Molecular Phylogenetics and Evolution

Papers
(The TQCC of Molecular Phylogenetics and Evolution is 11. The table below lists those papers that are above that threshold based on CrossRef citation counts [max. 250 papers]. The publications cover those that have been published in the past four years, i.e., from 2022-08-01 to 2026-08-01.)
ArticleCitations
The systematics and evolution of the Sri Lankan rainforest land snail Corilla: New insights from RADseq-based phylogenetics135
Resolving the phylogenetic relationship among recently diverged members of the rockfish subgenus Sebastosomus84
The distribution and characteristic of two transposable elements in the genome of Cydia pomonella granulovirus and codling moth57
Species delimitation within a taxonomically complex group: An example from the genus Apodemus (Rodentia: Muridae)53
Erratum to “Disentangling historical relationships within Poeciliidae (Teleostei: Cyprinodontiformes) using ultraconserved elements” [Mol. Phylogenet. Evol. 190 (2024) 107965]51
Recent evolution of extreme sexual dimorphism in the huia (Heteralocha acutirostris; Callaeidae)49
Phylogenomic insights into historical biogeography and species delimitation of African Ampelocissus (Vitaceae)49
Diversification and introgression in four chromosomal taxa of the Pearson’s horseshoe bat (Rhinolophus pearsoni) group43
Revisiting evolutionary relationships of Antrodiaetus (Araneae, Mygalomorphae, Antrodiaetidae) using phylogenomics; implications for species diversity and biogeography of a persistent Holarctic lineag42
Disconnecting trapdoors: Phylogenomic analyses reveal evolutionary contrasts in trapdoor spiders with intercontinental distribution (Idiopidae, Idiopinae)41
Corrigendum to “Evolution of the genetic code in the mitochondria of Labyrinthulea (Stramenopiles)” [Mol. Phylogenet. Evol. 152 (2020) 106908]40
When colors mislead: Genomics and bioacoustics prompt re-classification of Asian flycatcher radiation (Aves: Niltavinae)38
Machine learning can be as good as maximum likelihood when reconstructing phylogenetic trees and determining the best evolutionary model on four taxon alignments38
Population genomics indicate three different modes of divergence and speciation with gene flow in the green-winged teal duck complex37
Resolving the deep phylogeny: Implications for early adaptive radiation, cryptic, and present-day ecological diversity of Papuan microhylid frogs36
Multiple origins, singular success: genomic evidence for past recurrent hybridization in Chenopodium album s. str. (Amaranthaceae)36
Hidden in the sand: Phylogenomics unravel an unexpected evolutionary history for the desert-adapted vipers of the genus Cerastes35
Peering through the hedge: Multiple datasets yield insights into the phylogenetic relationships and incongruences in the tribe Lilieae (Liliaceae)35
Phylogeny, population structure, and conservation genomics of Galapagos vermilion flycatchers (genus Pyrocephalus)33
ModelRevelator: Fast phylogenetic model estimation via deep learning33
Phylogenomics and biogeography of arid-adapted Chlamydogobius goby fishes33
Whole genome phylogenomics helps to resolve the phylogenetic position of the Zygothrica genus group (Diptera, Drosophilidae) and the causes of previous incongruences32
Incomplete lineage sorting and hybridization underlie tree discordance in Petunia and related genera (Petunieae, Solanaceae)32
The evolution of primate malaria parasites: A study on the origin and diversification of Plasmodium in lemurs31
Phylogenomics and taxon-rich phylogenies of new and historical specimens shed light on the systematics of Hypnea (Cystocloniaceae, Rhodophyta)30
Genomic insights into the evolutionary history and cryptic diversity of two-toed sloths (Choloepus) in Amazonia30
Genomic phylogeography illuminates deep cyto-nuclear discordances in midwife toads (Alytes)30
Redefining Chlorobotryaceae as one of the principal and most diverse lineages of eustigmatophyte algae29
Substrate specialisation drives an unexpectedly diverse radiation in barking geckos (Ptenopus: Gekkonidae)29
Evolution, range formation and a revised taxonomy of the disjunctly distributed European members of Astragalus sect. Caprini, an intricate group including highly endangered species of dry grasslands29
Discordance between phylogenomic methods in Near Eastern mountain newts (Neurergus, Salamandridae)28
Repeat-based phylogenomics shed light on unclear relationships in the monocentric genus Juncus L. (Juncaceae)28
Mitochondrial genome and ultraconserved elements reveal a species complex within the Central American brocket deer Mazama temama (Artiodactyla: Cervidae)27
Out of North Africa: Evolution and biogeography of Afro-Arabian dwarf tarantulas (Theraphosidae, Ischnocolinae)27
Corrigendum to “Phylogeography, hybridization, and species discovery in the Etheostoma nigrum complex (Percidae: Etheostoma: Boleosoma)” [Mol. Phylogenet. Evol. 178 (2023) 107645]27
Phylotranscriptomic relationships of the Oophila clade of green algae associated to amphibian egg masses27
A phylogenomic and morphometric reassessment of Ovulidae highlights host-related shell shape evolution27
Geological events and climate change drive diversification and speciation of mute cicadas in eastern continental Asia26
Plastid-nuclear coevolution of ribosomal protein genes in papilionoid legumes25
Phylogenomics and divergence pattern of Polygonatum (Asparagaceae: Polygonateae) in the north temperate region25
Scaling the high latitudes: evolution, diversification, and dispersal of Coryphella nudibranchs across the Northern Hemisphere25
Temporal and spatial diversification along the Amazonia-Cerrado transition in Neotropical treefrogs of the Boana albopunctata species group24
Phylogenomics and biogeography of sawflies and woodwasps (Hymenoptera, Symphyta)24
Sink or swim: Phylogenomic analysis of Baikal sculpins reveals multiple transformations to pelagic, bathybenthic, and lotic ecomorphologies24
Phylogenomic reconstruction of Solenogastres (Mollusca, Aplacophora) informs hypotheses on body size evolution24
Comprehensive taxon sampling and vetted fossils help clarify the time tree of shorebirds (Aves, Charadriiformes)23
Exon-capture data resolve relationships resulting from a rapid radiation within family Gobiidae23
Molecular phylogenetics of the fresh water sleepers Odontobutis (Gobiiformes: Odontobutidae) and its implications on biogeography of freshwater ichthyofauna of East Asia22
Molecular phylogeny of deep-sea blind lobsters of the family Polychelidae (Decapoda: Polychelida), with implications for the origin and evolution of these “living fossils”22
Congruent patterns of cryptic cladogenesis revealed using RADseq and Sanger sequencing in a velvet worm species complex (Onychophora: Peripatopsidae: Peripatopsis sedgwicki)22
Corrigendum to “Molecular systematics and global phylogeography of angel sharks (genus Squatina)” [Mol. Phylogenetics Evol. 54 (2010) 395–404]21
Phylogenetic placement and species delimitation of the crab spider genus Phrynarachne (Araneae: Thomisidae) from China21
Phylogenetic relationships and historical biogeography of silkmoths (Lepidoptera: Bombycidae) suggest an origin in Southern Gondwana21
Different expansion events of the actin and tubulin gene families within spirotrichean ciliates (Alveolate, Ciliophora)21
Nuclear phylogenomics of Eperua (Leguminosae) highlights the role of habitat and morphological lability in dispersal and diversification across Amazonia and in the Caatinga-Cerrado ecotone20
Genomic SNPs resolve the phylogeny of an ancient amphibian island radiation from the Seychelles20
Ocean crossers: A tale of disjunctions and speciation in the dwarf-fruticose Lichina (lichenized Ascomycota)20
Recurrent founder-event speciation across the Mediterranean likely shaped the species diversity and geographic distribution of the freshwater snail genus Mercuria Boeters, 1971 (Caenogastropoda: Hydro20
Phylogenetic relationships of the Geoplaninae land planarians (Platyhelminthes, Tricladida) assessed with a total evidence approach, with the description of a new species of Gigantea20
UCE phylogenomics reveals orogenic vicariance and introgression shaping diversification in the montane Mexican lizard genus Barisia (Squamata: Anguidae)20
Phylogeny and historical biogeography of neotropical catfishes Trichomycterus (Siluriformes: Trichomycteridae) from eastern Brazil20
Cenozoic colonisation of the Indian Ocean region by the Australian freshwater-originating glassperch family Ambassidae (Teleostei)20
Deconstructing Difflugia: The tangled evolution of lobose testate amoebae shells (Amoebozoa: Arcellinida) illustrates the importance of convergent evolution in protist phylogeny19
Dynamics and timing of diversification events of ciliated eukaryotes from a large phylogenomic perspective19
Shining new light on naupliar eyes: A novel molecular phylogeny for Pleuromamma (Family: Metridinidae) and the characterization of luciferase and opsin expression19
Interspecific gene flow obscures phylogenetic relationships in an important insect pest species complex19
Editorial Board18
Phylogenomics AND biogeography of Castanea (chestnut) and Hamamelis (witch-hazel) – Choosing between RAD-seq and Hyb-Seq approaches18
Molecular phylogeny, historical biogeography, and classification of Pseudocoladenia butterflies (Lepidoptera: Hesperiidae)18
Resolving reticulate evolutionary histories of polyploid species of Azorella (Apiaceae) endemic to New Zealand18
Slippery slopes: Montane isolation and elevational shifts shape the evolution and diversity of Iberolacerta lizards18
A new bunting species in South China revealed by an integrative taxonomic investigation of the Emberiza godlewskii complex (Aves, Emberidae)18
A phylogenomic framework of Gastrotricha evolutionary relationships18
The hybridization origin of the Chinese endemic herb genus Notopterygium (Apiaceae): Evidence from population genomics and ecological niche analysis18
Population structure in Mixornis tit-babblers across Sunda Shelf matches interfluvia of paleo-rivers17
A new species of Populus and the extensive hybrid speciation arising from it on the Qinghai-Tibet Plateau17
Study of epiphytic non-geniculate coralline algae Reveals an Evolutionarily significant Genus, Pseudoderma gen. nov. (Lithophylloideae, Corallinophycidae)17
The phylogeny and evolutionary ecology of hoverflies (Diptera: Syrphidae) inferred from mitochondrial genomes17
Genomic insights into the biogeography and evolution of Galápagos iguanas17
Endogean habits drove cryptic diversification in Appalachian Lathrobium Gravenhorst (Coleoptera, Staphylinidae)17
Editorial Board17
A deceitful claw: Erection of Synonyx gen. Nov. and Synonyxidae fam. Nov. in Hypsibioidea (Eutardigrada: Parachela)17
Divergence time and biogeography of the fungal genus Porodaedalea (Basidiomycota, Hymenochaetales), obligate phytopathogens on coniferous trees17
Non-reciprocal coevolution in a fungus-gardening ant17
Editorial Board17
Diversity and population connectivity of members of the family eunicidae inhabiting deep-water corals in the North Atlantic17
Phylogenomics reveals climate-driven range expansion of the antlion tribe Megistopini (Neuroptera: Myrmeleontidae: Nemoleontinae) during the Oligocene-Miocene transition17
A phylotranscriptome study using silica gel-dried leaf tissues produces an updated robust phylogeny of Ranunculaceae17
Phylogenomic analysis of Stylops reveals the evolutionary history of a Holarctic Strepsiptera radiation parasitizing wild bees16
Out of the desert: Paleoclimatic changes drove the diversification of arid-adapted Ocymyrmex ants in southern Africa16
Rearranging and completing the puzzle: Phylogenomic analysis of bark beetles Dendroctonus reveals new hypotheses about genus diversification16
Macroevolutionary analyses point to a key role of hosts in diversification of the highly speciose eriophyoid mite superfamily16
Structural dynamics of chloroplast genome in Paphiopedilum (Orchidaceae): in response to natural hybridization16
The Sela macaque (Macaca selai) is a distinct phylogenetic species that evolved from the Arunachal macaque following allopatric speciation16
Diverse origins of peptidoglycan biosynthesis enzymes in Glaucophyta and Viridiplantae16
Multilocus phylogeny of the land snail Helix differs substantially from the mitochondrial gene tree16
Whole-genome resequencing unveils the phylogeographic coevolution of Oncomelania hupensis with Yangtze River dynamics in China16
Deeply divergent freshwater fish species within a single river system in central Sulawesi16
Under the hood: Phylogenomics of hooded tick spiders (Arachnida, Ricinulei) uncovers discordance between morphology and molecules16
Phylogeny and biogeography of harmochirine jumping spiders (Araneae: Salticidae)16
Deciphering the drivers of speciation in Alpine Noccaea (Brassicaceae) reveal an evolution predominantly shaped by geography16
Identifying a potentially invasive population in the native range of a species: The enlightenment from the phylogeography of the yellow spotted stink bug, Erthesina fullo (Hemiptera: Pentatomidae)15
Editorial Board15
Ancient gene flow shapes phylogenetic discordance in a genus of wood-warblers (Aves: Parulidae: Leiothlypis)15
Novel oceanic cyanobacterium isolated from Bangaram island with profound acid neutralizing ability is proposed as Leptolyngbya iicbica sp. nov. strain LK15
Integrative phylogenetic, phylogeographic and morphological characterisation of the Unio crassus species complex reveals cryptic diversity with important conservation implications15
Phylogeny and evolution of dissimilatory sulfite reduction in prokaryotes15
Phylogenomics and historical biogeography of West Indian Rock Iguanas (genus Cyclura)15
Integrative approach to species delimitation in Rhizophydiales: Novel species of Angulomyces, Gorgonomyces, and Terramyces from northern Thailand15
Corrigendum to “Molecular phylogeny and trait evolution in an ancient terrestrial arthropod lineage: Systematic revision and implications for ecological divergence (Collembola, Tomocerinae)” [Mol. Phy15
Phylogenetic relationships and the origin of New World soles (Teleostei: Pleuronectiformes: Achiridae): The role of estuarine habitats15
Following the aridity: Historical biogeography and diversification of the Philodromidae spider genus Petrichus in South America15
Genomic data provide a robust phylogeny backbone for Rhodiola L. (Crassulaceae) and reveal extensive reticulate evolution during its rapid radiation15
Imperiled wanderlust lichens in steppe habitats of western North America comprise geographically structured mycobiont lineages and a reversal to sexual reproduction within this asexual clade15
New evidence of consistency between phylogeny and morphology for two taxa in ciliated protists, the subclasses Oligotrichia and Choreotrichia (Protista, Ciliophora)15
Ecological speciation by sympatric host shifts in a clade of herbivorous sea slugs, with introgression and localized mitochondrial capture between species15
Plastid phylogenomic analyses of the Selaginella sanguinolenta group (Selaginellaceae) reveal conflict signatures resulting from sequence types, outlier genes, and pervasive RNA editing15
Exceptional levels of species discovery ameliorate inferences of the biogeography and diversification of an Afrotropical catfish family14
Molecular data and museum collections reframe Pleuroceridae (Gastropoda: Cerithioidea) diversity and conservation priorities in an overlooked freshwater biodiversity hotspot14
Genomic footprints of ancient multi‐species introgression events among allopatric cave-adapted Triplophysa species14
Ultraconserved elements-based phylogenomic systematics of the snake superfamily Elapoidea, with the description of a new Afro-Asian family14
Mixed, not stirred: Genomic data confirm the first case of interspecific hybridization in planarian triclads (Platyhelminthes: Tricladida) and raise questions about a possibly novel form of hybrid spe14
Skeleton phylogeny reconstructed with transcriptomes for the tribe Drosophilini (Diptera: Drosophilidae)14
Population genomics of the southern giraffe14
Diversification of the sleepers (Gobiiformes: Gobioidei: Eleotridae) and evolution of the root gobioid families14
Single cell transcriptomics reveals UAR codon reassignment in Palmarella salina (Metopida, Armophorea) and confirms Armophorida belongs to APM clade14
Expanding Acutuncus: Phylogenetics and morphological analyses reveal a considerably wider distribution for this tardigrade genus14
A thorny tale: The origin and diversification of Cirsium (Compositae)14
A global blueberry phylogeny: Evolution, diversification, and biogeography of Vaccinieae (Ericaceae)14
Phylogeny and diversification of the subfamily Acheilognathinae (Cypriniformes: Cyprinidae) from China based on a comprehensive molecular dataset14
Explosion of goby fish diversity at the Eocene-Oligocene transition14
Synchronous Miocene radiations and geographic-dependent diversification of pantropical Xylopia (Annonaceae)14
A story of vicariance? how the geology of oceanic archipelagos influenced the evolutionary history of endemic damselflies14
Editorial Board14
In the land of the blind: Exceptional subterranean speciation of cryptic troglobitic spiders of the genus Tegenaria (Araneae: Agelenidae) in Israel14
Genomic and phenotypic characterization of Thermosynechococcus-like strains reveals eight species within the genus Thermosynechococcus and a novel genus Parathermosynechococcus gen. nov.14
Phylogenomic loci define the generic boundaries of Gochnatieae and improve resolution at the species level in Moquiniastrum (Compositae)14
Overwater dispersal from a single source island shaped the diversity of green anole lizards (Anolis carolinensis subgroup)14
Corrigendum to “Employing exon capture to resolve species-level relationships in Australian Arid Zone camaenid land snails” [Mol. Phylogenetics Evol. 218 (2026) 108570]13
Molecular phylogenetics of the Clupeiformes based on exon-capture data and a new classification of the order13
Integrative taxonomy in a rapid speciation group associated with mating system transition: A case study in the Primula cicutariifolia complex13
Phylogenetic origin of dioecious Callicarpa (Lamiaceae) species endemic to the Ogasawara Islands revealed by chloroplast and nuclear whole genome analyses13
Integrative taxonomy of the subfamily Orbioninae (Crustacea: Isopoda) based on mitochondrial and nuclear data with evidence that supports Epicaridea as a suborder13
Australia’s hidden radiation: Phylogenomics analysis reveals rapid Miocene radiation of blindsnakes13
Phylogenomic conflict analyses of the plastid and mitochondrial genomes via deep genome skimming highlight their independent evolutionary histories: A case study in the cinquefoil genus Potentilla sen13
Plastid phylogenomics of the tribe potentilleae (Rosaceae)13
Evolution of androdioecy in Berchemia (Rhamnaceae) revealed by phylogenomics and ancestral character reconstruction13
Genomic data reveals cryptic diversity and suggests five putative species in the broad-snouted caiman in South America13
The phylogeny and global biogeography of Primulaceae based on high-throughput DNA sequence data13
Paraphyly and cryptic diversity unveils unexpected challenges in the “naked lichens” (Calvitimela, Lecanoromycetes, Ascomycota)13
A model of hybrid speciation process drawn from three new poplar species originating from distant hybridization between sections13
Molecular systematics and phylogenetics of the spider genus Mastigusa Menge, 1854 (Araneae, Cybaeidae)13
Historical DNA solves century-old mystery on sessility in freshwater gastropods13
Spider nest-retreat origin, diversification, and architectural plasticity link to historical and current temperature fluctuations13
Multi-locus phylogeny and species delimitations of the striped-back shrew group (Eulipotyphla: Soricidae): Implications for cryptic diversity, taxonomy and multiple speciation patterns13
Horizontally transferred glycoside hydrolase 26 may aid hemipteran insects in plant tissue digestion12
Genomic data reveal local endemism in Southern California Rubber Boas (Serpentes: Boidae, Charina) and the critical need for enhanced conservation actions12
Editorial Board12
Abundant incongruence in a clade endemic to a biodiversity hotspot: Phylogenetics of the scrub mint clade (Lamiaceae)12
Diversification and evolutionary history of the African laminated-toothed rats (Rodentia, Otomyini)12
When lizards shift to a more plant-based lifestyle: The macroevolution of mutualistic lizard-plant-interactions (Squamata: Sauria/Lacertilia)12
Phylogenomic evolutionary insights in the fern family Gleicheniaceae12
Phylogenomics offers new insights into the classification of Phytoseiidae (Acari: Mesostigmata)12
Phylogenomic analyses of ochrophytes (stramenopiles) with an emphasis on neglected lineages12
Phylogenomics of Anguis and Pseudopus (Squamata, Anguidae) indicates Balkan-Apennine mitochondrial capture associated with the Messinian event12
Molecular phylogeny and divergence time of Harpalyce (Leguminosae, Papilionoideae), a lineage with amphitropical diversification in seasonally dry forests and savannas12
A comprehensive molecular phylogeny of the genus Sylvirana (Anura: Ranidae) highlights unrecognized diversity, revised classification and historical biogeography12
Phylogenomic analyses of hamsters (Cricetinae) inferred from GBS data and mitochondrial genomes12
Integrated morphological and phylogenomic analyses revealed a novel genus Paramicrotoena (Lamiaceae − Pogostemoneae) discovered in the Pan-Himalaya12
Evaluating species boundaries using coalescent delimitation in pine-killing Monochamus (Coleoptera: Cerambycidae) sawyer beetles12
Phylogenomics and morphology of Celmisiinae (Asteraceae: Astereae): Taxonomic and evolutionary implications12
Phylogeny, character evolution, and biogeography of the fern genus Bolbitis (Dryopteridaceae)12
Disentangling conflicting molecular phylogenetic signals in nuclear and plastid DNA of the western Eurasian-Mediterranean grass genus Cynosurus and its relatives (Poaceae subtribes Cynosurinae and Par12
Intra-island patterns of cryptic diversity within an oceanic island: Insights from the differentiation of Schizidium Verhoeff, 1901 (Oniscidea, Armadillidiidae) within Cyprus, with descriptions of two12
Biogeography and evolution of social parasitism in Australian Myrmecia bulldog ants revealed by phylogenomics12
Independent recruitment of FRUITFULL-like transcription factors in the convergent origins of vernalization-responsive grass flowering12
Out of southern Africa: Origins and cryptic speciation in Chamaeleo, the most widespread chameleon genus12
A supermatrix phylogeny of the world’s bees (Hymenoptera: Anthophila)12
Hidden species diversity and mito-nuclear discordance within the Mediterranean cone snail, Lautoconus ventricosus12
Taxonomic insights and evolutionary history in East Asian terrestrial slugs of the genus Meghimatium11
Phylogeny and evolution of morphological structures in a highly diverse lineage of fruiting-body-forming amoebae, order Trichiales (Myxomycetes, Amoebozoa)11
Two new tardigrade genera from New Zealand’s Southern Alp glaciers display morphological stasis and parallel evolution11
Phylotranscriptomics reveals conflicts of deep nodes in Saxifragales11
Phylogenomics and genome size evolution in Amomum s. s. (Zingiberaceae): Comparison of traditional and modern sequencing methods11
Space explorer: floral evolution and lineage diversification of the Neotropical Sapranthinae clade (Annonaceae)11
Evolutionary insights from the pangenome and pigment profiles of Parasynechococcus11
Species delimitation using genomic data to resolve taxonomic uncertainties in a speciation continuum of pelagic seabirds11
A subfunctionalisation model of gene family evolution predicts balanced tree shapes11
The role of introgressive hybridization in shaping the geographically isolated gene pools of wax palm populations (genus Ceroxylon)11
The phylogenomics and evolutionary dynamics of the organellar genomes in carnivorous Utricularia and Genlisea species (Lentibulariaceae)11
Genome skimming elucidates the evolutionary history of Octopoda11
Geographic isolation, ecological adaptation, and hybridization influenced fast divergence of a Solanaceae plant group from subtropical highland grasslands11
Out of the ancient lake: Multiple riverine colonizations and diversification of the freshwater snails in the genus Semisulcospira around Lake Biwa11
Editorial Board11
A straightforward workflow to explore species diversity using the Patagonian lizards of the Diplolaemus genus (Iguania: Leiosauridae) as a study case, with the description of a new species11
Phylogenomics resolves the puzzling phylogeny of banded newts (genus Ommatotriton)11
Diversification in the mountains: Evolutionary history and molecular phylogeny of Anatolian rock lizards11
Jumping through hoops: Structural rearrangements and accelerated mutation rates on Dendrodorididae (Mollusca: Nudibranchia) mitogenomes rumble their evolution11
Phylogenomics of the woodland salamanders (Plethodon): Reticulate evolution and indistinct species boundaries11
Diversity of Wolbachia infection and its influence on mitochondrial DNA variation in the diamondback moth, Plutella xylostella11
Deciphering phylogenetic relationships of and delimiting species boundaries within the controversial ciliate genus Conchophthirus using an integrative morpho-evo approach11
Phylogenomics of Amazonian squirrel monkeys (Saimiri: Primates, Cebidae)11
Biome conservatism prevailed in repeated long-distance colonization of Madagascar’s mountains by Helichrysum (Compositae, Gnaphalieae)11
Phylogenomic insights into the historical biogeography, character-state evolution, and species diversification rates of Cypripedioideae (Orchidaceae)11
Harnessing transposable elements: A new frontier in insect systematics11
Editorial Board11
An ultraconserved element probe set for velvet worms (Onychophora)11
1.1676959991455