With the increasing availability of molecular data, maximum likelihood approaches have gained a new central role in phylogenetic reconstructions. Extremely fast tree-search algorithms have been developed to handle data sets of ample size in reasonable time. In the past few years, RAxML has achieved great relevance in this field and obtained wide distribution among evolutionary biologists and taxonomists because of its high computational performance and accuracy. However, there are certain drawbacks with regard to its usability, since the program is exclusively command-line based. To overcome this problem, we developed raxmlGUI, a graphical user interface that makes the use of RAxML easier and highly intuitive, enabling the user to perform phylogenetic analyses of varying complexity. The GUI includes all main options of RAxML, and a number of functions are automated or simplified. In addition, some features extend the standard use of RAxML, like assembling concatenated alignments with automatic partitioning. RaxmlGUI is an open source Python program, available in a cross-platform package that incorporates RAxML executables for the main operating systems. It can be downloaded from http://sourceforge.net/projects/raxmlgui/ .
Metazoa comprises 35–40 phyla that include some 1.3 million described species. Phylogenetic analyses of metazoan interrelationships have progressed in the past two decades from those based on morphology and/or targeted-gene approaches using single and then multiple loci to the more recent phylogenomic approaches that use hundreds or thousands of genes from genome and transcriptome sequencing projects. A stable core of the tree for bilaterian animals is now at hand, and instability and conflict are becoming restricted to a key set of important but contentious relationships. Acoelomorph flatworms (Acoela + Nemertodermatida) and Xenoturbella are sister groups. The position of this clade remains controversial, with different analyses supporting either a sister-group relation to other bilaterians (=Nephrozoa, composed of Protostomia and Deuterostomia) or membership in Deuterostomia. The main clades of deuterostomes (Ambulacraria and Chordata) and protostomes (Ecdysozoa and Spiralia) are recovered in numerous analyses based on varied molecular samples, and also receive anatomical and developmental support. Outstanding issues in protostome phylogenetics are the position of Chaetognatha within the protostome clade, and the monophyly of a group of spiralians collectively named Platyzoa. In contrast to the broad consensus over key questions in bilaterian phylogeny, the relationships of the five main metazoan lineages—Porifera, Ctenophora, Placozoa, Cnidaria and Bilateria—remain subject to conflicting topologies according to different taxonomic samples and analytical approaches. Whether deep bilaterian divergences such as the split between protostome and deuterostome clades date to the Cryogenian or Ediacaran (and, thus, the extent to which the pre-Cambrian fossil record is incomplete) is sensitive to dating methodology.
Diatoms are present in all types of water bodies and their species diversity is influenced greatly by environmental conditions. This means that diatom occurrence and abundances are suitable indicators of water quality. Furthermore, continuous screening of algal biodiversity can provide information about diversity changes in ecosystems. Thus, diatoms represent a desirable group for which to develop an easy to use, quick, efficient, and standardised organism identification tool to serve routine water quality assessments. Because conventional morphological identification of diatoms demands specialised in-depth knowledge, we have established standard laboratory procedures for DNA barcoding in diatoms. We (1) identified a short segment (about 400 bp) of the SSU (18S) rRNA gene which is applicable for the identification of diatom taxa, and (2) elaborated a routine protocol including standard primers for this group of microalgae. To test the universality of the primer binding sites and the discriminatory power of the proposed barcode region, 123 taxa, representing limnic diatom diversity, were included in the study and identified at species level. The effectiveness of the barcode was also scrutinised within a closely related species group, namely the Sellaphora pupula taxon complex and relatives.
Annelida is an ecologically and morphologically diverse phylum within the Lophotrochozoa whose members occupy a wide range of environments and show diverse life styles. The phylogeny of this group comprising more than 17,000 species remained controversial for a long time. By using next-generation sequencing and phylogenomic analyses of huge data matrices, it was finally possible to reach a well-supported and resolved annelid backbone tree. Most annelid diversity is comprised in two reciprocal monophyletic groups, Sedentaria and Errantia, which are named after the predominant life style of their members. Errantia include Aciculata (Phyllodocida + Eunicida) and Protodriliformia, which is a taxon of interstitial polychaetes. Sedentaria comprise most of the polychaete families formerly classified as Canalipalpata or Scolecida, as well as the Clitellata. Six taxa branch as a basal grade outside of this major radiation: Oweniidae, Magelonidae, Chaetopteridae, Sipuncula, Amphinomida, and Lobatocerebrum. Oweniidae and Magelonidae form a monophyletic group which we name Palaeoannelida, which constitutes the sister taxon of the remaining annelids. The early splits of annelid phylogeny date back to the Cambrian. The new annelid phylogeny highlights the variability and lability of annelid body plans, and many instances of simplifications of body plan as adaptations to new life styles can be found. Therefore, annelids will be an appropriate model to understand major transitions in the evolution of Bilateria in general. Evolutionary developmental studies are one way to investigate macroevolutionary transition in annelids. We briefly summarize the state of developmental model organisms in Annelida and also propose new candidates on the background of the phylogeny.
Opisthobranchia have experienced an unsettled taxonomic history. At the moment their taxonomy is in state of dramatic flux as recent phylogenetic studies have revealed traditional Opisthobranchia to be paraphyletic or even polyphyletic, allocating some traditional opisthobranch taxa to other groups of Heterobranchia, e.g. Pulmonata. Here we review the history of Opisthobranchia and their subgroups, explain their traditionally proposed relationships, and outline the most recent phylogenetic analyses based on various methods (morphology, single gene and multiple gene analyses, as well as genomic data). We also present a phylogenetic hypothesis on Heterobranchia that, according to the latest results, represents a consensus and is the most probable one available to date. The proposed phylogeny supports the Acteonoidea outside of monophyletic Euthyneura, the basal euthyneuran split into Nudipleura (Nudibranchia plus Pleurobranchoidea) and the recently established taxon Tectipleura. The latter divides into the Euopisthobranchia, containing most of the major traditional opisthobranch clades, and the Panpulmonata, with a mix of the former opisthobranch, putative allogastropod and pulmonate taxa. This “new euthyneuran tree” rejects the traditional taxa Opisthobranchia and Pulmonata, and, in particular, has profound implications for preconceived textbook scenarios of opisthobranch and pulmonate evolution, which must now be reconsidered. In the absence of systematic barriers, research communities—which have traditionally investigated marine and non-marine heterobranchs separately—need to interact and finally merge for the sake of science.
Many doubts still exist about which freshwater mussel Unio species inhabit Northwest Africa. While some authors refer to the presence of Unio delphinus in the Atlantic North African basins of Morocco, a recent International Union for Conservation of Nature (IUCN) assessment performed on Moroccan Unio species, recognised the existence of a distinct species, Unio foucauldianus, with a critically endangered conservation status. The present study delivered new genetic, morphological, and geographical distribution data on two Unio species (i.e. U. delphinus and U. foucauldianus) greatly increasing the almost non-existent data on these taxa. Bayesian phylogenetic analysis revealed two highly supported geographically concordant clades, which diverged by 3.2 ± 0.6 % (uncorrected p distance): the first distributed across Iberia and corresponding to U. delphinus, and the second distributed across Morocco, corresponding to U. foucauldianus. These results were corroborated by the analysis of ten newly developed microsatellite loci as well as shell morphometry. We suggest that the IUCN critically endangered conservation status of U. foucauldianus should be revised and probably down-listed since its actual distribution is much wider than previously described. Phylogenetic relationships with the other Unio species were resolved, showing that U. delphinus and U. foucauldianus fall inside the pictorum lineage. The estimated molecular rate reported herein (0.265 ± 0.06 % per million years) represents the first for the Unionida and could be used as a reference in future studies.
Molecular data are increasingly being used to resolve cryptic species complexes; however, subsequent formal species description and taxonomic revisions often remain incomplete. Given that most species are described based on morphology-based alpha taxonomy, one cannot resolve nomenclatural issues of species complexes without the aid of morphology. In this study, we examined the taxonomic status of a long-known human commensal and species complex, Hemidactylus brookii. To this end, samples of H. cf. brookii and related species were collected across India. We analyzed molecular as well as morphological data to resolve the taxonomy of this species complex. Seven deeply divergent, well-supported clades were recovered using the mitochondrial phylogeny, five of which were also retrieved in the nuclear tree. One of these consists of five morphologically distinct species of ground-dwelling Hemidactylus. The genetic distances across each clade of putative species of H. brookii sensu lato were comparable to that between morphologically distinct species of ground-dwelling Hemidactylus. Meristic characters such as number of precloacal-femoral pores, number of non-pore bearing scales interrupting the series of pored scales, dorsal pholidosis, and presence/absence of divided lamellae can be used to distinguish these putative species from each other. However, morphological characters of H. brookii sensu stricto did not correspond to any of the putative species studied. The study also revealed that the “H. brookii complex” in India includes two commensal species, Hemidactylus parvimaculatus and Hemidactylus murrayi. Furthermore, these two lineages have independently acquired adaptations that could have assisted them in exploiting human habitat. An identification key to diagnose species within this complex and rest of the Hemidactylus in India is proposed.
Lophotrochozoa is a protostome clade that includes disparate animals such as molluscs, annelids, bryozoans, and flatworms, giving it the distinction of including the most body plans of any of the three major clades of Bilateria. This extreme morphological disparity has prompted numerous conflicting phylogenetic hypotheses about relationships among lophotrochozoan phyla. Here, I review the current understanding of lophotrochozoan phylogeny with emphasis on recent insights gained through approaches taking advantage of high-throughput DNA sequencing (phylogenomics). Of significance, Platyzoa, a hypothesized clade of mostly small-bodied animals, appears to be an artifact of long-branch attraction. Recent studies recovered Gnathifera (Syndermata, Gnathostomulida, and Micrognathozoa) sister to all other lophotrochozoans and a clade called Rouphozoa (Platyhelminthes and Gastrotricha) sister to the remaining non-gnathiferan lophotrochozoans. Although Bryozoa was traditionally grouped with Brachiopoda and Phoronida (Lophophorata), most molecular studies have supported a clade including Entoprocta, Cycliophora, and Bryozoa (Polyzoa). However, recent phylogenomic work has shown that entoprocts and bryozoans have compositionally heterogeneous genomes that may cause systematic artifacts affecting their phylogenetic placement. Lastly, relationships within Trochozoa (Mollusca, Annelida, and relatives) largely remain ambiguous. Recent work has shown that phylogenomic studies must identify and reduce sources of systematic error, such as amino acid compositional heterogeneity and long-branch attraction. Still, other approaches such as the analysis of rare genomic changes may be needed to overcome challenges to standard phylogenomic approaches. Resolving lophotrochozoan phylogeny will provide important insight into how these complex and diverse body plans evolved and provide a much-needed framework for comparative studies.
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.
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.
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.
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.
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.
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.
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.
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.