Bayesian phylogenetic estimation of fossil ages

Recent advances have allowed for both morphological fossil evidence and molecular sequences to be integrated into a single combined inference of divergence dates under the rule of Bayesian probability. In particular, the fossilized birth–death tree prior and the Lewis-Mk model of discrete morphological evolution allow for the estimation of both divergence times and phylogenetic relationships between fossil and extant taxa. We exploit this statistical framework to investigate the internal consistency of these models by producing phylogenetic estimates of the age of each fossil in turn, within two rich and well-characterized datasets of fossil and extant species (penguins and canids). We find that the estimation accuracy of fossil ages is generally high with credible intervals seldom excluding the true age and median relative error in the two datasets of 5.7% and 13.2%, respectively. The median relative standard error (RSD) was 9.2% and 7.2%, respectively, suggesting good precision, although with some outliers. In fact, in the two datasets we analyse, the phylogenetic estimate of fossil age is on average less than 2 Myr from the mid-point age of the geological strata from which it was excavated. The high level of internal consistency found in our analyses suggests that the Bayesian statistical model employed is an adequate fit for both the geological and morphological data, and provides evidence from real data that the framework used can accurately model the evolution of discrete morphological traits coded from fossil and extant taxa. We anticipate that this approach will have diverse applications beyond divergence time dating, including dating fossils that are temporally unconstrained, testing of the ‘morphological clock'', and for uncovering potential model misspecification and/or data errors when controversial phylogenetic hypotheses are obtained based on combined divergence dating analyses.This article is part of the themed issue ‘Dating species divergences using rocks and clocks’.     

Oligocene ferns from the Rancahué Formation (Aluminé, Neuquén, Argentina): Cuyenopteris patagoniensis nov. gen., nov. sp. (Polypodiales: Blechnaceae/Dryopteridaceae) and Alsophilocaulis calveloi Menéndez emend. Vera (Cyatheales: Cyatheaceae)

The study of abundant permineralized fern remains collected in the Oligocene Rancahué Formation (Neuquén Province, Argentina) allowed the identification of two different taxa. The name Cuyenopteris patagoniensis nov. gen., nov. sp. is proposed for several stems and fronds characterized by the presence of caulinar dictyosteles with root gaps, producing C-shaped leaf traces composed by two hippocampiform bundles flanked by eight to ten small round bundles, half of them diverging from cauline meristeles and the rest from the hippocampiform bundles. The presence of these features, along with frond bases with adaxial grooves and a pair of pneumatophores, suggest affinities with the Blechnaceae or Dryopteridaceae. The second identified taxon is Alsophilocaulis calveloi Menéndez. Based on features observed in these new materials, including characteristics of the mantle of adventitious roots and anatomy of the petiole bases, an emended diagnosis for this latter species is proposed.     

A new phylogenetic classification for the gymnophthalmid genera Cercosaura , Pantodactylus and Prionodactylus (Reptilia: Squamata)

Because of the poor state of knowledge of many of the gymnophthalmid genera, systematic revision is necessary to render the classification consistent with evolutionary history. To that end, I conducted a review of the species of three genera of the Cercosaurinae which appear to form a monophyletic group: Cercosaura , Pantodactylus , and Prionodactylus . Phylogenetic analysis of 61 morphological characters was conducted after specimens of all species were examined to evaluate the composition of each taxon. The phylogenetic reconstruction suggested that the genus Prionodactylus was paraphyletic. A new phylogenetic classification is proposed that synonymizes Pantodactylus and Prionodactylus with Cercosaura. Cercosaura is redefined to include 11 species and seven subspecies. A key is provided to distinguish among species.  © 2003 The Linnean Society of London, Zoological Journal of the Linnean Society, 2003, 137 , 101−115.     

Phylogeny and classification of the shrimp genera Acetes,Peisos, and Sicyonella (Sergestidae: Crustacea: Decapoda)

Despite their role in marine systems, Sergestidae remain one of the most poorly understood families amongst planktonic shrimps with regard to phylogeny. Recent morphological and phylogenetic revisions of a number of sergestid genera have disentangled classificatory problems and emphasized the importance of reproductive structures for the taxonomy and phylogeny of the Sergestidae. Only three genera, Acetes, Peisos, and Sicyonella, remain unrevised phylogenetically. We undertook a phylogenetic analysis of these groups based on 124 morphological characters (120 binary, four multistate). Eighteen new characters were based on scanning electron microscopy studies of the clasping organ and petasma. The phylogenetic analysis revealed statistically supported monophyly of the clades Sicyonella and Acetes + Peisos. We combine Peisos and Acetes into a monophyletic genus Acetes, give emended diagnoses and keys to all species of Sicyonella and Acetes, and discuss morphological trends within these genera. We present maps of geographical distribution for all valid species of Acetes. © 2015 The Linnean Society of London     

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.     

上海市蕨类植物分布特点及其与环境因子关系分析

在查阅资料和标本基础上,对上海市33个样地蕨类植物进行了野外调查,初步确定了上海市自然分布的蕨类植物23科31属50种,并讨论了归化种与栽培种及曾有记录而可能消亡的种类。采用双向指示种法（TWINSPAN）和典范对应分析（CCA）方法对蕨类植物分布特点及其与环境因子关系进行了分析。结果表明：（1）蕨类分布的样点可分为3组,第1组为市区样点,种数为0～4种;第2组为市郊样点,种数为0～8种;第3组为佘山岛、佘山地区、大金山岛,是上海蕨类最丰富地区,种数达26种以上。（2）影响上海蕨类植物生长的主要环境因子为基质、郁闭度和人为干扰。     

多基因联合分析棒束孢属Isaria（Ascomycota,Cordycipitaceae）系统发育关系

对棒束孢属Isaria及近缘属物种开展5基因（nrSSU、nrLSU、tef-1α、rpb1和 rpb2）测序并联合分析,结合GenBank相关类群序列,探讨棒束孢属系统发育关系,最终获得95个菌株、58个明确分类群的2-5基因序列。利用MEGA和MrBayes软件进行多基因聚类分析,结果表明棒束孢属多系起源于虫草菌科中,分3个不同分支。A支主要由Isaria cicadae、I. teniupes、I. coleopterorum、I. fumosorosea和I. cateniannulata等组成;B支包括I. poprawkii、I. locustica、I. javanica、I. amoenerosea和I. cateniobliqua;C支仅有I. farinosa。分支间被Cordyceps militaris、C. ninchukispora、C. pruinosa等隔开。棒束孢在形态上,主要以瓶梗基部膨大、尖端变细及孢子呈链状等特征与其他类群分开,但同时也发现有棒状分生孢子梗和单孢子类型。基于节点的分歧时间预测分析,推测棒束孢属首次分化于70Mya,但棒束孢属主要物种形成却在60-55Mya,且3个分支的棒束孢物种为快速同时形成,而后大多数类群表现遗传稳定。同时发现,与Isaria Clade A较近一支有粉被玛利亚霉Mariannaea pruinosa（C. pruinosa无性型）和蛹草蚧霉Lecanicillium militaris（C. militaris无性型）;与粉棒束孢距离最近一支有Akanthomyces aculeatus（C. tuberculata无性型）和L. attenuatum（C. confragosa无性型）,是两个不同的属征分类群,且相互间遗传距离较近。根据棒束孢属及其近缘种属形态特征的复杂性推测,棒束孢属在快速物种形成中,其近缘类群存在一定程度的丢失和选择性演化。     

Comparative plastid genomics of Pinus species: Insights into sequence variations and phylogenetic relationships

Pinus L. is the largest genus of conifers and provides a classical model for studying species divergence and phylogenetic evolution by gymnosperms. However, our poor understanding of sequence divergence in the whole plastid genomes of Pinus species severely hinders studies of their evolution and phylogeny. Thus, we analyzed the sequences of 97 Pinus plastid genomes, including four newly sequenced genomes and 93 previously published plastomes, to explore the evolution and phylogenetic relationships in the genus Pinus. The complete chloroplast genomes of Pinus species ranged in size from 109 640 bp (P. cembra L.) to 121 976 bp (P. glabra Walter), and these genomes comprised circular DNA molecules in a similar manner to those of most gymnosperms. We identified 9108 repeats where most of the repeats comprised the dispersed type with 3983 (44%), followed by tandem repeats with 2999 (33%), and then palindromic repeats with 2126 (23%). Sixteen divergence hotspot regions were identified in Pinus plastid genomes, which could be useful molecular markers for future population genetics studies. Phylogenetic analysis showed that Pinus species could be divided into two diverged clades comprising the subgenera Strobus (single needle section) and Pinus (double needles section). Molecular dating suggested that the genus Pinus originated approximately 130.38 Mya during the late Cretaceous. The two subgenera subsequently split 85.86 Mya, which was largely consistent with the other molecular results based on partial DNA markers. These findings provide important insights into the sequence variations and phylogenetic evolution of Pinus plastid genomes.     

Molecular phylogenetic relationships of pangasiid and schilbid catfishes in Thailand

In this study, the phylogenetic relationships among 13 pangasiids and six schilbids of Thailand were reconstructed based on the almost complete mitochondrial cytochrome b (cyt b), 12S rRNA, tRNA-Val and 16S rRNA, as well as the partial nuclear recombination-activating gene 1 (rag1) sequences by using the maximum likelihood and the Bayesian inference methods of phylogenetic reconstruction. The reconstructed phylogeny based on the concatenated sequence data set recovered Pangasiidae and Schilbidae as reciprocally monophyletic groups. Within Pangasiidae, four major clades were recovered, which according to the cyt b genetic distances can be categorized into four genera: Pangasius, Pseudolais, Helicophagus and Pangasianodon. The genus Pangasianodon was strongly supported as the most basal taxon within pangasiids, whereas Pseudolais + Helicophagus were recovered as a sister group of Pangasius. Within the latter, the giant pangasius Pangasius sanitwongsei was recovered as a sister group of the spot pangasius Pangasius larnaudii, Pangasius krempfi as a sister group of Pangasius nasutus + Pangasius conchophilus and Pangasius polyuranodon as a sister species of Pangasius macronema. Other internal phylogenetic relationships, however, were unresolved. Within Schilbidae, Pseudeutropius was supported as the most basal lineage. Eutropiichthys was recovered as a sister group of Clupisoma. The enigmatic Clupisoma sinense was recognized as more closely related to Laides longibarbis than to Clupisoma prateri. Thus, based on the cyt b genetic distances, a recategorization of C. sinense to the genus Laides is suggested. On the basis of a relaxed clock fossil calibration, the divergence of pangasiids and schilbids was estimated to have occurred 14·93 million years before present (b.p.) during the Miocene epoch. The separation between Pangasiidae and Schilbidae took place c. 13·12 Mb.p. during the early middle Miocene. The estimated divergence time of pangasiids is similar to the age of the calibrated fossil, Cetopangasius chaetobranchus, which was discovered in north-central Thailand. This suggests that the oldest pangasiid ancestor diverged into diverse genera in the area.     

Picking holes in traditional species delimitations: an integrative taxonomic reassessment of the Parmotrema perforatum group (Parmeliaceae,Ascomycota)

Accurate species delimitation is important as species are a fundamental unit in ecological, evolutionary and conservation biology research. In lichenized fungi, species delimitation has been difficult due to a lack of taxonomically important characteristics and due to the limits of traditional, morphology‐based species concepts. In this study we reassess the current taxonomy of the Parmotrema perforatum group, which recognizes six closely related species divided into three species pairs, each pair comprising one apotheciate (sexual) and one sorediate (asexual) species. Each pair is further characterized by a distinct combination of secondary metabolites. It was hypothesized that the three apotheciate species are reproductively isolated sibling species and that each sorediate species evolved once from the chemically identical apotheciate species. In this study, species boundaries were re‐examined using an integrative approach incorporating morphological, chemical and molecular sequence data to delimit species boundaries. Phylogenetic trees were inferred from a seven‐locus DNA sequence dataset using concatenated gene tree and coalescent‐based species‐tree inference methods. Furthermore, we employed a multi‐species coalescent method to validate candidate species. Micromorphological measurements of conidia were found to be congruent with phylogenetic clusters. Each approach that we applied to the P. perforatum group consistently recovered four of the currently circumscribed species (P. perforatum, P. hypotropum, P. subrigidum and P. louisianae), whereas P. preperforatum and P. hypoleucinum were consistently combined and are thus interpreted as conspecific.     

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

Lobophylliidae is a family‐level clade of corals within the ‘robust’ lineage of Scleractinia. It comprises species traditionally classified as Indo‐Pacific ‘mussids’, ‘faviids’, and ‘pectiniids’. Following detailed revisions of the closely related families Merulinidae, Mussidae, Montastraeidae, and Diploastraeidae, this monograph focuses on the taxonomy of Lobophylliidae. Specifically, we studied 44 of a total of 54 living lobophylliid species from all 11 genera based on an integrative analysis of colony, corallite, and subcorallite morphology with molecular sequence data. By examining coral skeletal features at three distinct levels – macromorphology, micromorphology, and microstructure – we built a morphological matrix comprising 46 characters. Data were analysed via maximum parsimony and transformed onto a robust molecular phylogeny inferred using two nuclear (histone H3 and internal transcribed spacers) and one mitochondrial (cytochrome c oxidase subunit I) DNA loci. The results suggest that micromorphological characters exhibit the lowest level of homoplasy within Lobophylliidae. Molecular and morphological trees show that Symphyllia, Parascolymia, and Australomussa should be considered junior synonyms of Lobophyllia, whereas Lobophyllia pachysepta needs to be transferred to Acanthastrea. Our analyses also lend strong support to recent revisions of Acanthastrea, which has been reorganized into five separate genera (Lobophyllia, Acanthastrea, Homophyllia, Sclerophyllia, and Micromussa), and to the establishment of Australophyllia. Cynarina and the monotypic Moseleya remain unchanged, and there are insufficient data to redefine Oxypora, Echinophyllia, and Echinomorpha. Finally, all lobophylliid genera are diagnosed under the phylogenetic classification system proposed here, which will facilitate the placement of extinct taxa on the scleractinian tree of life.     

Spores in situ and problems of the classification of Mesozoic tree ferns

Although tree ferns dominated the Mesozoic flora, their taxonomic relationships are poorly understood at the generic level, and next to nothing can be said of evolutionary trends within the group. At least five genera are recognized based on the remains of spore-bearing structures. However, the dispersed spores belong to the same generalized morphotype, and cannot be assigned to genera based on macroscopic remains of fertile leaves. Electron microscopy of spores in situ may partly resolve these problems providing additional criteria for classification of spore-bearing structures and disperse spores. We studied in situ spores of the Early Cretaceous Alsophilites nipponensis (Oishi) Krassilov, which are comparable to dispersed spores Cyathidites minor Coup. Spore wall micromorphology and ultrastructure indicate their affinities with the modern genus Alsophila R. Brown. Only occasional poorly preserved striate sculptures survive the standard treatment of maceration of the perispore. Our data confirm the primitive status of the species with a great number of spores per sporangium, thick unsculptured exospore consisting of two ultrastructural layers, and the possibility that whole sporangia with unshed spores can function as dispersal units.     

Exploring the evolution of humus collecting leaves in drynarioid ferns (Polypodiaceae, Polypodiidae) based on phylogenetic evidence

Most species of the paleotropic fern genera Aglaomorpha and Drynaria, together constituting a monophyletic clade (drynarioid ferns), possess humus-collecting structures as an adaptation to their epiphytic life form. Humus-collectors are either present as a specialized foliar structure (external leaf dimorphism) or as a specialized leaf part (internal dimorphism). Apart from these basic patterns there are several forms of reduction and an internal fertile – sterile dimorphism in Aglaomorpha. We present a phylogeny of drynarioid ferns based on morphological and molecular (cpDNA) markers. The genus Aglaomorpha was found to be monophyletic, whereas Drynaria is likely to be a paraphyletic assemblage including a grade of Himalayan to Southern Chinese taxa basal to Aglaomorpha. The evolution of humus-collectors is reconstructed by plotting their character state changes onto the obtained phylogeny. Despite the complex morphological pattern across species, evolution of drynarioid humus-collecting structures can be reconstructed postulating a simple sequence of character state changes based on only a few elementary processes.     

Spores of Serpocaulon (Polypodiaceae): morphometric and phylogenetic analyses

The morphometry and sculpture pattern of Serpocaulon spores was studied in a phylogenetic context. The species studied were those used in a published phylogenetic analysis based on chloroplast DNA regions. Four additional Polypodiaceae species were examined for comparative purposes. We used scanning electron microscopy to image 580 specimens of spores from 29 species of the 48 recognised taxa. Four discrete and ten continuous characters were scored for each species and optimised on to the previously published molecular tree. Canonical correspondence analysis (CCA) showed that verrucae width/verrucae length and verrucae width/spore length index and outline were the most important morphological characters. The first two axes explain, respectively, 56.3% and 20.5% of the total variance. Regular depressed and irregular prominent verrucae were present in derived species. However, the morphology does not support any molecular clades. According to our analyses, the evolutionary pathway of the ornamentation of the spores is represented by depressed irregularly verrucae to folded perispore to depressed regular verrucae to irregularly prominent verrucae.     

The phylogenetic relationships and natural classificition of the Vespoidea (Hymenptera)

Abstract. Phylogenetic relationships of the subfamilies and tribes of the Vespoidea (= Diploptera) are investigated using cladistic methods. A natural classification is proposed, sequencing seven tribes in six subfamilies within the single family Vespidae. Euparagia is the sister-group of the rest of the Vespidae. The Gayellinae and Masarinae are sister-groups, and are reduced in rank to tribes within the subfamily Masarinae. This is the sister-group of the Eumeninae + Stenogastrinae + Polistinae + Vespinae. The Zethinae is a paraphyletic group; both it and the Raphiglossinae are deleted and included in the Eumeninae. The Stenogastrinae is regarded as the sister-group of the Vespinae + Polistinae.     

A new phylogenetic tribal classification of the grape family (Vitaceae)

Vitaceae (the grape family) consist of 16 genera and ca. 950 species primarily distributed in tropical regions. The family is well‐known for the economic importance of grapes, and is also ecologically significant with many species as dominant climbers in tropical and temperate forests. Recent phylogenetic and phylogenomic analyses of sequence data from all three genomes have supported five major clades within Vitaceae: (i) the clade of Ampelopsis, Nekemias, Rhoicissus, and Clematicissus; (ii) the Cissus clade; (iii) the clade of Cayratia, Causonis, Cyphostemma, Pseudocayratia, Tetrastigma, and an undescribed genus “Afrocayratia”; (iv) the clade of Parthenocissus and Yua; and (v) the grape genus Vitis and its close tropical relatives Ampelocissus, Pterisanthes and Nothocissus, with Nothocissus and Pterisanthes nested within Ampelocissus. Based on the phylogenetic and morphological (mostly inflorescence, floral and seed characters) evidence, the new classification places the 950 species and 16 genera into five tribes: (i) tribe Ampelopsideae J.Wen & Z.L.Nie, trib. nov. (47 species in four genera; Ampelopsis, Nekemias, Rhoicissus and Clematicissus); (ii) tribe Cisseae Rchb. (300 species in one genus; Cissus); (iii) tribe Cayratieae J.Wen & L.M.Lu, trib. nov. (370 species in seven genera; Cayratia, Causonis, “Afrocayratia”, Pseudocayratia, Acareosperma, Cyphostemma and Tetrastigma); (iv) tribe Parthenocisseae J.Wen & Z.D.Chen, trib. nov. (ca. 16 spp. in two genera; Parthenocissus and Yua); and (v) tribe Viteae Dumort. (ca. 190 species in two genera; Ampelocissus and Vitis).     

Towards a natural classification of the subtribe Philonthina (Coleoptera: Staphylinidae: Staphylinini): a phylogenetic analysis of the Neotropical genera

Philonthina, the largest subtribe of the rove beetle tribe Staphylinini, is a hyperdiverse group in the Neotropical Region, accounting for about half of the genera of the subtribe. Despite such diversity, Neotropical Philonthina have never been analysed phylogenetically, deterring formulation of a modern classification of the Staphylinini. A cladistic analysis of Neotropical Philonthina was performed based on 110 morphological characters and 77 terminal taxa. Representatives of Philonthina from other regions and other main lineages of Staphylinini, Arrowinini and Platyprosopini were included to test their relationships with Neotropical Philonthina. The major results are the monophyly of 11 of the 17 endemic Neotropical genera of Philonthina, the placement of Holisus Erichson (Hyptiomina) into this clade showing a sister group relationship to myrmecophile genera, and the position of Erichsonius Fauvel outside of Philonthina within Staphylinini. Six of the current seven species of Endeius Coiffait & Sáiz group with Neotropical species of Philonthus Stephens. The separation of Gondwana about 65 my and major landscape modifications in the vast interior of northern South America during the past 25 my is proposed to explain the evolution of the endemic Neotropical genera of Philonthina. The following taxonomic changes are proposed: Erichsonius Fauvel, 1874 now placed as incertae sedis in Staphylinini; Endeius Coiffait & Sáiz, 1968, n.syn. of Philonthus Stephens, 1929 and Endeius nitidipennis (Solier, 1849) placed as incertae sedis in Philonthina. The following new combinations are proposed: Philonthus franzi (Sáiz, 1971), comb.n. , Philonthus loensis (Coiffait & Sáiz, 1968), comb.n. , Philonthus lugubris (Sáiz, 1971), comb.n. , Philonthus ovaliceps (Coiffait, 1981), comb.n. , Philonthus punctipennis (Solier, 1849), comb.res. and Philonthus subpunctipennis (Coiffait & Sáiz, 1968), comb.n. Philonthus herberti, n.nov., is proposed for Philonthus franzi Schillhammer, 1998 , which is a junior secondary homonym of Philonthus franzi (Sáiz, 1971).     

Taxon sampling effects on the quantification and comparison of community phylogenetic diversity

Ecologists are increasingly making use of molecular phylogenies, especially in the fields of community ecology and conservation. However, these phylogenies are often used without full appreciation of their underlying assumptions and uncertainties. A frequent practice in ecological studies is inferring a phylogeny with molecular data from taxa only within the community of interest. These “inferred community phylogenies” are inherently biased in their taxon sampling. Despite the importance of comprehensive sampling in constructing phylogenies, the implications of using inferred community phylogenies in ecological studies have not been examined. Here, we evaluate how taxon sampling affects the quantification and comparison of community phylogenetic diversity using both simulated and empirical data sets. We demonstrate that inferred community trees greatly underestimate phylogenetic diversity and that the probability of incorrectly ranking community diversity can reach up to 25%, depending on the dating methods employed. We argue that to reach reliable conclusions, ecological studies must improve their taxon sampling and generate the best phylogeny possible.