phylogenetic tools for learning about common ancestors based on evolutionary closeness and branch lengths. Phylogenetics, thus, helps us understand phylogenetic diversity and phylogenetic history of various groups of organisms. The phylogenetic approach of studying evolutionary relatedness and histories of organisms makes use of a phylogenetic tree. As already discussed above, the phylogenetic tree depicts how a group of organisms can be related to another group and molecular sequencing is applied to provide a genetic basis for their relatedness. Thus, phylogenetics is mainly concerned with the phylogenetic relationships and molecular evolution of organisms according to evolutionary similarities and differences.
[7] Phylogenetics - an overview | ScienceDirect Topics — Phylogenetics is the study of the evolutionary relatedness among groups of organisms. Molecular phylogenetics uses sequence data to infer these relationships for both organisms and the genes they maintain. With the large amount of publicly available sequence data, phylogenetic inference has become increasingly important in all fields of biology.
[8] Advantages and Disadvantages of Molecular Phylogenetics: A Case Study ... — Abstract. The advantages of nucleotide sequence data for studying phylogeny have been shown to include number of potential characters available for comparison, rate independence between molecular and morphological evolution, and utility of molecular data for modeling patterns of nucleotide substitution.
[9] Molecular phylogenetics - Wikipedia — Molecular phylogenetics (/ m ə ˈ l ɛ k j ʊ l ər ˌ f aɪ l oʊ dʒ ə ˈ n ɛ t ɪ k s, m ɒ-, m oʊ-/ ) is the branch of phylogeny that analyzes genetic, hereditary molecular differences, predominantly in DNA sequences, to gain information on an organism's evolutionary relationships. From these analyses, it is possible to determine the processes by which diversity among species
[10] What evidence can we use to show relatedness between species? — Phylogenetics is the study of the evolutionary history and the relationships between groups of organisms. It involves the collection of morphological, behavioural and molecular (DNA, RNA, amino acid) data, to then compare the number of similarities or differences between them and use this information to construct phylogenetic trees.
[17] Next-Generation Sequencing Reveals the Impact of Repetitive DNA Across ... — We used next-generation sequencing to characterize the genomes of nine species of Orobanchaceae of known phylogenetic relationships, different life forms, and including a polyploid species. ... Next-Generation Sequencing Reveals the Impact of Repetitive DNA Across Phylogenetically Closely Related Genomes of Orobanchaceae.
[18] Applications of next-generation sequencing to phylogeography and ... — Despite this obvious potential, NGS has been slow to take root in phylogeography and phylogenetics compared to other fields like metagenomics and disease genetics (Mardis, 2008).We suggest that this lag has been caused by four specific aspects of phylogeographic and phylogenetic research: the predominant focus on non-model organisms, the need for sequencing large numbers of samples per species
[20] Phylogenomics: Current Biology - Cell Press — Phylogenomics can be summed up as a number of exciting theoretical and methodological advances that greatly expand traditional phylogenetics in two directions: first, by exploiting the increasing availability of genomic sequencing products and computational power; second, in modelling the multiple sources of heterogeneity in signals across
[23] Morphological Phylogenetics in the Genomic Age - ScienceDirect — For example, tracing the evolution of phenotypic traits along phylogenetic trees is essential for revealing the molecular basis of morphological change . Similarly, fossils provide the best window into vast expanses of extinct biodiversity and associated evolutionary dynamics, which are largely or totally inaccessible to genetic data .
[24] Integrative Phylogenetics: Tools for Palaeontologists to Explore the ... — Moreover, the integration of both morphological and molecular data for Bayesian relaxed clock analysis (total-evidence dating) provides a joint estimate of tree topology, divergence times, and evolutionary rates in a multivariate statistical framework . Complementary methodologies that combine morphological and molecular approaches can provide novel answers to broad evolutionary and deep-time questions with methods to infer the dynamics of speciation and extinction, as well as the variation in species diversification among lineages, using time-calibrated phylogenetic trees. 17.Simões T.R., Caldwell M.W., Pierce S.E. Sphenodontian phylogeny and the impact of model choice in Bayesian morphological clock estimates of divergence times and evolutionary rates. 94.Wood H.M., Matzke N.J., Gillespie R.G., Griswold C.E. Treating Fossils as Terminal Taxa in Divergence Time Estimation Reveals Ancient Vicariance Patterns in the Palpimanoid Spiders.
[37] Estimating the Age of Poorly Dated Fossil Specimens and Deposits Using ... — The proportion of imprecise-date fossils has a strong impact on the accuracy of fossil age estimates. ... While phylogenetic analyses using the FBD model have largely focused on inferring phylogenetic trees and dating species divergences, our study shows that these methods can harness indirect information in an integrative and hierarchical
[38] Calibrating the Tree of Life: fossils, molecules and evolutionary ... — The incompleteness of the fossil record also leads inevitably to the underestimation of node ages in a phylogenetic tree (Springer, 1995), presenting significant discrepancies between estimates obtained from the fossil record and molecular dating (e.g. Benton and Ayala, 2003). The selectivity of fossilization is largely responsible for this
[44] PDF — This led to the development of phylogenetics, a field that seeks to reconstruct the evolutionary history of organisms and classify them based on shared ancestry. Early phylogenetic trees, or cladograms, ... One of the key developments during this period was the introduction of cladistics by the German entomologist Willi Hennig in the mid-
[45] Current Advances in Molecular Phylogenetics - PMC — Since its inception some 50 years ago, phylogenetics has permeated nearly every branch of biology. Initially developed to classify objects based on a set of cladistic rules, it has now become the central paradigm of evolutionary biology and a key framework for making sense of a wide range of disciplines [], such as genomics [], community ecology [], epidemiology [], conservation biology
[49] Phylogeny and beyond: Scientific, historical, and conceptual ... — Abstract In 1977, Carl Woese and George Fox published a brief paper in PNAS that established, for the first time, that the overall phylogenetic structure of the living world is tripartite. We describe the way in which this monumental discovery was made, its context within the historical development of evolutionary thought, and how it has impacted our understanding of the emergence of life and
[50] The geography of phylogenetic paleoecology: integrating data and ... — However, designing methods that integrate modern and fossil occurrence data bolster our ability to make inferences using information from multiple taxonomic and phylogenetic scales (Hunt and Slater Reference Hunt and Slater2016), strengthen our ability to use findings from paleontological studies as past anchoring points to investigate ongoing ecological and evolutionary processes (Lawing and Matzke Reference Lawing and Matzke2014), and help us translate findings from paleontological studies to inform conservation practices (Dietl and Flessa Reference Dietl and Flessa2011; Barnosky et al. I will frame the discussion focusing on PaleoPhyloGeographic species distribution Models (PPGMs) as an organizing theme that integrates multiple lines of evidence to infer species past geographic response to climate change and to estimate where and when there were hotspots of ancient diversification (Lawing and Polly Reference Lawing and Polly2011; Rödder et al.
[52] Integrating Fossil Observations Into Phylogenetics Using the Fossilized ... — Over the past decade, a new set of methods for estimating dated trees has emerged. Originally referred to as the fossilized birth-death (FBD) process, this single model has expanded to a family of models that allows researchers to coestimate evolutionary parameters (e.g., diversification, sampling) and patterns alongside divergence times for a variety of applications from paleobiology to
[53] Integrative Phylogenetics: Tools for Palaeontologists to Explore the ... — Moreover, the integration of both morphological and molecular data for Bayesian relaxed clock analysis (total-evidence dating) provides a joint estimate of tree topology, divergence times, and evolutionary rates in a multivariate statistical framework . Complementary methodologies that combine morphological and molecular approaches can provide novel answers to broad evolutionary and deep-time questions with methods to infer the dynamics of speciation and extinction, as well as the variation in species diversification among lineages, using time-calibrated phylogenetic trees. 17.Simões T.R., Caldwell M.W., Pierce S.E. Sphenodontian phylogeny and the impact of model choice in Bayesian morphological clock estimates of divergence times and evolutionary rates. 94.Wood H.M., Matzke N.J., Gillespie R.G., Griswold C.E. Treating Fossils as Terminal Taxa in Divergence Time Estimation Reveals Ancient Vicariance Patterns in the Palpimanoid Spiders.
[54] Phylogenomics — principles, opportunities and pitfalls of big‐data ... — Next-generation sequencing techniques, developed in the mid-2000s, revolutionized DNA sequencing and led to a dramatic reduction in sequencing cost per nucleotide and a sharp increase in data generation speed. As a result, the generation of unprecedented amounts of sequence data for both model and nonmodel organisms has become affordable.
[55] Phylogenetics is the New Genetics (for Most of Biodiversity) — Genome sequencing is rapidly spreading beyond model organisms, opening the door to comparative studies that can reveal the genetic basis for phenotypic variation across species. We argue that phylogenetic methods and theory provide tremendous power to identify the functional genetic variation underlying trait evolution. We anticipate that existing statistical comparative approaches will be more commonly applied to studying the genetic basis for phenotypic evolution as whole genomes continue to populate the tree of life. Enabled by recent advances in sequencing technology, comparative genomic studies have emerged as an important avenue for detecting genetic changes responsible for trait variation across species. In our view, the applications of comparative methods to genotype–phenotype mapping described above constitute the tip of the iceberg in terms of potential synergies between phylogenetics and genetic studies of trait evolution.
[56] Applications of next-generation sequencing to phylogeography and ... — Restriction-site Associated DNA (RAD) sequencing is the NGS method that has made the most impact on phylogeography and phylogenetics to date. As with other similar methods described below, DNA is digested with restriction enzymes and the resulting fragmented are size-selected from an agarose gel and sequenced via NGS.
[82] Phylogenomics: Current Biology - Cell Press — Phylogenomics can be summed up as a number of exciting theoretical and methodological advances that greatly expand traditional phylogenetics in two directions: first, by exploiting the increasing availability of genomic sequencing products and computational power; second, in modelling the multiple sources of heterogeneity in signals across
[85] Recent advances in computational phylodynamics - ScienceDirect — The computational and methodological advances that made phylodynamic inference possible for increasingly large data sets have also created a need to visualize large phylogenetic trees as well as any annotated information (e.g. virus and patient data). iTol and PhyloGeoTool are particular examples that address this need by supporting interactive
[86] Scalable Bayesian phylogenetics - PMC - PubMed Central (PMC) — Recent advances in Bayesian phylogenetics offer substantial computational savings to accommodate increased genomic sampling that challenges traditional inference methods. In this review, we begin with a brief summary of the Bayesian phylogenetic framework, and then conceptualize a variety of methods to improve posterior approximations via
[87] Phylogenomics: Current Biology - Cell Press — Phylogenomics can be summed up as a number of exciting theoretical and methodological advances that greatly expand traditional phylogenetics in two directions: first, by exploiting the increasing availability of genomic sequencing products and computational power; second, in modelling the multiple sources of heterogeneity in signals across
[88] Advances in Computational Methods for Phylogenetic Networks in the ... — With the availability of data from multiple genomic regions, and increasingly often from whole genomes, a wide array of methods for inferring species trees, mainly based on the multispecies coalescent (MSC) model [], have been developed .Building on these methods, and often extending them in novel ways, the development of computational methods for inferring phylogenetic networks
[89] Phylogenomics: Intersection of Evolution and Genomics | Science - AAAS — Genome analysis can even help resolve relationships within species, such as by providing new genetic markers for population genetics studies in the bacteria causing anthrax or tuberculosis (5, 6). In all these studies, it is the additional data provided by a complete genome sequence that allows one to separate the phylogenetic signal from the
[90] A Practical Guide to Design and Assess a Phylogenomic Study — Over the last decade, molecular systematics has undergone a change of paradigm as high-throughput sequencing now makes it possible to reconstruct evolutionary relationships using genome-scale datasets. The advent of "big data" molecular phylogenetics provided a battery of new tools for biologists bu …
[91] Phylogenetic tree building in the genomic age - Nature — Phylogenetic tree building in the genomic age | Nature Reviews Genetics Here, we discuss the major steps of phylogenetic analysis, including identification of orthologous genes or proteins, multiple sequence alignment, and choice of substitution models and inference methodologies. D. PANTHER in 2013: modeling the evolution of gene function, and other gene attributes, in the context of phylogenetic trees. J. A class frequency mixture model that adjusts for site-specific amino acid frequencies and improves inference of protein phylogeny. J. Guided tree topology proposals for Bayesian phylogenetic inference. K.P., Z.Y. and M.J.T. contributed to all aspects of the article. The phylogenetic or genealogical tree of sequences at a gene locus or genomic region. & Telford, M.J. Phylogenetic tree building in the genomic age.
[129] Forensic application of phylogenetic analyses - Exploration of ... — Results of phylogenetic analysis as forensic evidence in criminal HIV transmission prosecutions were first used in court of low in Sweden in 1992 . In order to give strong forensic evidence regarding transmission, phylogenetic analysis needs to be enhanced with application of several methods and conducted under strictly controlled
[131] Forensic application of phylogenetic analysis - exploration of ... — Phylogenetic analysis may serve as a valuable tool in assessing the epidemiological relation between viral DNA sequences. In order to increase the likelihood of observing phylogenetic separation of sequences as well as to give strong forensic evidence regarding transmission, phylogenetic analysis needs to be performed on appropriate local control sequences and by sequencing of at least two
[132] Forensic application of phylogenetic analyses - Academia.edu — Forensic application of phylogenetic analyses - Exploration of suspected HIV-1 transmission case. Slobodan Nikolic. 2017, Forensic Science International: Genetics.
[134] Genome sequencing of endangered species - Wikipedia — By understanding the chromosomal basis of sex of those species, it is possible to reconstruct the phylogenetic history of those families and use more efficient strategies in their conservation. By using the ddRADseq method scientists found new sex-related loci in a 56 Gb genome of the family Cryptobranchidae.
[135] Keeping All the PIECES: Phylogenetically Informed Ex Situ Conservation ... — Ex situ conservation in germplasm and living collections is a major focus of global plant conservation strategies. Prioritizing species for ex situ collection is a necessary component of this effort for which sound strategies are needed. Phylogenetic considerations can play an important role in prioritization. Collections that are more phylogenetically diverse are likely to encompass more
[141] Phylogenetic analysis of SARS‐CoV‐2 in the first few months since its ... — The phylogenetic characterization of an emerging virus is crucial to understand the way the virus and the pandemic will evolve. Thus, a detailed study of the SARS CoV‐2 genome allows, on the one hand, to contribute to the knowledge of viral diversity to detect the most suitable regions to be used as antivirals or vaccines targets.
[142] Insights into the evolutionary and prophylactic analysis of SARS-CoV-2 ... — In this regard, the D614 G, S477 N, and E484 K variants of the S protein are thought to cause a threat to immune system or amplified ACE2 binding by the virus, thus affecting COVID-19 vaccine development and antibody treatment (Koyama et al., 2020). Particularly, E484 is a region in the RBD where mutations typically influence the binding and
[144] Emerging Technologies in Forensic DNA Analysis — This manuscript reviews the emerging technologies that are reshaping the field of forensic DNA analysis, including next-generation sequencing (NGS), rapid DNA analysis, AI-driven forensic workflows, 3D genomics, and mobile DNA platforms. Keywords: Forensic DNA analysis; Next-Generation Sequencing (NGS); AI in forensics; Rapid DNA analysis; 3D genomics; Mobile DNA platforms; Forensic databases; Ethical issues in DNA analysis; Phenotypic prediction; Spatial DNA analysis; Criminal investigations; Genetic privacy; DNA contamination; Emerging forensic Technologies; Legal considerations in forensics The continued advancement of DNA technologies, including next-generation sequencing (NGS), AI-driven analysis, 3D genomics, and mobile DNA platforms, has further expanded the capabilities of forensic scientists.
[146] The interface between forensic science and technology: how technology ... — 4. Concluding remarks on the future of forensic science. Further advancements in forensic science in combination with the introduction of new technology and methods that create an added value (innovation) for the end-user will definitely be able to cause a paradigm shift within the criminal justice system.
[147] (PDF) Predicting Viral Evolution Using Phylogenetic Trees and ... — Genomic data from Influenza, HIV, and SARS-CoV-2 were analyzed to reconstruct phylogenetic relationships and simulate mutation rates under varying selective pressures.
[148] Phylogenetic analysis of HA and NA genes of influenza A viruses in ... — A (H1N1) pdm09 and H3N2 are currently main circulating strains of influenza A virus. The hemagglutinin (HA) gene has the fastest mutation of the eight genes in influenza A viruses, followed by the neuraminidase (NA) gene . The main mechanism of influenza A virus variation are antigenic drift and genetic reassortments .
[149] Phylogenetic identification of influenza virus candidates for seasonal ... — The seasonal influenza (flu) vaccine is designed to protect against those influenza viruses predicted to circulate during the upcoming flu season, but identifying which viruses are likely to circulate is challenging. We use features from phylogenetic trees reconstructed from hemagglutinin (HA) and neuraminidase (NA) sequences, together with a support vector machine, to predict future
[151] Predictive evolutionary modelling for influenza virus by site-based ... — Therefore, influenza vaccine strains need to be updated annually for the upcoming flu season to ensure vaccine effectiveness. We develop a computational approach, beth-1, to forecast virus evolution and select representative virus for influenza vaccine. The method involves modelling site-wise mutation fitness.
[156] The Use of Phylogenetic Diversity in Conservation Biology and Community ... — Abstract The use of phylogenetic tools and studies has strongly increased in the last two decades especially in conservation biology and community ecology. Phylogenetic trees are essential to understand the processes of community or network assembly, to identify centers of diversification, and to help protect Earth's evolutionary heritage. Despite two decades of research and syntheses, there
[157] The Importance of Phylogeny in Conservation - Academic library — The practical contribution of phylogeny to conservation actions has recently been discussed (Cardillo and Meijaard 2012; Winter et al. 2013). In part, the conservation value of the phylogenetic approach is in its ability to guide pre-emptive actions towards identifying and prioritizing the most at-risk species.
[158] Phylogenetic diversity in conservation: A brief history, critical ... — Species that are evolutionarily distinct have long been valued for their unique and irreplaceable contribution to biodiversity. About 30 years ago, this idea was extended to the concept of phylogenetic diversity (PD): a quantitative, continuous-scale index of conservation value for a set of species, calculated by summing the phylogenetic branch lengths that connect them.
[159] Advances in the reconstruction of the spider tree of life: A roadmap ... — In the last decade and a half, advances in genetic sequencing technologies have revolutionized systematics, transforming the field from studying morphological characters or a few genetic markers, to genomic datasets in the phylogenomic era. A plethora of molecular phylogenetic studies on many taxono …
[170] Horizontal gene transfer and phylogenetics - ScienceDirect — The initial analysis of complete genomes has suggested that horizontal gene transfer events are very frequent between microorganisms. ... and time-consuming phylogenetic analysis should be preferred ... one expects that stochastic effects and also the impact of tree reconstruction artifacts are very important and therefore that different genes
[171] Detecting horizontal gene transfer: a probabilistic approach — Horizontal gene transfer (HGT) is the event of a DNA sequence being transferred between species not by inheritance. HGT is a crucial factor in prokaryotic evolution and is a significant source for genomic novelty resulting in antibiotic resistance or the outbreak of virulent strains. Detection of HGT and the mechanisms responsible and enabling it, is hence of prime importance.Existing
[173] Impact of gene family evolutionary histories on phylogenetic species ... — Complicated history of gene duplication and loss brings challenge to molecular phylogenetic inference, especially in deep phylogenies. ... but accuracy of GTP and phylogenetic signal in the context of different gene families with distinct histories of duplication and loss are unclear. To evaluate how different evolutionary properties of
[175] PDF — One of the challenges in phylogenetic analysis is the handling of large datasets, which have become more common with the availability of high-throughput sequencing technologies. The computational demands of analyzing these large datasets require eficient algorithms and software tools that can process vast amounts of data in a reasonable timeframe.
[176] Algorithms, data structures, and numerics for likelihood-based ... — Background The rapid accumulation of molecular sequence data, driven by novel wet-lab sequencing technologies, poses new challenges for large-scale maximum likelihood-based phylogenetic analyses on trees with more than 30,000 taxa and several genes. The three main computational challenges are: numerical stability, the scalability of search algorithms, and the high memory requirements for
[177] The challenge of constructing large phylogenetic trees — The amount of sequence data available to reconstruct the evolutionary history of genes and species has increased 20-fold in the past decade. Consequently the size of phylogenetic analyses has grown as well, and phylogenetic methods, algorithms and their implementations have struggled to keep pace. Computational and other challenges raised by this burgeoning database emerge at several stages of
[178] The challenge of constructing large phylogenetic trees — The two issues of concern in reconstructing phylogenetic trees from large data matrices are computation time and reliability. Multiple sequence alignment, the necessary precursor to tree building, and phylogenetic inference are notoriously time-consuming computational problems.
[179] Phylogenetic Analysis: Methods, Tools, and Best Practices — The complexity of phylogenetic analysis can vary depending on several factors, such as the size of the dataset, the diversity of the organisms being studied, the type of data available (genetic sequences, morphological traits, etc.), and the specific research question being addressed. Best Practices for Phylogenetic Analysis
[213] (PDF) Insect phylogenetics in the digital age - Academia.edu — Insect systematists have long used digital data management tools to facilitate phylogenetic research. Web-based platforms developed over the past several years support creation of comprehensive, openly accessible data repositories and analytical tools that support large-scale collaboration, accelerating efforts to document Earth's biota and reconstruct the Tree of Life.
[214] Mobilizing and integrating big data in studies of spatial and ... — These biodiversity challenges demand approaches that meld bioinformatics, large-scale phylogeny reconstruction, use of digitized specimen data, and complex post-tree analyses (e.g. niche modeling, niche diversification, and other ecological analyses). BiotaPhy (www.biotaphy.org) is an ongoing project creating the linkages required for this integration, enabling novel data collection and analysis pipelines blending the existing resources provided by Open Tree of Life, iDigBio, and Lifemapper. Lifemapper computes Species Distribution Models (SDMs) for the most current GBIF terrestrial taxa occurrence data, joined with observed climate data from Worldclim (Hijmans et al., 2005), and predicted future climate data based on International Panel on Climate Change (IPCC) scenarios, as inputs for ecological niche algorithms, resulting in publicly accessible species distribution maps. These biodiversity challenges demand approaches that meld bioinformatics, large-scale phylogeny reconstruction, use of digitized specimen data, and complex post-tree analyses (e.g. niche modeling, niche diversification, and other ecological analyses).
[218] Journal of Biodiversity, Bioprospecting and Development — Integrating machine learning algorithms with traditional phylogenetic methods could lead to improved accuracy and efficiency in tree inference [ 4 ]. As the field of computational phylogenetics evolves, the demand for skilled researchers who can harness the power of big data continues to grow.
[219] Evaluating Feature Impact Prior to Phylogenetic Analysis Using ... - MDPI — While effective, these methods require substantial computational power, especially with the increasing amount of data involved in phylogenetic studies. Recently, integrating machine learning with phylogenetic analysis has shown promise in addressing these challenges, enhancing both the efficiency and accuracy of phylogenetic tree construction
[220] Phylogenomics: Current Biology - Cell Press — Phylogenomics can be summed up as a number of exciting theoretical and methodological advances that greatly expand traditional phylogenetics in two directions: first, by exploiting the increasing availability of genomic sequencing products and computational power; second, in modelling the multiple sources of heterogeneity in signals across
[221] Phylogeny, extinction and conservation: embracing uncertainties in a ... — The main goal of the present discussion meeting issue is to offer a platform to present the available methods allow-ing the integration of phylogenetic and extinction risk data in conservation planning.
[222] Phylogenetic diversity meets conservation policy: small areas are key ... — Evolutionary and genetic knowledge is increasingly being valued in conservation theory, but is rarely considered in conservation planning and policy. Here, we integrate phylogenetic diversity (PD) with spatial reserve prioritization to evaluate how well
[224] Climate-Driven Reshuffling of Species and Genes: Potential Conservation ... — However, the integration of genomics and phylogenetics into conservation management may not be as rapid as climate change. The genetics of hybrid introgression as a source of novel variation for ecological divergence and evolutionary speciation (and resilience) may generate adaptive potential and diversity fast enough to respond to locally
[225] Projected climate change impacts on the phylogenetic diversity of the ... — The projected impacts of climate change not only affect the amount of evolutionary history stored within species assemblages but might also have significant impact on the phylogenetic structure of species communities, which plays an important role in shaping ecological processes and ecosystem functioning because phylogenetic composition is
[226] Applications of machine learning in phylogenetics — Supervised machine learning approaches that rely on simulated training data have been used to infer tree topologies and branch lengths, to select substitution models, and to perform downstream inferences of introgression and diversification. Here, we review how researchers have used several promising machine learning approaches to make phylogenetic inferences. In the future, we expect that the application of careful network designs and data encodings will allow supervised machine learning to accommodate the complex processes that continue to confound traditional phylogenetic methods. In addition to phylogenetic tree inference, machine learning approaches have been applied to both upstream and downstream tasks in phylogenetics. Moving forward, careful considerations of training datasets, network architectures, and data encodings will facilitate the use of machine learning to address fundamental challenges in phylogenetic inference.
[227] Applications of machine learning in phylogenetics - PubMed — Machine learning has increasingly been applied to a wide range of questions in phylogenetic inference. Supervised machine learning approaches that rely on simulated training data have been used to infer tree topologies and branch lengths, to select substitution models, and to perform downstream inferences of introgression and diversification.
[231] Phylogenetic diversity and nature conservation: where are we? — More than two decades ago, Richard Vane-Wright et al. proposed phylogenetic diversity (see Glossary) as an additional component for nature conservation.The idea was to integrate information on the phylogenetic positions of species as a legacy of evolutionary processes (e.g., speciation, radiation) into conservation assessments .Research on the applicability of aspects of phylogenetic
[232] American Journal of Botany - Botanical Society of America — More than 20 years ago, Vane-Wright, Humphries, and Williams (1991) first proposed that phylogeny—the evolutionary history of organisms—should inform biodiversity conservation priorities. Since then, the use of phylogenetic diversity or distinctiveness as a conservation criterion has been hypothesized to help maintain biodiversity (Rosauer and Mooers, 2013), preserve evolutionary potential
[233] Plant species richness and phylogenetic diversity can favor the ... — Plant communities with higher species richness and phylogenetic diversity can increase the diversity of herbivores and their enemies through trophic interactions. However, whether these two features of plant communities have the same positive influence on other guilds through non-trophic mechanisms requires further exploration. Dung beetles represent an ideal system for testing such impacts