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opencc-zeroFeb 2022View details →

Highly resolved papilionoid legume phylogeny based on plastid phylogenomics

Comprising 501 genera and around 14,000 species, Papilionoideae is not only the largest subfamily of Fabaceae (Leguminosae; legumes), but also one of the most extraordinarily diverse clades among angiosperms. Papilionoids are a major source of food and forage, are ecologically successful in all major biomes, and display dramatic variation in both floral architecture and plastid genome (plastome) structure. Plastid DNA-based phylogenetic analyses have greatly improved our understanding of relationships among the major groups of Papilionoideae, yet the backbone of the subfamily phylogeny remains unresolved. In this study, we sequenced and assembled 39 new plastomes that are covering key genera of evolution and morphological diversity in the subfamily. From 244 total taxa, we produced eight datasets for maximum likelihood (ML) analyses based on entire plastomes and/or concatenated sequences of 77 protein-coding sequences (CDS) and two datasets for multispecies coalescent (MSC) analyses based on individual gene trees. We additionally produced a combined nucleotide dataset comprising CDS plus matK gene sequences only, in which most papilionoid genera were sampled. An ML tree based on the entire plastome maximally supported all of the deep and most recent divergences of papilionoids (223 out of 236 nodes). The Swartzieae, ADA (Angylocalyceae, Dipterygeae, and Amburaneae), Cladrastis, Andira, and Exostyleae clades formed a grade to the remainder of the Papilionoideae, concordant with nine ML and two MSC trees. Phylogenetic relationships among the remaining five papilionoid lineages (Vataireoid, Dermatophyllum, Genistoid s.l., Dalbergioid s.l., and Baphieae + Non-Protein Amino Acid Accumulating or NPAAA clade) remained uncertain, because of insufficient support and/or conflicting relationships among trees. Our study fully resolved most of the deep nodes of Papilionoideae, however some relationships require further exploration. More genome-scale data and rigorous analyses are needed to disentangle phylogenetic relationships among the five remaining lineages.

opencc-by-4.0Apr 2022View details →

Three New Species of Hypoxylon (Xylariales, Ascomycota) on a multigene phylogeny from Medog in China

Figure S1: ML phylogram inferred from ITS-TUB2 sequences. ML bootstrap support (BS) ≥ 50% and Bayesian posterior probabilities (PP) ≥ 0.95 are labelled above or below the respective branches (BS/PP). Species in bold were sequenced in the this study.

opencc-zeroApr 2022View details →

Molecular phylogeny reveals the past transoceanic voyages of drywood termites (Isoptera, Kalotermitidae)

Termites are major decomposers in terrestrial ecosystems and the second most diverse lineage of social insects. The Kalotermitidae form the second-largest termite family and are distributed across tropical and subtropical ecosystems, where they typically live in small colonies confined to single wood items inhabited by individuals with no foraging abilities. How the Kalotermitidae have acquired their global distribution patterns remains unresolved. Similarly, it is unclear whether foraging is ancestral to Kalotermitidae or was secondarily acquired in a few species. These questions can be addressed in a phylogenetic framework. We inferred time-calibrated phylogenetic trees of Kalotermitidae using mitochondrial genomes of ~120 species, about 27% of kalotermitid diversity, including representatives of 21 of the 23 kalotermitid genera. Our mitochondrial genome phylogenetic trees were corroborated by phylogenies inferred from nuclear ultraconserved elements derived from a subset of 28 species. We found that extant kalotermitids shared a common ancestor 84 Mya (75–93 Mya 95% HPD), indicating that a few disjunctions among early-diverging kalotermitid lineages may predate Gondwana breakup. However, most of the ~40 disjunctions among biogeographic realms were dated at less than 50 Mya, indicating that transoceanic dispersals, and more recently human-mediated dispersals, have been the major drivers of the global distribution of Kalotermitidae. Our phylogeny also revealed that the capacity to forage is often found in early-diverging kalotermitid lineages, implying the ancestors of Kalotermitidae were able to forage among multiple wood pieces. Our phylogenetic estimates provide a platform for critical taxonomic revision and future comparative analyses of Kalotermitidae.

opencc-by-4.0Dec 2021View details →

A quantitative assessment of the patterns of integration in the mandible of bovids and their relationships with trophic ecology, phylogeny, and evolutionary rates

Dataset and R script supporting the findings of the study "A quantitative assessment of the patterns of integration in the mandible of bovids and their relationships with trophic ecology, phylogeny, and evolutionary rates".

A new phylogeny of Rumex (Polygonaceae) adds evolutionary context to the diversity of reproductive systems present in the genus

Rumex is a unique member of the Polygonaceae family of plants. A source of intrigue for Rumex lies in the diversity of the reproductive systems associated with this genus. Four previously circumscribed subgenera and some two-hundred species comprise the collective Rumex genus. These species exhibit monoecious, dioecious, synoecious (hermaphroditic), and polygamous reproductive systems. Moreover, some of the dioecious species contain heteromorphic sex chromosomes, a phenomenon that is very rare in angiosperms. Apart from these confirmed morphological and phytogeographical distinctions, two of the four described subgenera, Rumex subg. Acetosa and Rumex subg. Acetosella, are distinctive in their sex chromosome systems. For this study, we used three chloroplast markers, rbcL, trnH-psbA, trnL-F, and dense taxon sampling, to reconstruct the most comprehensive molecular phylogeny of Rumex to date. The reconstructed phylogeny for this work resolves six major clades and one large grade in Rumex subg. Rumex. In addition, the species with known dioecious reproductive systems are resolved within a broader clade termed "the dioecious clade". These results suggest that the species with divergent reproductive systems are more closely related to each other than to other species comprising the rest of the Rumex genus. Furthermore, some species with known synoecious reproductive systems are resolved in a single clade which is also nested within "the dioecious clade". These results imply a possible reversal occurring over time which suggests the highly plastic nature of the reproductive systems in Rumex species.

The rediscovery of a relict unlocks the first global phylogeny of whip spiders (Amblypygi)

Asymmetrical rates of cladogenesis and extinction abound in the Tree of Life, resulting in numerous minute clades that are dwarfed by larger sister groups. Such taxa are commonly regarded as phylogenetic relicts or "living fossils" when they exhibit an ancient first appearance in the fossil record and prolonged external morphological stasis, particularly in comparison to their more diversified sister groups. Due to their special status, various phylogenetic relicts tend to be well-studied and prioritized for conservation. A notable exception to this trend is found within Amblypygi ("whip spiders"), a visually striking order of functionally hexapodous arachnids that are notable for their antenniform first walking leg pair (the eponymous "whips"). Paleoamblypygi, the putative sister group to the remaining Amblypygi, is known from Late Carboniferous and Eocene deposits, but is survived by a single living species, Paracharon caecus Hansen, 1921, that was last collected in 1899. Due to the absence of genomic sequence-grade tissue for this vital taxon, there is no global molecular phylogeny for Amblypygi to date, nor a fossil-calibrated estimation of divergences within the group. Here, we report several individuals of a previously unknown species of Paleoamblypygi from a cave site in Colombia. Capitalizing upon this discovery, we generated the first molecular phylogeny of Amblypygi, integrating ultraconserved element sequencing with legacy Sanger datasets and including described extant genera. To quantify the impact of sampling Paleoamblypygi on divergence time estimation, we performed in silico experiments with pruning of Paracharon. We demonstrate that the omission of relicts has a significant impact on the accuracy of node dating approaches that outweighs the impact of excluding ingroup fossils. Our results underscore the imperative for biodiversity discovery efforts in elucidating the phylogenetic relationships of " dark taxa", and especially phylogenetic relicts in tropical and subtropical habitats.

New non-native pseudocryptic Cyclorhipidion species (Coleoptera: Curculionidae: Scolytinae: Xyleborini) found in the United States as revealed in a multigene phylogeny

Pseudocryptic species, those that are difficult to diagnose using traditional taxonomic methods, are serious impediments for recognizing the introduction of non-native species. Rapid identification of species facilitates a rapid response to newly introduced species which can lessen their damaging effects. This situation is acute for known pest species such as xyleborine ambrosia beetles which are difficult to identify given minute morphological, often variable, diagnostic characters. These beetles have been introduced into non-native temperate regions and have caused economic and ecological havoc. In this study, we produced DNA-based phylogenies using four genes for individuals of Cyclorhipidion bodoanum (Reitter, 1913), C. distinguendum (Eggers, 1930), and C. pelliculosum (Eichhoff, 1878) sampled from their introduced and native Asian ranges and as well as other Cyclorhipidion species. In addition, we review subtle morphological characters for diagnostic potential for these similar species. Bayesian phylogenetic analysis produced well-resolved and supported phylogeny that provided evidence for multiple introductions of C. bodoanum and C. distinguendum into the US and the occurrence of pseudocryptic species. The ambrosia beetles Cyclorhipidion tenuigraphum (Schedl, 1953) and C. nemesis Smith & Cognato, sp. nov. are reported in North America for the first time. We find that the pattern of elytral interstrial setae is an unrealized source for the identification of Cyclorhipidion species. This study resulted in the recognition of six species adventive to the US with the revised status of C. californicum (Wood, 1975). All species known from North American are diagnosed, illustrated and a key is provided.

On the computational reproducibility of molecular phylogenies

Reports on the lack of computational reproducibility of molecular phylogenies, produced in multiple runs of the same program or by different programs, cast a long shadow on downstream research using these phylogenies and on efforts to build the tree of life. We show that this irreproducibility does not decrease the accuracy of the reconstructed evolutionary relationships. Also, we find inferred molecular phylogenies to have log-likelihoods comparable to or better than the true phylogeny. Therefore, the lack of computational reproducibility of molecular phylogenies is not a problem for evolutionary studies.

opencc-zeroJun 2022View details →

Zehneria neorensis: Additional phylogenies and sequence information

Basic data and supplement for Ranjan et al. 2022, Biogeography of Zehneria (Cucurbitaceae) and a New Species from India, Systematic Botany. Zehneria is one of the most diverse genera in Cucurbitaceae with 75 accepted species mainly in Southeast Asia and tropical Africa. We describe Zehneria neorensis, a new species from Neora Valley in the mountains of West Bengal, India, which has 7–10 cm long twisted fruiting pedicels, the longest pedicels reported in the genus so far. Based on morphological data, we also suggest the transfer of Melothria morobensis to the genus Zehneria. With a molecular phylogenetic and global biogeographic analysis based on 3856 nucleotides of plastid and nuclear ribosomal DNA, we demonstrate that the genus Zehneria most likely originated on the African continent 24 (30-19) million years ago and spread from there at least five times to Madagascar and three times to Asia. Zehneria neorensis represents an independent colonization event from Africa to India about 11 (15–7) million years ago. Three lineages reached New Guinea/Australia and finally moved into Polynesia. We infer a rate of at least 20 long-distance dispersal (LDD) events per 10 million years in the genus. This high LDD frequency is most likely a result of the small berry fruits and small flattened seeds of Zehneria, which seem perfectly adapted to long-distance bird dispersal. Field observations are needed to investigate a potential effect of the newly discovered extended and coiling pedicels in Zehneria neorensis on seed dispersal efficiency. The new species adds to a growing list of rather old Cucurbitaceae lineages in the Himalayan foothills, supporting the hypothesis of long climatic stability in the region.

opencc-zeroJun 2022View details →

Data for a preliminary molecular phylogeny of the family Hydroptilidae (Trichoptera): exploring the combination of targeted enrichment data and legacy Sanger sequence data

The purpose of this study is to provide a proof-of-concept that the use of molecular data, particularly targeted enrichment data, and statistically supported methods of analysis can result in the construction of a stable phylogenetic framework for the microcaddisflies (Trichoptera: Hydroptilidae). Here, we use a combination of targeted enrichment data for ca. 300 nuclear protein-coding genes and legacy (Sanger-based) sequence data for the mitochondrial COI gene and partial sequence from the 28S rRNA gene.

opencc-zeroJun 2022View details →

Craniodental morphology and phylogeny of marsupials

The current literature on marsupial phylogenetics includes numerous studies based on analyses of morphological data with limited sampling of Recent and fossil taxa and many studies based on analyses of molecular data with dense sampling of Recent taxa, but few studies have combined both data types. Another dichotomy in the marsupial phylogenetic literature is between studies focused on New World taxa, and those focused on Sahulian taxa. To date, there has been no attempt to assess the phylogenetic relationships of the global marsupial fauna based on combined analyses of morphology and molecular sequences for a dense sampling of Recent and fossil taxa. For this report, we compiled morphological and molecular data from an unprecedented number of Recent and fossil marsupials. Our morphological data consist of 180 craniodental characters that we scored for 97 terminals representing every currently recognized Recent genus, 42 additional ingroup (crown-clade marsupial) terminals represented by well-preserved fossils, and 5 outgroups (nonmarsupial metatherians). Our molecular data comprise 24.5 kb of DNA sequences from whole-mitochondrial genomes and six nuclear loci (APOB, BRCA1, GHR, RAG1, RBP3, and VWF) for 97 marsupial terminals (the same Recent taxa scored for craniodental morphology) and several placental and monotreme outgroups. The results of separate and combined analyses of these data using a wide range of phylogenetic methods support many currently accepted hypotheses of ingroup (marsupial) relationships, but they also underscore the difficulty of placing fossils with key missing data (e.g., †Evolestes), and the unique difficulty of placing others that exhibit mosaics of plesiomorphic and autapomorphic traits (e.g., †Yalkaparidon). Unique contributions of our study are (1) critical discussions and illustrations of marsupial craniodental morphology including features never previously coded for phylogenetic analysis; (2) critical assessments of relative support for many suprageneric clades; (3) estimates of divergence times derived from tip-and-node dating based on uniquely taxon-dense analyses; and (4) a revised, higher-order classification of marsupials accompanied by lists of supporting craniodental synapomorphies. Far from the last word on these topics, this report lays the foundation for future research that may be enabled by the discovery of new fossil taxa, better-preserved material of previously described taxa, novel morphological characters (e.g., from the postcranium), and improved methods of phylogenetic analysis.

opencc-zeroJul 2022View details →

Genetic variation data to explore the phylogeny of Iberian weedy rice

Weedy rice, a damaging conspecific weed of cultivated rice, has arisen multiple times independently around the world. Understanding all weedy rice origins is necessary to create more effective weed management strategies. The origins of weedy rice in Spain and Portugal, where there are no native Oryza species are unknown. We used genotyping-by-sequencing (GBS) to understand the origin of Iberian weedy rice and its relationship to other weedy, wild, and cultivated rice groups worldwide. This is the variant call format (vcf) file for all 481 accessions including weedy, wild, and cultivated rice. We used this dataset to understand the phylogenetic relationships and population structure among these different populations, especially the Iberian weedy rice. We find that weedy rice in the Iberian Peninsula has primarily evolved through de-domestication of temperate japonica cultivars, with minor origins from exotic weedy rice.

opencc-by-4.0Jul 2022View details →

Data collected by citizen scientists reveal the role of climate and phylogeny on the frequency of shelter types used by frogs across the Americas

Supplementary Material  of the manuscript on frog shelters across americas. Raw data and figures. Table S1. The number of all anuran observations per species per country in the iNaturalist dataset on July 1, 2021. Table S2. Distribution of shelter types among frog species retrieved from the iNaturalist platform across the Americas. Species with shelter first time reports are marked with *, shelter types are: AH = Holes in an artificial material; AS = Artificial surface; HG = Hole in the ground; HR = Among rocks; VBa = Hollow in bamboo; VBr = Bromelias or bromelia-like plants; VL = Live vegetation; VT = Tree trunk; VD = Leaf litter; WA = Water Table S3. Anuran shelter sites around the world based on our literature review. *indicates the reference is secondary literature

opencc-zeroAug 2022View details →

Evolutionary rates and shape variation along the anuran vertebral column with attention to phylogeny, body size, and ecology

The vertebral column is critical to a vertebrate species' flexibility and skeletal support, making vertebrae a clear target for selection. Anurans (frogs and toads) have a unique, truncated vertebral column that appears constrained to provide axial rigidity for efficient jumping. However, no study has examined how presacral vertebrae shape varies among anuran species at the macroevolutionary scale nor how intrinsic (developmental and phylogenetic) and extrinsic (ecological) factors may have influenced vertebrae shape evolution. We used microCT scans and phylogenetic comparative methods to examine the vertebrae of hundreds of anuran species that vary in body size as well as adult and larval ecology. We found variation in shape and evolutionary rates among anuran vertebrae, dispelling any notion that trunk vertebrae evolve uniformly. We discovered the highest evolutionary rates in the cervical vertebrae and in the more caudal trunk vertebrae. We found little evidence for selection pressures related to adult or larval ecology affecting vertebrae evolution, but we did find body size was highly associated with vertebrae shape and microhabitat (mainly burrowing) affected those allometric relationships. Our results provide an interesting comparison to vertebrae evolution in other clades and a jumping-off point for studies of anuran vertebrae evolution and development.

opencc-zeroSep 2022View details →

Phylogenies related to: Codiversification of gut microbiota with humans

The gut microbiomes of human populations worldwide have many core microbial species in common. However, within a species, some strains can show remarkable population specificity. The question is whether such specificity arises from a shared evolutionary history (codiversification) between humans and their microbes. To test for codiversification of host and microbiota, we analyzed paired gut metagenomes and human genomes for 1225 individuals in Europe, Asia, and Africa, including mothers and their children. Between and within countries, signals of codiversification were evident for humans and their gut microbes. Moreover, species displaying the strongest codiversification independently evolved traits characteristic of host dependency, including reduced genomes, and oxygen and temperature sensitivity. These findings all point to the importance of understanding the potential role of population-specific microbial strains in microbiome-mediated disease phenotypes.

opencc-zeroOct 2022View details →

Data from: Resolution, conflict and rate shifts: Insights from a densely sampled plastome phylogeny for Rhododendron (Ericaceae)

Background and Aims Rhododendron is a species-rich and taxonomically challenging genus due to recent adaptive radiation and frequent hybridization. A well-resolved phylogenetic tree would help to understand the diverse history of Rhododendron in the Himalaya–Hengduan Mountains where the genus is most diverse. Methods We reconstructed the phylogeny based on plastid genomes with broad taxon sampling, covering 161 species representing all eight subgenera and all 12 sections, including ~45 % of the Rhododendron species native to the Himalaya–Hengduan Mountains. We compared this phylogeny with nuclear phylogenies to elucidate reticulate evolutionary events and clarify relationships at all levels within the genus. We also estimated the timing and diversification history of Rhododendron, especially the two species-rich subgenera Rhododendron and Hymenanthes that comprise >90 % of Rhododendron species in the Himalaya–Hengduan Mountains. Key Results The full plastid dataset produced a well-resolved and supported phylogeny of Rhododendron. We identified 13 clades that were almost always monophyletic across all published phylogenies. The conflicts between nuclear and plastid phylogenies strongly suggested that reticulation events may have occurred in the deep lineage history of the genus. Within Rhododendron, subgenus Therorhodion diverged first at 56 Mya, then a burst of diversification occurred from 23.8 to 17.6 Mya, generating ten lineages among the component 12 clades of core Rhododendron. Diversification in subgenus Rhododendron accelerated c. 16.6 Mya and then became fairly continuous. Conversely, Hymenanthes diversification was slow at first, then accelerated very rapidly around 5 Mya. In the Himalaya–Hengduan Mountains, subgenus Rhododendron contained one major clade adapted to high altitudes and another to low altitudes, whereas most clades in Hymenanthes contained both low- and high-altitude species, indicating greater ecological plasticity during its diversification. Conclusions The 13 clades proposed here may help to identify specific ancient hybridization events. This study will help to establish a stable and reliable taxonomic framework for Rhododendron, and provides insight into what drove its diversification and ecological adaption. Denser sampling of taxa, examining both organelle and nuclear genomes, is needed to better understand the divergence and diversification history of Rhododendron.

opencc-zeroOct 2022View details →

The phylogeny of Errazurizia (Fabaceae: Amorpheae) and description of the new monotypic genus Pictarena

Errazurizia (Fabaceae) is a genus comprised of four species of New World desert shrubs with an ambiguous evolutionary history. Prior studies determined the North American species of Errazurizia were polyphyletic and the relationship of E. rotundata with other genera in the tribe Amorpheae remained undetermined. The sole South American species, which is also the type species, has never been included in a molecular study. We inferred the phylogenetic relationships of Errazurizia and six closely related genera using data from the cpDNA genome and nrDNA cistron from reference-guided assemblies. Maximum likelihood and Bayesian analyses found two of the North American and the South American species were a monophyletic group, but that E. rotundata was sister to the monotypic genus Parryella. Gland and pollen surface characters confirm the close relationship between P. filifolia and E. rotundata. Cytonuclear discordance yielded partially incongruent tree topologies, and while the cpDNA phylogeny indicated a monophyletic Amorpha was sister to the E. rotundata and P. filifolia clade, the nrDNA cistron phylogeny recovered a paraphyletic Amorpha, with A. californica sister to the E. rotundata and P. filifolia clade. Molecular and morphological evidence support the elevation of E. rotundata to its own monotypic genus, Pictarena. The new genus Pictarena is defined by subsessile, suborbicular leaflets, mammiform leaflet glands, spicate inflorescences, and flowers with either all petals absent or rarely with a banner petal. Elevating E. rotundata to Pictarena resolves the confusing classification of the species, an imperiled endemic known only from four localities in northern Arizona and lends support for continued conservation.

opencc-zeroOct 2022View details →

Molecular phylogeny of Dermestidae (Coleoptera) reveals the polyphyletic nature of Trogoderma Latreille, and the taxonomic placement of the Khapra Beetle Trogoderma granarium Everts

The hide, larder and carpet beetles (Coleoptera: Dermestidae) are a family of mainly scavenger beetles, with numerous species such as the khapra beetle (Trogoderma granarium Everts, 1898), the black carpet beetle (Attagenus unicolor (Brahm, 1791)) and the hide beetle (Dermestes maculatus De Geer, 1774) being widely recognised as serious economic pests of stored products and museum collections (Fig. 1). A stable classification and reliable identification of genera and species of these pests and their 1,700 relatives are of great relevance for trade restrictions, biosecurity, pest management, forensics and biodiversity surveys. In this study, we examined and sequenced mitochondrial genomes of 477 dermestid specimens, representing all subfamilies and 90% of the globally recognised tribes and subtribes. Our study provides the most comprehensive, taxonomically verified and vouchered resource of mitochondrial reference sequences linked to specimen images and occurrence records of pests and their relatives, enabling eDNA surveys, metabarcoding and molecular species identification. It also reconstructs the phylogeny of Dermestidae based on molecular and morphological data for the first time, thereby providing robust phylogenetic hypotheses for a stable classification system from family to genus-level. Accordingly, a revised classification of Dermestidae with formal nomenclatural changes is proposed, recognising six subfamilies: Orphilinae, Trinodinae, Trogoparvinae subfam. nov. (type genus Trogoparvus Háva, 2001), Dermestinae, Attageninae and Megatominae. Trinodinae is recovered towards the base of Dermestidae with three tribes: Trinodini (=Trinoparvini syn. nov.), Thylodriini and Trichelodini. Dermestinae is the only subfamily with adults lacking a median ocellus, and it includes the tribes Thorictini stat. nov. (that is downgraded from Thorictinae), Marioutini and Dermestini. The endemic Australian genus Derbyana Lawrence and Ślipiński, was recovered within Holarctic Dermestes Linnaeus. Attageninae is strongly supported and includes the monogeneric Adelaidiini and polygenic Attagenini. Former subgenera of Attagenus Latreille, i.e., Lanorus Mulsant and Rey (= Paranovelsis Casey syn. nov.), Telopes Redtenbacher, and Aethriostoma Motschulsky, are elevated to generic level. The largest clade, Megatominae, is confirmed as monophyletic and is divided into three tribes: Anthrenini, Ctesiini and Megatomini. Megatomini is divided into three subtribes: Megatomina, Orphinina subtribe nov. (type genus Orphinus Motschulsky) and Trogodermina. Within the economically important lineage Trogodermina, Trogoderma Latreille, is delimited to contain only Holarctic species including the Khapra beetle T. granarium Everts, while a Southern Hemisphere clade is here recognised as Eurhopalus Solier in Gay, 1849 (= Anthrenocerus Arrow, 1915; Myrmeanthrenus Armstrong, 1945; Neoanthrenus Armstrong, 1941; Sodaliatoma Háva, 2013; Reesa Beal, 1967 syn. nov.). A revised classification of the extant genera of Dermestidae is also provided.

opencc-by-4.0Aug 2017View details →

Multiple origin of the Phaenonotum beetles in the Greater Antilles (Coleoptera: Hydrophilidae): phylogeny, biogeography and systematics

The systematics and the phylogenetic position of the Caribbean representatives of Phaenonotum Sharp (Coleoptera: Hydrophilidae) are investigated in order to understand the composition of the Caribbean fauna and its origin. Phylogenetic analysis based on mitochondrial and nuclear genes has revealed the Caribbean species to be situated in three deeply nested clades, inferring multiple colonization of Caribbean islands from the continent. Time-tree analysis and BioGeoBEARS analyses of ancestral ranges estimated the oldest clade, consisting of wingless single-island endemics of Cuba (P. delgadoi), Jamaica (P. ondreji sp. nov.) and Hispaniola (P. laterale sp. nov.), to have diverged ca. 46.6 Ma from the South American ancestor and subsequently colonizing the Caribbean most likely via the GAARlandia land bridge connecting South America with Greater Antilles. The remaining three Caribbean species, including the Puerto Rican endemic, P. borinquenum sp. nov., are of more recent (Miocene to Pliocene) origin and colonized the Greater Antilles by over-water dispersal. All the Caribbean species are illustrated and diagnosed and three new species are described. The genus Phaenonotum, excluding P. caribense Archangelsky, is confirmed as a monophylum. We demonstrate that species-level taxonomy of Phaenonotum is difficult to solve by morphology alone, and ideally requires the combination of morphology and molecular markers.