Monophyly or polyphyly of the order Rodentia: Possible conflict between morphological and molecular interpretations

Recent analyses of amino acid sequence data from selected proteins inCavia, Rattus, Homo, Bos, Sus, and a few additional rodents and other eutherians suggested that Rodentia is not a monophyletic taxon and thatCavia and other hystricognaths may have branched off earlier than the separation between Muroidea and Primates during mammalian evolution. Because this hypothesis of polyphyly is contrary to the otherwise unanimous recognition of rodent monophyly, we have reevaluated the morphological and developmental evidence from the cranium, dentition, postcranial skeleton, and fetal membranes for the taxa Hystricognathi, Muroidea, other Rodentia, Primates, Artiodactyla, and Lagomorpha, as well as for the eutherian morphotype. Our character analyses provide strong corroboration for the traditional hypothesis of rodent monophyly and lend additional support to the suggestion that Lagomorpha is the sister taxon of Rodentia. Our survey of published molecular data furnishes little or no support for the proposed hypothesis of rodent polyphyly. We conclude that this hypothesis is the result of poor sampling of sequence data from rodents and other eutherians, rather than any inherent difficulties in the use of molecular evidence for the assessment of mammalian evolution. The available molecular data suggest thatCavia differs considerably from other hystricognaths in many proteins, but the reasons for this remain to be investigated.     

Phylogenetics and seed morphology of African Nymphoides (Menyanthaceae)

We evaluated the boundaries among Nymphoides (Menyanthaceae) species in Africa, a region where the genus has received relatively little attention. We gathered morphological data from seeds using light and scanning electron microscopy, and we conducted molecular phylogenetic analyses using nuclear sequence data from the internal transcribed spacer (ITS) region. Morphological and molecular features distinguished six species and affirmed their respective geographic ranges. No African specimens were attributable to Nymphoides indica, even though this paleotropical species previously had been understood to grow in Africa. We establish the new combination Nymphoides senegalensis (G. Don) Tippery, based on an established African basionym, to accommodate the specimens formerly identified as N. indica. Phylogenetic analyses resolved two distinct clades containing African species. The majority of African species are closely related to neotropical species, with which they share similar petal ornamentation. The morphologically distinct N. ezannoi shares floral and phylogenetic similarity with species from North America and Asia. Results presented here support prior hypotheses that allopolyploid species in the Americas may have originated from one or more parental lineages in Africa. Seed morphological characters remain some of the most reliable features for identifying species, particularly for herbarium specimens lacking observable floral characters.     

长孢假小蜜环菌，一种孢子杆状的亚洲产新种

根据形态和分子系统发育证据,描述采自我国西南的新种长孢假小蜜环菌Pseudoarmillariella bacillaris.与假小蜜环菌属Pseudoarmillariella已知分布于北美-中美洲和大洋洲的2个物种相比,该新种的突出特征是担孢子杆状.在亚洲发现假小蜜环菌属真菌,表明该属的地理分布范围与过去已知的相比要广泛得多.     

A new Late Cretaceous family of Hymenoptera, and phylogeny of the Plumariidae and Chrysidoidea (Aculeata)

The taxonomic placement of an enigmatic species of wasp known from two specimens in Late Cretaceous New Jersey amber is investigated through cladistic analyses of 90 morphological characters for 33 terminals ranging across non-Aculeata, non-Chrysidoidea, most subfamilies of Chrysidoidea and all genera of Plumariidae (the family to which the fossils were initially assigned), based on use of exemplars. The fossil taxon is apparently basal in Chrysidoidea, most likely sister to Plumariidae, but perhaps sister to the remaining chrysidoids, or even sister to Chrysidoidea as a whole. It is described as representing a new family, Plumalexiidaefam. n., containing a single species, Plumalexius rasnitsynigen. et sp. n. Previous estimates of relationships for the genera of Plumariidae and for the higher taxa of Chrysidoidea are mostly confirmed. The importance of outgroup choice, and additivity and weighting of characters are demonstrated.     

First report of Melanoides tuberculata (Mollusca: Thiaridae) harboring a xiphidiocercaria in Brazil: A new parasite introduced in the Americas?

Xiphidiocercariae were found in the invasive snail Melanoides tuberculata collected during a malacological survey in Ceará-Mirim, State of Rio Grande do Norte, Northeastern Brazil in November 2018 and submitted to morphological and molecular analyses. The morphology revealed similarities between the larvae here reported for the first time in M. tuberculata from Brazil and other xiphidiocercariae described in thiarid snails from Asia and Africa. Phylogenetic analyses based on 28S and ITS-2 sequences revealed that the larvae correspond to an unidentified species of the family Lecithodendriidae. Aspects related to the morphology and taxonomy of xiphidiocercariae found in M. tuberculata are briefly discussed. It is possible that the parasite here reported is a newly introduced species transmitted by M. tuberculata in the American continent.     

The use of molecular and morphological characters to resolve the taxonomic identity of cryptic species: the case of Miniopterus manavi (Chiroptera, Miniopteridae)

Based on recent molecular phylogenetic studies, the Old World bat family Miniopteridae, composed of species in the genus Miniopterus , has been shown to contain complex paraphyletic species, many of which are cryptic based on convergent morphological characters. Herein we resolve the phylogenetic relationships and taxonomy of the species complex M . manavi on Madagascar and in the Comoro Archipelago, where these animals occur in different bioclimatic zones. First using mitochondrial cytochrome- b sequence data to define clades and then morphology to corroborate the molecular data, including comparisons to type specimens, we demonstrate that animals identified as this taxon are a minimum of three species: M . manavi sensu stricto occurs in at least the central portion of the Central Highlands; M . griveaudi has a broad distribution in lowland northern and central western Madagascar and the Comoros (Anjouan and Grande Comore), and M . aelleni sp. n. has been found in northern and western Madagascar and the Comoros (Anjouan). In each case, these three clades were genetically divergent and monophyletic and the taxa are diagnosable based on different external and craniodental characters. One aspect that helped to define the systematics of this group was isolation of DNA from one of the paratypes of M. manavi collected in 1896 and new topotypic material. Miniopterus manavi is most closely allied to a recently described species, M. petersoni . At several localities, M . griveaudi and M . aelleni have been found in strict sympatry, and together with M. manavi sensu stricto show considerable convergence in morphological characters, but are not immediate sister taxa. In defining and resolving the systematics of cryptic species, such as miniopterid bats, the process of defining clades with molecular tools, segregating the specimens accordingly, and identifying corroborative morphological characters has been notably efficient.     

Taxonomic classification of the reef coral family Mussidae (Cnidaria: Anthozoa: Scleractinia)

Molecular analyses are transforming our understanding of the evolution of scleractinian corals and conflict with traditional classification, which is based on skeletal morphology. A new classification system, which integrates molecular and morphological data, is essential for documenting patterns of biodiversity and establishing priorities for marine conservation, as well as providing the morphological characters needed for linking present‐day corals with fossil species. The present monograph is the first in a series whose goal is to develop such an integrated system. It addresses the taxonomic relationships of 55 Recent zooxanthellate genera (one new) in seven families (one new), which were previously assigned to the suborder Faviina (eight genera are transferred to incertae sedis). The present monograph has two objectives. First, we introduce the higher‐level classification system for the 46 genera whose relationships are clear. Second, we formally revise the taxonomy of those corals belonging to the newly discovered family‐level clade (restricted today to the western Atlantic and Caribbean regions); this revised family Mussidae consists of ten genera (one of which is new) and 26 species that were previously assigned to the ‘traditional’ families Faviidae and Mussidae. To guide in discovering morphologic characters diagnostic of higher‐level taxa, we mapped a total of 38 morphologic characters [19 macromorphology, eight micromorphology, 11 microstructure] onto a molecular tree consisting of 67 species [22 Indo‐Pacific and seven Atlantic species in the traditional family Faviidae; 13 Indo‐Pacific and ten Atlantic species in the traditional family Mussidae; 13 species in the traditional families Merulinidae (5), Pectiniidae (7), and Trachyphylliidae (1); two Atlantic species of traditional Montastraea], and trace character histories using parsimony. To evaluate the overall effectiveness of morphological data in phylogeny reconstruction, we performed morphology‐based phylogenetic analyses using 27 (80 states) of the 38 characters, and compared morphological trees with molecular trees. The results of the ancestral state reconstructions revealed extensive homoplasy in almost all morphological characters. Family‐ and subfamily‐level molecular clades [previously identified as XVII?XXI] are best distinguished on the basis of the shapes of septal teeth and corresponding microstructure. The newly revised family Mussidae (XXI) has septal teeth with regular pointed tips (a symplesiomorphy) and a stout blocky appearance. It has two subfamilies, Mussinae and Faviinae. The subfamily Mussinae is distinguished by spine‐shaped teeth and widely spaced costoseptal clusters of calcification centres. The subfamily Faviinae is distinguished by blocky, pointed tricorne or paddle‐shaped teeth with elliptical bases, transverse structures such as carinae that cross the septal plane, and well‐developed aligned granules. Defining diagnostic characters for the broader data set is more challenging. In analyses of taxonomic subsets of the data set that were defined by clade, morphological phylogenetic analyses clearly distinguished the families Mussidae (XXI) and Lobophylliidae (XIX), as well as the two subfamilies of Mussidae (Mussinae, Faviinae), with one exception (Homophyllia australis). However, analyses of the entire 67‐species data set distinguished the family Lobophylliidae (XIX), but not the Merulinidae (XVII) and not the newly defined Mussidae (XXI), although the subfamily Mussinae was recovered as monophyletic. Some lower‐level relationships within the Merulinidae (XVII) agree with molecular results, but this particular family is especially problematic and requires additional molecular and morphological study. Future work including fossils will not only allow estimation of divergence times but also facilitate examination of the relationship between these divergences and changes in the environment and biogeography. Published 2012. This article is a U.S. Government work and is in the public domain in the USA. Zoological Journal of the Linnean Society, 2012, 166 , 465–529.     

Taxonomic revision of the humpback dolphins (Sousa spp.), and description of a new species from Australia

The taxonomy of the humpback dolphin genus Sousa has been controversial and unsettled for centuries, but recent work indicates that there are several valid species. A review of multiple lines of evidence from skeletal morphology, external morphology, coloration, molecular genetics, and biogeography, in combination provides strong support for the recognition of four species of Sousa. These include S. teuszii (Kükenthal, 1892), a species with uniform gray coloration and a prominent dorsal hump, which is found in the Atlantic Ocean off West Africa. The species S. plumbea (G. Cuvier, 1829) has similar external appearance to S. teuszii, but has a more pointed dorsal fin. It occurs in the Indian Ocean from South Africa to Myanmar (Burma). The original taxon, S. chinensis (Osbeck, 1765), is reserved for the species that has a larger dorsal fin with no prominent hump, and largely white adult coloration. It ranges from eastern India to central China and throughout Southeast Asia. Finally, we describe a new species of Sousa, the Australian humpback dolphin, which occurs in the waters of the Sahul Shelf from northern Australia to southern New Guinea. It has a lower dorsal fin, more extensive dark color on the body, and a dorsal “cape.” It is separated from the Indo‐Pacific humpback dolphin by a wide distributional gap that coincides with Wallace's Line.     

A new sea cow record from the lower Oligocene of western Germany: new indications on the skeletal morphology of Halitherium schinzii (Mammalia: Sirenia)

Since the discovery of the extinct species Halitherium schinzii in the Mainz Basin, sirenian remains from the German Oligocene are usually assigned to this taxon according to the assumption that this would be the only sea cow species there. The attempts of several authors to determine morphological distinctions on the species level remain unconsidered until today. The new find of a partial sea cow skeleton from the lower Oligocene of Bottrop-Kirchheller Heide (western Germany) stirs up the debate on splitting the species currently referred to as H. schinzii. The Bottrop specimen morphologically corresponds to skullcaps from the Mainz Basin and the Belgian Oligocene, which were the basis for the introduction of new species in the past, but are considered synonymous with H. schinzii today. Despite its fragmentary preservation, the new sirenian record reveals shared morphological features mainly referring to the supraoccipital, such as a distinctly rostrad indenting nuchal crest and a reduced external occipital protuberance. These features are in contrast to the prominent morphology of the specimens generally associated with H. schinzii and support the assumed presence of at least two morphotypes in the Oligocene of Central Europe. Additionally, the sea cow from Bottrop-Kirchheller Heide represents the first occurrence of skeletal elements, which are not preserved in the known specimens from this morphotype so far and may contribute to a better understanding of intra- and/or interspecific differences within Sirenia.     

RHIPILIA COPPEJANSII,A NEW CORAL REEF‐ASSOCIATED SPECIES FROM GUAM (BRYOPSIDALES,CHLOROPHYTA)1

The new species Rhipilia coppejansii is described from Guam. This species, which has the external appearance of a Chlorodesmis species, features tenacula upon microscopical examination, a diagnostic character of Rhipilia. This unique morphology, along with the tufA and rbcL data presented herein, set this species apart from others in the respective genera. Phylogenetic analyses show that the taxon is nested within the Rhipiliaceae. We discuss the diversity and possible adaptation of morphological types in the Udoteaceae and Rhipiliaceae.     

Molecules,morphology, missing data and the phylogenetic position of a recently extinct madtom catfish (Actinopterygii: Ictaluridae)

Taxa missing large amounts of data pose challenges that may hinder the recovery of a well‐resolved, accurate phylogeny and leave questions surrounding their phylogenetic position. Systematists commonly have to contend with one or two species in a group for which there is little or no material available suitable for recovering molecular data. It is unclear whether these taxa can be better placed using analyses based on morphological data only, or should be included in broader analyses based on both morphological and molecular data. The extinct madtom catfish Noturus trautmani is known from few specimens for which molecular data are unavailable. We included this taxon in parsimony and Bayesian analyses of relationships of madtom catfishes based on a combination of morphological and molecular data. Results indicate that using a combination of morphological and molecular data does a better job at providing a phylogenetic placement for N. trautmani than morphology alone, even though it is missing all of its molecular characters. We provide a novel hypothesis of relationships among Noturus species and recommendations for classification within the group. © 2009 The Linnean Society of London, Zoological Journal of the Linnean Society, 2009, 155 , 60–75.     

TWO NEW SOREDIATE TAXA OFPELTIGERA

Examination of specimens ofPeltigera didactyla, from Africa, Asia, Europe and North America revealed that this sorediate species includes three entities that can be separated on morphological characters. A new species,P. lambinonii, is described from East Africa, and a new combinationP. didactylavar.extenuata, is proposed to accommodate morphs from mesic forest habitats in Asia, Europe and North America. Despite this taxonomic reduction,P. didactylavar.didactylaremains a ubiquitous taxon. The former two taxa often produce methyl gyrophorate, which can co-occur with traces of gyrophoric acid. These tridepsides were only rarely detected in var.didactyla; their occasional presence seems to be best explained by hybridization. The taxonomic and ecological significance of these substances is discussed.     

Intra‐specific variability in Rhinoleucophenga punctulata populations (Diptera: Drosophilidae) from Neotropical biomes: Combined analyses of morphological and molecular data

Despite the fact that Drosophilidae is a very diverse and well‐studied taxon, the New World genus Rhinoleucophenga is yet poorly understood even in regard to species distribution and morphological variability pattern. In this sense, R. punctulata is a species widely distributed in the Neotropical region. Specimens of R. punctulata were collected from different biomes in Brazil: Pampa, Cerrado and Caatinga sensu strictu, and a southern Amazonian savannah enclave area. Geographical variations in the external body morphology and in the morphology of spermatheca were noticed among the different populations. The hypothesis that each population could be a different species was tested through molecular data. A fragment of the mitochondrial cytochrome c oxydase subunit I (COI) gene was sequenced to perform phylogenetic analyses through neighbor‐joining and Bayesian inferences. Pairwise genetic divergences of COI sequences were calculated using DNA barcode premises. The analyzed populations presented different variation levels in both morphology and molecular traits. However, new species were not proposed because the intra‐population nucleotide variations exceeded the inter‐population ones. The noticeable morphological and genetic variations revealed among the four studied populations of R. punctulata in different biomes of Brazil suggest the necessity that morphological, distributional and molecular data at the population level should be integrated into complementary datasets to better understand the biological diversity of Rhinoleucophenga through Neotropical environments.     

Phylogeny and taxonomy of European funnel‐web spiders of the Tegenaria−Malthonica complex (Araneae: Agelenidae) based upon morphological and molecular data

The taxonomy and systematics of European house spiders, currently constituting the ill‐defined Tegenaria?Malthonica complex (including Aterigena) in the family Agelenidae, are revised. In Europe four monophyletic genera and 81 species are defined. One genus, Eratigena gen. nov. , and seven species are described as new; at species level 17 new synonyms and 20 new combinations are proposed, and the original combination of 14 species is reinstated. Five species could not be placed (incertae sedis) because of insufficient material and one taxon is regarded as ‘nomen dubium’. On the basis of a detailed morphological assessment, 88 characters were chosen for a cladistic analysis. Phylogenetically informative characters include mostly spination patterns as well as spinneret and genital structures. In addition to morphology, three gene sections [cytochrome c oxidase subunit 1 (CO1), nicotinamide adenine dinucleotide dehydrogenase subunit 1 (NADH1) 28S] were analysed. Morphological and molecular analyses were performed individually and in combination applying maximum parsimony and Bayesian tree search methods. In all resulting trees Malthonica and Tegenaria in their present composition are either polyphyletic or paraphyletic. Consequently, we redefined the two genera and erected a new genus, Eratigena gen. nov. Identification keys are provided for the European agelenid genera as well as for the European species of Tegenaria and Eratigena gen. nov. The genera and most of the constituent species are described and illustrated. The new classification has also been applied to some extra European members of the Tegenaria‐Malthonica complex resulting in additional three new synonyms, seven reversals to the original combination, and four new combinations. © 2013 The Linnean Society of London     

Pattern of shape variation in the eastern African gerbils of the genus Gerbilliscus (Rodentia,Muridae): Environmental correlations and implication for taxonomy and systematics

Gerbilliscus has been in recent years the subject of new molecular and karyological investigations that shed new light on the evolutionary processes of this taxon. However, the patterns of phenotypic diversification of Gerbilliscus remain poorly understood. Furthermore, the molecular phylogenetic analyses posed new questions concerning the systematics and taxonomy of the whole genus and revealed the possible occurrence of cryptic species and hence the need to carry out a taxonomic revision.We used geometric morphometrics to investigate the adaptive value of morphological changes and to elucidate the systematic relationships and taxonomic status of the Gerbilliscus species of east Africa.Our results show concordance between morphological and genetic species boundaries. However, the observed morphological differences appear not only related to hereditary characters. In fact, the correlation with the climatic variables suggests an adaptive value of shape changes related to different trophic resources availability.Finally, discriminant analysis of the eastern Africa Gerbilliscus species highlight the distinctiveness of G. vicinus, clearly separated from G. robustus and G. nigricaudus.     

Craniodental morphology and systematics of a new family of hystricognathous rodents (Gaudeamuridae) from the late eocene and early oligocene of Egypt

Background

Gaudeamus is an enigmatic hystricognathous rodent that was, until recently, known solely from fragmentary material from early Oligocene sites in Egypt, Oman, and Libya. Gaudeamus'' molars are similar to those of the extant cane rat Thryonomys, and multiple authorities have aligned Gaudeamus with Thryonomys to the exclusion of other living and extinct African hystricognaths; recent phylogenetic analyses have, however, also suggested affinities with South American caviomorphs or Old World porcupines (Hystricidae).

Methodology/Principal Findings

Here we describe the oldest known remains of Gaudeamus, including largely complete but crushed crania and complete upper and lower dentitions. Unlike younger Gaudeamus species, the primitive species described here have relatively complex occlusal patterns, and retain a number of plesiomorphic features. Unconstrained parsimony analysis nests Gaudeamus and Hystrix within the South American caviomorph radiation, implying what we consider to be an implausible back-dispersal across the Atlantic Ocean to account for Gaudeamus'' presence in the late Eocene of Africa. An analysis that was constrained to recover the biogeographically more plausible hypothesis of caviomorph monophyly does not place Gaudeamus as a stem caviomorph, but rather as a sister taxon of hystricids.

Conclusions/Significance

We place Gaudeamus species in a new family, Gaudeamuridae, and consider it likely that the group originated, diversified, and then went extinct over a geologically brief period of time during the latest Eocene and early Oligocene in Afro-Arabia. Gaudeamurids are the only known crown hystricognaths from Afro-Arabia that are likely to be aligned with non-phiomorph members of that clade, and as such provide additional support for an Afro-Arabian origin of advanced stem and basal crown members of Hystricognathi.     

Phylogeny and biogeography of Oriolidae (Aves: Passeriformes)

Understanding oscine passerine dispersal patterns out of their Australian area of origin is hampered by a paucity of robust phylogenies. We constructed a molecular phylogeny of the oscine family, Oriolidae, which is distributed from Australia through to the Old World. We used the phylogeny to assess direction and timing of dispersal and whether dispersal can be linked with the well‐documented movements of geological terranes in the Indonesian Archipelago. We sampled 29 of 33 species of Oriolidae from fresh tissue and from toe pads from museum specimens, and examined two nuclear introns and two mitochondrial genes. Model‐based phylogenetic analyses yielded strong support for clades that generally mirrored classical systematics. Biogeographical analyses and divergence time estimates demonstrated that the family originated in the Australo‐Papuan region from where it dispersed first to Asia and then onwards to Africa and the Philippines before back‐colonising Asia and the Indonesian archipelago. Thus, contrary to several other avian families in the region, Oriolidae represents a sequential dispersal pattern from Australia to Africa via Asia. However, it is noteworthy that the Pacific islands and archipelagos remain uncolonised and that members inhabiting Wallacea are recent colonisers suggesting that Oriolidae are poorly adapted to island life.