Phylogenetic Hypothesis Research Articles

Molecular Phylogeny of Dermestidae (Coleoptera) Reveals the Polyphyletic Nature ofTrogodermaLatreille and the Taxonomic Placement of the Khapra BeetleTrogoderma granariumEverts

AbstractThe 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 recognized as serious economic pests of stored products and museum collections. 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 recognized 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, recognizing six subfamilies: Orphilinae, Trinodinae, Trogoparvinae subfam. nov. (type genus TrogoparvusHáva, 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 recognized as Eurhopalus Solier in Gay, 1849 (= AnthrenocerusArrow, 1915; Myrmeanthrenus Armstrong, 1945; Neoanthrenus Armstrong, 1941; SodaliatomaHáva, 2013; Reesa Beal, 1967 syn. nov.). A revised classification of the extant genera of Dermestidae is also provided.

Synchrotron tomography of a stem lizard elucidates early squamate anatomy.

Squamates (lizards and snakes) include more than 10,000 living species, descended from an ancestor that diverged more than 240 million years ago from that of their closest living relative, Sphenodon. However, a deficiency of fossil evidence1-7, combined with serious conflicts between molecular and morphological accounts of squamate phylogeny8-13 (but see ref. 14), has caused uncertainty about the origins and evolutionary assembly of squamate anatomy. Here we report the near-complete skeleton of a stem squamate, Bellairsia gracilis, from the Middle Jurassic epoch of Scotland, documented using high-resolution synchrotron phase-contrast tomography. Bellairsia shares numerous features of the crown group, including traits related to cranial kinesis (an important functional feature of many extant squamates) and those of the braincase and shoulder girdle. Alongside these derived traits, Bellairsia also retains inferred ancestral features including a pterygoid-vomer contact and the presence of both cervical and dorsal intercentra. Phylogenetic analyses return strong support for Bellairsia as a stem squamate, suggesting that several features that it shares with extant gekkotans are plesiomorphies, consistent with the molecular phylogenetic hypothesis that gekkotans are early-diverging squamates. We also provide confident support of stem squamate affinities for the enigmatic Oculudentavis. Our findings indicate that squamate-like functional features of the suspensorium, braincase and shoulder girdle preceded the origin of their palatal and vertebral traits and indicate the presence of advanced stem squamates as persistent components of terrestrial assemblages up to at least the middle of the Cretaceous period.

Phylogenetic relationships and species delimitation in Haemopis (Annelida: Hirudinea: Haemopidae)

The Holarctic leech genus Haemopis currently includes 11 species, all of which are macrophagous, as opposed to their more infamous bloodfeeding counterparts among hirudiniform leeches. In spite of their ecological importance as fish food and predators of freshwater invertebrates, there is a paucity of data regarding morphology and genetic variation that might guide future identification efforts for members of the genus. The lack of detailed descriptions of distinguishing morphological features, coupled with the absence of a robust phylogenetic hypothesis for the genus, have conspired to prevent meaningful inferences on the natural history of the group. In an attempt to remedy this, we present new genetic (using COI, 12S rDNA, 28S rDNA and 18S rDNA) data for the majority of the known species diversity within the genus in order to both infer a phylogenetic hypothesis and to introduce authoritative DNA barcodes for the newly collected species. The potential of these barcodes is increased through rigorous morphological investigations of the specimens, with comparisons to the original literature. Our resulting phylogenetic hypothesis is agnostic as to the geographic origin of the genus, with equal probability afforded to both a Nearctic and Palearctic origin. Beyond this, we show that there is a strong tendency towards a barcoding gap within the genus, but that a distinct gap is lacking due to the relatively high genetic variation found within H. marmorata. Taken together, our results shed light on species delimitation within, and evolutionary history of, this often-neglected group of leeches.

A New Species of Brachycephalus (Anura, Brachycephalidae) from a Montane Atlantic Rainforest of Southeastern Brazil, with a Reappraisal of the Species Groups in the Genus

Toadlets of the genus Brachycephalus are endemic to the Brazilian Atlantic Rainforest, where they inhabit the forest floor leaf litter. These miniaturized frogs are commonly known as flea-toads or pumpkin toadlets depending on their phenotypic characteristics. Herein, we describe a new species of the genus Brachycephalus from montane forests (970–1200 m a.s.l.) in the Serra dos Órgãos mountain range, in the state of Rio de Janeiro, southeastern Brazil. The new species is characterized by having a small body size within the genus (maximum SVL 9.6 mm in males and 10.9 mm in females), a noticeably granular dorsum with an X-shaped mark and a median row of small yellow tubercles, a yellow background color with red blotches on ventral surfaces, a lateral dark brown stripe, and the absence of hyperossification in the skeleton. Morphological features of the new taxon resemble those of both flea-toads and pumpkin toadlets. Based on our molecular phylogenetic hypothesis, the new species is recovered sister to the clade formed by the monophyletic B. ephippium and B. vertebralis species groups (previously considered as lineages of a more inclusive B. ephippium group). We also reinforce the suggestion of not using the name B. didactylus group because it does not represent a monophyletic taxon. The new species probably has an extremely restricted geographic distribution, and its discovery reinforces the importance of the Serra dos Órgãos mountains for the conservation of the Atlantic Rainforest anuran biodiversity.

Diversification of chiles (Capsicum, Solanaceae) through time and space: New insights from genome-wide RAD-seq data.

Capsicum L. encompasses 43 American species, including the five domesticated worldwide consumed sweet and hot chiles. This study presents new, updated and age-calibrated phylogenetic hypothesis on the genus evolution incorporating nearly all currently accepted Capsicum species. A new model of spatial diversification of Capsicum is proposed based on analyses of several thousands of genome-wide RAD-seq derived SNPs. Maximum likelihood approaches were used to reconstruct phylogenies and to estimate dates of all major splits. Ancestral ranges were inferred and diversification events were modeled in a time frame using a Bayesian approach. Nine clades corresponding to genetically and (mostly) geographically well-defined lineages, which diversified starting around mid-upper Miocene, were recovered with strong support. The Northern and Central Andes were inferred to represent the most likely ancestral range of the genus Capsicum. A few early vicariant and dispersal events were estimated to have driven the geographic divergence of the main Capsicum clades. Each lineage was inferred to have diversified within a distinct region of South America and expanded geographically to different extent. Extant species diversification was inferred to have begun at the beginning of Pliocene and continued through the Pleistocene. The Central Andes, represented mainly by the territory of present-day Bolivia, were proposed to play a central role in the diversification of lineages comprising domesticated capsicums and their wild allies. The genome-wide approach allowed for high resolution and support of deep phylogenetic nodes providing novel insights into the affinities of major lineages and clades as well as on the geographic expansion of Capsicum. This study provides the first dated evolutionary history of the genus encompassing most of the chile species diversity.

Molecular phylogeny of the tropical wandering spiders (Araneae, Ctenidae) and the evolution of eye conformation in the RTA clade.

Tropical wandering spiders (Ctenidae) are a diverse group of cursorial predators with its greatest species richness in the tropics. Traditionally, Ctenidae are diagnosed based on the presence of eight eyes arranged in three rows (a 2-4-2 pattern). We present a molecular phylogeny of Ctenidae, including for the first time representatives of all of its subfamilies. The molecular phylogeny was inferred using five nuclear (histone H3, 28S, 18S, Actin and ITS-2) and four mitochondrial (NADH, COI, 12S and 16S) markers. The final matrix includes 259 terminals, 103 of which belong to Ctenidae and represent 28 of the current 49 described genera. We estimated divergence times by including fossils as calibration points and biogeographic events, and used the phylogenetic hypothesis obtained to reconstruct the evolution of the eye conformation in the retrolateral tibial apophysis (RTA) clade. Ctenidae and its main lineages originated during the Paleocene-Eocene and have diversified in the tropics since then. However, in some analyses Ctenidae was recovered as polyphyletic as the genus Ancylometes Bertkau, 1880 was placed as sister to Oxyopidae. Except for Acantheinae, in which the type genus Acantheis Thorell, 1891 is placed inside Cteninae, the four recognized subfamilies of Ctenidae are monophyletic in most analyses. The ancestral reconstruction of the ocular conformation in the retrolateral tibial apophysis clade suggests that the ocular pattern of Ctenidae has evolved convergently seven times and that it has originated from ocular conformations of two rows of four eyes (4-4) and the ocular pattern of lycosids (4-2-2). We also synonymize the monotypic genus Parabatinga Polotov & Brescovit, 2009 with Centroctenus Mello-Leitão, 1929. We discuss some of the putative morphological synapomorphies of the main ctenid lineages within the phylogenetic framework offered by the molecular phylogenetic results of the study.

Systematics of Thraupis (Aves, Passeriformes) reveals an extensive hybrid zone between T. episcopus (Blue-gray Tanager) and T. sayaca (Sayaca Tanager).

The Neotropical avian genus Thraupis (Passeriformes, Thraupidae) currently comprises seven species that are widespread and abundant throughout their ranges. However, no phylogenetic hypothesis with comprehensive intraspecific sampling is available for the group and, therefore, currently accepted species limits remain untested. We obtained sequence data for two mitochondrial (ND2, cyt-b) and three non-coding nuclear (TGFB2, MUSK, and βF5) markers from 118 vouchered museum specimens. We conducted population structure and coalescent-based species-tree analyses using a molecular clock calibration. We integrated these results with morphometric and coloration analyses of 1,003 museum specimens to assess species limits within Thraupis. Our results confirm that Thraupis is a monophyletic group and support its origin in the late Miocene and subsequent diversification during the Pleistocene. However, we found conflicts with previous phylogenies. We recovered Thraupis glaucocolpa to be sister to all other species in the genus, and T. cyanoptera to the remaining five species. Our phylogenetic trees and population structure analyses uncovered phylogeographic structure within Thraupis episcopus that is congruent with geographic patterns of phenotypic variation and distributions of some named taxa. The first genetic and phenotypic cluster in T. episcopus occurs east of the Andes and is diagnosed by the white patch on the lesser and median wing coverts, whereas the second group has a blue patch on the wing and distributes to the west of Colombia's eastern Andes. Finally, we present evidence of hybridization and ongoing gene flow between several taxa at different taxonomic levels and discuss its taxonomic implications.

Phylogenetic resolution of the fly superfamily Ephydroidea-Molecular systematics of the enigmatic and diverse relatives of Drosophilidae.

The schizophoran superfamily Ephydroidea (Diptera: Cyclorrhapha) includes eight families, ranging from the well-known vinegar flies (Drosophilidae) and shore flies (Ephydridae), to several small, relatively unusual groups, the phylogenetic placement of which has been particularly challenging for systematists. An extraordinary diversity in life histories, feeding habits and morphology are a hallmark of fly biology, and the Ephydroidea are no exception. Extreme specialization can lead to “orphaned” taxa with no clear evidence for their phylogenetic position. To resolve relationships among a diverse sample of Ephydroidea, including the highly modified flies in the families Braulidae and Mormotomyiidae, we conducted phylogenomic sampling. Using exon capture from Anchored Hybrid Enrichment and transcriptomics to obtain 320 orthologous nuclear genes sampled for 32 species of Ephydroidea and 11 outgroups, we evaluate a new phylogenetic hypothesis for representatives of the superfamily. These data strongly support monophyly of Ephydroidea with Ephydridae as an early branching radiation and the placement of Mormotomyiidae as a family-level lineage sister to all remaining families. We confirm placement of Cryptochetidae as sister taxon to a large clade containing both Drosophilidae and Braulidae–the latter a family of honeybee ectoparasites. Our results reaffirm that sampling of both taxa and characters is critical in hyperdiverse clades and that these factors have a major influence on phylogenomic reconstruction of the history of the schizophoran fly radiation.

Slow and steady wins the race: Diversification rate is independent from body size and lifestyle in Malagasy skinks (Squamata: Scincidae: Scincinae)

Most of the unique and diverse vertebrate fauna that inhabits Madagascar derives from in situ diversification from colonisers that reached this continental island through overseas dispersal. The endemic Malagasy Scincinae lizards are amongst the most species-rich squamate groups on the island. They colonised all bioclimatic zones and display many ecomorphological adaptations to a fossorial (burrowing) lifestyle. Here we propose a new phylogenetic hypothesis for their diversification based on the largest taxon sampling so far compiled for this group. We estimated divergence times and investigated several aspects of their diversification (diversification rate, body size and fossorial lifestyle evolution, and biogeography). We found that diversification rate was constant throughout most of the evolutionary history of the group, but decreased over the last 6–4 million years and independently from body size and fossorial lifestyle evolution. Fossoriality has evolved from fully quadrupedal ancestors at least five times independently, which demonstrates that even complex morphological syndromes – in this case involving traits such as limb regression, body elongation, modification of cephalic scalation, depigmentation, and eyes and ear-opening regression – can evolve repeatedly and independently given enough time and eco-evolutionary advantages. Initial diversification of the group likely occurred in forests, and the divergence of sand-swimmer genera around 20 Ma appears linked to a period of aridification. Our results show that the large phenotypic variability of Malagasy Scincinae has not influenced diversification rate and that their rich species diversity results from a constant accumulation of lineages through time. By compiling large geographic and trait-related datasets together with the computation of a new time tree for the group, our study contributes important insights on the diversification of Malagasy vertebrates.

Museomics and the holotype of a critically endangered cricetid rodent provide key evidence of an undescribed genus

Historical DNA obtained from voucher specimens housed in natural history museums worldwide have allowed the study of elusive, rare or even extinct species that in many cases are solely represented by museum holdings. This has resulted in the increase of taxonomic representation of many taxa, has led to the discovery of new species, and has yielded stunning novel insights into the evolutionary history of cryptic or even undescribed species. Peromyscus mekisturus, is a critically endangered cricetid rodent endemic to Mexico and is only known from two museum specimens collected in 1898 and 1947. Intensive field work efforts to attempt to determine if viable populations still exist have failed, suggesting that this species is extinct or is nearing extinction. In addition, a recent study using mitogenomes demonstrated that P. mekisturus forms a well-supported clade outside the genus Peromyscus and hypothesized that this taxon is the sister group of the genus Reithrodontomys. Here, we used target enrichment and high-throughput sequencing of several thousand nuclear ultraconserved elements and mitogenomes to reconstruct dated phylogenies to test the previous phylogenetic hypothesis. We analyzed the holotype and the only other known specimen of P. mekisturus and museum samples from other peromyscine rodents to test the phylogenetic position of the species. Our results confirm that the only two specimens known to science of P. mekisturus belong to the same species and support the hypothesis that this species belongs to an undescribed genus of cricetid rodents that is sister to the genus Reithrodontomys. We dated the origin of P. mekisturus together with other speciation events in peromyscines during the late Pliocene – early Pleistocene and related these events with the Pleistocene climatic cycles. In light of our results, we recommend a taxonomic re-evaluation of this enigmatic species to properly recognize its taxonomic status as a new genus. We also acknowledge the relevance of generating genomic data from type specimens and highlight the need and importance of continuing to build the scientific heritage of the collections to study and better understand past, present, and future biodiversity.

Integrative taxonomy tests possible hybridisation between Central Asian cerambycids (Coleoptera)

AbstractHybridisation can lead to the formation of new evolutionary lineages and some described insect species may in fact be first‐generation hybrids of their parental species. Anoplistes forticornis and A. galusoi are two closely related cerambycid taxa endemic to Central Asia that exhibit a peculiar geographical distribution. Although the common diagnostic elytral pattern makes these beetles superficially easily distinguishable, there are marked resemblances in their morphology. By applying an integrative taxonomy approach, we verify the taxonomic status of A. forticornis and A. galusoi and test the possibility of hybridisation. The results of our comprehensive morphological examination and molecular analyses targeting mitochondrial (COI, 16S rRNA) and nuclear (arginine kinase, CAD, 28S rRNA) genes support the specific status of these taxa. In mtDNA, the putative hybrid specimen is more closely related to A. forticornis, which indicates that a female of this species bred with a male of A. galusoi. The supposed ecotypic variability (manifested in elytral pattern) is apparently not related to the topography or spatial structure of habitat. The phylogenetic hypothesis supports a peripatric scenario in which populations of the common ancestor had been separated for a significant period of time, first by the mountain ranges of Dzungarian Alatau (~11–10 Ma) and ultimately by the Ili River. The diverged taxa came into recent secondary contact following these isolation events. The methodology presented herein can be widely applied to identify first‐generation hybridisation in Coleoptera.

The Hind Wing of Coleoptera (Insecta): Morphology, Nomenclature and Phylogenetic Significance: Part 2. Further Discussion, Histeroidea, Bostrichoidea to Curculionoidea

Part 2 of this work includes a review of morphological and systematic work on Histeridae (G07, revision), Bostrichoidea (G15), Coccinelloidea (G16), Lymexyloidea + Tenebrionoidea (G17), Cleroidea (G18), Cucujoidea (G19), Chrysomeloidea (G20) and Curculionoidea (G21), discussions of hind wing structure in each group based on 702 wing images, references to additional published figures and comments on wing morphology and, if possible, how these wing features may or may not be correlated with recent phylogenetic hypotheses. The introduction is followed by brief discussions of some important works not mentioned in Part 1, particularly those dealing with relationships of extinct taxa.

Molecular systematics of Poaceae based on eight chloroplast markers, emphasizing the phylogenetic positions of Korean taxa

This study was conducted to clarify the phylogenetic position and relationships of Korean Poaceae taxa. A total of 438 taxa including 155 accessions of Korean Poaceae (representing 92% and 72% of Korean Poaceous genera and species, respectively) were employed for phylogeny reconstruction. Sequence data of eight chloroplast DNA markers were used for molecular phylogenetic analyses. The resulted phylogeny was mostly concordant with previous phylogenetic hypotheses, especially in terms of subfamilial and tribal relationships. Several taxa-specific indels were detected in the molecular phylogeny, including a 45 bp deletion in rps3 (PACMAD [Panicoideae, Arundinoideae, Chloridoideae, Micrairoideae, Aristidoideae, Danthonioideae] clade), a 15 bp deletion in ndhF (Oryzeae + Phyllorachideae), a 6 bp deletion in trnLF (Poeae s.l.), and two (17 bp and 378 bp) deletions in atpF-H (Pooideae). The Korean Poaceae members were classified into 23 tribes, representing eight subfamilies. The subfamilial and tribal classifications of the Korean taxa were generally congruent with a recently published system, whereas some subtribes and genera were found to be non-monophyletic. The taxa included in the PACMAD clade (especially Andropogoneae) showed very weak and uncertain phylogenetic relationships, presumably to be due to evolutionary radiation and polyploidization. The reconstructed phylogeny can be utilized to update the taxonomic positions of the newly examined grass accessions.

Craniomandibular osteology of Manidens condorensis (Ornithischia: Heterodontosauridae) from the upper Lower Jurassic of Argentina

ABSTRACT Heterodontosauridae is a clade that appears early in the ornithischian fossil record, and includes small-bodied, highly specialized species characterized by an unusual heterodont dentition. Although known from relatively few taxa, the early representation of the clade and unsolved phylogenetic relationships within heterodontosaurids and among early ornithischians implies that novel information has a marked effect on broader phylogenetic hypotheses and our understanding of early diversification patterns within Ornithischia. This paper describes the cranial osteology of the heterodontosaurid Manidens condorensis based on computed micro-tomographic scans of MPEF-PV 3211 and MPEF-PV 3809. This enabled more detailed descriptions of previously recognized bones, corrections to the literature, and the identification of undescribed elements. We present a new skull reconstruction and propose an emended diagnosis in light of novel anatomical information. Areas of jaw muscle attachment were identified and compared with Heterodontosaurus and Lesothosaurus, and mandibular function among heterodontosaurids is discussed. Our results indicate that diverse skull morphologies and functions existed among Early Jurassic ornithischians, with Manidens being intermediate between the plesiomorphic cranial shape and function associated with a generalist diet in ornithischians such as Tianyulong and Lesothosaurus, and the more derived cranial construction specialized for herbivory identified in heterodontosaurids from South Africa such as Heterodontosaurus.

Evolution and Biogeographic History of Rubyspot Damselflies (Hetaerininae: Calopterygidae: Odonata)

The damselflies Hetaerininae, a subfamily of Calopterygidae, comprise four genera distributed from North to South America: Hetaerina, Mnesarete, Ormenophlebia and Bryoplathanon. While several studies have focused on the intriguing behavioral and morphological modifications within Hetaerina, little of the evolutionary history of the group is well understood. Understanding the biogeographical history of Hetaerininae is further complicated by uncertainty in important geological events, such as the closure of the Central American Seaway (CAS). We generated a phylogenetic hypothesis to test the relationships and divergence times within Hetaerininae using IQtree and BEAST2 and found that Mnesarete and Ormenophlebia render Hetaerina paraphyletic. Reclassification of the genera within Hetaerininae is necessary based on our results. We also tested the fit to our dataset of two different hypotheses for the closure of CAS. Our results supported a gradual closure, starting in the Oligocene and ending in the Pliocene. Using Ancestral Character State Reconstruction, we found that the rubyspot, which is associated with higher fecundity in several species, was ancestral for Hetaerininae and subsequently lost four times. Estimates of diversification in association with the rubyspot are needed to understand the plasticity of this important character. Forest habitat was the ancestral state for Hetaerininae, with transitions to generalist species of Hetaerina found primarily in the Mesoamerican region. These results add to our understanding of the relationship between morphology, biogeography and habitat in a charismatic group of damselflies.

Cranial osteology of a juvenile specimen of Acratocnus ye (Mammalia, Xenarthra, Folivora) and its ontogenetic and phylogenetic implications.

The present study comprises a description of the skull and jaw anatomy of a juvenile specimen of the Antillean sloth Acratocnus ye, from the Holocene of Haiti. Detailed descriptions and illustrations are provided of the skull bones and their sutural connections, which normally fuse in adults. Descriptions are also provided for the mandible and ear ossicles, as well as endocranial surfaces and sinuses exposed by breaks. The anatomy of our juvenile A. ye is compared to that of adult A. ye to assess ontogenetic changes in the skull. Several of these ontogenetic features are significant new observations that impact the relationships within Xenarthra as a whole, or between Xenarthrans and other placental mammals, most notably, the presence of a separate mesethmoid element, the presence of alveoli for a lower deciduous canine and anterior incisor, and the presence of separate rostral and caudal entotympanic elements. A full list of such changes are provided. In addition, the specimen provides information on phylogenetically relevant characters, including features unique to the genus Acratocnus, and features of the clade Choloepodini, including Acratocnus, the smaller extinct Antillean sloth Neocnus, and the extant two-toed sloth Choloepus. Contrary to previous studies, Acratocnus shares as many features with Choloepus as it does with its fellow Antillean form Neocnus in the present study, which is consistent with current morphology-based phylogenetic hypotheses regarding the relationships within Choloepodini. The current study highlights the need for further anatomical and phylogenetic investigations of Antillean sloths (Megalocnidae/Megalonychidae), and juvenile sloths in general.

Target capture data resolve recalcitrant relationships in the coffee family (Rubioideae, Rubiaceae).

Subfamily Rubioideae is the largest of the main lineages in the coffee family (Rubiaceae), with over 8,000 species and 29 tribes. Phylogenetic relationships among tribes and other major clades within this group of plants are still only partly resolved despite considerable efforts. While previous studies have mainly utilized data from the organellar genomes and nuclear ribosomal DNA, we here use a large number of low-copy nuclear genes obtained via a target capture approach to infer phylogenetic relationships within Rubioideae. We included 101 Rubioideae species representing all but two (the monogeneric tribes Foonchewieae and Aitchinsonieae) of the currently recognized tribes, and all but one non-monogeneric tribe were represented by more than one genus. Using data from the 353 genes targeted with the universal Angiosperms353 probe set we investigated the impact of data type, analytical approach, and potential paralogs on phylogenetic reconstruction. We inferred a robust phylogenetic hypothesis of Rubioideae with the vast majority (or all) nodes being highly supported across all analyses and datasets and few incongruences between the inferred topologies. The results were similar to those of previous studies but novel relationships were also identified. We found that supercontigs [coding sequence (CDS) + non-coding sequence] clearly outperformed CDS data in levels of support and gene tree congruence. The full datasets (353 genes) outperformed the datasets with potentially paralogous genes removed (186 genes) in levels of support but increased gene tree incongruence slightly. The pattern of gene tree conflict at short internal branches were often consistent with high levels of incomplete lineage sorting (ILS) due to rapid speciation in the group. While concatenation- and coalescence-based trees mainly agreed, the observed phylogenetic discordance between the two approaches may be best explained by their differences in accounting for ILS. The use of target capture data greatly improved our confidence and understanding of the Rubioideae phylogeny, highlighted by the increased support for previously uncertain relationships and the increased possibility to explore sources of underlying phylogenetic discordance.

Origin and diversification of free-living stick spiders of Sri Lanka including the description of four new species of Rhomphaea L. Koch, 1872 and two new species of Neospintharus Exline, 1950.

Sri Lanka is a biologically diverse South Asian island, and together with the Western Ghats (Southern India) is one of the 36 world’s most biologically diverse areas. Here, we investigated the origin and diversification of Rhomphaea and Neospintharus of Sri Lanka using sequences of three genes: mitochondrial cytochrome c oxidase I (COI) and 16S rRNA (16S); and nuclear 28S rRNA (28S). Our phylogeny included 32 taxa (30 ingroup and 2 outgroup). We used Bayesian Inference and maximum likelihood methods to reconstruct the placement of species, divergence time estimations and their foraging behavior with an emphasis on species from Sri Lanka. Our phylogenetic hypothesis support the monophyly of Argyrodinae as well as the monophyly of Rhomphaea, where Rhomphaea is a sister group of Neospintharus. Further, our analysis also suggests that Sri Lanka was colonized by Argyrodinae several times. Additionally, the following new species are described: Rhomphaea shanthi sp. nov., Rhomphaea jacko sp. nov., Rhomphaea martini sp. nov., Rhomphaea marani sp. nov., Neospintharus kandelensis sp. nov. and Neospintharus ohiyiaensis sp. nov.

Revisiting trends in morphology of antennal sensilla in scarabaeoid beetles

Phytophagous scarab beetles associated with angiosperms have characteristically enlarged lamellate antennae and exhibit a striking morphological variation of sensilla. In this study, we compared the morphology of antennal surface of 62 species Scarabaeoidea using SEM microscopy, particularly also in light of their evolution in association with angiosperms. We investigated the correlation of antennal sensilla morphology, i.e., their structure and distribution, with species diversity and lineage diversification rates. A high diversity of sensilla was observed but also multiple transitional forms, even on the same antennomere. We interpreted this as evidence for a high evolutionary plasticity. We recognized clear patterns of convergence and repeated evolution of certain types of placoid sensilla. One main tendency found in the phytophagous Pleurostict chafers was a shift from sensilla trichodea to placoid-like sensilla, apparently also enhanced by the increase of the lamellate antennal surface, either by size or number of the lamellae. This trend occurred not only in the Pleurosticts, but also in Glaphyridae, a second angiosperm-associated lineage of Scarabaeoidea. However, our results suggest no direct relation between species diversity or the rate of diversification and general sensilla morphology, i.e., the origin of placoid sensilla. This could be explained not only by species-poor lineages also possessing placoid sensilla but also by otherwise successful and species rich groups having sensilla trichodea (e.g., dung beetles). Results further reveal the need to refine current phylogenetic hypotheses by more comprehensive taxon sampling and to expand the molecular characterization of pheromones and odor binding proteins to better understand the role of chemical communication in scarab diversification.

Relative performance of Bayesian morphological clock and parsimony methods for phylogenetic reconstructions: Insights from the case of Myomiminae and Dryomyinae glirid rodents.

Extinct organisms provide crucial information about the origin and time of origination of extant groups. The importance of morphological phylogenetics for rigorously dating the tree of life is now widely recognized and has been revitalized by methodological developments such as the application of tip-dating Bayesian approaches. Traditionally, molecular clocks have been node calibrated. However, node calibrations are often unsatisfactory because they do not allow the fossil age to inform about phylogenetic hypothesis. The introduction of tip calibrations allow fossil species to be included alongside their living relatives, and the absence of molecular sequence data for these taxa to be remedied by supplementing the sequence alignments for living taxa with phenotype character matrices for both living and fossil taxa. Therefore, only phylogenetic analyses that take into account morphological characters can incorporate both fossil and extant species. Herein we present an unprecedented morphological dataset for a vast group of glirid rodents, to which different phylogenetic methodologies have been applied. We have compared the tree topologies resulting from traditional parsimony and Bayesian phylogenetic approaches and calculate stratigraphic congruence indices for each. Bayesian tip-dated clock methods seem to outperform parsimony with our dataset. The strict consensus tree recovered by tip dating invalidates the classic classification and allows dates to be proposed for the divergence and origin of the different clades.