Received: 03 August 2018 / Accepted: 02 January 2019 / Published online: 06 February 2019
Exploring the evolution and terrestrialization of scorpions (Arachnida: Scorpiones) with rocks and clocksDownload PDFAbstract
Scorpions (Arachnida: Scorpiones Koch, 1837) are an ancient chelicerate arthropod lineage characterised by distinctive subdivision of the opisthosoma and venomous toxicity. The crown group is represented by over 2400 extant species, and unambiguous fossil representatives are known at least from the Cretaceous Period. However, a number of extinct scorpion lineages existed in the Palaeozoic Era, many of which are of a contentious marine (or at least semi-aquatic) lifestyle, and have long caused confusion regarding the nature of arachnid terrestrialization and arachnid phylogeny more broadly. To clarify the process of terrestrialization, there is a need to marry fossil and extant scorpions in a common evolutionary framework utilising modern advances in phylogenetics. Here, we review phylogenetic hypotheses of arachnid and scorpion interrelationships, relevant advances in phylogenetic divergence time estimation and the scorpion fossil record—especially with reference to terrestrialization. In addition, we provide a list of scorpion fossil calibrations for use in molecular dating and demonstrate their utility in deriving a novel scorpion time tree using Bayesian relaxed-clock methods. Our results reveal a window of divergence from 335 to 266 Mya for the scorpion crown group, consistent with a Pangean origin of crown scorpions inferred from the biogeographical distribution of the extant fauna.
Received: 18 May 2018 / Accepted: 27 February 2019 / Published online: 11 March 2019
Inferring host-cleptoparasite complexes of South American Centridine bees (Hymenoptera: Apidae) using macroecological perspectivesDownload PDFAbstract
Bees are normally regarded as social insects that build hives and visit flowers to collect pollen to feed their offspring. However, throughout their evolutionary history, several lineages have lost these characteristics, and have instead, become cleptoparasites, depending on other bee species to raise their offspring. Since cleptoparasites depend on hosts to persist in a location, we could expect that the geographic distribution of the later also influences the distribution the former, mainly in specialized forms of parasitism. Moreover, we could also expect that cleptoparasites ecological niches would evolve to overlap with its respective host(s). Here, we applied multivariate bioclimatic niche analyses and species distribution models to evaluate the effects of host-cleptoparasite relationships on the distribution and ecological niche of Centris and Epiclopus from Chile. Based on our results, considering the species’ distribution range and multivariate niche overlaps, we were able to (1) evaluate the specificity of cleptoparasitism among host-parasite complexes and (2) infer the existence of still uncaptured relationships between the available host and cleptoparasite species. With our results in hand, it is possible to start discussing and decreasing the so-called Eltonian shortfall (lack of proper knowledge on the interactions each species maintains with others). Although not conclusive, these results support the need for continuous sampling of bees and insect species in general, in order to allow the unveiling and better description of their biological relationships.
Received: 24 October 2018 / Accepted: 06 March 2019 / Published online: 22 March 2019
Adrift across tectonic plates: molecular phylogenetics supports the ancient Laurasian origin of old limnic crangonyctid amphipodsDownload PDFAbstract
Crangonyctidae is a speciose and almost exclusively freshwater Holarctic family of amphipod crustaceans. Its members inhabit groundwater as well as epigean biotopes with groundwater connections, and often exhibit endemic, relict distributions. Therefore, it has been proposed that this poorly dispersing, yet intercontinentally distributed family must have ancient Mesozoic origins. Here, we test the hypothesis that Crangonyctidae originated before the final break-up of Laurasia at the end of the Cretaceous. We used molecular phylogenetic analyses based on mitochondrial and nuclear markers and incorporated six out of the seven recognized genera. We calculated divergence times using a novel calibration scheme based exclusively on fossils and, for comparison, also applied substitution rates previously inferred for other arthropods. Our results indicate that crangonyctids originated during the Early Cretaceous in a northerly temperate area comprising nowadays North America and Europe, supporting the Laurasian origin hypothesis. Moreover, high latitude lineages were found to be generally older than the ones at lower latitudes, further supporting the boreal origin of the group and its relict biogeography. The estimated substitution rate of 1.773% Ma for the COI marker agrees well with other arthropod rates, making it appropriate for dating divergences at various phylogenetic levels within the Amphipoda. Furthermore, our extensive phylogeny reinforces the polyphyly of the intercontinental genera Crangonyx, Stygobromus, and Synurella, supports the monophyly of Bactrurus, and elucidates the position of Lyurella. We conclude that crangonyctids are an ideal model for testing continental-level vicariance hypotheses and should be in the focus of future phylogenomic studies.
Received: 30 October 2018 / Accepted: 01 June 2019 / Published online: 22 June 2019
Comparative analysis of peripheral blood reveals transcriptomic adaptations to extreme environments on the Qinghai-Tibetan Plateau in the gray wolf (Canis lupus chanco)Download PDFAbstract
Molecular adaptations to life on the Qinghai-Tibetan Plateau (QTP) have been detected in the genomes of many native animals, but the contribution of variations in gene expression to high-altitude adaptation remains to be determined. Here, we sequenced the peripheral blood transcriptomes of the lowland wolf and the Tibetan wolf (Canis lupus chanco), an endemic top predator on the QTP, and analyzed how the gene expression pattern has become modified to cope with the extreme plateau environments. Comparisons of the transcriptomes of Tibetan wolves and their lowland counterparts revealed 90 differentially expressed genes (DEGs), including 6 genes (ATP6, ATP8, COX3, CYTB, ND2, and ND4) located in the mitochondrial respiratory chain. Several DEGs are functionally involved in DNA repair (RAD52 and NUPR1), reactive oxygen species (ROS) regulation (GSTP1 and RETSAT), and cardiovascular homeostasis (ACTA2, CD151, DDX6, HPSE, and YOD1). Further functional enrichment analyses demonstrated that the identified DEGs were significantly enriched in specific functional categories related to energy metabolism, hypoxic response, and cardiovascular homeostasis, indicating that the gene expression variation in Tibetan wolves may contribute to their adaptation to life on the QTP. The phylogenetic topology of worldwide populations based on 12 mitochondrial protein-coding genes (MPGs) is inconsistent with the patterns revealed by a previous genome-wide study, implying that adaptive evolution may have occurred in the MPGs of Tibetan wolves. Wolf ATP8 was shown to have a higher dN/dS (ω) ratio (ω = 0.712) than the other 11 genes (ω ≤ 0.272). Overall, our study provides new insights into the mechanisms underlying high-altitude adaptations in a wild carnivore with not only mitochondrial gene adaptation but also fine-tuned gene expression responses.
Published online: 30 April 2019
Correction to: Adrift across tectonic plates: molecular phylogenetics supports the ancient Laurasian origin of old limnic crangonyctid amphipodsDownload PDFAbstract
The above article was originally published with an error. Figures 1 and 2 were shown in the wrong order. The original article has been corrected.
Received: 07 November 2018 / Accepted: 27 February 2019 / Published online: 16 March 2019
Multigene fossil-calibrated analysis of the African lampeyes (Cyprinodontoidei: Procatopodidae) reveals an early Oligocene origin and Neogene diversification driven by palaeogeographic and palaeoclimatic eventsDownload PDFAbstract
Here, we present the first molecular and fossil-dated analysis focusing in the Procatopodidae, a widely distributed and little known African oviparous killifish family. The analysis included 36 species representing all Procatopodidae genera except the monotypic Aapticheilichthys. Procatopodidae relationships were established through maximum likelihood and bayesian inference approaches based on fragments of one mitochondrial and five nuclear genes, a total of 5691 bp. The Procatopodidae is herein considered a monophyletic group, sister to the Old world Valenciidae and Aphaniidae. The genus Plataplochilus represent the most basal procatopodid lineage and the brackish water species Aplocheilichthys spilauchen is placed within the Procatopodidae. A clade including the morphologically distinct species of Congopanchax, Lacustricola, and Lamprichthys is herein suggested for the first time, and the genera Micropanchax, Poropanchax, Lacustricola, and Hypsopanchax revealed to be paraphyletic. A fossil-calibrated analysis, based on the same dataset, provided the first information about the evolution of the Procatopodidae in Africa. Our estimates indicate an early Oligocene origin for the Procatopodidae, as a consequence of the Eocene trans-Saharan epicontinental sea retreat, and also indicated that major Neogene paleogeographical and paleoenvironmental events influenced procatopodids diversification (e.g., increase activity in the African rift; late Miocene aridification; Pliocene and Pleistocene climatic instability).
Received: 04 May 2018 / Accepted: 27 February 2019 / Published online: 23 March 2019
COI-based species delimitation in Indochinese Tetraserica chafers reveal hybridisation despite strong divergence in male copulation organsDownload PDFAbstract
Species of Tetraserica chafers (Coleoptera: Scarabaeidae: Sericini) can easily be distinguished by the distinct shape of strongly divergent male genitalia; however, it was so far unclear if such divergent copulation organs may avoid hybridisation. Here, we analysed an 826 bp fragment of the mitochondrial cytochrome c oxidase subunit 1 (COI) for a total of 113 Tetraserica individuals out of 38 morphospecies from 33 localities in Southeast Asia. DNA-based species delimitation was performed using statistical parsimony network analysis (TCS), Poisson tree processes (PTP) model, Automatic Barcode Gap Discovery (ABGD) and the generalised mixed Yule-coalescent (GMYC) model. The different approaches for DNA-based species delimitation revealed different numbers of molecular operational taxonomic units (MOTUs) and showed low congruence with a priori assigned morphospecies. GMYC and PTP generally tended to lump morphospecies while ABGD and TCS more often split morphospecies. TCS revealed the highest congruence between MOTUs and morphospecies. While incongruence of species hypotheses was discussed in the context of incomplete lineage sorting and introgression, we could identify two unexpected cases in which introgression occurred between species with highly dissimilar morphology of the male genitalia and that resulted in lumping with DNA-based species delimitation. Most other cases of not matching morphospecies and MOTUs represent young speciation in which standard markers (CO1) do not yet fit the morphological signal of divergence, as reflected by male copulation organs.
Received: 16 July 2018 / Accepted: 05 December 2018 / Published online: 03 January 2019
Setting the records straight: the ventral receptacle and the spermathecae of Piophila casei (Diptera: Piophilidae)Download PDFAbstract
Piophila casei has been reported repeatedly, but incorrectly, to have only a single spermatheca—an extremely rare condition in the higher flies. This error is based on the misinterpretation of the large sclerotized ventral receptacle as a single spermatheca combined with the failure to detect the two present but unsclerotized spermathecae. This misconception is of importance not only in the context of studies regarding recurrent trends in the evolution of the ventral receptacle. It also led to a set of erroneous character codings in a phylogenetic analysis of the family. To set the records straight, previous more accurate literature is revisited and the ventral receptacle of Piophila casei is described and illustrated in detail together with other aspects of the female reproductive tract such as the spermathecae, accessory glands, vagina, and anterior ventral vagina pouch.
Received: 01 November 2018 / Accepted: 27 February 2019 / Published online: 13 March 2019
Composition of the canid auditory bulla and a new look at the evolution of carnivoran entotympanicsDownload PDFAbstract
The higher carnivoran taxa significantly differ in the morphology of the auditory bulla, but little is known about its non-ectotympanic elements and their contribution to phylogenetically informative bullar characters. The ventral entotympanic sinus, a principal hypotympanic compartment unique to Canidae, expands in post-ossification ontogeny from a distinct portion, rather than the whole, of what is considered the ‘caudal entotympanic’. To trace the earlier development of this sinus and to clarify the potential roles of individual entotympanics in formation of the canid auditory bulla, osteological observations were made on younger skulls of Canis lupus and four additional species. The ventral entotympanic sinus was found to invariably originate at a separate bone provisionally designated the ventral entotympanic. The rest of the caudal entotympanic is a fusion of the posterior (or the proper) caudal entotympanic ossifying near the tympanohyal, and the anterior caudal entotympanic ossifying between the ectotympanic and rostral entotympanic. Examination of the rostral entotympanic also revealed previously unknown details. In sum, the canid auditory bulla includes at least four rather than earlier recognised two (or suspected three) entotympanics. Based on these findings, the composition of the canid intrabullar septum and the homologies of the carnivoran entotympanics are discussed. Within the established phylogenetic framework, the rostral entotympanic and posterior caudal entotympanic appear as plesiomorphic for crown-group Carnivora, while the anterior caudal entotympanic is synapomorphic for Caniformia, and the ventral entotympanic is autapomorphic for Cynoidea. This hypothesis implies that the carnivoran entotympanic patterns may have emerged before complete fusions of bullar bones observed in the fossil record.
Received: 17 May 2018 / Accepted: 19 November 2018 / Published online: 28 November 2018
Rinistachya hilleri gen. et sp. nov. (Sphenophyllales), from the upper Devonian of South AfricaDownload PDFAbstract
A rich and diverse plant assemblage has been excavated from latest Devonian (Famennian) black shales of the Witpoort Formation (Witteberg Group) at Waterloo Farm, close to the city of Grahamstown (South Africa). Several specimens of a new sphenopsid have been collected. The description of this as a new taxon, here named Rinistachya hilleri, gen. et sp. nov., provides an important addition to the scarce early record of the group. Rinistachya hilleri presents a novel architecture that include apparently plesiomorphic characters, reminiscent of the organisation of the Iridopteridales (including the production of two types of laterals at one node, the location of fertile parts in loose whorls on lateral branches and an organisation of the fertile parts in which they branch several times before bearing distally elongate sporangia). Other characters unambiguously nest Rinistachya within the Sphenopsida (including presence of planate and slightly webbed ultimate appendages and lateral strobili made of successive whorls of fertile leaves with fertile parts located at their axil). This provides strong support for a close relationship between Sphenopsida and Iridopteridales. Rinistachya furthermore represents the first record of a Devonian sphenopsid from Gondwana and extends the known distribution of the Sphenopsida from the tropics to very high palaeolatitudes. It is a new sphenopsid with a peculiar organisation. The new taxon allows better characterization of the initial evolutionary radiation at the base of the group.
Received: 19 January 2019 / Accepted: 20 June 2019 / Published online: 29 June 2019
The first known fossils of the Platydesmida—an extant American genus in Cretaceous amber from Myanmar (Diplopoda: Platydesmida: Andrognathidae)Download PDFAbstract
Millipedes have been inhabiting the earth for more than 400 my and show a great diversity regarding their morphology and ecology. For a better understanding of the timing and pattern of millipede evolution, Burmese amber offers a unique window into the Cretaceous period, ca. 99 Ma. Here, we describe the first known fossil of the colobognathan order Platydesmida, the species Andrognathus burmiticus n. sp. based on 15 specimens from Cretaceous Burmese amber. We combine classical light-microscopy and modern micro-computer tomography (μCT) with computer aided 3D-reconstructions. These non-invasive techniques allow us to describe the fossil millipedes as detailed as is general practice for extant species, and to grant the scientific community open access to the deposited “Cybertypes”. Based on the combination of unique morphological characters such as surface structures, body type, the unique size and shape of tergite 5, the absence of a hypoproct at the anal segment, and detailed gonopod characteristics, the studied fossils can be placed in the family Andrognathidae and the extant genus Andrognathus, which nowadays is restricted to the eastern USA and Mexico with three extant species. Therefore, the minimum age of the genus Andrognathus is pushed to the Cenomanian, 99 Ma. It can be assumed that the genus was much more diverse and wider distributed in the past and migrated between Asia and America via one of the once existing land bridges. These unique fossils prove the unusual relictual distribution of Andrognathus and can serve as key-fossils for the dating of the diplopod phylogeny.
Received: 06 April 2019 / Accepted: 11 August 2019 / Published online: 04 September 2019
Intraspecific variation in digit reduction in Testudo: the case of the Hermann’s tortoiseDownload PDFAbstract
Phalangeal reduction is a common and widespread phenomenon among tortoises that has been associated with the adaptation to terrestrial life. While reduced manual digit 1 appears characteristic in almost all Testudo species, it is uncertain why the metacarpal I and distal carpal of the same digit are completely missing in some individuals of Hermann’s tortoise (Testudo hermanni hermanni). To clarify this issue, we investigated the number of manual claws in six populations of Hermann’s tortoise (one from the Ebro Delta in the Iberian Peninsula and five from Minorca Island), their age, sex, genetic lineage, and the substrate type that they inhabit. The number of claws was ascertained based on direct counts (n > 1500 individuals) and by X-rays (n = 32 individuals), obtaining three different phalangeal formulae: (1-2-2-2-1, D-2-2-2-1, 0-2-2-2-1). Thus, claw counts through both methodologies (direct count and X-ray) further confirm that the observed claws serve as a good proxy to assess the actual number of digits. Our results show no loss of phalanges, metacarpal and carpal bones in digit 1 associated with age, sex, or substrate, contrary to some previous authors who hypothesized a relationship between this loss and sexual dimorphism. Therefore, variations in the number of manual digits and the loss of metacarpal I and distal carpal in digit 1 in Hermann’s tortoise are related to population and genetic lineage. More detailed comparisons with other Testudo hermanni populations from elsewhere in Europe would be required to understand the evolutionary significance concerning the intrapopulation variability in the number of digits remaining.
Received: 19 November 2018 / Accepted: 27 February 2019 / Published online: 07 March 2019
The phylogenomic revolution and its conceptual innovations: a text mining approachDownload PDFAbstract
Natural language processing provides a quantitative framework with which to explore human cultural dynamics. Although this approach is less commonly used in the natural sciences, the text employed in scientific publications preserves a historical record of the development of disciplines as they evolve and mature. A high-throughput text mining study was performed here to investigate patterns of word use in publications dealing with phylogenomics. Over 2000 research articles in the field were surveyed, revealing the words whose frequency of use has shown the strongest positive correlation with time. Notably, concepts such as gene tree discordance and the susceptibility and discriminatory power of phylogenomic datasets were found to be among the strongest trending topics in the field. As systematics transitioned into a big data science, such obstacles to phylogenetic reconstruction were not left behind. On the contrary, phylogenomics opened a new door to explore these phenomena and their biological significance, becoming the focus of new theoretical and practical developments.
Received: 23 April 2018 / Accepted: 07 November 2018 / Published online: 03 December 2018
The origin and diversification of the Entorrhizales: deep evolutionary roots but recent speciation with a phylogenetic and phenotypic split between associates of the Cyperaceae and JuncaceaeDownload PDFAbstract
Fungi belonging to the Entorrhizales (Entorrhizomycota) comprise biotrophic pathogens associated with roots of the Cyperaceae and Juncaceae plant species. They are nearly globally distributed but rarely studied due to a hidden lifestyle without causing visible effects on host plants. Therefore, the evolutionary origin and phylogenetic relationships of the group are still poorly understood and it is not known whether species diversification was the result of co-evolution with their hosts or the result of host jumps. To infer hypotheses about the evolutionary history of the Entorrhizales, divergence times were estimated and plant-fungal tanglegrams calculated. Relaxed molecular clock analyses suggest that the Entorrhizomycota originated around the Neoproterozoic-Palaeozoic and diverged during the Late Cretaceous-Paleogene into the extant orders Entorrhizales and Talbotiomycetales. The split of the major lineages within the Entorrhizales took place in the Eocene, somewhat later than the divergence of the host families Cyperaceae and Juncaceae. Topology- and distance-based co-phylogenetic analyses of the fungi and their hosts revealed a large number of co-speciation and lineage sorting events in early fungal speciation, which resulted in a phylogenetic split corresponding to species infecting Cyperaceae or Juncaceae. Given that this split is congruent with spore differences, Entorrhiza s. str. is emended for species infecting hosts in the Cyperaceae, and a new genus Juncorrhiza is described for species restricted to hosts in the Juncaceae. Additionally, three new species are described: Entorrhiza fuirenae, Juncorrhiza maritima and J. oxycarpi.
Received: 16 July 2018 / Accepted: 20 December 2018 / Published online: 22 March 2019
Taxonomic revision of the dwarf spider genus Shaanxinus Tanasevitch, 2006 (Araneae, Linyphiidae, Erigoninae), with new species from Taiwan and VietnamDownload PDFAbstract
Dwarf spiders are of special interest due to their sexually dimorphic prosomal structures in males. Glandular secretions within these structures serve as nuptial gifts, and thus sexual selection may have contributed to their high species richness. However, species diversity of dwarf spiders in East Asia is yet understudied. Here, we review the erigonine genus Shaanxinus Tanasevitch, 2006, and describe 13 new species from Taiwan: S. magniclypeus sp. n. (♂♀), S. shihchoensis sp. n. (♂♀), S. shoukaensis sp. n. (♂♀), S. hirticephalus sp. n. (♂♀), S. mingchihensis sp. n. (♂♀), S. makauyensis sp. n. (♂♀), S. lixiangae sp. n. (♂♀), S. curviductus sp. n. (♂♀), S. tsou sp. n. (♂♀), S. hehuanensis sp. n. (♂♀), S. seediq sp. n. (♂♀), S. meifengensis sp. n. (♂♀), and S. atayal sp. n. (♂♀). In addition, one new species from Vietnam, S. tamdaoensis sp. n. (♂), is described from museum material. We reconstructed the dimension of glandular tissues associated with male prosoma modifications in Shaanxinus, as well as the detailed palpal structure by micro-computer tomography. Placement within Shaanxinus and intrageneric relationships were inferred by means of a cladistic analysis based on morphological characters. Sequences of COI, 16S, and 28S genetic markers corroborated the monophyly of some species, as well as male-female matching. Poly-/paraphyly of morphologically delimitated species in the mitochondrial DNA (mtDNA) trees led to the discovery of two seemingly identical species, for which diagnostic morphological features could then be further identified. We discuss incomplete lineage sorting and introgression as possible causes of mtDNA poly-/paraphyly in morphologically indistinguishable specimens.
Received: 03 August 2018 / Accepted: 03 December 2018 / Published online: 04 January 2019
Pseudovermis paradoxus 2.0—3D microanatomy and ultrastructure of a vermiform, meiofaunal nudibranch (Gastropoda, Heterobranchia)Download PDFAbstract
Pseudovermidae is the only clade of nudibranchs entirely comprised of mesopsammic species probably resulting from paedomorphosis. These minute slugs show a worldwide distribution with most lineages described from European waters. The present study redescribes the type species of Pseudovermidae, Pseudovermis paradoxus Pereyaslavtzeva, 1891, from the Black Sea with modern methodology. We provide computer-based 3D reconstructions of all organ systems and ultrastructural data on the digestive and renopericardial systems. Several aspects of the external morphology and the highly concentrated central nervous system in P. paradoxus are paedomorphic. The presence of a vestigial pericardium without a heart is interpreted as co-adaptation to the minute, vermiform body with a relatively large surface. The (partially) triaulic hermaphroditic genital system shows a small penis, suggesting true copulation as mode of sperm transfer. We provide a molecular barcode and a neotype in line with our detailed 3D microanatomy and ultrastructural data to establish a baseline for revision of Pseudovermidae. The current taxonomy of Pseudovermidae in European waters is likely artificially inflated, impeding a better understanding of distribution and diversification within the clade. Our study highlights the need for a taxonomic revision of European pseudovermid species based on molecular data, as traditional taxonomic characters mostly present a higher intraspecific rather than interspecific variation or might present artifacts (i.e., “denticulated” jaws).
Received: 18 March 2019 / Accepted: 25 July 2019 / Published online: 06 August 2019
Phylogenetic relationships within the flatworm genus Matuxia (Platyhelminthes, Tricladida, Continenticola) inferred from molecular data with the description of a southern lineage of the genusDownload PDFAbstract
The genus Matuxia Carbayo et al., 2013 currently comprises two species with distribution restricted to southeastern Brazil. In the present study, based on an integrative approach, we examine the genetic diversity within the genus and describe a new species, Matuxia tymbyra Rossi and Leal-Zanchet, sp. nov., representing a southern lineage of the genus. We employed one mitochondrial (cytochrome c oxidase subunit I, COI) and other nuclear (elongation factor 1a, EF-1a) markers to investigate the phylogenetic relationships within the genus. Maximum-parsimony analysis in a segment of the COI gene of 676 nucleotides showed 79 (11.68%) nucleotide positions exhibiting autapomorphic characters that support the occurrence of three independent evolutionary molecular operational taxonomic units in the genus. Similar evaluation for the dataset of the EF-1a gene showed a much smaller number of autapomorphies. Bayesian inference, maximum-likelihood and delimitation approaches, based on evolutionary models, showed that M. tymbyra is the sister species of the type-species of the genus, Matuxia tuxaua. They should be considered sibling species, only distinguishable based on details regarding eye arrangement and prostatic vesicle. The existence of 15 and 23 molecular autapomorphies, as revealed by maximum-parsimony analysis in a segment of the COI gene for M. tymbyra and M. tuxaua, respectively, allowed us to propose a molecular diagnosis for the new species, which is essential in cases of sibling species. The new species seems to be endemic from areas of Araucaria Forest in southern Brazil; the record augments the known distribution of the genus to the south.
Received: 14 November 2018 / Accepted: 01 June 2019 / Published online: 26 July 2019
Molecular and morphological recognition of species boundaries in the neglected ant genus Brachymyrmex (Hymenoptera: Formicidae): toward a taxonomic revisionDownload PDFAbstract
Brachymyrmex is a neglected genus of Formicinae because of its small body size, soft mesosoma, and superficially monotonous external morphology. These features have complicated the documentation of morphological variation, resulting in poorly defined and incompletely described species. Consequently, the taxonomy of the genus is complex and problematic, which has impeded research and conservation efforts. Here, we integrate molecular and morphological data to recognize species boundaries in Brachymyrmex and to guide its long-overdue revision. Specifically, we (1) redefine the limits of all described species, subspecies, and varieties based on intra- and interspecific morphological variation in workers; (2) document this variation quantitatively by constructing morphospace occupation and statistically analyzing measurements; (3) synthesize our findings on diagnostic traits in a dichotomous, illustrated identification key; and (4) examine the significance of our morphological identification system with molecular evidence from four gene fragments (EF1aEF1, EF1aEF2, WG, and COI). We recognize 40 species, of which four are new to science: Brachymyrmex bahamensis, Brachymyrmex bicolor, Brachymyrmex iridescens, and Brachymyrmex sosai. Furthermore, Brachymyrmex attenuatus and Brachymyrmex bonariensis are raised to species, and we propose 25 new synonyms. Morphometrics indicated that even poorly distinguishable species pairs show statistically significant differences in some traits, and that taxonomically problematic cases relate to taxa that demonstrate large intraspecific trait variance. Our molecular analysis supports the monophyly of the genus based on increased taxon sampling, and of the 19 species that were included 18 were retrieved as monophyletic. The single case of incongruence was also flagged in morphological analyses and requires extended geographic sampling before it can be resolved. In conclusion, the molecular work corroborates the morphologically recognized species boundaries. We also document the presence of worker dimorphism and putative worker-queen intercastes in several Brachymyrmex species, which indicates that the genus may present a promising study system to understand caste evolution in ants.
Received: 06 August 2018 / Accepted: 12 February 2019 / Published online: 05 March 2019
The hills are alive with geckos! A radiation of a dozen species on sky islands across peninsular India (Squamata: Gekkonidae, Hemiphyllodactylus) with the description of three new speciesDownload PDFAbstract
Sky Islands are high-elevation environments that are separated by warmer, low elevations, forming natural patches of unique montane habitat that often persist through changing climates. Peninsular India was ancestrally forested and has gradually become more arid since at least the Oligocene, and open landscapes have dominated since the middle-late Miocene. Mesic forests today are largely restricted to coastal mountains and some other montane habitats. A mitochondrial phylogeny and fossil-calibrated timetree of Indian Hemiphyllodactylus reveal an Indochinese origin and an endemic radiation with 12 species-level lineages, where a single species was known, that diversified in the Oligocene-Miocene across montane forest habitats in the Eastern Ghats and south India. The phylogeny also suggests the discontinuous Eastern Ghats mountain range encompasses two distinct biogeographic entities: north and south of the Pennar/Krishna-Godavari River basins. This study highlights the deep history of the region and the importance of montane habitats as islands of unique biodiversity that have persisted through millions of years of changing climates. We describe three new species: Hemiphyllodactylus arakuensis sp. nov., H. jnana sp. nov. and H. kolliensis sp. nov. from montane habitats above 1000 m. The montane habitats of these species are emerging hotspots of reptile endemism, and this study emphasizes the need for systematic biodiversity inventory across India to uncover basic patterns of diversity and distribution.
Received: 28 November 2018 / Accepted: 11 August 2019 / Published online: 17 August 2019
Phylogenetic and functional diversity of African muroid rodents at different spatial scalesDownload PDFAbstract
Considering the interplay between regional diversification and local community processes is a relatively nascent field of study. Here, I examined the phylogenetic and functional structure of African muroid assemblages at both regional (eight bioregions) and local (72 communities) levels to assess the relative roles of historical processes, environmental filtering and ecological interactions in community assembly. In addition, I used patterns of phylogenetic and functional β diversity to separate the factors that structure muroid assemblages. At the regional scale, none of the regions showed evidence of phylogenetic evenness, while two of them (Congolian, Southern African) exhibited phylogenetic structure, probably due to the fact that the opportunity for in situ speciation has been greater in these biogeographic regions, mostly in the Congolian rainforests. Functional clustering was detected in the two northernmost regions, where conditions are more extreme, suggesting the existence of environmental filtering. At a finer (local) scale, ~ 6% of the examined muroid communities had net relatedness index (NRI) values significantly greater than expected by chance (NRI > 2), whereas no localities harboured muroid communities with NRI values significantly lower than expected by chance (NRI < − 2). Thus, there was no evidence in support of a more prominent role of competition as the scale decreases. Regional patterns of β diversity and phylogenetic β diversity suggest that phylogenetic structure in African muroid assemblages may be explained by the history of speciation and dispersal of this taxonomic group. Finally, the lack of concordance between phylogenetic and functional structure highlights the importance of considering the multiple facets of biodiversity to study community assembly processes from an integrative point of view.
Received: 09 August 2018 / Accepted: 30 January 2019 / Published online: 08 February 2019
In defence of taxonomic governanceDownload PDFAbstract
It is well known that taxonomists rely on many different methods and criteria for species delimitation, leading to different kinds of groups being recognised as species. While this state of relative disorder is widely acknowledged, there is no similar agreement about how it should be resolved. This paper considers the view that the disorder in species classification should be resolved by a system of taxonomic governance. I argue that such a system of governance is best seen as a combination of standardisation, unification and regulation, each of which can be implemented in different forms. I investigate the forms that these three components should take for taxonomic governance by looking into two successfully governed classification systems, namely, virus classification and enzyme classification. The last part of the paper then defends the governance view against five objections.
Received: 22 April 2019 / Accepted: 11 August 2019 / Published online: 22 August 2019
Description of Calliactis tigris sp. nov.: reconciling taxonomy and phylogeny in hermit-crab symbiotic anemones (Cnidaria: Actiniaria: Hormathiidae)Download PDFAbstract
The symbiosis between sea anemones and hermit crabs is ubiquitous in the marine environment (except in the poles), occurring from shallow to deep waters; it involves one or more anemones living on a shell inhabited by a hermit crab. The anemone-crab partnership is a mutualism in which hermit crabs provide a hard substrate, increased access to oxygenated waters and food supply, in exchange for defense by the anemone. The vast majority of the sea anemone partners belong to three genera in family Hormathiidae: Adamsia, Calliactis, Paracalliactis. Given the remarkable nature of the symbiosis, hormathiid partners have been hypothesized to represent a monophyletic group. This has been rejected by Gusmão and Daly et al. () and confirmed by our phylogenetic analysis using molecular markers (12S, 16S, 18S, 28S, COIII). We expand the results of Gusmão and Daly et al. () by finding a monophyletic Paracalliactis, which was left untested in their analyses. Thus, characters of taxonomic significance associated to the symbiotic habit are interpreted as functional rather than phylogenetic. We reconcile taxonomy and the present evolutionary framework to avoid defining taxonomic groups based on characters prone to convergence. We formalize the synonymy of Adamsia and Calliactis and provide updated diagnoses for the valid genera Calliactis and Paracalliactis to bring more stability to the group. Under this new framework, we describe Calliactis tigris sp. nov. from Australia based on 21 specimens collected off the coast of New South Wales and Queensland and differentiate it from congeners and other hermit crab symbionts recorded in the Pacific Ocean.
Received: 16 August 2018 / Accepted: 27 February 2019 / Published online: 06 April 2019
An integrative taxonomic study reveals carychiid microsnails of the troglobitic genus Zospeum in the Eastern and Dinaric Alps (Gastropoda, Ellobioidea, Carychiinae)Download PDFAbstract
The minute snails of the troglobitic genus Zospeum are known from the southeastern Alps through the Dinarides and from the Pyrenees to the Cantabrian Mountains. The majority of Zospeum has been described from the northernmost region of Southeast Europe, the geographical focus of our study. The taxonomic value of the few available morphological shell characters has been debated for nearly as long as the genus is known. Recent results of genetic studies questioned the established taxonomic system based on morphological characters in the 1970s, with one species (Z. isselianum) appearing to be polyphyletic. Here, we present a comprehensive revision of Zospeum from the Alpine and Dinaride regions, using an integrative approach including genetic methods, morphometry, X-ray micro computer tomography (micro-CT), and SEM. We reveal 25 species and describe 5 new to science. Genetic analysis separated the genus into five clades, strongly challenging the previously valid taxonomic system and revealing several species polyphyletic. The various methods used for morphological characterization often proved useful in separating species showing high incidence of cryptic speciation in the genus. Radular investigation, using SEM, uncovered new insights about the taxonomic value of the configuration of the radular ribbon within Zospeum as well as Zospeum’s dentitional affinity within the Ellobioidea.
Received: 30 July 2018 / Accepted: 12 February 2019 / Published online: 27 February 2019
The reduced limbed lizards of the genus Bachia (Reptilia, Squamata, Gymnophthalmidae); biogeography, cryptic diversity, and morphological convergence in the eastern CaribbeanDownload PDFAbstract
The phylogenetic and systematic relationships of the reduced limbed lizards of the genus Bachia are poorly understood. Here, we investigate the eastern Caribbean Bachia assigned to the B. heteropa and B. flavescens groups, whose members are characterized by a band of hexagonal or quadrangular scales on the dorsum, respectively. The polytypic Bachia heteropa is redefined, and the previous subspecies in the Grenadines (Bachia heteropa alleni) and Trinidad (B. h. trinitatis) are demonstrated to be species-level lineages. One new species of hex-scaled Bachia was formerly assigned intergrade status between B. heteropa and Bachia trinitatis. Here, it is described as a new species from Caripito, Venezuela. Bachia h. heteropa, B. h. lineata, and B. h. marcelae are elevated to species status. The Tobago species formerly considered a member of the Bachia flavescens species group is described as a new species. In this paper, we increase the number of species in the genus Bachia from 25 to 31 with the description of two new species and the elevation of four previously described species from the synonymy of Bachia heteropa. This work will greatly improve the understanding of the systematics and evolution of Bachia in the eastern Caribbean.
Received: 29 March 2019 / Accepted: 11 August 2019 / Published online: 22 August 2019
Recent progress in reconstructing lophotrochozoan (spiralian) phylogenyDownload PDFAbstract
Lophotrochozoa (also called Spiralia), the sister taxon of Ecdysozoa, includes animal taxa with disparate body plans such as the segmented annelids, the shell bearing molluscs and brachiopods, the colonial bryozoans, the endoparasitic acanthocephalans and the acoelomate platyhelminths. Phylogenetic relationships within Lophotrochozoa have been notoriously difficult to resolve leading to the point that they are often represented as polytomy. Recent studies focussing on phylogenomics, Hox genes and fossils provided new insights into the evolutionary history of this difficult group. New evidence supporting the inclusion of chaetognaths within gnathiferans, the phylogenetic position of Orthonectida and Dicyemida, as well as the general phylogeny of lophotrochozoans is reviewed. Several taxa formerly erected based on morphological synapomorphies (e.g. Lophophorata, Tetraneuralia, Parenchymia) seem (finally) to get additional support from phylogenomic analyses.
Received: 22 July 2018 / Accepted: 28 June 2019 / Published online: 16 July 2019
Phylogeography of ants from the Brazilian Atlantic ForestDownload PDFAbstract
Known for its remarkable biodiversity and high levels of endemism, the Brazilian Atlantic Rainforest has been characterized as one of the most threatened biomes on the planet. Despite strong interest in recent years, we still lack a comprehensive scenario to explain the origin and maintenance of diversity in this region, partially given the relatively low power of analyses involving few independent genetic loci. In this study, we examine a phylogenomic dataset of five ant species to investigate phylogeographical patterns across the Brazilian Atlantic Forest. We sequenced ultraconserved elements to generate hundreds of loci using a bait set developed specifically for hymenopterans. We analyzed the data using Bayesian and maximum likelihood approaches of phylogenetic inference. Results were then integrated with environmental niche modeling of current and past climates, including the Last Glacial Maximum and the last interglacial period. The studied species showed differentiation patterns that were consistent with the north/south division of the Atlantic Rainforest indicated in previous studies for other taxa. However, there were differences among species, both in the location of phylogeographic breaks and in the pattern of genetic variation within these areas. Samples from southern localities tended to show recent genetic structure, although a site in Tapiraí (state of São Paulo) repeatedly showed an intriguing older history of differentiation. All species experienced shifts in areas of suitability through the time. Our study suggests that distinct groups may have responded idiosyncratically to the climatic changes that took place in the Brazilian Atlantic Forest. The amount of intraspecific genetic structure was related to the inferred geographical distribution of habitat suitability according to current and past times. Also, a parallel between the amount of Quaternary climatic suitability and the level of interspecific differentiation was detected for four species. Finally, despite strong contractions at the northeastern region of the forest, the remaining areas appear to have been able to act as refugia.
Received: 10 December 2018 / Accepted: 17 March 2019 / Published online: 11 April 2019
The popular model annelid Enchytraeus albidus is only one species in a complex of seashore white worms (Clitellata, Enchytraeidae)Download PDFAbstract
The white worm Enchytraeus albidus Henle, 1837 (Clitellata, Enchytraeidae) is easy to keep in laboratory cultures, and has therefore been employed as a model organism in basic and applied biological research. Its natural habitat includes terrestrial composts and wrack beds on seashores. However, the name E. albidus is currently used for a complex of morphologically similar and closely related species. We here revise the components of the E. albidus species complex based on a sample of 100 Enchytraeus specimens from 56 sites, most of which are across Europe. These samples were DNA-barcoded for the mitochondrial COI gene. A subset of them was sequenced for the nuclear ITS2 and H3 markers. Six species were delimited with strong support by the COI and ITS2 gene trees, as well as by a multi-locus species delimitation analysis. These species are identified morphologically and described as E. albidus s. str. (with designation of a neotype); Enchytraeus moebiiMichaelsen, 1885); Enchytraeus albellus Klinth, Erséus and Rota, sp. nov., E. cf. krumbachi (Čejka, 1913), E. sp. 1 (unnamed), and Enchytraeus polatdemiri Arslan and Timm, 2018. The last-mentioned species is a soda lake specialist, whereas E. albidus s. str. is both terrestrial and marine littoral; all other species occur only in seashores. The phylogeny of this group was estimated using the multi-species coalescent model. Monophyly of the E. albidus complex was recovered. Within this complex, three groups were recovered as monophyletic, but the relationship between them is unclear. One group comprises E. albidus s. str., E. albellus, and E. moebii; the second group E. cf. krumbachi and the unnamed E. sp. 1, and the third consists of only E. polatdemiri. This study serves as a framework for genetic identification of white worms used for experimental purposes.
Received: 12 April 2019 / Accepted: 14 August 2019 / Published online: 16 September 2019
Polyclad phylogeny persists to be problematicDownload PDFAbstract
Two conflicting morphological approaches to polyclad systematics highlight the relevance of molecular data for resolving the interrelationships of Polycladida. In the present study, phylogenetic trees were reconstructed based on a short alignment of the 28S rDNA marker gene with 118 polyclad terminals (24 new) including 100 different polyclad species from 44 genera and 22 families, as well as on a combined dataset using 18S and 28S rDNA genes with 27 polyclad terminals (19 new) covering 26 different polyclad species. In both approaches, Theamatidae and Cestoplanidae were included, two families that have previously been shown to switch from Acotylea to Cotylea. Three different alignment methods were used, both with and without alignment curation by Gblocks, and all alignments were subjected to Bayesian inference and maximum likelihood tree calculations. Over all trees of the combined dataset, an extended majority-rule consensus tree had weak support for Theamatidae and Cestoplanidae as acotyleans, and also the cotylean genera Boninia, Chromyella and Pericelis appeared as acotyleans. With the most inclusive short 28S dataset, on the other hand, there is good support for the aforementioned taxa as cotyleans. Especially with the short 28S matrix, taxon sampling, outgroup selection, alignment method and curation, as well as model choice were all decisive for tree topology. Well-supported parts of the phylogeny over all trees include Pseudocerotoidea, Prosthiostomoidea, Stylochoidea, Leptoplanoidea and Cryptoceloidea, the latter three with new definitions. Unstable positions in the tree were found not only for Theamatidae, Cestoplanidae, Boninia, Chromyella and Pericelis, but also for Anonymus, Chromoplana and Cycloporus.
Received: 07 February 2019 / Accepted: 11 May 2019 / Published online: 29 May 2019
Family Tylenchidae (Nematoda): an overview and perspectivesDownload PDFAbstract
Nematodes in the Tylenchidae family are one of the most important soil-inhabiting species, yet little is known about this intriguing group. The present review examines newly collected samples of Tylenchidae from worldwide sources as well as slides from museum collections. Together with all available literature, detailed morphology among genera are summarized and compared, allowing us to explore the importance of each morphological character in a phylogenetic framework. An updated phylogeny inferred from concatenated 18S and 28S ribosomal RNA dataset is reconstructed; the results suggest that not all didelphic genera may be included in Tylenchidae. In fact, our analyses suggest Tylenchidae should be split into several families, although their phylogeny has not yet fully been resolved. Currently, the Tylenchidae family comprises 44 genera and 412 nominal species; however, diversity estimations for the group ranged from 2000 to 10,000 species, meaning that 75–95% of the species remains undiscovered. This is partially because the biased sampling in agro-ecosystems with most Tylenchidae may present in neglected habitats. Finally, we discussed current difficulties in morphology, taxonomy, and molecular phylogeny research of Tylenchidae and the need for multi-gene phylogeny or phylogenomic approaches to resolve the deep phylogeny in Tylenchidae.
Received: 15 November 2018 / Accepted: 22 August 2019 / Published online: 04 September 2019
The Caribbean enigma: the presence of unusual cryptic diversity in intertidal mites (Arachnida, Acari, Oribatida)Download PDFAbstract
The definition, as well as the existence of cryptic species, is still a subject of controversial debates. Some scientists claim that cryptic diversity is a real phenomenon that should be extensively studied while others argue that cryptic species do not exist as they are nothing more than an incompatibility of species concepts. We investigated the enigmatic case of two widely distributed Caribbean intertidal oribatid mites, Carinozetes bermudensis and Carinozetes mangrovi, consisting of five distinct genetic lineages. Morphological features allowing to clearly distinguish between these lineages are absent, and despite certain congruence with genetic data, comprehensive morphometric analyses also do not show clear separation. Species delimitation analyses based on COI sequence data, on the other hand, suggest five distinct genetic species. Despite the lack of diagnostic characters for these suggested species, the lineages can be classified at least into two morphological groups, the bermudensis and the mangrovi group which can only be distinguished by the arrangement of cuticular ventral carinae. Specimens within a group show nearly identical phenotypes, impeding morphological identification and hence rendering the found diversity cryptic. Stabilizing selection caused by the extreme conditions of the intertidal environment is suggested to be responsible for the found morphological stasis. The genetic lineages show more or less clear geographic patterns; in C. mangrovi, there is a northern, an Antillean, and a Pacific lineage, whereas in C. bermudensis, there is a Bermudian and a Caribbean lineage. In a few places, e.g., the Bahamas and Panama, distributions may overlap. Neither the found biogeographic pattern nor the observed ecological needs could explain the reason for the genetic diversification of Caribbean Carinozetes.
Received: 15 October 2018 / Accepted: 05 June 2019 / Published online: 28 June 2019
Systematics and evolution of the parasitoid wasp genera of the tribe Holcobraconini (Hymenoptera: Braconidae: Doryctinae)Download PDFAbstract
The tribe Holcobraconini (Braconidae: Doryctinae) is a group of parasitoid wasps mainly found in the tropical and subtropical regions of the world. It contains seven genera (Holcobracon Cameron, Ivondrovia Shenefelt & Marsh, Liodoryctes Szépligeti, Monarea Szépligeti, Nervellius Roman, Odontobracon Cameron and Zombrus Marshall), most of which are characterized by having the m-cu vein of the hind wing long and strongly curved towards the apex of wing. Some studies, however, found that three doryctine genera that lack the above feature (Binarea Brullé, Liobracon Szépligeti and Odontodoryctes Granger) might be closely related to holcobraconines. Here, we reconstructed the phylogenetic relationships among species of six holcobraconine genera and the three putative closely related genera using four gene markers and estimated the times of origin and diversification within the tribe. The holcobraconine genera were intermingled in a clade with the above three genera. Liobracon and Zombrus were not recovered as monophyletic. Acanthodoryctes Turner, Antidoryctes Belokobylskij & Quicke and Priosphys Enderlein were also included within the Holcobraconini based on morphology. Based on molecular evidence and on morphological examination of the genera involved, Holcobraconini is proposed to comprise 13 genera for which we include morphological diagnoses. The origin of the tribe probably occurred during the late Palaeocene to mid Eocene, 44.43 to 58.15 Mya. At least two main dispersal events from the Ethiopian to the other biogeographic regions could have led to the current geographic distribution of the Holcobraconini associated with the global increase of temperature during the Late Palaeocene to Middle Eocene.
Received: 26 August 2018 / Accepted: 07 December 2018 / Published online: 18 December 2018
Organization of the lophophore in the deep-sea brachiopod Pelagodiscus atlanticus and evolution of the lophophore in the BrachiozoaDownload PDFAbstract
Molecular data indicate that brachiopods and phoronids form a clade Brachiozoa. In both groups, the lophophore consists of a brachial axis that bears a row of tentacles and does take different forms. Pelagodiscus atlanticus is a brachiopod with an unusual lophophore combining primitive (horseshoe-shaped brachial axis) and advanced (brachial axis forms two arms that are raised freely into the mantle cavity) features. The organization of the lophophore of P. atlanticus was studied by histological and MicroCT methods. Lophophoral arms of P. atlanticus are directed posteriorly. Each arm is formed by a looped brachial axis. As in the lateral arm of a zygolophe in terebratulids, the two parts of the looped brachial axis run in a common extracellular matrix. Apparently, P. atlanticus demonstrates a distinct path in the evolution of the brachiopod lophophore. Although the lophophore of P. atlanticus is a result of the paedomorphic morphology of this brachiopod, a lophophore of similar shape could be an initial step for the development of the lophophore of other discinids. We suggest based on morphological analyses of phoronid and brachiopod lophophores that a crescent-shaped taxolophe with one coelomic canal and a single row of tentacles may represent an initial stage in the evolution of the lophophores in the Brachiozoa. In brachiopods, the brachial axis apparently became more complex with a double row of tentacles and large and small coelomic canals. In phoronids, the brachial axis preserved a simple organization that occurs in the taxolophe and the trocholophe of brachiopods. During the evolution of the phoronid lophophore, the brachial axis obtained a shape of horseshoe with two loops, in which two parts of the looped brachial axis were fused. Such a structure resembles the zygolophe of brachiopods.
Received: 30 July 2018 / Accepted: 27 February 2019 / Published online: 09 March 2019
New fossil data and phylogenetic inferences shed light on the morphological disparity of Mesozoic Sinoalidae (Hemiptera, Cicadomorpha)Download PDFAbstract
Like many fossil insect groups, the systematic framework of extinct ‘Homoptera’ is mainly based on venational traits of isolated wings; most taxa of Mesozoic Sinoalidae, however, were erected with whole-bodied specimens. On the basis of new fossil data and phylogenetic analyses, this froghopper family is herein chosen as a case study to discuss the potential influence of the absence and/or neglect of body information in palaeoentomological studies. Mesodorus orientalis Chen et Wang, gen. et sp. nov., found in the mid-Cretaceous Burmese amber, bears a venational topology of fore- and hindwings similar to that of the genus Fangyuania from the same horizon and locality, but distinctly differs from the latter and other known sinoalids in possessing a series of unique body characters. Given the similar wing features, Jiania crebra and J. gracila were proposed to be synonyms in a recent study; these two congeners, however, are apparently discernable in their ovipositor and so the synonym should be rejected. Three main clades were recovered within the Sinoalidae in our cladistic analyses, including Clade I (Stictocercopis + Chengdecercopis), Clade II (Huabeicercopis + Luanpingia + Sinoala + Jiania + Shufania), and Clade III (Fangyuania + Mesodorus), and their relationship is as following: Clade I + (Clade II + Clade III). The Jurassic Clade I, as the basal lineage, is remarkably different from other sinoalids in bearing wings with complex venation, but similar to the Jurassic Clade II in body structures. The Cretaceous Clade III possesses a reduced wing topology similar to Clade II, but differs from the latter in possessing a series of novel body characteristics for each taxon (i.e., Fangyuania and Mesodorus). Unsurprisingly, our finds confirm that the information from body structures, vital to understanding the biodiversity and evolutionary history of extinct insects, should not be ignored in palaeoentomological studies.