The effects of fossil taxa, hypothetical predicted ancestors, and a molecular scaffold on pseudoextinction analyses of extant placental orders

Pseudoextinction analyses, which simulate extinction in extant taxa, use molecular phylogenetics to assess the accuracy of morphological phylogenetics. Previous pseudoextinction analyses have shown a failure of morphological phylogenetics to place some individual placental orders in the correct superordinal clade. Recent work suggests that the inclusion of hypothetical ancestors of extant placental clades, estimated by ancestral state reconstructions of morphological characters, may increase the accuracy of morphological phylogenetic analyses. However, these studies reconstructed direct hypothetical ancestors for each extant taxon based on a well-corroborated molecular phylogeny, which is not possible for extinct taxa that lack molecular data. It remains to be determined if pseudoextinct taxa, and by proxy extinct taxa, can be accurately placed when their immediate hypothetical ancestors are unknown. To investigate this, we employed molecular scaffolds with the largest available morphological data set for placental mammals. Each placental order was sequentially treated as pseudoextinct by exempting it from the molecular scaffold and recoding soft morphological characters as missing for all its constituent species. For each pseudoextinct data set, we omitted the pseudoextinct taxon and performed a parsimony ancestral state reconstruction to obtain hypothetical predicted ancestors. Each pseudoextinct order was then evaluated in seven parsimony analyses that employed combinations of fossil taxa, hypothetical predicted ancestors, and a molecular scaffold. In treatments that included fossils, hypothetical predicted ancestors, and a molecular scaffold, only 8 of 19 pseudoextinct placental orders (42%) retained the same interordinal placement as on the molecular scaffold. In treatments that included hypothetical predicted ancestors but not fossils or a scaffold, only four placental orders (21%) were recovered in positions that are congruent with the scaffold. These results indicate that hypothetical predicted ancestors do not increase the accuracy of pseudoextinct taxon placement when the immediate hypothetical ancestor of the taxon is unknown. Hypothetical predicted ancestors are not a panacea for morphological phylogenetics.

The burrowing origin of modern snakes

Modern snakes probably originated as habitat specialists, but it controversial unclear whether they were ancestrally terrestrial burrowers or marine swimmers. We used x-ray virtual models of the inner ear to predict the habit ofDinilysia patagonica, a stem snake closely related to the origin of modern snakes. Previous work has shown that modern snakes perceive substrate vibrations via their inner ear. Our data show thatD. patagonicaand modern burrowing squamates share a unique spherical vestibule in the inner ear, as compared with swimmers and habitat generalists. We built predictive models for snake habit based on their vestibular shape, which estimatedD. patagonicaand the hypothetical ancestor of crown snakes as burrowers with high probabilities. This study provides an extensive comparative data set to test fossoriality quantitatively in stem snakes, and it shows that burrowing was predominant in the lineages leading to modern crown snakes.

Layers of Chinese Loanwords in Protosouthwestern Tai as Evidence for the Dating of the Spread of Southwestern Tai

The current ethno-linguistic landscape of mainland Southeast Asia is a result of the spread of Tai speakers from southern China. This study examines Chinese loanwords in Proto-Southwestern Tai, the hypothetical ancestor of all modern Southwestern Tai varieties and proposes a dating of the spread of Southwestern Tai languages. By comparing the reconstructed Proto-Southwestern Tai forms with corresponding Chinese forms, four layers of Chinese loanwords existed in Proto- Southwestern Tai, namely Pre-Later Han, Later Han Chinese, Early Middle Chinese, and Late Middle Chinese layers. These layers indicate that Proto-Southwestern Tai was in contact with Chinese at least until the Tang era. In collaboration with non-linguistic evidence, this paper therefore proposes that Southwestern Tai languages began to spread southward sometime during the eighth and the tenth centuries CE.

Clonal Species Trichoderma parareesei sp. nov. Likely Resembles the Ancestor of the Cellulase Producer Hypocrea jecorina/T. reesei

ABSTRACT We have previously reported that the prominent industrial enzyme producer Trichoderma reesei (teleomorph Hypocrea jecorina; Hypocreales, Ascomycota, Dikarya) has a genetically isolated, sympatric sister species devoid of sexual reproduction and which is constituted by the majority of anamorphic strains previously attributed to H. jecorina/T. reesei. In this paper we present the formal taxonomic description of this new species, T. parareesei, complemented by multivariate phenotype profiling and molecular evolutionary examination. A phylogenetic analysis of relatively conserved loci, such as coding fragments of the RNA polymerase B subunit II (rpb2) and GH18 chitinase (chi18-5), showed that T. parareesei is genetically invariable and likely resembles the ancestor which gave raise to H. jecorina. This and the fact that at least one mating type gene of T. parareesei has previously been found to be essentially altered compared to the sequence of H. jecorina/T. reesei indicate that divergence probably occurred due to the impaired functionality of the mating system in the hypothetical ancestor of both species. In contrast, we show that the sexually reproducing and correspondingly more polymorphic H. jecorina/T. reesei is essentially evolutionarily derived. Phenotype microarray analyses performed at seven temperature regimens support our previous speculations that T. parareesei possesses a relatively high opportunistic potential, which probably ensured the survival of this species in ancient and sustainable environment such as tropical forests.

Biology and Management of Dogfish Sharks

Abstract.—Squaliform sharks constitute a monophyletic group of predominantly deep-water neoselachians. Their fossil record mainly consists of isolated teeth; complete skeletons or skeletal remains are very rare. The quality of the fossil record of squaliform sharks is analyzed using a phylogenetic hypothesis based on a supertree to establish the timing of cladogenetic events, those related to descent from a common ancestor, and gaps in the fossil record. The supertree is the most inclusive estimate of squaliform interrelationships that has been proposed to date and contains 23 fossil and extant members of all major groups. In addition, the simple completeness metric is used to examine the quality of the fossil record of squaliforms as an independent measure. Although different (48% and 61%, respectively), both measures indicate that the fossil record of squaliforms is very incomplete considering that most living and extinct squaliforms are deep-water sharks and corresponding sediments are very scarce. Gaps in the fossil record range from 5 to 100 million years. The most basal and stratigraphically oldest group within Squaliformes consists of <em>Squalus </em>and †<em>Protosqualus</em>¹<em>. </em>The phylogenetic hypothesis indicates a gap in the fossil record of <em>Squalus </em>spp. of about 25–30 million years. Our results show a postJurassic origination of squaliforms in the shallow waters of the northern Tethyal margin. The hypothetical ancestor of squaliforms is characterized by two dorsal fin spines and absence of dignathic heterodonty (the morphology of upper and lower teeth differs significantly). Lower teeth are characterized by a slightly oblique basal root face and overlapping upper teeth. Although disappearance and appearance of organisms is a fact of life, the very long geologic range and success of <em>Squalus </em>highlights the need for very careful management of its current population crisis, which is due to causes that never occurred before in Earth’s history–the anthropogenetic impact.

Cytogenetics and morphotaxonomy of the Simulium (Gomphostilbia) ceylonicum species group (Diptera: Simuliidae) in Thailand

The polytene chromosomes of 1,612 larvae of three described morphospecies in the Simulium (Gomphostilbia) ceylonicum species group—S. asakoae, S. inthanonense, and S. sheilae—were examined from 52 sites in Thailand. A standard map for the S. ceylonicum group was established. Ten cytoforms, plus an eleventh from the literature, are revealed on the basis of unique suites of fixed and floating inversions; sex chromosomes are microscopically undifferentiated in all cytoforms. A cytodendrogram, based on shared inversions, shows seven lineages in a polytomy derived from a hypothetical ancestor. Morphological descriptions of the known life stages of each cytoform and keys to larvae, pupae, and polytene chromosomes also are provided. Despite small sample sizes for some cytoforms, all segregates appear to be good species, supported by both chromosomal and morphological evidence. Three reproductively isolated cytoforms for which adequate material is available are formally described as new species. The existence of chromosomally distinct entities within established morphospecies of the S. ceylonicum group supports a recurrent trend of hidden biodiversity in Southeast Asian black flies. The differentiation of taxa that we found in the S. ceylonicum group between northern and southern Thailand conforms to a similar biogeographic trend in diverse organisms.

The spondylium and related structures in the clitambonitidine brachiopods

Development of the ventral muscle field has been studied in 12 genera of clitambonitidine brachiopods: Eremotoechia, Clitambonites, Vellamo, Pahlenella, Lacunarites, Oslogonites, Gonambonites, Estlandia, Anchigonites, Kullervo, Antigonambonites, and Raunites. The last two have a pseudospondylium instead of spondylium, which links them to polytoechiids. The spondylium of the studied genera is not derived from convergent dental plates, but develops from the free plate in the early phase of morphogenesis. The early growth stages of spondylium triplex and simplex are identical. The hypothetical ancestor of clitambonitidines with spondylium was presumably a protorthid-like brachiopod probably of the mid-Cambrian age. On the contrary, polytoechiids, as well as Antigonambonites and Raunites, may have been derived from a late Cambrian billingsellid with dental plates. The polyphyly of clitambonitidines follows from development of their ventral muscle field.

Evolution of the Major Pilus Gene Cluster ofHaemophilus influenzae

ABSTRACT Haemophilus influenzae is a ubiquitous colonizer of the human respiratory tract and causes diseases ranging from otitis media to meningitis. Many H. influenzae isolates express pili (fimbriae), which mediate adherence to epithelial cells and facilitate colonization. The pilus gene (hif) cluster of H. influenzae type b maps between purE andpepN and resembles a pathogenicity island: it is present in invasive strains, absent from the nonpathogenic Rd strain, and flanked by direct repeats of sequence at the insertion site. To investigate the evolution and role in pathogenesis of the hif cluster, we compared the purE-pepN regions of various H. influenzae laboratory strains and clinical isolates. Unlike Rd, most strains had an insert at this site, which usually was the only chromosomal locus of hif DNA. The inserts are diverse in length and organization: among 20 strains, nine different arrangements were found. Several nontypeable isolates lack hif genes but have two conserved open reading frames (hicA andhicB) upstream of purE; their inferred products are small proteins with no data bank homologs. Other isolates havehif genes but lack hic DNA or have combinations of hif and hic genes. By comparing these arrangements, we have reconstructed a hypothetical ancestral genotype, the extended hif cluster. The hif region of INT1, an invasive nontypeable isolate, resembles the hypothetical ancestor. We propose that a progenitor strain acquired the extended cluster by horizontal transfer and that other variants arose as deletions. The structure of the hif cluster may correlate with colonization site or pathogenicity.

The Australian moth family Lophocoronidae and the basal phylogeny of the Lepidoptera – Glossata

The endemic Australian primitive moth family Lophocoronidae is reviewed. The family was previously known from three species represented by male 'museum' specimens only. The family now consists of one genus, Lophocorona Common, with six species of which three (L. robinsoni, L. commoni and L. flavicosta) are here described as new. L. robinsoni differs markedly from the remaining species in wing pattern and phenology, but all species have very similar male genitalia. Females of two species (L. robinsoni and L. commoni) are described. All species and parts of their male genitalia are illustrated; a key to all species is given. All new distribution records are listed and the known Australian range of the family now extends from east of Perth to south of Sydney. Lophocoronid structure is surveyed, including information on aspects of the soft anatomy of L. pediasia Common: cephalic, spiracular, abdominal base and male genital musculature, male internal genitalia, alimentary canal, gross structure of the central nervous system (CNS) and thoracic aorta. The most significant findings include the following: extrinsic labral muscles are absent; the relatively well-developed mandibles have no musculature, hence the (unknown) lophocoronid pupa must be adecticous; there is no intrinsic proboscis musculature; the posterolateral comer of the laterocervicale covers the anepisternal tooth; an anterior pronotal plate is present; the mesobasistemum is markedly produced anteriorly; wingsurface scales are largely hollow; a sizeable metapostphragma is present; the female has a piercing oviscapt similar to that of Eriocraniidae and Acanthopteroctetidae; a stomodaeal crop is well developed, extending into the abdomen, and followed by a narrow tubular portion in front of the mesenteron; there are four malpighian tubules, each opening into the gut; the deutocerebral lobes meet in front of the posterionnost pharyngeal sucking pump dilator (forming a 'deutocerebral loop'); the abdominal nerve cord has five ganglionic masses and thick connective tissue on top; the metathoracic aorta touches the dorsal pulsatile diaphragm. Six basal clades are recognised within the Lepidoptera-Glossata: (1) Eriocraniidae, (2) Acanthopteroctetidae (including Catapterix), (3) Lophocoronidae, (4) Neopseustidae, (5) Exoporia and (6) Heteroneura. Putative autapomorphies are listed and discussed for each. Several structural traits are compared throughout the six clades, and 47 potentially phylogenetically informative characters are identified (Appendices 1 and 2). Analysis of these characters with Hennig86, by using a hypothetical ancestor (reconstructed on the basis of character state distribution within the non-glossatan moth grade), yields a single shortest tree: Eriocraniidae + (Acanthopteroctetidae + (Lophocoronidae + (Neopseustidae + (Exoporia + Heteroneura)))). This tree is compared with a number of competing trees; it is concluded to be the most biologically meaningful one. The formal classification of the Glossata is discussed. The Acanthopteroctetidae are assigned to a superfamily of their own. Redundant taxon names above familygroup (Dacnonypha, Lophocoronina and Neopseustina) are discarded. The new name Coelolepida is introduced for the high-rank taxon comprising all Glossata except the Eriocraniidae; it is characterised primarily by the acquisition of hollow wing-surface scales and an apomorphic configuration of the first thoracic spiracle. Some ecological and conservation-related implications of the new insights in glossatan phylogeny are outlined.