Discordant mitochondrial and nuclear gene phylogenies in emydid turtles: implications for speciation and conservation

Do phylogenies and branch lengths based on mitochondrial DNA (mtDNA) provide a reasonable approximation to those based on multiple nuclear loci? In the present study, we show widespread discordance between phylogenies based on mtDNA (two genes) and nuclear DNA (nucDNA; six loci) in a phylogenetic analysis of the turtle family Emydidae. We also find an unusual type of discordance involving the unexpected homogeneity of mtDNA sequences across species within genera. Of the 36 clades in the combined nucDNA phylogeny, 24 are contradicted by the mtDNA phylogeny, and six are strongly contested by each data set. Two genera (Graptemys, Pseudemys) show remarkably low mtDNA divergence among species, whereas the combined nuclear data show deep divergences and (for Pseudemys) strongly supported clades. These latter results suggest that the mitochondrial data alone are highly misleading about the rate of speciation in these genera and also about the species status of endangered Graptemys and Pseudemys species. In addition, despite a strongly supported phylogeny from the combined nuclear genes, we find extensive discordance between this tree and individual nuclear gene trees. Overall, the results obtained illustrate the potential dangers of making inferences about phylogeny, speciation, divergence times, and conservation from mtDNA data alone (or even from single nuclear genes), and suggest the benefits of using large numbers of unlinked nuclear loci. © 2010 The Linnean Society of London, Biological Journal of the Linnean Society, 2010, 99 , 445–461.     

Phylogenetic patterns in larval host plant and ant association of Indo-Australian Arhopalini butterflies (Lycaenidae: Theclinae)

The Oriental butterfly genus Arhopala is by far the most species‐rich genus within the subfamily Theclinae. We investigated whether biotic interactions with larval host plants or ants are phylogenetically constrained in the evolutionary history of Arhopala, by collating available information on the ecology of Arhopala from the literature as well as from personal observations, and analysing and interpreting these data rigorously in a phylogenetic context. Larvae of all species in the sister‐group of Arhopala and Flos feed on Fabaceae. However, the predominant feeding preference of Arhopala s.l., with the exception of a particular monophyletic and species‐rich group, called ‘Group A’, appears to be centred on Fagaceae, with additional records of Dipterocarpaceae feeding. The preference for Fagaceae has strong phylogenetic inertia, as indicated by T‐PTP tests designed to test for phylogenetic signal. Adding all available life‐history data, using the phylogeny presented before as scaffolding, further increased the phylogenetic signal in host plant data. Feeding on Fabaceae (mainly in the outgroup) and Euphorbiaceae also showed significant phylogenetic signal, but feeding on Dipterocarpaceae did not and was found scattered across the phylogeny. Except for the Dipterocarpaceae, phylogenetic signal in feeding preferences was very clear, even despite uneven taxon sampling and apparent lability in host plant use. Ant association also demonstrated historical constraint, but based on the phylogenetic hypothesis presented here it was not clear whether increased ant association intimacy emerged independently various times in Group A, as well as in several basal groups. Our finding of distinct phylogenetic patterns in the host plant and to a lesser degree in ant association data contradicts the hypothesis that life‐history traits are very labile in the Lycaenidae. © 2005 The Linnean Society of London, Biological Journal of the Linnean Society, 2005, 84 , 225–241.     

A global phylogeny of apple snails: Gondwanan origin, generic relationships, and the influence of outgroup choice (Caenogastropoda: Ampullariidae)

Apple snails (Ampullariidae) are a diverse family of pantropical freshwater snails and an important evolutionary link to the common ancestor of the largest group of living gastropods, the Caenogastropoda. A clear understanding of relationships within the Ampullariidae, and identification of their sister taxon, is therefore important for interpreting gastropod evolution in general. Unfortunately, the overall pattern has been clouded by confused systematics within the family and equivocal results regarding the family's sister group relationships. To clarify the relationships among ampullariid genera and to evaluate the influence of including or excluding possible sister taxa, we used data from five genes, three nuclear and two mitochondrial, from representatives of all nine extant ampullariid genera, and species of Viviparidae, Cyclophoridae, and Campanilidae, to reconstruct the phylogeny of apple snails, and determine their affinities to these possible sister groups. The results obtained indicate that the Old and New World ampullariids are reciprocally monophyletic with probable Gondwanan origins. All four Old World genera, Afropomus, Saulea, Pila, and Lanistes, were recovered as monophyletic, but only Asolene, Felipponea, and Pomella were monophyletic among the five New World genera, with Marisa paraphyletic and Pomacea polyphyletic. Estimates of divergence times among New World taxa suggest that diversification began shortly after the separation of Africa and South America and has probably been influenced by hydrogeological events over the last 90 Myr. The sister group of the Ampullariidae remains unresolved, but analyses omitting certain outgroup taxa suggest the need for dense taxonomic sampling to increase phylogenetic accuracy within the ingroup. The results obtained also indicate that defining the sister group of the Ampullariidae and clarifying relationships among basal caenogastropods will require increased taxon sampling within these four families, and synthesis of both morphological and molecular data. © 2009 The Linnean Society of London, Biological Journal of the Linnean Society, 2009, 98 , 61–76.     

Congruence between molecular phylogeny and cuticular design in Echiniscoidea (Tardigrada,Heterotardigrada)

Although morphological characters distinguishing echiniscid genera and species are well understood, the phylogenetic relationships of these taxa are not well established. We thus investigated the phylogeny of Echiniscidae, assessed the monophyly of Echiniscus, and explored the value of cuticular ornamentation as a phylogenetic character within Echiniscus. To do this, DNA was extracted from single individuals for multiple Echiniscus species, and 18S and 28S rRNA gene fragments were sequenced. Each specimen was photographed, and published in an open database prior to DNA extraction, to make morphological evidence available for future inquiries. An updated phylogeny of the class Heterotardigrada is provided, and conflict between the obtained molecular trees and the distribution of dorsal plates among echiniscid genera is highlighted. The monophyly of Echiniscus was corroborated by the data, with the recent genus Diploechiniscus inferred as its sister group, and Testechiniscus as the sister group of this assemblage. Three groups that closely correspond to specific types of cuticular design in Echiniscus have been found with a parsimony network constructed with 18S rRNA data. © 2013 The Linnean Society of London     

A phylogenetic analysis of palm subtribe Archontophoenicinae (Arecaceae) based on 14 DNA regions

Subtribe Archontophoenicinae belongs to Areceae, the largest of all palm tribes. It includes 15 species distributed in five genera, all found in the south‐western Pacific Region. Archontophoenicinae are rather homogeneous in morphology, making phylogenetic relationships problematic to reconstruct using morphological characters. In this study we investigated phylogenetic relationships in Archontophoenicinae based on all 15 species of the subtribe, using a combination of nine plastid and five nuclear DNA sequence markers. The plastid regions used were the coding rbcL, matK, ndhF and rpoC1 (exon 2) and the non‐coding rps16 intron, atpF‐atpH, psbK‐psbI, trnL‐trnF and trnQ‐rps16. The nuclear regions used were AG1, BRSC, ITS2, PRK and RPB2, which have all proved useful in palm systematics. We compared the phylogenetic hypotheses resulting from the plastid versus nuclear datasets, and combined both datasets to retrieve as much phylogenetic information as possible. Our results strongly support a clade composed of all species of Archontophoenix, Actinokentia, Chambeyronia and Kentiopsis, but raise the question of whether Actinorhytis, the fifth genus, should remain in Archontophoenicinae. Interspecific relationships in ‘core Archontophoenicinae’ still remain incompletely resolved, despite the gene and taxon sampling being substantially greater than in previous studies, and question the monophyly of the New Caledonian genera Chambeyronia and Kentiopsis. © 2014 The Linnean Society of London, Botanical Journal of the Linnean Society, 2014, 175 , 469–481.     

Breaking family ties: taxon sampling and molecular phylogeny of chromodorid nudibranchs (Mollusca,Gastropoda)

Johnson, R. F. (2010). Breaking family ties: taxon sampling and molecular phylogeny of chromodorid nudibranchs (Mollusca, Gastropoda). —Zoologica Scripta, 40, 137–157. Although researchers have debated the monophyly of the diverse chromodorid nudibranchs (Chromodorididae) for over 100 years, the monophyly of this family has not been properly tested. Recent morphological and molecular phylogenetic studies have added to the debate, but have not used appropriate methods to resolve this issue. I investigate how outgroup choice and taxon sampling influences tree topology and in turn the recovery of chromodorid monophyly. As a demonstration of these potential methodological problems, I then present phylogenies resulting from different taxon‐sampling schemes using the same molecular data. Taxon sampling has a strong influence on the resulting phylogenies. With comprehensive taxon sampling and outgroup selection, Cadlina is not a member of the Chromodorididae. The chromodorid nudibranchs without Cadlina are monophyletic and possibly sister to the Actinocyclidae. Additionally, I found, for the first time, support for most current family groupings in the Doridoidea. I propose a new classification in which Cadlina is not considered a member of the Chromodorididae. Instead, I resurrect the family name Cadlinidae to include the genera Cadlina and Aldisa.     

Interspecific relationships in co‐occurring populations of social parasites and their host ants

Myrmica ant colonies host numerous insect species, including the larvae of Maculinea butterflies and Microdon myrmicae hoverflies. Little is known about the interspecific relationships among these social parasites and their host ants occurring in sympatric populations. We investigated communities of social parasites to assess the strategies allowing them to share the same pool of resources (i.e. Myrmica colonies). The present study was carried out at five sites inhabited by different social parasite communities, each comprising varying proportions of Maculinea teleius, Maculinea nausithous, Maculinea alcon, and Microdon myrmicae. We investigated their spatial distributions, host segregation, the degree of chemical similarity between social parasites and hosts, and temporal overlaps in colony resource exploitation. Spatial segregation among social parasites was found in two populations and it arises from microhabitat preferences and biological interactions. Local conditions can drive selection on one social parasite to use a Myrmica host species that is not exploited by other social parasites. Myrmica scabrinodis and Myrmica rubra nests infested by larvae of two social parasite species were found and the most common co‐occurrence was between Ma. teleius and Mi. myrmicae. The successful coexistence of these two species derives from their exploitation of the host colony resources at different times of the year. © 2013 The Linnean Society of London, Biological Journal of the Linnean Society, 2013, 109 , 699–709.     

A molecular phylogeny and a revised classification of tribe Lepisoreae (Polypodiaceae) based on an analysis of four plastid DNA regions

Phylogenetic relationships within the palaeotropical tribe Lepisoroideae (Polypodiaceae) were investigated by studying sequence variation of four plastid DNA regions: rbcL, rps4 plus rps4‐trnS IGS, trnL intron plus trnL‐F IGS, rbcL‐atpB IGS plus part of atpB. In total, over 4000 nucleotides were sequenced for 39 species. Seven well‐supported clades were found in the analyses of the combined data set. We provide a new classification of Lepisoroideae by integrating phylogenetic results and known variation of morphological characters. The two small genera Neocheiropteris and Tricholepidium are supported as monophyletic, the genus Paragramma is resurrected and the genera Lepisorus, Neolepisorus, Lemmaphyllum and Lepidomicrosorium are re‐circumscribed. We proposed 14 new combinations, among which Caobangia is treated as a synonym of Lemmaphyllum. A key for identifying the recognized genera is presented. © 2010 The Linnean Society of London, Botanical Journal of the Linnean Society, 2010, 162 , 28–38.     

Molecular phylogeny and divergence times of Malagasy tenrecs: Influence of data partitioning and taxon sampling on dating analyses

Background  

Malagasy tenrecs belong to the Afrotherian clade of placental mammals and comprise three subfamilies divided in eight genera (Tenrecinae: Tenrec, Echinops, Setifer and Hemicentetes; Oryzorictinae: Oryzorictes, Limnogale and Microgale; Geogalinae: Geogale). The diversity of their morphology and incomplete taxon sampling made it difficult until now to resolve phylogenies based on either morphology or molecular data for this group. Therefore, in order to delineate the evolutionary history of this family, phylogenetic and dating analyses were performed on a four nuclear genes dataset (ADRA2B, AR, GHR and vWF) including all Malagasy tenrec genera. Moreover, the influence of both taxon sampling and data partitioning on the accuracy of the estimated ages were assessed.     

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     

Contrasting evolutionary history of hedgehogs and gymnures (Mammalia: Erinaceomorpha) as inferred from a multigene study

The subfamilies Erinaceinae and Galericinae of the extant family Erinaceidae are the only living representatives of the once diverse taxon Erinaceomorpha. In the present study, we performed the first multilocus analysis of phylogenetic relationships among genera of Erinaceidae and estimated the split times between and within the two subfamilies. The analyses of five nuclear and two mitochondrial genes produced a well‐resolved molecular phylogeny. Generally, the molecular tree is compatible with the morphology‐based taxonomy proposed by Frost, Wozencraft & Hoffmann with the exception of the position of Mesechinus, which is placed as the closest sister taxon of Hemiechinus. Another point of contradiction between molecular and morphological phylogenies is the position of Hylomys megalotis, which was consistently placed as the most basal branch among all gymnures in molecular analyses. Genetic relationships between Erinaceus and Atelerix remain unclear, suggesting a hard trichotomy among these two lineages and Hemiechinus + Paraechinus. Molecular dating suggests an ancient origin of the extant gymnure lineages, which date back to the late Eocene to early Oligocene. The age of the basal split within spiny hedgehogs is relatively recent and corresponds to the Miocene–Pliocene boundary. Possible changes to the erinaceid taxonomy are considered. © 2014 The Linnean Society of London, Biological Journal of the Linnean Society, 2014, 112 , 499–519.     

Snake evolution in Melanesia: origin of the Hydrophiinae (Serpentes,Elapidae), and the evolutionary history of the enigmatic New Guinean elapid Toxicocalamus

The venomous snake subfamily Hydrophiinae includes more than 40 genera and approximately 200 species. Most members of this clade inhabit Australia, and have been well studied. But, because of poor taxon sampling of Melanesian taxa, basal evolutionary relationships have remained poorly resolved. The Melanesian genera Ogmodon, Loveridgelaps, and Salomonelaps have not been included in recent phylogenetic studies, and the New Guinean endemic, Toxicocalamus, has been poorly sampled and sometimes recovered as polyphyletic. We generated a multilocus phylogeny for the subfamily using three mitochondrial and four nuclear loci so as to investigate relationships among the basal hydrophiine genera and to determine the status of Toxicocalamus. We sequenced these loci for eight of the 12 described species within Toxicocalamus, representing the largest molecular data set for this genus. We found that a system of offshore island arcs in Melanesia was the centre of origin for terrestrial species of Hydrophiinae, and we recovered Toxicocalamus as monophyletic. Toxicocalamus demonstrates high genetic and morphological diversity, but some of the molecular diversity is not accompanied by diagnostic morphological change. We document at least five undescribed species that all key morphologically to Toxicocalamus loriae (Boulenger, 1898), rendering this species polyphyletic. Continued work on Toxicocalamus is needed to document the diversity of this genus, and is likely to result in the discovery of additional species. Our increased taxon sampling allowed us to better understand the evolution and biogeography of Hydrophiinae; however, several unsampled lineages remain, the later study of which may be used to test our biogeographic hypothesis.     

Morphological and molecular evidence for phylogeny and classification of South American pitvipers,genera Bothrops,Bothriopsis, and Bothrocophias (Serpentes: Viperidae)

Species in the genus Bothrops s. l. are extraordinarily variable in ecology and geography, compared with other genera in the subfamily Crotalinae. In contrast to the trend of splitting large and variable groups into smaller, more ecologically and phenotypically cohesive genera, the genus Bothrops has remained speciose. In addition, previous phylogenetic analyses have found Bothrops to be paraphyletic with respect to the genus Bothriopsis. Taxonomic arguments exist for synonymizing Bothriopsis with Bothrops, and for splitting Bothrops into smaller genera, but the greatest hindrance to taxonomic revision has been incomplete phylogenetic information. We present a phylogeny of Bothrops, Bothriopsis, and Bothrocophias based on 85 characters of morphology and 2343 bp of four mitochondrial gene regions, and with significantly greater taxonomic coverage than previous studies. The combined data provide improved support over independent datasets, and support the existence of discrete species groups within Bothrops. The monophyly and distinctness of these groups warrant recognition at the generic level, and we propose a new taxonomic arrangement to reflect these findings. © 2009 The Linnean Society of London, Zoological Journal of the Linnean Society, 2009, 156 , 617–640.     

Phylogenetics of Eulophiinae (Orchidaceae: Epidendroideae): evolutionary patterns and implications for generic delimitation

Eulophiinae comprise c. 270 species divided into nine genera, with the species‐rich terrestrial genus Eulophia representing 60% of this diversity. Remarkable ecological and morphological variation, and an absence of clear diagnostic characters have led to uncertain generic delimitation in the subtribe. Using a combination of new and previously published DNA sequences, we created a dataset representing 122 taxa and all genera of Eulophiinae and inferred a complete generic‐level phylogeny for the subtribe for the first time. Our sampling focused on analysing Afro‐Madagascan taxa and therefore included representatives of the four mostly epiphytic Madagascan endemic genera, the near Madagascan endemic Oeceoclades and additional sampling of the predominantly African genera Eulophia and Orthochilus. In total, 104 new accessions were collected for this study in Zambia and Madagascar (88 of which represented 36 Eulophia spp. and 12 Oeceoclades spp.). Independent plastid and nuclear phylogenetic trees were inferred using Bayesian and maximum‐likelihood algorithms, which recovered strong support for a monophyletic Eulophiinae, the first‐branching position of the mostly epiphytic Madagascan endemic genera, and increased support for recognition of the terrestrial genera Oeceoclades and Orthochilus. Eulophia, the largest genus in the group, was recovered as polyphyletic, but with implications for its classification and that of Geodorum, that was nested in the main Eulophia clade. Although relationships among several genera were resolved with some confidence, the positions of the South African endemic genus Acrolophia and the epiphytic Madagascan endemic Paralophia require further work. Taxon sampling of Asian Eulophia is a priority for future work on the systematics of this group. © 2015 The Linnean Society of London, Botanical Journal of the Linnean Society, 2015, 179 , 43–56.     

A new Oligocene Ctenodactylinae (Rodentia: Mammalia) from Ulantatal (nei Mongol): new insight on the phylogenetic origins of the modern Ctenodactylidae

The four living genera of Ctenodactylidae (Rodentia) are the only survivors of a flourishing Tertiary group. In this paper, we describe a new Oligocene species from Ulantatal (Chinese Mongolia) that highlights the origins of crown ctenodactylids. This species, Helanshania deserta gen. et sp. nov. , is lophodont and displays semi‐hypsodont teeth, a dental pattern that is somewhat transitional between that of primitive Oligocene ctenodactylids and the later hypsodont genera. We perform here a cladistic assessment of the dental evidence for species produced by the successive radiations of the group. In order to get new data, to decipher homologies for the dental pattern of modern ctenodactylids, and to specify their dental replacement, we describe additional dental material of Ctenodactylus, Massoutiera, and Felovia. The phylogenetic analysis (using PAUP) considered 45 characters (mainly dental) and 31 species. The performed heuristic searches yielded 596 equally most parsimonious trees. Protataromys and Karakoromys are stem ctenodactylids and appear as the earliest offshoots of the Ctenodactylidae clade, which represents a well‐supported family rank. Within this family, the Tataromyinae appear paraphyletic, whereas the Ctenodactylinae sensu lato are a clade including the new taxon Helanshania. As such, a revision of the Tataromyinae is envisaged and a new subfamily is erected (Yindirtemyinae). Amongst the Ctenodactylinae, a tribe Ctenodactylini encompassing the crown ctenodactylines is proposed. © 2010 The Linnean Society of London, Zoological Journal of the Linnean Society, 2010, 160 , 531–550.     

Molecular systematics of peppermint and cleaner shrimps: phylogeny and taxonomy of the genera Lysmata and Exhippolysmata (Crustacea: Caridea: Hippolytidae)

Shrimps from the ecologically diverse genera Lysmata and Exhippolysmata are rare among marine invertebrates because they are protandric simultaneous hermaphrodites: shrimps initially mature and reproduce solely as males, and later in life become functional simultaneous hermaphrodites. Considerable progress on the reproductive ecology of members from these two genera has been achieved during the last decade. However, several outstanding issues of systematic nature remain to be addressed. Here, a molecular phylogeny of these two genera was used to examine the overall evolutionary relationship within and between species and genera, and to answer various questions related to the systematic status of several species. The present phylogenetic analysis, including 53 sequences and 26 species of Lysmata and Exhippolysmata, indicates that semiterrestrial shrimps from the genus Merguia represent the sister group to a second natural clade composed by shrimps from the genera Lysmata and Exhippolysmata. Also, the phylogenetic analysis confirmed that the genus Lysmata is paraphyletic, and includes the genus Exhippolysmata, as noted in a preliminary study. The tree partially supports the separation of species with or without a developed accessory branch into two different genera or subgenera (i.e. Lysmata and Hippolysmata having a well‐developed accessory branch, or not, respectively). The genetic distance between the cleaner shrimps Lysmata amboinensis and Lysmata grabhami was smaller than has been observed between other sister species. On the other hand, the topology of the tree indicates that these two entities are reciprocally monophyletic. Thus, this latter result, together with minor but constant differences in the colour pattern reported for these two entities, indicates that there is no reason to stop treating them as different valid species. This study enabled the long overdue resolution of standing taxonomic questions in shrimps from the genera Lysmata and Exhippolysmata. In the future, this phylogeny will help to reveal the conditions favouring the origins of several behavioural and morphological novelties in these unique shrimps. © 2010 The Linnean Society of London, Zoological Journal of the Linnean Society, 2010, 160 , 254–265.