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Paraphyly

Paraphyly is a concept in phylogenetics and cladistics that describes a taxonomic group consisting of an ancestral species and some, but not all, of its descendant lineages, thereby excluding one or more monophyletic subgroups derived from that ancestor.^[1] This contrasts with monophyly, where a group includes the common ancestor and all descendants, forming a complete clade, and polyphyly, where a group derives from multiple distinct ancestors without a shared recent common origin.^[2] The term was introduced by German entomologist Willi Hennig in his foundational work on phylogenetic systematics, published in 1966, as part of an effort to establish a rigorous method for classifying organisms based on shared derived characteristics (synapomorphies) rather than overall similarity.^[3] Hennig's framework emphasized that only monophyletic groups represent natural evolutionary units, rendering paraphyletic assemblages artificial and misleading for understanding evolutionary relationships.^[4] Common examples of paraphyletic groups include the traditional class Reptilia, which encompasses lizards, snakes, turtles, and crocodiles but excludes birds—descendants of theropod dinosaurs—despite their shared reptilian ancestry; similarly, "fish" as a category often omits tetrapods (amphibians, reptiles, birds, and mammals), which evolved from lobe-finned fish ancestors.^[5] These groupings arose from pre-cladistic classifications based on grades of organization or Linnaean ranks, but cladistic analysis reveals their incompleteness.^[1] In modern systematics, recognizing paraphyly is crucial for refining classifications to reflect true evolutionary history, though some evolutionary taxonomists argue for retaining certain paraphyletic groups when they capture significant adaptive radiations or practical utility in fields like conservation and agriculture.^[6] Debates persist on whether paraphyly undermines biodiversity assessments, as many species-level taxa may prove paraphyletic under strict cladistic criteria, potentially underrepresenting evolutionary diversity.^[7]

Core Concepts

Definition

In phylogenetics, paraphyly describes a taxonomic grouping that includes a common ancestor and some, but not all, of its descendant lineages, thereby excluding at least one monophyletic subgroup derived from that ancestor.^[1]^[2] This exclusion typically occurs when a derived lineage is recognized separately due to distinct evolutionary innovations, leaving the remaining assemblage incomplete.^[8] A key characteristic of paraphyletic groups is the absence of a single most recent common ancestor (MRCA) shared exclusively by all members; instead, the MRCA of the group is also ancestral to the excluded descendants, making the grouping non-exclusive in its descent.^[2]^[8] This often results from evolutionary divergence where one or more lineages evolve traits that warrant separation, fragmenting what would otherwise be a complete clade.^[9] In cladograms, paraphyletic groups are visually represented as a monophyletic clade minus one or more derived subclades, such as a branching tree where a terminal lineage or subgroup is detached from the main stem, leaving the remainder as the paraphyletic assemblage.^[8] This depiction highlights the incomplete nature of the group relative to the full phylogenetic topology. Paraphyly constitutes a topological property within phylogenetic trees, defined by the structure of descent and branching patterns rather than reliance on Linnaean taxonomic ranks or hierarchies.^[2] In contrast to monophyly, which encompasses all descendants of an MRCA, paraphyly deliberately omits portions of that descent.^[1] Paraphyly is distinguished from monophyly primarily by its incomplete inclusion of descendants from a shared ancestor. A monophyletic group, also known as a clade or holophyletic taxon, comprises an ancestral species and all of its descendant species, ensuring that the group shares an exclusive most recent common ancestor (MRCA) with no external taxa intervening.^[1] In contrast, a paraphyletic group includes the MRCA but excludes one or more descendant lineages, resulting in a structure that can be visualized as a monophyletic assemblage with deliberate "gaps" where certain branches are omitted.^[10] This partial monophyly often arises in classifications that prioritize shared ancestral traits (symplesiomorphies) over derived ones, leading to groupings that reflect evolutionary grades rather than complete lineages.^[11] Polyphyly differs more fundamentally from both monophyly and paraphyly by lacking a single unifying ancestor altogether. A polyphyletic group consists of organisms derived from two or more distinct ancestral lineages, without including their MRCA, and is typically assembled based on superficial similarities due to convergent evolution or homoplasy rather than shared descent.^[12] For instance, the informal category of "flying animals" encompassing birds, bats, and pterosaurs is polyphyletic, as these taxa evolved powered flight independently from separate reptilian and mammalian ancestors.^[13] Unlike paraphyly's retention of a common ancestor but incomplete descendants, polyphyly represents an artificial convergence of unrelated forms, creating disjointed branches on a phylogenetic tree without any proximal MRCA binding the group.^[14] Evolutionarily, these distinctions carry significant implications for understanding biodiversity. Monophyletic groups align with natural evolutionary units, capturing complete adaptive radiations and facilitating accurate reconstructions of phylogenetic history in cladistic analysis. Paraphyletic assemblages, by excluding key descendant clades, often correspond to transitional "grade taxa" that highlight sequential evolutionary progressions, such as stem groups leading to more derived forms, though they are considered unnatural in strict cladistics for obscuring true relationships.^[11] Polyphyletic groups, conversely, mask independent evolutionary events and are rejected in modern systematics as they promote misleading inferences about ancestry and adaptation.^[15] The following table summarizes the core structural and cladistic differences among these taxonomic groupings:

Criterion	Monophyly	Paraphyly	Polyphyly
Ancestor Inclusion	Includes the MRCA and all descendants	Includes the MRCA but excludes some descendants	Excludes the MRCA; members from multiple ancestors
Descendant Completeness	Complete (all lineages represented)	Incomplete (gaps in descendant clades)	Disjoint (lineages from separate MRCAs)
Cladistic Validity	Valid natural group (clade)	Invalid; reflects grades or symplesiomorphy	Invalid; based on homoplasy or convergence

Historical Development

Etymology

The term "paraphyly" derives from the Ancient Greek prefix pará- (παρά), meaning "beside," "near," or "alongside," combined with phŷlon (φῦλον), denoting "tribe," "race," "clan," or "kindred," thereby suggesting a grouping positioned adjacent to or incomplete relative to a full tribal or lineage unit, akin to "beside the tribe" or an "almost-phylum."^[16] This etymological structure highlights the concept's emphasis on proximity to but exclusion from a complete monophyletic assemblage in phylogenetic terms. The term was coined by German entomologist and cladistics pioneer Willi Hennig in his 1966 English translation of Phylogenetic Systematics, where he introduced "paraphyletic group" to describe assemblages comprising a common ancestor and some, but not all, of its descendants, contrasting with his earlier German terminology in pre-1966 works. Hennig's innovation addressed limitations in pre-cladistic taxonomy, formalizing distinctions from earlier informal concepts like evolutionary grades or stem groups that bundled organisms by shared primitive traits without capturing full descent.^[17] The term gained traction in the 1970s amid debates on cladistic versus evolutionary systematics, with early English usages appearing in 1971 in Systematic Zoology, including Peter D. Ashlock's paper redefining monophyly to incorporate paraphyly as a subset, and subsequent applications in avian taxonomy papers from 1972 onward that highlighted paraphyletic arrangements in traditional bird classifications, such as non-monophyletic orders excluding derived lineages.^[18] These initial adoptions by Hennig's followers and critics, including evolutionary biologist Ernst Mayr in his 1974 critique of strict cladism, marked the term's integration into broader taxonomic discourse. Etymologically parallel to "paraphyly," the related term "monophyly" combines the prefix mono- (μόνο, "single" or "alone") with phŷlon to denote a complete "single tribe," while "polyphyly" merges poly- (πολύ, "many") with phŷlon for groups from multiple ancestral lines, or "many tribes," forming a consistent terminological triad rooted in Greek morphology to classify phylogenetic relationships.

Evolution of the Concept in Cladistics

Prior to the formalization of cladistics, evolutionary taxonomists like George Gaylord Simpson conceptualized paraphyletic groups as "grades" or adaptive zones in his 1945 monograph The Principles of Classification and a Classification of Mammals, where such assemblages captured evolutionary stages by grouping organisms with similar adaptive traits while excluding more specialized descendants, as seen in his treatment of mammalian orders.^[19] This approach tolerated paraphyly to reflect perceived evolutionary progression, contrasting with later cladistic rigor.^[20] Willi Hennig's seminal 1950 work Grundzüge einer Theorie der phylogenetischen Systematik introduced the principles of phylogenetic systematics, emphasizing monophyletic groups defined by shared derived characters (synapomorphies) and critiquing paraphyletic assemblages as deviations from true evolutionary lineages.^[21] The 1966 English translation, Phylogenetic Systematics, explicitly defined paraphyly as a group comprising an ancestor and some but not all descendants, rendering it invalid for cladistic classification and highlighting its pitfalls in misrepresenting ancestry. This shift marked a key milestone, establishing cladograms as tools to detect and avoid paraphyly. In the 1970s and 1980s, the rise of computational phylogenetics amplified debates on paraphyly through parsimony-based methods, with James S. Farris and Arnold G. Kluge's 1969 development of the Wagner algorithm enabling efficient tree searches that exposed paraphyletic groupings as suboptimal explanations requiring additional evolutionary steps.^[12] Their 1979 paper on the avian genus Alectura further critiqued paraphyly in cladistic analysis, arguing it undermined explanatory power, while 1985 work reinforced parsimony's role in prioritizing monophyly.^[22] Software like Hennig86 (1980s) and PAUP (1990s implementations) facilitated widespread detection of paraphyletic pitfalls in empirical datasets.^[23] Post-2000 refinements in Bayesian and likelihood-based phylogenetics have nuanced paraphyly's treatment, particularly for fossil records where incomplete sampling may produce apparent paraphyletic signals. Critiques in these approaches emphasize that paraphyly often reflects methodological artifacts rather than biological reality, advancing cladistics toward probabilistic robustness.

Applications in Biology

Role in Phylogenetic Analysis

In phylogenetic analysis, paraphyly serves as a key diagnostic indicator for evaluating the evolutionary coherence of hypothesized groups within tree topologies. Detection primarily relies on the identification of synapomorphies—shared derived traits that unite all descendants of a common ancestor—to reveal exclusions that render a group paraphyletic. A taxon is deemed paraphyletic when it encompasses the most recent common ancestor and some, but not all, descendants, typically unified by symplesiomorphies (shared ancestral traits) rather than synapomorphies, as the excluded lineages acquire novel derived characters not present in the group.^[1] Computational tools employing maximum parsimony further aid detection by scoring potential trees; paraphyletic arrangements are treated as suboptimal because they necessitate extra evolutionary steps (homoplasies) to accommodate the data, favoring monophyletic alternatives that minimize changes.^[24] The implications of paraphyly for tree topology are significant, often highlighting methodological challenges such as incomplete taxon sampling, where key descendants are omitted, or convergent evolution, which mimics shared ancestry through independent trait acquisition. Such patterns disrupt the hierarchical structure of phylogenies, potentially leading to misleading inferences about evolutionary relationships. Resolution typically involves outgroup comparison, wherein taxa external to the ingroup are incorporated to root the tree and polarize characters, distinguishing plesiomorphic (ancestral) from apomorphic (derived) states and clarifying whether exclusions reflect genuine divergence or artifacts of analysis.^[25]^[26] Within cladistics, paraphyly plays a central role in enforcing classificatory rigor, as the framework—pioneered by Willi Hennig—rejects paraphyletic taxa in formal hierarchies to prioritize monophyletic clades that fully capture phylogenetic branching. This rejection ensures classifications mirror the tree of life without artificial grades, though informal usage persists for evolutionary stages, such as the grade "fish" encompassing non-tetrapod vertebrates. Quantitative metrics like the consistency index (CI) and retention index (RI) penalize paraphyletic resolutions by quantifying character fit: CI measures homoplasy as the ratio of minimum possible steps to observed steps on a tree (with values approaching 1 indicating low homoplasy and optimal monophyly), while RI assesses retained synapomorphies as (maximum steps - observed steps) / (maximum steps - minimum steps), where deviations signal suboptimal topologies often tied to paraphyly.^[17]^[27]^[28] A standard workflow integrates paraphyly assessment to refine phylogenies: it commences with character coding, polarizing traits via outgroup criteria to establish homology; proceeds to tree search using heuristic algorithms (e.g., branch-and-bound or genetic methods) to generate candidate topologies under parsimony or likelihood; and culminates in evaluation, where monophyly constraints are tested on predefined groups to detect and rectify paraphyly through resampling or expanded sampling.^[25]^[29]

Examples of Paraphyletic Taxa

One prominent example of a paraphyletic taxon is the traditional class Reptilia, which encompasses lizards, snakes, turtles, crocodilians, and tuatara but excludes birds (class Aves), despite birds sharing a most recent common ancestor with crocodilians within the reptilian lineage. This grouping arose from Linnaean classifications based on morphological traits like ectothermy and scaly skin, but cladistic analysis reveals that birds evolved from theropod dinosaurs, rendering Reptilia incomplete as it omits a descendant clade. To resolve this, Reptilia is often redefined phylogenetically to include birds, forming the monophyletic Sauropsida (or broader Reptilia including Aves), as proposed in early cladistic revisions. In a typical cladogram of amniotes, the common ancestor of sauropsids branches into synapsids (leading to mammals) and a sauropsid stem; within sauropsids, the traditional Reptilia forms a grade excluding the avian branch from archosauria (crocodilians + birds), highlighting the paraphyletic structure by showing the avian lineage nested within what would otherwise be a continuous reptilian clade.^[2]^[30] Another classic case is the informal group "fish" (Pisces), traditionally comprising all aquatic vertebrates with gills and fins but excluding tetrapods (amphibians, reptiles, birds, and mammals), even though tetrapods descended from lobe-finned fish (sarcopterygians). This paraphyly stems from the evolutionary transition from aquatic to terrestrial life, where sarcopterygian ancestors like Eusthenopteron gave rise to tetrapodomorphs such as Tiktaalik, which are not included in the "fish" category despite sharing the common ancestor. Cladistic resolution groups all jawed vertebrates (Gnathostomata) monophyletically, with "fish" forming a basal grade excluding the tetrapod subclade from Sarcopterygii; in a cladogram, the gnathostome ancestor branches to chondrichthyans (sharks/rays), actinopterygians (ray-finned fish), and sarcopterygians, from which coelacanths, lungfish, and tetrapods diverge, illustrating how excluding tetrapods leaves "fish" without all descendants.^[2]^[31] The term "invertebrates" represents a broad paraphyletic assemblage of animals lacking a vertebral column, including diverse phyla like arthropods, mollusks, annelids, and cnidarians, but excluding vertebrates (the chordate subphylum Vertebrata) despite all sharing a common bilaterian or metazoan ancestor. This grouping, which constitutes about 97% of animal species, originated from early zoological classifications emphasizing the absence of a backbone rather than shared derived traits, but phylogenetic trees show vertebrates nested within deuterostomes, making invertebrates incomplete. A cladogram of Metazoa typically roots at sponges or ctenophores, branching to non-bilaterians (cnidarians, placozoans) and bilaterians; within bilaterians, protostomes (e.g., arthropods, mollusks) and deuterostomes diverge, with deuterostomes further splitting into echinoderms, hemichordates, and chordates—the latter including tunicates, lancelets, and vertebrates—thus excluding vertebrates fragments the full metazoan clade.^[32]^[33] In plants, gymnosperms illustrate paraphyly as a group of seed-producing plants with "naked" seeds (not enclosed in ovaries), including conifers, cycads, ginkgo, and gnetophytes, but excluding angiosperms (flowering plants), which evolved from within the gymnosperm lineage. This traditional division, based on reproductive structures, fails cladistically because molecular and fossil evidence places angiosperms as derived from an extinct gymnosperm-like ancestor, similar to how gnetophytes are closely related to the angiosperm lineage. The resolution forms the monophyletic Acrogymnospermae or broader seed plant clades; a cladogram of seed plants shows the common ancestor branching to progymnosperms, then to ferns and seed ferns, with gymnosperms forming a grade where cycads, ginkgo, conifers, and gnetophytes diverge, but the angiosperm branch emerges from near the gnetophyte position, excluding it renders gymnosperms paraphyletic.^[34] A contemporary example from microbial systematics involves prokaryotes, particularly the domain Archaea, which becomes paraphyletic when excluding eukaryotes, as revealed by genomic studies since the 2010s identifying the Asgard archaea as the closest prokaryotic relatives to eukaryotes. Eukaryotes arose through an archaeal-bacterial symbiosis, with the host likely an Asgard archaeon, meaning traditional Archaea includes the ancestor but not its eukaryotic descendants, challenging the three-domain tree of life. This was supported by phylogenomic analyses of Asgard genomes, showing eukaryotic signature proteins in these archaea; in a tree of life cladogram, the bacterial domain branches separately, while Archaea + Eukarya form a supergroup, with Asgard archaea (e.g., Lokiarchaeota) basal to eukaryotes within archaea, making non-Asgard archaea a paraphyletic grade excluding the eukaryotic lineage.^[35]^[36]

Paraphyly in Species Concepts

Under the biological species concept (BSC), introduced by Ernst Mayr in 1942, species are defined as groups of actually or potentially interbreeding natural populations that are reproductively isolated from other such groups.^[37] This definition can lead to paraphyletic species because it may exclude divergent populations that have evolved reproductive isolation, even if they share a recent common ancestor with the main group, thereby omitting some descendant lineages from the species boundary.^[38] For instance, in cases where peripheral isolates develop barriers to gene flow, the core population might be classified as the species while the isolates form separate taxa, rendering the original grouping paraphyletic with respect to phylogeny.^[39] Ring species exemplify how paraphyly emerges under the BSC due to clinal variation and incomplete isolation. In the Ensatina eschscholtzii complex of salamanders, populations form a geographic ring around California's Central Valley, with adjacent forms interbreeding but terminal populations reproductively isolated, creating a chain of overlapping gene flow.^[40] Phylogenetic analyses reveal that some subspecies, such as the deeply diverged and paraphyletic assemblage of E. e. oregonensis, nest other forms like E. e. picta within them, challenging strict monophyly while fitting BSC criteria through localized interbreeding.^[41] Similarly, hybrid zones in plant species complexes, such as European white oaks (Quercus section Quercus), blur boundaries due to frequent hybridization and introgression, often resulting in paraphyletic assemblages where morphological or ecological cohesion maintains species identity despite shared ancestry with excluded hybrids.^[42] Plastome data from these oaks further indicate paraphyly across geographic partitions, underscoring how gene flow in hybrid zones can exclude divergent lineages from formal species designations.^[43] The phylogenetic species concept (PSC), which emphasizes monophyly based on shared derived characters or diagnosable clusters, critiques the BSC for frequently producing paraphyletic species that distort evolutionary history.^[38] Under the PSC, many BSC-defined species, including those with hybridizing populations, would be split into monophyletic units, highlighting paraphyly as a flaw in cohesion-based definitions.^[44] Genomic evidence from introgression often exacerbates this, as gene flow can cause paraphyly in mitochondrial DNA (mtDNA) trees; for example, historical admixture between Neanderthals and modern humans introduced Neanderthal nuclear alleles, rendering human lineages paraphyletic at certain loci despite monophyletic mtDNA overall.^[45] In broader cases, such as skipper butterflies (Erynnis spp.), mtDNA introgression between allopatric species directly causes paraphyly, where one species' mtDNA haplotypes nest within another's, complicating species delimitation.^[45] Debates surrounding paraphyly in species concepts contrast Mayr's 1942 emphasis on reproductive isolation as the primary criterion, which tolerated potential paraphyly to prioritize gene flow dynamics, with modern coalescent models that integrate phylogenetic history and incomplete lineage sorting.^[37] Coalescent theory, as applied in critiques of the BSC, reveals that gene tree discordance due to ancestral polymorphism can mimic paraphyly even without recent introgression, urging a reconciliation where species boundaries account for both isolation and shared ancestry.^[39] This evolution in thinking underscores ongoing tensions, as Mayr's framework excels in explaining cohesion but underemphasizes the phylogenetic signals now illuminated by genomic data.^[38]

Practical Uses and Limitations

Paraphyletic groups serve practical purposes in biological education by providing simplified frameworks for introducing evolutionary concepts before delving into more precise cladistic analyses. For instance, traditional classifications like "reptiles," which exclude birds despite their shared ancestry, allow educators to highlight key morphological and ecological transitions without overwhelming students with complex phylogenetic revisions. This approach facilitates initial understanding of shared primitive traits (symplesiomorphies) and is commonly reflected in student-drawn phylogenies, where up to 31% of branch names refer to paraphyletic groups.^[46] In ecological contexts, paraphyletic groupings are retained as "grades" that capture functional similarities among organisms sharing ancestral adaptations, aiding studies of community dynamics and succession. Such grades, like pioneer species in primary succession (e.g., lichens and mosses initiating soil formation), often form paraphyletic assemblages because they emphasize ecological roles over strict monophyly, enabling researchers to model environmental responses without requiring exhaustive lineage tracing. This utility persists in ecomorphological analyses, where paraphyletic taxa like "lizards" (excluding snakes) reveal patterns of morphological diversification linked to habitat use.^[47] Conservation efforts frequently rely on paraphyletic units within traditional taxonomic frameworks to assess biodiversity and prioritize threats, as seen in IUCN Red List categories that incorporate widespread species encompassing distinct endemics. For example, cave-dwelling forms of fish like the Mexican tetra (Astyanax mexicanus) are often classified under paraphyletic parent species, leading to "Least Concern" statuses that overlook localized vulnerabilities and underestimate overall diversity in adaptive radiations. This practice supports rapid policy decisions but can dilute focus on endemic subpopulations.^[48] Despite these applications, paraphyly poses significant limitations by fostering misleading evolutionary inferences, as groups defined by shared ancestry but excluding key descendants obscure true phylogenetic relationships and adaptive histories. In predictive systematics, paraphyletic taxa hinder accurate forecasting of traits or responses to environmental changes, since monophyletic clades better enable extrapolations based on shared derived characters (apomorphies), whereas paraphyly introduces inconsistencies incompatible with cladistic principles.^[49]^[50] Alternatives to retaining paraphyly include apomorphy-based naming under the PhyloCode, which defines taxa via explicit phylogenetic specifiers (e.g., node- or stem-based) to ensure monophyly and avoid rank-induced exclusions. In contrast, the Linnaean system, with its hierarchical ranks, often perpetuates paraphyletic groups by prioritizing morphological similarity over complete descent lineages, leading to nomenclatural instability when phylogenies are revised. The PhyloCode thus promotes a rank-free approach tailored to evolutionary trees.^[51] In the 2020s, paraphyly has seen renewed integration in ecomorphology, where it aids functional studies by grouping organisms by ecological performance rather than strict phylogeny, such as analyzing convergent traits in "warm-blooded" endotherms (e.g., birds and mammals, excluding some reptiles with partial endothermy). This trend enhances understanding of adaptive convergences in carnivorans and squamates, balancing cladistic rigor with practical ecological insights.^[52]^[47]

Extensions Beyond Biology

In Linguistics

In linguistics, paraphyly describes a grouping of languages that includes a proto-language and some, but not all, of its descendant branches, often arising from phylogenetic analyses that reveal non-monophyletic assemblages. This concept, borrowed from biological cladistics, aids in understanding language family structures where certain subgroups are excluded due to early divergences.^[53] A prominent example is the Formosan languages within the Austronesian family, which comprise nine primary branches but exclude the tenth branch ancestral to all extra-Formosan Austronesian languages (Malayo-Polynesian); this renders Formosan paraphyletic, as the branches do not share unique innovations post-dating their common ancestor with Malayo-Polynesian. Similarly, the Baltic languages form a paraphyletic group within Balto-Slavic, consisting of all non-Slavic descendants of Proto-Balto-Slavic, with no distinct Proto-Baltic stage separate from Proto-Balto-Slavic itself; East Baltic (Lithuanian, Latvian) and West Baltic (extinct Old Prussian) diverged directly alongside Slavic.^[54] In the Indo-European family, excluding the early Anatolian branch (e.g., Hittite) creates a paraphyletic "core" Indo-European grouping, highlighting divergences from the proto-language before other major branches like Indo-Iranian or Germanic emerged.^[55] Applications of paraphyly in historical linguistics include reconstructing proto-languages and tracing divergences, as seen in Austronesian subgrouping where recognizing Formosan paraphyly refines models of Taiwan as the family's origin and subsequent expansions. Methods such as comparative reconstruction identify shared retentions and innovations that expose paraphyletic subgroups, while glottochronology estimates divergence times based on lexical retention rates, though it assumes tree-like evolution and can overlook contact effects. For instance, Bayesian phylogenetic analyses of Austronesian basic vocabulary datasets confirm Formosan paraphyly and support dispersal models from Taiwan.^[56] Critiques from areal linguistics emphasize that language evolution differs from biological phylogenies due to extensive borrowing, which introduces horizontal transmission and can artificially create or obscure paraphyletic patterns; for example, in Bantu languages, contact-induced similarities make northwestern groups paraphyletic despite rapid vertical divergence.^[53] Unlike biological cladistics, where inheritance is strictly vertical, linguistic paraphyly often reflects reticulate networks from borrowing rather than pure branching.^[53]

In Other Disciplines

In social sciences, particularly in anthropology and population genetics, the concept of paraphyly has been analogously applied to human populations and ethnic groups to describe evolutionary relationships based on genetic or cultural descent. For instance, supertree approaches to human population history have identified paraphyletic groups of populations, where a common ancestral population is included but some descendant lineages are excluded, reflecting complex migration and admixture patterns.^[57] Such applications highlight how paraphyly can model incomplete lineages in human history without implying strict biological taxonomy. In computing, analogous concepts appear in phylogenomic software, where data structures may represent paraphyletic assemblages by including base trees but excluding optimized subtrees or branches to simplify analysis. Tools like ParaPhylo, designed for reconstructing species trees from paralogous genes, handle paraphyly by resolving NP-hard problems in tree inference, but this is tied to biological computation rather than general computer science paradigms.^[58] The term's application here is limited to specialized phylogenetic algorithms, with little extension to broader data structure design. Critiques of extending paraphyly beyond biology emphasize the risk of over-analogizing evolutionary terms to non-descent-based systems, potentially leading to misleading classifications in fields like social sciences where ancestry is not literal. Philosophers of science argue that while monophyly and paraphyly offer theoretical insights under scientific realism, their application to "the world around us" requires caution to avoid conflating biological realism with approximate truths in unrelated domains.^[59] Overall, formal adoption remains limited, confined mostly to metaphorical or auxiliary roles in interdisciplinary work.

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Retention Index (RI). RI = MaxSteps − ObsSteps. MaxSteps − MinSteps. • defined to be 0 for parsimony uninformative characters. • RI=1 if the character fits ...
[30]
Common Methods for Phylogenetic Tree Construction and Their ...
May 11, 2024 · In this review, we summarize common methods for constructing phylogenetic trees, including distance methods, maximum parsimony, maximum likelihood, Bayesian ...Missing: paraphyly | Show results with:paraphyly
[31]
Phylogenetic Definition of Reptilia | Systematic Biology
Whereas our definition is equivalent to Gauthier's (1994) for Sauropsida (“reptiles plus all other amniotes more closely related to them than they are to ...
[32]
Introduction to the Sarcopterygii
Sarcopterygii are lobe-finned fish and tetrapods, with flexible fins containing a central appendage and enamel on their teeth.Missing: paraphyletic | Show results with:paraphyletic
[33]
The Global Invertebrate Genomics Alliance (GIGA) - PubMed Central
Although invertebrates clearly represent a paraphyletic assemblage, the term “invertebrate” persists, and the distinction between vertebrates and invertebrates ...
[34]
There is no universal molecular clock for invertebrates, but ... - PNAS
Here, we use the term “invertebrates” to refer to all metazoans except those in subphylum Vertebrata. Although invertebrate is a paraphyletic taxonomic division ...
[35]
Asgard archaea are the closest prokaryotic relatives of eukaryotes
We provided extensive phylogenomic evidence for the emergence of eukaryotes from within the Asgard archaea (thus supporting the two-domains [2D] tree of life).
[36]
A Briefly Argued Case That Asgard Archaea Are Part of the ... - NIH
Aug 15, 2018 · ... archaea,” with eukaryotes evolving from within a paraphyletic Archaea ... Asgard archaea are the closest prokaryotic relatives of eukaryotes.
[37]
Ernst Mayr and the modern concept of species - PNAS
Apr 25, 2005 · For example, the biological species concept emphasizes the property of reproductive isolation (9, 21), the ecological species concept emphasizes ...
[38]
Species concepts should not conflict with evolutionary history, but ...
Many phylogenetic systematists have criticized the Biological Species Concept (BSC) because it distorts evolutionary history.
[39]
Phylogenetics and the origin of species - PMC - NIH
A recent criticism that the biological species concept (BSC) unduly neglects phylogeny is examined under a novel modification of coalescent theory.
[40]
Incipient species formation in salamanders of the Ensatina complex
The Ensatina eschscholtzii complex of plethodontid salamanders, a well-known “ring species,” is thought to illustrate stages in the speciation process.
[41]
s of the salamander ring species Ensatina - jstor
... Ensatina complex: that oregonensis is a deeply diverged, paraphyletic assemblage of lineages, that picta is nested within oregonensis, and that platensis is ...
[42]
Oaks: an evolutionary success story - Kremer - 2020 - New Phytologist
Oct 20, 2019 · Reproductive patterns shape introgression dynamics and species succession within the European white oak species complex. Evolution 65: 156 ...Missing: paraphyly | Show results with:paraphyly
[43]
Plastome data reveal multiple geographic origins of Quercus Group ...
Several members of this oak group appeared paraphyletic with Groups Cerris and Quercus, and an underlying geographic partitioning was suggested in addition to ...
[44]
Species concepts: the basis for controversy and reconciliation - 2002
Oct 17, 2002 · Phylogenetic species are either entire biological species, or parts of biological species.
[45]
Introgression as a likely cause of mtDNA paraphyly in two allopatric ...
Mar 18, 2009 · Here we describe a unique case of mitochondrial DNA (mtDNA) paraphyly in the skipper genus, Erynnis, that involves well-diverged allopatric species.
[46]
Tree thinking cannot taken for granted: challenges for teaching ... - NIH
Tree thinking is an integral part of modern evolutionary biology, and a necessary precondition for phylogenetics and comparative analyses.Results · Discussion · Fig. 3
[47]
Ecomorphological diversification in squamates from conserved ...
Jul 1, 2019 · With >10,000 known extant species, Squamata (snakes and paraphyletic “lizards”) is an excellent clade in which to investigate this topic because ...Ecomorphological... · Results · Discussion<|control11|><|separator|>
[48]
[PDF] PERSPECTIVE Cladistic species definitions can lead to under ...
Abstract: Many species are paraphyletic, but current taxonomic practices often do not recognise this, and attempts are made to apply a monophyletic species ...
[49]
(PDF) Paraphyly Is Bad Taxonomy - ResearchGate
Aug 9, 2025 · While some evolutionary systematists have argued for the maintenance of paraphyletic groups 52,53 , the precise location in the phylogeny where ...
[50]
Further Dogged Defense of Paraphyletic Taxa - ResearchGate
Aug 9, 2025 · I was invited to defend my views on cladistic classification at a symposium on Linnaean taxonomy at the Smithsonian Institution in 2001.Abstract · References (8) · Recommended Publications
[51]
[PDF] PhyloCode: A Phylogenetic Code of Biological Nomenclature
In contrast to the preexisting codes based on the Linnaean system of nomenclature, the PhyloCode will provide rules for the express purpose of naming the parts ...
[52]
Evolutionary ecomorphology for the twenty-first century - NIH
Nov 29, 2023 · This review provides a synthesis of current research on carnivoran ecomorphology, with the goal of illustrating the complex interaction between ecology and ...
[53]
[PDF] Evolutionary Linguistics - Santa Fe Institute Events Wiki
Jun 17, 2008 · In historical linguistics, the parallels between biological and linguistic evolution have been observed since Darwin himself first took notice.<|control11|><|separator|>
[54]
https://annamalaiuniversity.ac.in/studport/download/indlang/resources/Historical%20Linguistics%20and%20South%20Asian%20Languages.pdf
[55]
[PDF] Ancestry-constrained phylogenetic analysis supports the Indo ...
Since these languages are contiguous but paraphyletic, contact must have played a role in causing them to gain the trait [*mand-, 'eat'], but this also ...Missing: paraphyly | Show results with:paraphyly
[56]
Human population history revealed by a supertree approach - Nature
Jul 19, 2016 · A few populations were identified as highly unstable “wildcard taxa” (e.g. Andamanese, Malagasy). The linguistic classification fits rather ...
[57]
Dense sampling of ethnic groups within African countries reveals ...
Mar 29, 2023 · There is controversy over the early splits in the Bantu language phylum, such that proto-Bantu is likely to be paraphyletic ... Social Sciences, ...
[58]
ParaPhylo - Swarm Intelligence and Complex Systems
ParaPhylo is a tool for reconstructing phylogenetic species trees based on information about paralogous genes. It relies on solving three intertwined NP-hard ...
[59]
Harnessing machine learning to guide phylogenetic-tree search ...
Mar 31, 2021 · Our analyses suggest that machine learning can guide tree-search methodologies towards the most promising candidate trees.
[60]
Monophyly, paraphyly, and the world around us - ScienceDirect.com
This paper addresses the theoretical relevance of monophyletic, paraphyletic and polyphyletic groups under the paradigm of sophisticated scientific realism.