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Taxonomic revision of the Australian stick insect genus Candovia (Phasmida: Necrosciinae): insight from molecular systematics and species-delimitation approaches
Abstract
The Phasmida genus Candovia comprises nine traditionally recognized species, all endemic to Australia. In this study, Candovia diversity is explored through molecular species-delimitation analyses using the COIFol gene fragment and phylogenetic inferences leveraging seven additional mitochondrial and nuclear loci. Molecular results were integrated with morphological observations, leading us to confirm the already described species and to the delineation of several new taxa and of the new genus Paracandovia. New Candovia species from various parts of Queensland and New South Wales are described and illustrated (C. alata sp. nov., C. byfieldensis sp. nov., C. dalgleishae sp. nov., C. eungellensis sp. nov., C. karasi sp. nov., C. koensi sp. nov. andC. wollumbinensis sp. nov.). New combinations are proposed and species removed from synonymy with the erection of the new genus Paracandovia (P. cercata stat. rev., comb. nov., P. longipes stat. rev., comb. nov., P. pallida comb. nov., P. peridromes comb. nov., P. tenera stat. rev., comb. nov.). Phylogenetic analyses suggest that the egg capitulum may have independently evolved multiple times throughout the evolutionary history of these insects. Furthermore, two newly described species represent the first taxa with fully developed wings in this previously considered apterous clade.
... The sampling locations of specimens used in the current study are indicated on the maps with their unique identifiers (see Table 2). and hinders progress in almost all areas of biology (e.g., Hernández et al. 2020;Forni et al. 2023;Wilkerson et al. 2015). Here we examine the current taxonomic grouping of the alpine radiation of New Zealand grasshoppers into four genera. ...
Aotearoa New Zealand has a fauna of endemic alpine grasshoppers, consisting of thirteen species distributed among four genera. The many re-classifications of species within this group and the presence of species complexes highlight the uncertainty that surrounds relationships within and between these genera. High-throughput Next Generation Sequencing was used to assemble the complete mitochondrial genomes, 45S ribosomal cassettes and histone sequences of New Zealand’s four endemic alpine genera: Alpinacris, Brachaspis, Paprides and Sigaus. Phylogenetic analysis of these molecular datasets, as individual genes, partitions and combinations returned a consistent topology that is incompatible with the current classification. The genera Sigaus, Alpinacris, and Paprides all exhibit paraphyly. A consideration of the pronotum, epiphallus and terminalia of adult specimens reveals species-specific differences, but fails to provide compelling evidence for species groups justifying distinct genera. In combination with phylogenetic, morphological and spatial evidence we propose a simplified taxonomy consisting of a single genus for the māwhitiwhiti Aotearoa species radiation.
... Recent studies on Australian genera (Forni et al., 2022;Jones et al., 2022) show the value of detailed research by drastically changing what we know about under studied groups, including similar-looking species; other genera would benefit from similar work. ...
Studies on the genus Xeroderus have revealed a new species from Papua New Guinea: Xeroderus conlei sp. n., which is described and figured from the holotype female only. Keys are provided to compare it with X. kirbyi Gray, 1835 from Australia, the only other species in the genus. Lectotypes are designated for X. kirbyi and the synonym Cooktownia plana Sjöstedt, 1918. Xeroderus brevipennis Redtenbacher, 1908 is found to be a member of Nisyrus Stål, 1877 and is here removed from Xeroderus and transferred to Nisyrus Stål, 1877. N. brevipennis (Redtenbacher, 1908) comb. n. is the first record of Nisyrus from the Solomon Islands. Various additional Australian localities are recorded for X. kirbyi Gray, 1835.
Two species of stick insect with a distinctive morphology, Candovia evoneobertii (Zompro & Adis, 2001) and Echetlus fulgens Zompro, 2004, were considered to be native to Australia and introduced into Brazil. However, Heteronemia dubia (Caudell, 1904) and Heteronemia fragilis (Brunner von Wattenwyl, 1907), both described more than a hundred years ago from South America, exhibit striking similarities with the two purportedly introduced species and are found to be conspecific with C. evoneobertii. Careful analysis of the literature and specimens revealed that these species belong to the Neotropical tribe Diapheromerini (Diapheromeridae) and represent a new genus, Arumatia Ghirotto gen. nov. We therefore propose Arumatia fulgens (Zompro, 2004) gen. et comb. nov. and Arumatia dubia (Caudell, 1904) gen. et comb. nov. We further redescribe A. dubia (Caudell, 1904) gen. et comb. nov. based on several specimens and synonymize Heteronemia fragilis syn. nov. and Candovia evoneobertii syn. nov. under it. Additionally, five new Brazilian species are described: Arumatia diamante Ghirotto gen. et sp. nov. from Abaíra, Bahia; Arumatia aramatia Ghirotto gen. et sp. nov. from Porto Nacional, Tocantins; Arumatia motenata Ghirotto gen. et sp. nov. from Serra do Cipó, Minas Gerais; Arumatia crassicercata Ghirotto, Crispino & Engelking gen. et sp. nov. from Alto Paraíso de Goiás, Goiás; and Arumatia anyami Ghirotto, Crispino & Neves gen. et sp. nov. from Costa Marques, Rondônia. Species of Arumatia gen. nov. occur mostly in the Cerrado domain, and represent the first Diapheromeridae recorded in this area. Most species are known exclusively from females with only A. aramatia gen. et sp. nov. and A. motenata gen. et sp. nov. known from both sexes. Adult and egg morphology are described and illustrated in detail for all species, as well as the nymph stages for A. dubia. Biological observations are presented, including parthenogeny in A. dubia and one of the few detailed accounts of sexual behaviour in Euphasmatodea (for A. motenata gen. et sp. nov.). Finally, a species of Diapheromerini described in error from Brazil, Diapheromera armata Piza, 1973, is synonymized under the North American Megaphasma denticrus (Stål, 1875) (syn. nov.).
Background
The re-evolution of complex characters is generally considered impossible, yet, studies of recent years have provided several examples of phenotypic reversals shown to violate Dollo’s law. Along these lines, the regain of wings in stick and leaf insects (Phasmatodea) was hypothesised to have occurred several times independently after an ancestral loss, a scenario controversially discussed among evolutionary biologists due to overestimation of the potential for trait reacquisition as well as to the lack of taxonomic data.
Results
We revisited the recovery of wings by reconstructing a phylogeny based on a comprehensive taxon sample of over 500 representative phasmatodean species to infer the evolutionary history of wings. We additionally explored the presence of ocelli, the photoreceptive organs used for flight stabilisation in winged insects, which might provide further information for interpreting flight evolution. Our findings support an ancestral loss of wings and that the ancestors of most major lineages were wingless. While the evolution of ocelli was estimated to be dependent on the presence of (fully-developed) wings, ocelli are nevertheless absent in the majority of all examined winged species and only appear in the members of few subordinate clades, albeit winged and volant taxa are found in every euphasmatodean lineage.
Conclusion
In this study, we explored the evolutionary history of wings in Phasmatodea and demonstrate that the disjunct distribution of ocelli substantiates the hypothesis on their regain and thus on trait reacquisition in general. Evidence from the fossil record as well as future studies focussing on the underlying genetic mechanisms are needed to validate our findings and to further assess the evolutionary process of phenotypic reversals.
The insect order Phasmatodea is known for large slender insects masquerading as twigs or bark. In contrast to these so-called stick insects, the subordinated clade of leaf insects (Phylliidae) are dorso-ventrally flattened and therefore resemble leaves in a unique way. Here we show that the origin of extant leaf insects lies in the Australasian/Pacific region with subsequent dispersal westwards to mainland Asia and colonisation of most Southeast Asian landmasses. We further hypothesise that the clade originated in the Early Eocene after the emergence of angiosperm-dominated rainforests. The genus Phyllium to which most of thẽ 100 described species pertain is recovered as paraphyletic and its three non-nominate subgenera are recovered as distinct, monophyletic groups and are consequently elevated to genus rank. This first phylogeny covering all major phylliid groups provides the basis for future studies on their taxonomy and a framework to unveil more of their cryptic and underestimated diversity.
While the leaf insects (Phylliidae) are a well-supported group within Phasmatodea, the genus Phyllium Illiger, 1798 has repeatedly been recovered as paraphyletic. Here, the Phyllium (Phyllium) celebicum species group is reviewed and its distinctiveness from the remaining Phylliini genera and subgenera in a phyloge- netic context based on morphological review and a phylogenetic analysis of three genes (nuclear gene 28S and mitochondrial genes COI and 16S) from most known and multiple undescribed species is shown. A new genus, Cryptophyllium gen. nov., is erected to partially accommodate the former members of the celebicum species group. Two species, Phyllium ericoriai Hennemann et al., 2009 and Phyllium bonifacioi Lit & Eusebio, 2014 morphologically and molecularly do not fall within this clade and are therefore left within Phyllium (Phyllium). The transfer of the remaining celebicum group members from Phyllium Illiger, 1798 to this new genus creates the following new combinations; Cryptophyllium athanysus (Westwood, 1859), comb. nov.; Cryptophyllium celebicum (de Haan, 1842), comb. nov.; Cryptophyllium chrisangi (Seow-Choen, 2017), comb. nov.; Cryptophyllium drunganum (Yang, 1995), comb. nov.; Cryptophyl- lium oyae (Cumming & Le Tirant, 2020), comb. nov.; Cryptophyllium parum (Liu, 1993), comb. nov.; Cryptophyllium rarum (Liu, 1993), comb. nov.; Cryptophyllium tibetense (Liu, 1993), comb. nov.; Crypto- phyllium westwoodii (Wood-Mason, 1875), comb. nov.; Cryptophyllium yapicum (Cumming & Teemsma, 2018), comb. nov.; and Cryptophyllium yunnanense (Liu, 1993), comb. nov.
The review of specimens belonging to this clade also revealed 13 undescribed species, which are described within as: Cryptophyllium animatum gen. et sp. nov. from Vietnam: Quang Nam Province; Cryptophyllium bankoi gen. et sp. nov. from Vietnam: Quang Ngai, Thua Thien Hue, Da Nang, Gia Lai, Quang Nam, and Dak Nong Provinces; Cryptophyllium bollensi gen. et sp. nov. from Vietnam: Ninh Thuan Province; Cryptophyllium daparo gen. et sp. nov. from China: Yunnan Province; Cryptophyllium echidna gen. et sp. nov. from Indonesia: Wangi-wangi Island; Cryptophyllium faulkneri gen. et sp. nov. from Vietnam: Quang Ngai and Lam Dong Provinces; Cryptophyllium icarus gen. et sp. nov. from Vi- etnam: Lam Dong and Dak Lak Provinces; Cryptophyllium khmer gen. et sp. nov. from Cambodia: Koh Kong and Siem Reap Provinces; Cryptophyllium limogesi gen. et sp. nov. from Vietnam: Lam Dong, Dak Lak, and Dak Nong Provinces; Cryptophyllium liyananae gen. et sp. nov. from China: Guangxi Province; Cryptophyllium nuichuaense gen. et sp. nov. from Vietnam: Ninh Thuan Province; Cryptophyllium phami gen. et sp. nov. from Vietnam: Dong Nai and Ninh Thuan Provinces; and Cryptophyllium wennae gen. et sp. nov. from China: Yunnan Province. All newly described species are morphologically described, il- lustrated, and molecularly compared to congenerics.
With the molecular results revealing cryptic taxa, it was found necessary for Cryptophyllium westwoo- dii (Wood-Mason, 1875), comb. nov. to have a neotype specimen designated to allow accurate differen- tiation from congenerics. To conclude, male and female dichotomous keys to species for the Cryptophyl- lium gen. nov. are presented.
The egg stages of animal life cycles are underappreciated in terms of their capacity for dispersal, protection, and biotic and abiotic interactions. Some of the most intriguing egg morphologies are seen in stick and leaf insects (Phasmatodea). Phasmids are charismatic insects, particularly due to their incredible camouflage, though a lesser-known fact is that their eggs are incredibly diverse in shape and structure, reflecting varying ecological niches. Perhaps most remarkable are those eggs which appear to resemble plant seeds in both their appearance and means of dispersal, such as via water and animal vectors. Numerous hypotheses surrounding the function of these egg morphologies and their apparent convergence with seeds have been proposed; however, empirical evidence remains lacking. Here, we present an initial synthesis of available evidence surrounding the ecology and dispersal strategies of phasmid eggs and weigh up the evidence for convergent evolution between phasmid eggs and seeds. In doing so, we highlight areas where further research is needed and discuss how the ecology of phasmid eggs may interplay with other aspects of phasmid ecology, distribution, and evolution.
Morphology of Phasmatodea eggs is remarkably diverse and highly valuable in taxonomic research. Two alterative hypotheses have been proposed to describe the phylogenetic relationship of the species from the genus Agathemera Stål. Additionally, descriptions of the egg morphology within Agathemera have been done based on the eggs of two species. This small sample size does not represent the diverse egg morphology along the genus, thus we attempt to describe the eggs from all the known Agathemera species. The main goal of the present study is to determine whether the evolution of the eggs occurred through either divergent or convergent evolution. We based our descriptions on morphometrics, morphology and the ultrastructure. For data analysis, principal component analysis (PCA) was performed on morphometric variables and the characters emerged from the morphological and ultrastructure were mapped over the molecular phylogeny. The results show that it is possible to discriminate among species using the morphology of the different egg structures, and furthermore, a divergent event at the base of the tree, differentiate the overall egg shape and the internal micropylar plate shape. Finally, we conclude that both divergent and convergent evolution are shaping the different structures of the Agathemera eggs.
Elaboration of Bayesian phylogenetic inference methods has continued at pace in recent years with major new advances in nearly all aspects of the joint modelling of evolutionary data. It is increasingly appreciated that some evolutionary questions can only be adequately answered by combining evidence from multiple independent sources of data, including genome sequences, sampling dates, phenotypic data, radiocarbon dates, fossil occurrences, and biogeographic range information among others. Including all relevant data into a single joint model is very challenging both conceptually and computationally. Advanced computational software packages that allow robust development of compatible (sub-)models which can be composed into a full model hierarchy have played a key role in these developments. Developing such software frameworks is increasingly a major scientific activity in its own right, and comes with specific challenges, from practical software design, development and engineering challenges to statistical and conceptual modelling challenges. BEAST 2 is one such computational software platform, and was first announced over 4 years ago. Here we describe a series of major new developments in the BEAST 2 core platform and model hierarchy that have occurred since the first release of the software, culminating in the recent 2.5 release.
Achrioptera is a taxon of extremely large and exceptionally colorful stick insects endemic to Madagascar and the Comoros Archipelago. We studied the phylogenetic position of the Achriopterini, comprising the genera Achrioptera and Glawiana, based on a multigene phylogeny and concluded that it is a sister group to other Madagascan phasmids (Anisacanthidae) rather than to Neotropical or Australo-Pacific groups as was suggested in a previous study based on morphology. Our results also point to unresolved relationships (potential paraphyly of Achrioptera), taxonomic issues (elevation of A. punctipes cliquennoisi to species level), and detection of cryptic diversity (in A. impennis), demonstrating the need of additional research. A DNA barcoding approach based on COI sequences of Achrioptera species revealed a clear discrimination between closely related and morphologically similar species. Applying integrative taxonomy using multiple lines of evidence, we demonstrated that the well-known species with blue males from Montagne des Français and Foret d'Orangea in the far north of Madagascar, previously attributed to Achrioptera fallax, represents a new species, which we describe as Achrioptera manga sp. nov. based on morphological, chromatic, and genetic (mitochondrial and nuclear) differences. We also describe a second new giant species from this massif: Achrioptera maroloko sp. nov. is among the largest insects (females reaching up to 24 cm total length) and differs from its sister species A. spinosissima from western Madagascar in morphology, coloration, and substantial DNA barcode divergence. These magnificent new species confirm the significance of the Montagne des Français area as a hotspot of biodiversity and microendemism. The biogeographic pattern of the species pair A. fallax/A. manga is paralleled by species pairs of reptiles and amphibians suggesting a similar evolutionary history. Finally, we discuss the sexual dichromatism of Achrioptera species with conspicuous males and mostly cryptic females. As possible reasons, we consider female mate choice and divergent habits of males and females, but aposematism combined with toxic substances produced in defense glands or accumulated in the insect's body from nutritional plants are more plausible explanations for this phenomenon.
Australia has a rich diversity of phasmids – otherwise known as stick and leaf insects. Most of them are endemic, few have been studied and new species continue to be found. Stick insects are, by far, Australia’s longest insects – some of them reach up to 300 mm in body length, or more than half a metre if you include their outstretched legs. Many stick insects are very colourful, and some have quite elaborate, defensive behaviour. Increasingly they are being kept as pets. This is the first book on Australian phasmids for nearly 200 years and covers all known stick and leaf insects. It includes photographs of all species, notes on their ecology and biology as well as identification keys suitable for novices or professionals.
Stick and leaf insects (Phasmatodea) are large, tropical, predominantly nocturnal herbivores, which exhibit extreme masquerade crypsis, whereby they morphologically and behaviorally resemble twigs, bark, lichen, moss, and leaves. Females employ a wide range of egg-laying techniques, largely corresponding to their ecological niche, including dropping or flicking eggs to the forest floor, gluing eggs to plant substrate, skewering eggs through leaves, ovipositing directly into the soil, or even producing a complex ootheca. Phasmids are the only insects with highly species-specific egg morphology across the entire order, with specific egg forms that correspond to oviposition technique. We investigate the temporal, biogeographic, and phylogenetic pattern of evolution of egg-laying strategies in Phasmatodea. Our results unequivocally demonstrate that the ancestral oviposition strategy for female stick and leaf insects is to remain in the foliage and drop or flick eggs to the ground, a strategy that maintains their masquerade. Other major key innovations in the evolution of Phasmatodea include the (1) hardening of the egg capsule in Euphasmatodea; (2) the repeated evolution of capitulate eggs (which induce ant-mediated dispersal, or myrmecochory); (3) adapting to a ground or bark dwelling microhabitat with a corresponding shift in adult and egg phenotype and egg deposition directly into the soil; and (4) adhesion of eggs in a clade of Necrosciinae that led to subsequent diversification in oviposition modes and egg types. We infer at minimum 16 independent origins of a burying/inserting eggs into soil/crevices oviposition strategy, 7 origins of gluing eggs to substrate, and a single origin each of skewering eggs through leaves and producing an ootheca. We additionally discuss the systematic implications of our phylogenetic results. Aschiphasmatinae is strongly supported as the earliest diverging extant lineage of Euphasmatodea. Phylliinae and Diapheromerinae are both relatively early diverging euphasmatodean taxa. We formally transfer Otocrania from Cladomorphinae to Diapheromerinae and recognize only two tribes within Diapheromerinae: Diapheromerini sensu nov. and Oreophoetini sensu nov. We formally recognize the clade comprising Necrosciinae and Lonchodinae as Lonchodidae stat. rev. sensu nov.
Molecular approaches to species delimitation are increasingly used to ascertain the number of species in a sample prior to taxonomic, ecological or physiological studies. Although multilocus approaches are gaining fast in popularity, single‐gene methods still predominate in the literature. However, available simulation benchmarks of these methods focus exclusively on species‐poor samples and/or tree‐based approaches: as a result, travellers in the land of single‐locus species delimitation lack a comprehensive “hitchhiker's guide” highlighting the sweet spots and dangers on their road. To fill this gap, we compared the performances of distance‐based (ABGD, “automatic barcode gap discovery”), allele sharing‐based (haplowebs) and tree‐based approaches (GMYC, “generalized mixed Yule‐coalescent”, and PTP, “Poisson tree processes”) to detect interspecific boundaries in samples of 6, 60 and 120 simulated species with various speciation rates, effective population sizes, mutation rates and sampling patterns. We found that all approaches performed poorly when population sizes and speciation rates were large, with haplowebs yielding best results followed by ABGD then tree‐based approaches. The latter's error type was mostly oversplitting, whereas ABGD chiefly overlumped and haplowebs leaned either way depending on simulation parameters: such widely divergent error patterns suggest that, if all three types of methods agree, then the resulting delimitation is probably correct. Perfect congruence being quite rare, travellers in search of a one‐size‐fit‐all approach to single‐locus species delimitation should forget it; however, our hitchhiker's guide raises hope that such species delimitation's Holy Grail may be found in the relatively uncharted nearby land of multilocus species delimitation.
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Bayesian inference of phylogeny using Markov chain Monte Carlo (MCMC) (Drummond et al., 2002; Mau et al., 1999; Rannala and Yang, 1996) flourishes as a popular approach to uncover the evolutionary relationships among taxa, such as genes, genomes, individuals or species. MCMC approaches generate samples of model parameter values - including the phylogenetic tree -drawn from their posterior distribution given molecular sequence data and a selection of evolutionary models. Visualising, tabulating and marginalising these samples is critical for approximating the posterior quantities of interest that one reports as the outcome of a Bayesian phylogenetic analysis. To facilitate this task, we have developed the Tracer (version 1.7) software package to process MCMC trace files containing parameter samples and to interactively explore the high-dimensional posterior distribution. Tracer works automatically with sample output from BEAST (Drummond et al., 2012), BEAST2 (Bouckaert et al., 2014), LAMARC (Kuhner, 2006), Migrate (Beerli, 2006), MrBayes (Ronquist et al., 2012), RevBayes (Höhna et al., 2016) and possibly other MCMC programs from other domains.
Species are fundamental units in biological research and can be defined on the basis of various operational criteria. There has been growing use of molecular approaches for species delimitation. Among the most widely used methods, the generalized mixed Yule-coalescent (GMYC) and Poisson tree processes (PTP) were designed for the analysis of single-locus data but are often applied to concatenations of multilocus data. In contrast, the Bayesian multispecies coalescent approach in the software BPP explicitly models the evolution of multilocus data. In this study, we compare the performance of GMYC, PTP, and BPP using synthetic data generated by simulation under various speciation scenarios. We show that in the absence of gene flow, the main factor influencing the performance of these methods is the ratio of population size to divergence time, while number of loci and sample size per species have smaller effects. Given appropriate priors and correct guide trees, BPP shows lower rates of species overestimation and underestimation, and is generally robust to various potential confounding factors except high levels of gene flow. The single-threshold GMYC and the best strategy that we identified in PTP generally perform well for scenarios involving more than a single putative species when gene flow is absent, but PTP outperforms GMYC when fewer species are involved. Both methods are more sensitive than BPP to the effects of gene flow and potential confounding factors. Case studies of bears and bees further validate some of the findings from our simulation study, and reveal the importance of using an informed starting point for molecular species delimitation. Our results highlight the key factors affecting the performance of molecular species delimitation, with potential benefits for using these methods within an integrative taxonomic framework.
European dry-wood termites belong to the genus Kalotermes (Kalotermitidae), one of the two termite genera in Europe. Until the recent description of two new species, Kalotermes italicus in Italy and Kalotermes phoenicae in the eastern Mediterranean area, Kalotermes flavicollis was the only taxon known in this region. The presence of additional entities, suggested by morphological and physiological variation observed in K. flavicollis , was supported by molecular studies revealing four distinct genetic lineages: lineage A, K. flavicollis sensu strictu , from the Aegean area to Italy; lineage B, in Tuscany; lineage SC, in Sardinia and Corsica; lineage SF, in southern France. Lineages A and B may form mixed colonies, suggesting hybridization. To draw a more detailed picture of Kalotermes evolution and biogeography in Europe, we analyzed samples from previously unsampled areas, such as Spain and southern Italy, by means of the highly informative cox1/trnL/cox2 mitochondrial DNA marker. Overall, phylogenetic analyses confirmed previously identified lineages and taxa, but widened the distribution of the lineage SC to the mainland and of the lineage SF to Spain and Portugal. Results further provided evidence for the synonymy between lineage B and K. italicus . Species delimitation analysis suggested that the three K. flavicollis lineages, as well as K. italicus , can be separate taxa. Data also suggest a possible interspecific hybridization between K. italicus and both K. flavicollis lineages A and SC.
Crypsis is a widespread defensive mechanism for prey ambushed by visually oriented predators.
One well-documented consequence of this interaction is the formation of search
images by the predator that leads to the coexistence of multiple morphs in the prey population.
Libethra is a genus of stick insects whose ornamentation and coloration are decidedly
protective and exhibit exuberant intraspecific variation. Despite this fact, these traits have
been extensively used to support the boundaries between the species it includes. This is the
case in the north Andean species Libethra rabdota and Libethra rabdotula, delimited on the
basis of a specific arrangement of ornamental characters. To state whether such taxonomical
practice is meaningful and convenient, we evaluated the grouping of specimens of both species
by means of the independent inference of phylogenies obtained with mitochondrial
DNA sequences and ootaxonomy. This article synonymizes L. rabdota and L. rabdotula,
redescribes the adults and describes the egg of the species. Additionally, we demonstrate
that the characters related to crypsis used for the diagnosis of L. rabdota are not exclusive to
this species by describing Libethra rioblanco sp. n. and Libethra ucumariensis sp. n. Our findings
suggest that this genus requires extensive revision, but also provide support for the
usage of different tools that might produce more accurate and stable classification. Evolutionary
scenarios for both the extreme morphological variation and possible homoplastic
state of camouflage-related traits are discussed herein.
Motivation:
In recent years, molecular species delimitation has become a routine approach for quantifying and classifying biodiversity. Barcoding methods are of particular importance in large-scale surveys as they promote fast species discovery and biodiversity estimates. Among those, distance-based methods are the most common choice as they scale well with large datasets; however, they are sensitive to similarity threshold parameters and they ignore evolutionary relationships. The recently introduced "Poisson Tree Processes" (PTP) method is a phylogeny-aware approach that does not rely on such thresholds. Yet, two weaknesses of PTP impact its accuracy and practicality when applied to large datasets; it does not account for divergent intraspecific variation and is slow for a large number of sequences.
Results:
We introduce the multi-rate PTP (mPTP), an improved method that alleviates the theoretical and technical shortcomings of PTP. It incorporates different levels of intraspecific genetic diversity deriving from differences in either the evolutionary history or sampling of each species. Results on empirical data suggest that mPTP is superior to PTP and popular distance-based methods as it, consistently yields more accurate delimitations with respect to the taxonomy (i.e., identifies more taxonomic species, infers species numbers closer to the taxonomy). Moreover, mPTP does not require any similarity threshold as input. The novel dynamic programming algorithm attains a speedup of at least five orders of magnitude compared to PTP, allowing it to delimit species in large (meta-) barcoding data. In addition, Markov Chain Monte Carlo sampling provides a comprehensive evaluation of the inferred delimitation in just a few seconds for millions of steps, independently of tree size.
Availability and implementation:
mPTP is implemented in C and is available for download at http://github.com/Pas-Kapli/mptp under the GNU Affero 3 license. A web-service is available at http://mptp.h-its.org .
Contact:
: paschalia.kapli@h-its.org or alexandros.stamatakis@h-its.org or tomas.flouri@h-its.org.
Supplementary information:
Supplementary data are available at Bioinformatics online.
PartitionFinder 2 is a program for automatically selecting best-fit partitioning schemes and models of evolution for phylogenetic analyses. PartitionFinder 2 is substantially faster and more efficient than version 1, and incorporates many new methods and features. These include the ability to analyze morphological datasets, new methods to analyze genome-scale datasets, new output formats to facilitate interoperability with downstream software, and many new models of molecular evolution. PartitionFinder 2 is freely available under an open source license and works on Windows, OSX, and Linux operating systems. It can be downloaded from www.robertlanfear.com/partitionfinder The source code is available at https://github.com/brettc/partitionfinder.
DNA-based species delimitation may be compromised by limited sampling effort and species rarity, including ‘singleton’ representatives
of species, which hampers estimates of intra- vs. interspecies evolutionary processes. In a case study of southern African
chafers (beetles in the family Scarabaeidae) many species and subclades were poorly represented and 48.5% of species were
singletons. Using cox1 sequences from >500 specimens and ~100 species, the Generalized Mixed Yule Coalescent (GMYC) analysis as well as various
other approaches for DNA-based species delimitation (AGBD, PTP, Species Identifier, Statistical Parsimony), frequently produced
poor results if analyzing a narrow target group only, but the performance improved when several subclades were combined. Hence,
low sampling may be compensated for by “clade addition” of lineages outside of the focal group. Similar findings were obtained
in reanalysis of published datasets of taxonomically poorly known species assemblages of insects from Madagascar. The low
performance of undersampled trees is not due to high proportions of singletons per se, as shown in simulations (with 13%, 40% and 52% singletons). However, the GMYC method was highly sensitive to variable effective
population size (Ne), which was exacerbated by variable species abundances in the simulations. Hence, low sampling success and rarity of species
affect the power of the GMYC method only if they reflect great differences in Ne among species. Potential negative effects of skewed species abundances and prevalence of singletons are ultimately an issue
about the variation in Ne and the degree to which this is correlated with the census population size and sampling success. Clade addition beyond a
limited study group can overcome poor sampling for the GMYC method in particular under variable Ne. This effect was less pronounced for methods of species delimitation not based on coalescent models.
The Australian phasmid fauna has been revised prior to publication of a field guide by the same authors. Six new genera are described: Austrosipyloidea Brock & Hasenpusch, Cornicandovia Hasenpusch & Brock, Davidrentzia Brock & Hasenpusch, Micropodacanthus Brock & Hasenpusch, Paratropidoderus Brock & Hasenpusch and Spinosipyloidea Hasenpusch & Brock. Sixteen new species from various parts of Australia are described and figured: Candovia robinsoni Brock & Hasenpusch, Rhamphosipyloidea palumensis Hasenpusch & Brock, Scionecra milledgei Hasenpusch & Brock, Sipyloidea brevicerci Hasenpusch & Brock, Sipyloidea garradungensis Hasenpusch & Brock, Sipyloidea larryi Hasenpusch & Brock, Sipyloidea lewisensis Hasenpusch & Brock, Sipyloidea rentzi Brock & Hasenpusch, Sipyloidea whitei Brock & Hasenpusch, Spinosipyloidea doddi Hasenpusch & Brock [all Necrosciinae], Pachymorpha spinosa Brock & Hasenpusch [Pachymorphinae], Davidrentzia valida Brock & Hasenpusch [Platycraninae], Micropodacanthus mouldsi Brock & Hasenpusch, Micropodacanthus sztrakai Brock & Hasenpusch, Paratropidoderus spinosus Brock & Hasenpusch and Podacanthus keyi Brock & Hasenpusch [Tropidoderinae]. A number of new combinations are proposed, new synonyms and incorrect synonymy corrected following detailed examination of type and other material: 1. (Lonchodinae): Austrocarausius Brock, 2000: Carausius macerrimus Brunner, 1907 is a new synonym of Austrocarausius nigropunctatus (Kirby, 1896). Denhama Werner, 1912: D. austrocarinata (Otte & Brock, 2005), D. longiceps (Brunner, 1907), D. striata (Sjöstedt, 1918) and D. eutrachelia (Westwood, 1859) are transferred from Hyrtacus Stål, 1875, the latter species also removed from synonymy with Hyrtacus coenosa (Gray, 1833). D. gracilis (Sjöstedt, 1918), a former Marcenia species, is also transferred. Hyrtacus Stål, 1875 (= Marcenia Sjöstedt, 1918 syn. n.): H. caurus (Tepper, 1905) comb. n. transferred from Lonchodes Gray, 1835 (three new synonyms also reported for this species: Bacillus peristhenellus Tepper, 1905, Hyrtacus cunctatrix (Sjöstedt, 1918) and Hyrtacus nigrogranulosus Sjöstedt, 1918). Marcenia frenchi (Wood-Mason, 1877) is a new synonym of Hyrtacus tuberculatus Stål, 1875. 2. (Necrosciinae): Austrosipyloidea Brock & Hasenpusch, gen. n.: A. carterus (Westwood, 1859) comb. n., transferred from Sipyloidea Brunner, 1893 (= Sipyloidea filiformis Redtenbacher, 1908 syn. n.). Candovia Stål, 1875 is removed from synonymy with Hyrtacus, along with the type species, C. coenosa. This has resulted in all former Australian species placed in Parasipyloidea Redtenbacher, 1908 being transferred to Candovia i.e. C. aberrata (Brunner, 1907) comb. n., C. annulata (Brunner, 1907) comb. n., C. granulosa (Brunner, 1907) comb. n., C. pallida (Sjöstedt, 1918), comb. n., C. spurcata (Brunner, 1907) comb. n. and C. strumosa (Redtenbacher, 1908) comb. n. In addition, C. evoneobertii (Zompro & Adis, 2001) comb. n. and C. peridromes (Westwood, 1859) comb. n. (including its new synonyms Clitarchus longipes Brunner, 1907, Bacunculus tener Brunner, 1907 and E. cercatus (Redtenbacher, 1908)) are transferred from Echetlus Stål, 1875. Cornicandovia Hasenpusch & Brock gen n.: C. australica (Redtenbacher, 1908) comb. n. Sipyloidea Brunner, 1893: S. bella (Tepper, 1905) comb. n. (new synonym S. ovabdita Rentz & John, 1987) is transferred from Necroscia Serville, 1838, S. caeca Sjöstedt, 1918 rev. stat., is removed from synonymy with Sipyloidea carterus (Westwood, 1859). Rhamphosipyloidea Redtenbacher, 1908: R. queenslandica (Sjöstedt, 1918) comb. n. is transferred from Sipyloidea, also removed from synonymy with carterus. 3. (Pachymorphinae): Pachymorpha Gray, 1835: P. pasithoe (Westwood, 1859) is a new synonym of P. simplicipes Serville, 1838. 4. (Eurycanthinae). Eurycantha Boisduval, 1835: E. sifia (Westwood, 1859) is a new synonym of E. calcarata Lucas, 1870. 5. (Phasmatinae): Vetilia Stål, 1875 is a new synonym of Acrophylla Gray, 1835, resulting in the transfer of these species to Acrophylla: A. enceladus (Gray, 1835) comb. n. and A. thoon (Stål, 1875) comb. n. Vetilia ligia Redtenbacher, 1908 is a new synonym of Acrophylla wuelfingi Redtenbacher, 1908. A. paula (Tepper, 1905) and A. aliena Redtenbacher, 1908 are new synonyms of A. nubilosa Tepper, 1905. A. caprella (Westwood, 1859) comb. n. is transferred from Ctenomorpha Gray, 1833. Anchiale Stål, 1875 (= Ctenomorphodes Karny, 1923 syn. n.), resulting in the transfer of A. briareus (Gray, 1834) comb. n. and A. tessulata (Gray, 1835) which is renamed Anchiale austrotessulata name nov., as tessulata Gray is preoccupied by Anchiale tessulata (Goeze, 1778). Austroclonistria Redtenbacher, 1908 is a new synonym of Arphax Stål, 1875, as A. serrulataa Redtenbacher, 1908) is a new synonym of Arphax dolomedes (Westwood, 1859). Ctenomorpha Gray, 1833: Paractenomorpha macrotegmus (Tepper, 1887) is confirmed as a synonym of Ctenomorpha marginipennis Gray, 1833. Hermarchus Stål, 1875: H. polynesicus Redtenbacher, 1908 is a new synonym of H. insignis (Kaup, 1871). Paronchestus Redtenbacher, 1908: P. cornutus (Tepper, 1905) comb. n. is transferred from Acrophylla Gray, 1835 and P. pasimachus (Westwood, 1859) from Onchestus Stål, 1875. 6. (Platycraninae): Megacrania batesii (Kirby, 1896) is removed from synonymy with Megacrania alpheus (Westwood, 1859). 7. (Tropidoderinae): Didymuria Kirby 1904: D. virginea Stål, 1875 is removed from synonymy with D. violescens (Leach, 1814). Lysicles Stål, 1877: L. periphanes (Westwood, 1859) comb. n. is transferred from Echetlus Stål, 1875. Tropidoderus Gray 1835: T. michaelseni Werner, 1912 is removed from synonymy with T. childrenii (Gray, 1833). 8. (Xeroderinae): Cooktownia Sjöstedt, 1918 becomes a new synonym of Xeroderus Gray, 1835, as Cooktownia plana Sjöstedt, 1918 is a new synonym of Xeroderus kirbii Gray, 1835. Lectotypes are designated for Clitarchus longipes Brunner, 1907, Sipyloidea filiformis Redtenbacher, 1908 and Vetilia ligula Redtenbacher, 1908. As a result of this work, there are now 104 Australian species (+ 1 subspecies) and in order to facilitate further research on these insects, an updated checklist is provided, also a detailed bibliography.
Numerous tree species’ seeds contain an ‘elaiosome’ that acts as a food reward for ants and thus induces dispersal of the seeds. Many stick and leaf insect species appear to have evolved a convergent adaptation for dispersal whereby the egg ‘capitulum’ serves to induce ants to pick up and carry their eggs. Here, we investigated whether the capitulum facilitates egg dispersal by ants in the Australian stick insect Eurycnema goliath. The total fatty acid composition of E. goliath egg capsules and egg capitula were characterized to identify potential signaling compounds. Removing capitula from E. goliath eggs significantly reduced the likelihood of eggs being carried into the nests of Rhytidoponera metallica ants. Furthermore, attaching capitula to inert objects (polystyrene balls) resulted in these objects being carried into nests by R. metallica. Several fatty acids were present on the egg capsule surface in only trace amounts, whereas they made up over 10 % of the dry weight of egg capitula. The fatty acid composition of egg capitula consisted mostly of palmitic acid (C16:0), linoleic acid (C18: 2n6c), oleic acid (C18:1n9c), linolenic acid (C18:3n3), and stearic acid (C18:0). Previously reported research has found that a diglyceride lipid species of oleic acid induces carrying behavior in R. metallica when added to inert artificial stimuli. Therefore, we propose that the dispersal mechanism of E. goliath eggs has converged upon the same chemical signaling pathway used by plants to exploit ant behavior.
Large phylogenomics data sets require fast tree inference methods, especially for maximum-likelihood (ML) phylogenies. Fast
programs exist, but due to inherent heuristics to find optimal trees, it is not clear whether the best tree is found. Thus,
there is need for additional approaches that employ different search strategies to find ML trees and that are at the same
time as fast as currently available ML programs. We show that a combination of hill-climbing approaches and a stochastic perturbation
method can be time-efficiently implemented. If we allow the same CPU time as RAxML and PhyML, then our software IQ-TREE found
higher likelihoods between 62.2% and 87.1% of the studied alignments, thus efficiently exploring the tree-space. If we use
the IQ-TREE stopping rule, RAxML and PhyML are faster in 75.7% and 47.1% of the DNA alignments and 42.2% and 100% of the protein
alignments, respectively. However, the range of obtaining higher likelihoods with IQ-TREE improves to 73.3–97.1%. IQ-TREE
is freely available at http://www.cibiv.at/software/iqtree.
Coalescent-based species delimitation methods combine population genetic and phylogenetic theory to provide an objective means for delineating evolutionarily significant units of diversity. The generalised mixed Yule coalescent (GMYC) and the Poisson tree process (PTP) are methods that use ultrametric (GMYC or PTP) or non-ultrametric (PTP) gene trees as input, intended for use mostly with single-locus data such as DNA barcodes.
Here, we assess how robust the GMYC and PTP are to different phylogenetic reconstruction and branch smoothing methods. We reconstruct over 400 ultrametric trees using up to 30 different combinations of phylogenetic and smoothing methods and perform over 2000 separate species delimitation analyses across 16 empirical data sets. We then assess how variable diversity estimates are, in terms of richness and identity, with respect to species delimitation, phylogenetic and smoothing methods.
The PTP method generally generates diversity estimates that are more robust to different phylogenetic methods. The GMYC is more sensitive, but provides consistent estimates for BEAST trees. The lower consistency of GMYC estimates is likely a result of differences among gene trees introduced by the smoothing step. Unresolved nodes (real anomalies or methodological artefacts) affect both GMYC and PTP estimates, but have a greater effect on GMYC estimates. Branch smoothing is a difficult step and perhaps an underappreciated source of bias that may be widespread among studies of diversity and diversification.
Nevertheless, careful choice of phylogenetic method does produce equivalent PTP and GMYC diversity estimates. We recommend simultaneous use of the PTP model with any model-based gene tree (e.g. RAxML) and GMYC approaches with BEAST trees for obtaining species hypotheses.
AliView is an alignment viewer and editor designed to meet the requirements of next-generation sequencing era phylogenetic datasets. AliView handles alignments of unlimited size in the formats most commonly used, i.e. FASTA, Phylip, Nexus, Clustal and MSF. The intuitive graphical interface makes it easy to inspect, sort, delete, merge and realign sequences as part of the manual filtering process of large datasets. AliView also works as an easy-to-use alignment editor for small as well as large datasets.
Availability and implementation: AliView is released as open-source software under the GNU General Public License, version 3.0 (GPLv3), and is available at GitHub (www.github.com/AliView). The program is cross-platform and extensively tested on Linux, Mac OS X and Windows systems. Downloads and help are available at http://ormbunkar.se/aliview
Contact:
anders.larsson@ebc.uu.se
Supplementary information:
Supplementary data are available at Bioinformatics online.
Sequence-based methods to delimit species are central to DNA taxonomy, microbial community surveys, and DNA meta-barcoding studies. Current approaches either rely on simple sequence similarity thresholds (OTU-picking) or on complex and compute-intensive evolutionary models. OTU-picking methods scale well on large data sets, but the results are highly sensitive to the similarity threshold. Coalescent-based species delimitation approaches often rely on Bayesian statistics and MCMC sampling, and can therefore only be applied to small data sets.
We introduce the Poisson Tree Processes (PTP) model to infer putative species boundaries on a given phylogenetic input tree. We also integrate PTP with our Evolutionary Placement Algorithm (EPA-PTP) to count the number of species in phylogenetic placements. We compare our approaches to popular OTU-picking methods and the General Mixed Yule Coalescent (GMYC) model. For de novo species delimitation, the stand-alone PTP model generally outperforms GMYC as well as OTU-picking methods when evolutionary distances between species are small. PTP neither requires an ultrametric input tree, nor a sequence similarity threshold as input. In the open reference species delimitation approach, EPA-PTP yields more accurate results than de novo species delimitation methods. Finally, EPA-PTP scales on large datasets because it relies on the parallel implementations of the EPA and RAxML, thereby allowing to delimit species in high-throughput sequencing data.
The code is freely available at www.exelixis-lab.org/software.html.
Alexandros.Stamatakis@h-its.org SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics on-line.
The CIPRES Science Gateway (CSG) provides browser-based access to computationally demanding phylogenetic codes run on large HPC resources. Since its release in December 2009, there has been a sustained, near-linear growth in the rate of CSG use, both in terms of number of users submitting jobs each month and number of jobs submitted. The average amount of computational time used per month by CSG increased more than 5-fold since its initial release. As of April 2012, more than 4,000 unique users have run parallel tree inference jobs on TeraGrid/XSEDE resources using the CSG. The steady growth in resource use suggests that the CSG is meeting an important need for computational resources in the Systematics/Evolutionary Biology community.
To ensure that XSEDE resources accessed through the CSG are used effectively, policies for resource consumption were developed, and an advanced set of management tools was implemented. Studies of usage trends show that these new management tools helped in distributing XSEDE resources across a large user population that has low-to-moderate computational needs.
In the first quarter of 2012, 30% of all active XSEDE users accessed computational resources through the CSG, while the analyses conducted by these users accounted for 0.7% of all allocable XSEDE computational resources. User survey results showed that the easy access to XSEDE/TeraGrid resources through the CSG had a critical and measurable scientific impact: at least 300 scholarly publications spanning all major groups within the Tree of Life have been enabled by the CSG since 2009. The same users reported that 82% of these publications would not have been possible without access to computational resources available through the CSG. The results indicate that the CSG is a critical and cost-effective enabler of science for phylogenetic researchers with limited resources.
We report a major update of the MAFFT multiple sequence alignment program. This version has several new features, including
options for adding unaligned sequences into an existing alignment, adjustment of direction in nucleotide alignment, constrained
alignment and parallel processing, which were implemented after the previous major update. This report shows actual examples
to explain how these features work, alone and in combination. Some examples incorrectly aligned by MAFFT are also shown to
clarify its limitations. We discuss how to avoid misalignments, and our ongoing efforts to overcome such limitations.
Singletons—species only known from a single specimen—and uniques—species that have only been collected once—are very common in biodiversity samples. Recent reviews suggest that in tropical arthropod samples, 30% of all species are represented by only one specimen (Bickel 1999; Novotny and Basset 2000; Coddington et al. 2009), with additional sampling helping little with eliminating rarity. Usually, such sampling only converts some of the singleton species to doubletons, with new singleton species being discovered in the process (Scharff et al. 2003; Coddington et al. 2009). Here, we first demonstrate that rare species are similarly common in specimen samples used for taxonomic research before we argue that the phenomenon of rarity has been insufficiently considered by the new quantitative techniques for species delimitation. Addressing this disconnect between theory and reality is pressing given that the last decade has seen a renewed interest in methods for species identification and delimitation (Sites and Marshall 2004; O’Meara 2010). Much of this interest has been fuelled by the availability of DNA sequences (Meier 2008). However, many newly proposed techniques implicitly or explicitly assume that all populations and species can be well sampled. But what is the value of these techniques if many species have only been collected once and/or are only known from one specimen? Here, we argue that all existing techniques need to be modified to accommodate the commonness of rarity and that all future techniques should be explicit about how rare species can be discovered and treated.
Background:
The demand for scientific biodiversity data is increasing, but taxonomic expertise is often limited or not available. DNA sequencing is a potential remedy to overcome this taxonomic impediment. Mitochondrial DNA is most commonly used, e.g., for species identification ("DNA barcoding"). Here, we present the first study in arthropods based on a near-complete species sampling of a family-level taxon from the entire Australian region. We aimed to assess how reliably mtDNA data can capture species diversity when many sister species pairs are included. Then, we contrasted phylogenetic subsampling with the hitherto more commonly applied geographical subsampling, where sister species are not necessarily captured.
Methodology/principal findings:
We sequenced 800 bp cox1 for 1,439 individuals including 260 Australian species (78% species coverage). We used clustering with thresholds of 1 to 10% and general mixed Yule Coalescent (GMYC) analysis for the estimation of species richness. The performance metrics used were taxonomic accuracy and agreement between the morphological and molecular species richness estimation. Clustering (at the 3% level) and GMYC reliably estimated species diversity for single or multiple geographic regions, with an error for larger clades of lower than 10%, thus outperforming parataxonomy. However, the rates of error were higher for some individual genera, with values of up to 45% when very recent species formed nonmonophyletic clusters. Taxonomic accuracy was always lower, with error rates above 20% and a larger variation at the genus level (0 to 70%). Sørensen similarity indices calculated for morphospecies, 3% clusters and GMYC entities for different pairs of localities was consistent among methods and showed expected decrease over distance.
Conclusion/significance:
Cox1 sequence data are a powerful tool for large-scale species richness estimation, with a great potential for use in ecology and β-diversity studies and for setting conservation priorities. However, error rates can be high in individual lineages.
The capitulum on the eggs of the South African stick insect Bacillus? coccyx functions in a similar way as elaiosomes on seeds. Ants use the capitulum to carry the eggs, removing and eating it without reducing egg viability.
A new species of Phasmatodea, Echetlus evoneobertii ZOMPRO & ADIS n. sp., is described from Southern Brazil, where it is likely to have been introduced. This species is destructive to Eucalyptus urophylla S. T. BLAKE (Myrtaceae) which was imported from Australia. Ernodes sumatranus REDTENBACHER, 1908, is designated as type-species for Ernodes REDTENBACHER, 1908, which is restituted as valid genus. Bacunculus tener BRUNNER V. W., 1907, is a new synonym of the type-species Echetlus peristhenes (WESTWOOD, 1859). With that Echetlus includes the following species: Parasipyloidea cercata REDTENBACHER, 1908, Bacillus peridromes WESTWOOD, 1859, Anophelepis periphanes WESTWOOD, 1859, Bacillus peristhenes WESTWOOD, 1859.
A new approach to rapid sequence comparison, basic local alignment search tool (BLAST), directly approximates alignments that optimize a measure of local similarity, the maximal segment pair (MSP) score. Recent mathematical results on the stochastic properties of MSP scores allow an analysis of the performance of this method as well as the statistical significance of alignments it generates. The basic algorithm is simple and robust; it can be implemented in a number of ways and applied in a variety of contexts including straightforward DNA and protein sequence database searches, motif searches, gene identification searches, and in the analysis of multiple regions of similarity in long DNA sequences. In addition to its flexibility and tractability to mathematical analysis, BLAST is an order of magnitude faster than existing sequence comparison tools of comparable sensitivity.
We describe "universal" DNA primers for polymerase chain reaction (PCR) amplification of a 710-bp fragment of the mitochondrial cytochrome c oxidase subunit I gene (COI) from 11 invertebrate phyla: Echinodermata, Mollusca, Annelida, Pogonophora, Arthropoda, Nemertinea, Echiura, Sipuncula, Platyhelminthes, Tardigrada, and Coelenterata, as well as the putative phylum Vestimentifera. Preliminary comparisons revealed that these COI primers generate informative sequences for phylogenetic analyses at the species and higher taxonomic levels.
The evolution of wings was the central adaptation allowing insects to escape predators, exploit scattered resources, and disperse into new niches, resulting in radiations into vast numbers of species. Despite the presumed evolutionary advantages associated with full-sized wings (macroptery), nearly all pterygote (winged) orders have many partially winged (brachypterous) or wingless (apterous) lineages, and some entire orders are secondarily wingless (for example, fleas, lice, grylloblattids and mantophasmatids), with about 5% of extant pterygote species being flightless. Thousands of independent transitions from a winged form to winglessness have occurred during the course of insect evolution; however, an evolutionary reversal from a flightless to a volant form has never been demonstrated clearly for any pterygote lineage. Such a reversal is considered highly unlikely because complex interactions between nerves, muscles, sclerites and wing foils are required to accommodate flight. Here we show that stick insects (order Phasmatodea) diversified as wingless insects and that wings were derived secondarily, perhaps on many occasions. These results suggest that wing developmental pathways are conserved in wingless phasmids, and that 're-evolution' of wings has had an unrecognized role in insect diversification.
The concept that complex ancestral traits can never be recovered after their loss is still widely accepted, despite phylogenetic and molecular approaches suggest instances where phenotypes may have been lost throughout the evolutionary history of a clade and subsequently reverted back in derived lineages. One of the first and most notable examples of such a process is wing evolution in phasmids; this polyneopteran order of insects, which comprises stick and leaf insects, has played a central role in initiating a long-standing debate on the topic. In this study, a novel and comprehensive time tree including over 300 Phasmatodea species is used as a framework for investigating wing evolutionary patterns in the clade. Despite accounting for several possible biases and sources of uncertainty, macroevolutionary analyses consistently revealed multiple reversals to winged states taking place after their loss, and reversibility is coupled with higher species diversification rates. Our findings support a loss of or reduction in wings that occurred in the lineage leading to the extant phasmid most recent common ancestor, and brachyptery is inferred to be an unstable state unless co-opted for nonaerodynamic adaptations. We also explored how different assumptions of wing reversals probability could impact their inference: we found that until reversals are assumed to be over 30 times more unlikely than losses, they are consistently inferred despite uncertainty in tree and model parameters. Our findings demonstrate that wing evolution is a reversible and dynamic process in phasmids and contribute to our understanding of complex trait evolution.
http://phasmida.speciesfile.org
The Phasmida Species File (PSF) is a taxonomic database of the world's Phasmida (stick and leaf insects, known as walking sticks and walking leaves in the U.S.). There is full synonymic and taxonomic information for 3,350 valid species and 5,300 taxonomic names, 37,500 citations to 3,178 references, over 7,600 specimen records and 16,800 images of 75% of valid species, with more being added to on a regular basis. Another future aim of this database is to provide high quality images of living phasmids in the wild. The PSF is annually in fed into the catalogue of life (Species 2000: Naturalis, Leiden, the Netherlands).
Model-based molecular phylogenetics plays an important role in comparisons of genomic data, and model selection is a key step in all such analyses. We present ModelFinder, a fast model-selection method that greatly improves the accuracy of phylogenetic estimates by incorporating a model of rate heterogeneity across sites not previously considered in this context and by allowing concurrent searches of model space and tree space.
The eggs of many stick insect species (Phasmatodea) bear a striking resemblance to seeds. These eggs are not only similar in size, shape, colour and texture to seeds, but in many species bear a knob-like structure known as a capitulum. This structure resembles an elaiosome, a lipid-rich appendage on some seeds known to be an adaptation for burial by ants. Capitula, like elaiosomes, promote removal of eggs to ant nests and buried eggs suffer reduced rates of parasitism by wasps. Phasmatid nymphs are capable of emerging from eggs buried under 6 cm of soil. Capitula are found only in those phasmatid species which drop eggs freely on to litter and not in species which bury eggs or glue them to vegetation. Elaiosomes and capitula are both adaptations to use ant mutualists for burial, a striking example of evolutionary convergence between the plant and animal kingdoms. -from Authors
The barcoding approach was applied to analyze 16 Australian morphospecies of the order Phasmida, with the aim to test if it could be suitable as a tool for phasmid species identification and if its discrimination power would allow uncovering of cryptic diversity. Both goals were reached. Eighty-two specimens representing twelve morphospecies (Sipyloidea sp. A, Candovia annulata, Candovia sp. A, Candovia sp. B, Candovia sp. C, Denhama austrocarinata, Xeroderus kirbii, Parapodacanthus hasenpuschorum, Tropidoderus childrenii, Cigarrophasma tessellatum, Acrophylla wuelfingi, Eurycantha calcarata) were correctly recovered as clades through the molecular approach, their sequences forming monophyletic and well-supported clusters. In four instances, Neighbor-Joining tree and barcoding gap analyses supported either a specific (Austrocarausius mercurius, Anchiale briareus) or a subspecific (Anchiale austrotessulata, Extatosoma tiaratum) level of divergence within the analyzed morphospecies. The lack of an appropriate database of homologous coxI sequences prevented more detailed identification of undescribed taxa.
John Skelhorn introduces masquerade, a strategy of prey animals to resemble inanimate (and inedible) objects.
Copyright © 2015 Elsevier Ltd. All rights reserved.
1. The generalized mixed Yule-coalescent (GMYC) model has become one of the most popular approaches for species delimitation based on single-locus data, and it is widely used in biodiversity assessments and phylogenetic community ecology. We here examine an array of factors affecting GMYC resolution (tree reconstruction method, taxon sampling coverage/taxon richness, and geographic sampling intensity/geographic scale).
2. We test GMYC performance based on empirical data (DNA barcoding of the Romanian butterflies) on a solid taxonomic framework (i.e. all species are thought to be described and can be determined with independent sources of evidence). The dataset is comprehensive (176 species), and intensely and homogeneously sampled (1303 samples representing the main populations of butterflies in this country). Taxonomy was assessed based on morphology, including linear and geometric morphometry when needed.
3. The number of GMYC entities obtained constantly exceeds the total number of morphospecies in the dataset. We show that approximately 80% of the species studied are recognised as entities by GMYC. Interestingly, we show that this percentage is practically the maximum that a single threshold method can provide for this dataset. Thus the ca. 20% of failures are attributable to intrinsic properties of the COI polymorphism: overlap in inter- and intraspecific divergences and non-monophyly of the species likely because of introgression or lack of independent lineage sorting.
4. Our results demonstrate that this method is remarkably stable under a wide array of circumstances, including most phylogenetic reconstruction methods, high singleton presence (up to 95%), taxon richness (above five species), and presence of gaps in intraspecific sampling coverage (removal of intermediate haplotypes). Hence, the method is useful to designate an optimal divergence threshold in an objective manner, and to pinpoint potential cryptic species that are worth being studied in detail. However, the existence of a substantial percentage of species wrongly delimited indicates that GMYC cannot be used as sufficient evidence for evaluating the specific status of particular cases without additional data.
5. Finally, we provide a set of guidelines to maximize efficiency in GMYC analyses and discuss the range of studies that can take advantage of the method.
Species delimitation is the act of identifying species-level biological diversity. In recent years, the field has witnessed a dramatic increase in the number of methods available for delimiting species. However, most recent investigations only utilize a handful (i.e. 2-3) of the available methods, often for unstated reasons. Because the parameter space that is potentially relevant to species delimitation far exceeds the parameterization of any existing method, a given method necessarily makes a number of simplifying assumptions, any one of which could be violated in a particular system. We suggest that researchers should apply a wide range of species delimitation analyses to their data and place their trust in delimitations that are congruent across methods. Incongruence across the results from different methods is evidence of either a difference in the power to detect cryptic lineages across one or more of the approaches used to delimit species and could indicate that assumptions of one or more of the methods have been violated. In either case, the inferences drawn from species delimitation studies should be conservative, for in most contexts it is better to fail to delimit species than it is to falsely delimit entities that do not represent actual evolutionary lineages.
The holomediterranean species Bacillus rossius includes many subspecific taxa, which can be characterized both on the basis of electrophoretic allozyme frequencies and egg chorionic pattern. At present, 8 subspecies have been identified; they are, following a clock‐wise direction from the south‐eastern to the north‐western: B.r. tripolitanus A, B.r. tripolitanus B, B.r. lobipes, B.r. montalentii, B.r. medeae, B.r. catalauniae, B.r. rossius, and B.r. redtenbacheri. Opercular details do not unequivocally specify intraspecific taxa, however these taxa sea can be clearly recognized from the fine chorionic SEM patterns of eggs laid by field collected females. B.r. tripolitanus A and B.r. tripolitanus B show a pattern of single small mamelons, while all the others have a ribbon design, more often with a lace‐net distribution. In B.r. redtenbacheri such a pattern breaks down to give strings of different size mamelons. It would seem that the lace‐net ribbon pattern, owing to its frequent occurence and geographically wide distribution, is the ancestral one for the species. This also appears to be supported by comparative findings in related species such as B. grandii and all the eastern Bacillus species. The ootaxonomical observations confirm electrophoretic evidence demonstrating that in B. rossius parthenogenesis has arisen several times, independently in different areas of the species’ range.
Modern applications of Sanger DNA sequencing often require converting a large number of chromatogram trace files into high-quality DNA sequences for downstream analyses. Relatively few nonproprietary software tools are available to assist with this process. SeqTrace is a new, free, and open-source software application that is designed to automate the entire workflow by facilitating easy batch processing of large numbers of trace files. SeqTrace can identify, align, and compute consensus sequences from matching forward and reverse traces, filter low-quality base calls, and end-trim finished sequences. The software features a graphical interface that includes a full-featured chromatogram viewer and sequence editor. SeqTrace runs on most popular operating systems and is freely available, along with supporting documentation, at http://seqtrace.googlecode.com/.
The term capitulum is defined and a survey of the known eggs of the Phasmida is made to show the occurrence of this structure. Its value as a taxonomic criterion is considered.
The relationship between egg shape and presence or absence of a capitulum is considered. The distribution of capitula of different types within the order Phasmida is reviewed. These tend to confirm tribal and subfamily groupings but suggest that the suborder Anareolatae is polyphyletic and some suggestions are made for its regrouping. The species of Phasmida which have been recently studied from an ootaxonomic viewpoint are surveyed.
Within uncharacterized groups, DNA barcodes, short DNA sequences that are present in a wide range of species, can be used to assign organisms into species. We propose an automatic procedure that sorts the sequences into hypothetical species based on the barcode gap, which can be observed whenever the divergence among organisms belonging to the same species is smaller than divergence among organisms from different species. We use a range of prior intraspecific divergence to infer from the data a model-based one-sided confidence limit for intraspecific divergence. The method, called Automatic Barcode Gap Discovery (ABGD), then detects the barcode gap as the first significant gap beyond this limit and uses it to partition the data. Inference of the limit and gap detection are then recursively applied to previously obtained groups to get finer partitions until there is no further partitioning. Using six published data sets of metazoans, we show that ABGD is computationally efficient and performs well for standard prior maximum intraspecific divergences (a few per cent of divergence for the five data sets), except for one data set where less than three sequences per species were sampled. We further explore the theoretical limitations of ABGD through simulation of explicit speciation and population genetics scenarios. Our results emphasize in particular the sensitivity of the method to the presence of recent speciation events, via (unrealistically) high rates of speciation or large numbers of species. In conclusion, ABGD is fast, simple method to split a sequence alignment data set into candidate species that should be complemented with other evidence in an integrative taxonomic approach.