Outgroup Sampling Research Articles

A Revision of the New World Species ofParalimnaLoew (Diptera: Ephydridae)

The New World species of the genus Paralimna Loew are revised. Fifteen new species are described and four new synonyms are proposed ( Paralimna cilifera Hendel = Paralimna sana Cresson, Paralimna sticta Hendel = Paralimna taurus Cresson, and Paralimna bistriata Hendel = Paralimna molossus Schiner, P. multipunctata Williston = Paralimna thomae (Wiedemann)). A key to the 34 known, New World species of the subgenera Paralimna is provided, as is a key to the three New World species of the subgenus Phaiosterna Cresson. Diagnoses, detailed distributional data for the species of the genus, notes on the biology, and illustrations (photographs and drawings) are provided to assist species identification. A cladistic analysis was performed to examine the monophyly of the known species groups of Paralimna . The ingroup includes a total of 64 exemplar species. Outgroup sampling includes the following exemplar genera: Afrolimna Cogan Oedenops Becker, and Papuama Mathis and Zatwarnicki. The analyses of the 36 included characters recovered a monophyletic subgenus Phaiosterna Cresson and a paraphyletic subgenus Paralimna if the limbata species group is included. Except for the limbata species group, the remaining known species groups of Paralimna were not sustained. — Smithsonian Contributions to Zoology , number 643, x + 148 pages, 215 figures, 31 maps, 1 table, published 1 June 2015.

Resolving the phylogeny of a speciose spider group, the family Linyphiidae (Araneae)

For high-level molecular phylogenies, a comprehensive sampling design is a key factor for not only improving inferential accuracy, but also for maximizing the explanatory power of the resulting phylogeny. Two standing problems in molecular phylogenies are the unstable placements of some deep and long branches, and the phylogenetic relationships shown by robust supported clades conflict with recognized knowledge. Empirical and theoretical studies suggest that increasing taxon sampling is expected to ameliorate, if not resolve, both problems; however, sometimes neither the current taxonomic system nor the established phylogeny can provide sufficient information to guide additional sampling design. We examined the phylogeny of the spider family Linyphiidae, and selected ingroup species based on epigynal morphology, which can be reconstructed in a phylogenetic context. Our analyses resulted in seven robustly supported clades within linyphiids. The placements of four deep and long branches are sensitive to variations in both outgroup and ingroup sampling, suggesting the possibility of long branch attraction artifacts. Results of ancestral state reconstruction indicate that successive state transformations of the epigynal plate are associated with early cladogenetic events in linyphiid diversification. Representatives of different subfamilies were mixed together within well supported clades and examination revealed that their defining characters, as per traditional taxonomy, are homoplastic. Furthermore, our results demonstrated that increasing taxon sampling produced a more informative framework, which in turn helps to study character evolution and interpret the relationships among linyphiid lineages. Additional defining characters are needed to revise the linyphiid taxonomic system based on our phylogenetic hypothesis.

Intercontinental dissemination of azithromycin-resistant shigellosis through sexual transmission: a cross-sectional study

Shigellosis is an acute, severe bacterial colitis that, in high-income countries, is typically associated with travel to high-risk regions (Africa, Asia, and Latin America). Since the 1970s, shigellosis has also been reported as a sexually transmitted infection in men who have sex with men (MSM), in whom transmission is an important component of shigellosis epidemiology in high-income nations. We aimed to use sophisticated subtyping and international sampling to determine factors driving shigellosis emergence in MSM linked to an outbreak in the UK. We did a large-scale, cross-sectional genomic epidemiological study of shigellosis cases collected from 29 countries between December, 1995, and June 8, 2014. Focusing on an ongoing epidemic in the UK, we collected and whole-genome sequenced clinical isolates of Shigella flexneri serotype 3a from high-risk and low-risk regions, including cases associated with travel and sex between men. We examined relationships between geographical, demographic, and clinical patient data with the isolate antimicrobial susceptibility, genetic data, and inferred evolutionary relationships. We obtained 331 clinical isolates of S flexneri serotype 3a, including 275 from low-risk regions (44 from individuals who travelled to high-risk regions), 52 from high-risk regions, and four outgroup samples (ie, closely related, but genetically distinct isolates used to determine the root of the phylogenetic tree). We identified a recently emerged lineage of S flexneri 3a that has spread intercontinentally in less than 20 years throughout regions traditionally at low risk for shigellosis via sexual transmission in MSM. The lineage had acquired multiple antimicrobial resistance determinants, and prevailing sublineages were strongly associated with resistance to the macrolide azithromycin. Eight (4%) of 206 isolates from the MSM-associated lineage were obtained from patients who had previously provided an isolate; these serial isolations indicated atypical infection patterns (eg, reinfection). We identified transmission-facilitating behaviours and atypical course(s) of infection as precipitating factors in shigellosis-affected MSM. The intercontinental spread of antimicrobial-resistant shigella through established transmission routes emphasises the need for new approaches to tackle the public health challenge of sexually transmitted infections in MSM. Wellcome Trust (grant number 098051).

Phylogenetic analyses provide insights into the historical biogeography and evolution of Brachyrhaphis fishes

The livebearing fish genus Brachyrhaphis (Poeciliidae) has become an increasingly important model in evolution and ecology research, yet the phylogeny of this group is not well understood, nor has it been examined thoroughly using modern phylogenetic methods. Here, we present the first comprehensive phylogenetic analysis of Brachyrhaphis by using four molecular markers (3mtDNA, 1nucDNA) to infer relationships among species in this genus. We tested the validity of this genus as a monophyletic group using extensive outgroup sampling based on recent phylogenetic hypotheses of Poeciliidae. We also tested the validity of recently described species of Brachyrhaphis that are part of the B. episcopi complex in Panama. Finally, we examined the impact of historical events on diversification of Brachyrhaphis, and made predictions regarding the role of different ecological environments on evolutionary diversification where known historical events apparently fail to explain speciation. Based on our results, we reject the monophyly of Brachyrhaphis, and question the validity of two recently described species (B. hessfeldi and B. roswithae). Historical biogeography of Brachyrhaphis generally agrees with patterns found in other freshwater taxa in Lower Central America, which show that geological barriers frequently predict speciation. Specifically, we find evidence in support of an 'island' model of Lower Central American formation, which posits that the nascent isthmus was partitioned by several marine connections before linking North and South America. In some cases where historic events (e.g., vicariance) fail to explain allopatric species breaks in Brachyrhaphis, ecological processes (e.g., divergent predation environments) offer additional insight into our understanding of phylogenetic diversification in this group.

What's in an Outgroup? The Impact of Outgroup Choice on the Phylogenetic Position of Thalattosuchia (Crocodylomorpha) and the Origin of Crocodyliformes.

Outgroup sampling is a central issue in phylogenetic analysis. However, good justification is rarely given for outgroup selection in published analyses. Recent advances in our understanding of archosaur phylogeny suggest that many previous studies of crocodylomorph and crocodyliform relationships have rooted trees on outgroup taxa that are only very distantly related to the ingroup (e.g., Gracilisuchus stipanicicorum), or might actually belong within the ingroup. Thalattosuchia, a group of Mesozoic marine crocodylomorphs, has a controversial phylogenetic position--they are recovered as either the sister group to Crocodyliformes, in a basal position within Crocodyliformes, or nested high in the crocodyliform tree. Thalattosuchians lack several crocodyliform apomorphies, but share several character states with derived long-snouted forms with a similar ecological habit, suggesting their derived position may be the result of convergent evolution. Several of these "shared" characters may result from ambiguously worded character state definitions--structures that are superficially similar but anatomically different in detail are identically coded. A new analysis of crocodylomorphs with increased outgroup sampling recovers Thalattosuchia as the sister group to Crocodyliformes, distantly related to long-snouted crocodyliforms. I also demonstrate that expanding the outgroup sampling of previously published matrices results in the recovery of thalattosuchians as sister to Crocodyliformes. The exclusion of thalattosuchians from Crocodyliformes has numerous implications for large-scale evolutionary trends within the group, including extensive convergence in the evolution of the secondary palate characteristic of the group. These results demonstrate the importance of careful outgroup sampling and character construction, and their profound effect on the position of labile clades.

Reasoning over taxonomic change: exploring alignments for the Perelleschus use case.

Classifications and phylogenetic inferences of organismal groups change in light of new insights. Over time these changes can result in an imperfect tracking of taxonomic perspectives through the re-/use of Code-compliant or informal names. To mitigate these limitations, we introduce a novel approach for aligning taxonomies through the interaction of human experts and logic reasoners. We explore the performance of this approach with the Perelleschus use case of Franz & Cardona-Duque (2013). The use case includes six taxonomies published from 1936 to 2013, 54 taxonomic concepts (i.e., circumscriptions of names individuated according to their respective source publications), and 75 expert-asserted Region Connection Calculus articulations (e.g., congruence, proper inclusion, overlap, or exclusion). An Open Source reasoning toolkit is used to analyze 13 paired Perelleschus taxonomy alignments under heterogeneous constraints and interpretations. The reasoning workflow optimizes the logical consistency and expressiveness of the input and infers the set of maximally informative relations among the entailed taxonomic concepts. The latter are then used to produce merge visualizations that represent all congruent and non-congruent taxonomic elements among the aligned input trees. In this small use case with 6-53 input concepts per alignment, the information gained through the reasoning process is on average one order of magnitude greater than in the input. The approach offers scalable solutions for tracking provenance among succeeding taxonomic perspectives that may have differential biases in naming conventions, phylogenetic resolution, ingroup and outgroup sampling, or ostensive (member-referencing) versus intensional (property-referencing) concepts and articulations.

The species‐rich, paleotropical genus Memecylon (Melastomataceae): Molecular phylogenetics and revised infrageneric classification of the African species

AbstractThe internal and external transcribed spacers of nuclear ribosomal DNA were sequenced in 167 samples of Memecylon s.str. and 22 outgroup samples of Lijndenia, Mouriri, Spathandra, Votomita, and Warneckea. Maximum‐likelihood analyses of ETS, ITS1, 5.8S and ITS2 alignments yielded tree topologies that are not significantly incongruent, with one exception involving the Tanzanian sample Luke 9741. Monophyly of Memecylon s.str. is strongly supported in the separate ETS and the combined ETS + ITS1 + 5.8S + ITS2 analyses. Also supported in all analyses except 5.8S is a sister‐group relationship between a small species‐group from western and central Africa (Memecylon subg. Mouririoidea, ovary 4‐loculed) and the remaining taxa (M. subg. Memecylon, ovary unilocular). In the combined analysis, internal branches at the base of M. subg. Memecylon are short and weakly supported, yet within this large subgenus one finds a series of monophyletic groups representing different parts of the widespread paleotropical distribution (one group in western and central Africa; two separate groups in East Africa, one of these extending to southern Africa and disjunctly to western and northern Madagascar; one species‐rich group occurring exclusively on Madagascar and the neighboring Comoro and Mascarene islands; and three distinct groups in Indo‐Malesia, one of these also including the Seychelles endemic M. elaeagni). Within the western and central African clade, M. sect. Polyanthema sensu Jacques‐Félix is paraphyletic with respect to M. sect. Afzeliana, and at the morphological level it seems to be a group defined by symplesiomorphies (ovary unilocular, fruit globose). Three East African species (M. fragrans, M. greenwayi, M. semseii) are returned to Memecylon s.str. after being erroneously transferred to Lijndenia by Borhidi. The Madagascan endemic M. mocquerysii is no longer considered a taxonomic synonym of the distantly related, Tanzanian M. cogniauxii. In addition to elevating M. sect. Mouririoidea to subgeneric rank, the following changes are proposed in the infrageneric classification of African Memecylon: (1) the circumscription of sect. Polyanthema is narrowed to comprise only the members of the “M. polyanthemos complex” sensu Jacques‐Félix; (2) Engler's sections Tenuipedunculata, Cauliflora, and Obtusifolia are re‐instated with emended descriptions (in the case of sect. Cauliflora with an expanded circumscription); (3) seven new sections, Buxifolia, Diluviana, Felixiocylon, Germainiocylon, Magnifoliata, Montana, and Sitacylon, are described; (4) the purported occurrence of M. sect. Pseudonaxiandra in East Africa is rejected. A key is provided to the two subgenera and twelve sections currently recognized in African Memecylon. Further study is needed toward a sectional classification of Indo‐Malesian Memecylon, and for revision of the seven Madagascan sections recognized by Jacques‐Félix.

Crowdsourcing for large-scale mosquito (Diptera: Culicidae) sampling

AbstractSampling a cosmopolitan mosquito (Diptera: Culicidae) species throughout its range is logistically challenging and extremely resource intensive. Mosquito control programmes and regional networks operate at the local level and often conduct sampling activities across much of North America. A method for large-scale sampling of two mosquito species using crowdsourcing to network with these local and regional programmes is described. A total of 961 mosquito vector and control districts, health departments, and individual collectors across the United States of America and Canada were contacted in 2011 and 2012 of which 9% positively responded by sending mosquitoes. In total, 1101 unique population samples of Aedes vexans (Meigen) and Culex tarsalis Coquillett were collected throughout their range in these two countries. Aedes vexans outgroup samples were also submitted from Europe and Asia. This is the largest crowd-sourced collection of samples to date.

Maximum polyphyly: Multiple origins and delimitation with plesiomorphic characters require a new circumscription of Minuartia (Caryophyllaceae)

AbstractMinuartia is one of the larger genera of Caryophyllaceae with about 175 species distributed mainly in the Northern Hemisphere. The taxonomy of the genus has been studied by several authors, resulting in the recognition of numerous infrageneric groups. Previous phylogenies of the Caryophyllaceae showed that Minuartia is polyphyletic, but included only a limited sample of the genus. We here provide a molecular phylogeny of Minuartia including all infrageneric groups recognized in the last revision of the genus. We reconstructed the phylogeny of the genus using DNA sequences of nrITS and plastid matK from 160 ingroup and 105 outgroup samples. The evolution of the morphological character relevant for the delimitation of Minuartia (three styles plus three capsule valves/teeth) was reconstructed. Minuartiahas been defined with a plesiomorphic character and is highly polyphyletic. All four subgenera fall into different lineages containing other genera of the family, and M. subg. Minuartia, as by far the largest subgenus, falls into seven clades, which together do not form a monophylum. These clades are closely related to several other genera, e.g., Sagina, Colobanthus and Scleranthus. In several cases taxonomic groups below subgeneric rank are monophyletic. The type of Minuartia, M. dichotoma, is part of a clade containing M. sect. Plurinerviae and sect. Minuartia. We propose to retain this clade as Minuartia s.str. and to transfer the other species of Minuartia to the genera Cherleria, Eremogone, Facchinia, Mcneillia, Minuartiella, Mononeuria, Pseudocherleria, Rhodalsine, Sabulina and Triplateia.

From capsules to nutlets-phylogenetic relationships in the Boraginales.

Multiple family-level subdivisions of Boraginales have been proposed in the past. The relationships of several constituent genera have been enigmatic, including Codon (Codonaceae), Hoplestigma (Hoplestigmataceae), Pholisma (Lennoaceae), Vahlia (Vahliaceae), and Wellstedia (Wellstediaceae), all of which are included in the present study. We present a molecular analysis with four chloroplast loci, including 89 ingroup taxa and a broad outgroup sampling in the asterids. The genus Vahlia is excluded from Boraginales and appears to represent an early branching lineage of Lamiales. The study provides a well supported topology for the relationships within Boraginales, including all of the genera with previously unclear relationships. Within Boraginales, two major clades are recognized, with "herbaceaous" Boraginales I resolved as [Codonaceae,[Wellstediaceae,[Boraginaceae]]] and "woody" Boraginales II resolved as [Hydrophyllaceae I,[Hydrophyllaceae II,[Heliotropiaceae,[Cordiaceae,[Ehretiaceae,Lennoaceae]]]]. A close relationship between Ehretiaceae and Lennoaceae is well supported, but the exact placement of Lennoaceae remains unresolved. The Cordiaceae lineage includes the monotypic genus Coldenia and the aberrant western and central African genus Hoplestigma. Woody Boraginales II are retrieved in two highly supported clades. Hydrophyllaceae are retrieved in two separate clades, but with poor support. There appear to be clear morphological progressions in vegetative, floral, and fruit morphology in both major Boraginales lineages. Thus capsular fruits are found in the first branching lineages of both clades, whereas reduced seed numbers in indehiscent fruits predominate in the more derived phylogenetic positions. Based on these results, we advocate the recognition of eight morphologically well defined clades in the order, namely Boraginaceae s.str., Codonaceae, Cordiaceae (incl. Coldenia and Hoplestigmataceae), Ehretiaceae (incl. Lennoaceae), Heliotropiaceae, Hydrophyllaceae I and Hydrophyllaceae II, and Wellstediaceae.

The phylogeny of the European high mountain genus Adenostyles (Asteraceae‐Senecioneae) reveals that edaphic shifts coincide with dispersal events

Heterogeneity of edaphic conditions plays a large role in driving the diversification of many plant groups. In the Alps and other European high mountains, many closely related calcicole and calcifuge plant taxa exist. To better understand patterns and processes of edaphic differentiation, the phylogeny of the edaphically variable genus Adenostyles was studied. The genus contains three species, of which A. alpina has five subspecies. Each species and subspecies is largely confined to either calcareous or noncalcareous substrates. • We analyzed the phylogeny of Adenostyles using DNA sequences of nrITS, nrETS, nuclear chalcone synthase, and three plastid markers (rpl32-trnL, psbA-trnH, and ndhF-rpl32) from 45 in-group and five out-group samples. The phylogeny was used to reconstruct ancestral edaphic associations and distribution areas. • Within Adenostyles alpina, the shifts of edaphic association from calcicole to calcifuge in subsp. briquetii (Corsica) and in a clade of subsp. macrocephala (southernmost Italy) plus subsp. pyrenaica (Pyrenees) coincide with dispersal events. • We conclude that colonization of areas with novel edaphic conditions via dispersal can trigger shifts of edaphic association. Accordingly, edaphic niche shifts can result from chance events.

Beetles with ‘trochantelli’: phylogeny of Cephenniini (Coleoptera: Staphylinidae: Scydmaeninae) focussing on Neotropical genera

Neotropical genera of Cephenniini characterized by an additional leg ‘segment’ (‘trochantellus’) are revised, and the following new taxa are described: Shyrigen.n., Shyri pichinchasp.n. (type species of Shyri) (Ecuador), Shyri perversussp.n. (Ecuador), Shyri quitusp.n. (Ecuador), Shyri microphthalmussp.n. (Ecuador), Monstrophenniumgen.n. (type species: Cephennium spinicolle Schaufuss), Furcodesgen.n., Furcodes apicalissp.n. (type species of Furcodes) (Mexico), Furcodes tutulesp.n. (Honduras), Paracephennium pumiliosp.n. (Costa Rica), Pseudocephennium iwokramanumsp.n. (Guyana), Pseudocephennium trilineatumsp.n. (Guyana), Pseudocephennium araguanumsp.n. (Venezuela), Pseudocephennium maximumsp.n. (Venezuela), Pseudocephennium peruvianumsp.n. (Peru), Pseudocephennium cochabambanumsp.n. (Bolivia), Pseudocephennium saramaccanumsp.n. (Suriname) and Pseudocephennium brokopondonumsp.n. (Suriname). Pseudocephennium spinicolle (Schaufuss) is transferred to Monstrophennium. Cladistic analysis of characters from adult morphology of all genera of Cephenniini and a large outgroup sample from Cyrtoscydmini, Eutheiini, Scydmaenini, Clidicini and Mastigini strongly supported the monophyly of Cephenniini. However, only the Cephennomicrus group comprising nine genera was strongly supported as a monophyletic clade, while only weak support was found for the previously suggested Cephennodes group and Cephennium group. Two alternative hypotheses concerning the phylogeny of Cephenniini are put forward and discussed: (i) the Cephennium group is sister to all remaining Cephenniini; or (ii) the Cephennomicrus group is sister to all remaining Cephenniini. The Neotropical genera with ‘trochantellus’ form a well‐supported clade derived from the ancestral lineage of the Cephennodes group.

Revision of New World Species of the Shore-fly Subgenus Allotrichoma Becker of the Genus Allotrichoma with Description of the Subgenus Neotrichoma (Diptera, Ephydridae, Hecamedini).

The New World species of the subgenera Allotrichoma Becker and Neotrichoma (new subgenus) are revised, including a phylogenetic analysis of the species groups and subgenera within the genus Allotrichoma. For phylogenetic perspective and to document the monophyly of the genus Allotrichoma and its included subgenera and species groups, we also provide a cladistic analysis of genera within the tribe Hecamedini. The ingroup included seven exemplar congeners from within Allotrichoma. Outgroup sampling included exemplars of other genera within Hecamedini and from the putative sister group, Lipochaetini, and to root the analysis, we used an exemplar of the tribe Discocerinini. Analyses with successive weighting and implied weighting recovered a monophyletic Allotrichoma and indicated clades within the genus. Eight new species are described (type locality in parenthesis): Allotrichoma bifurcatum (Utah. Utah: Lake Shore (40°06.9'N, 111°41.8'W; 1370 m)), Allotrichoma dynatum (Oregon. Benton: Finley National Wildlife Refuge (44°24.6'N, 123°19.5'W)), Allotrichoma occidentale (Oregon. Lake: Lakeview (44 km E; Drake Creek; 42°11'N, 119°59.3'W)), Allotrichoma robustum (California. Kern: Kern River (35°16.1'N, 119°18.4'W)), Allotrichoma sabroskyi (New Mexico. Sandoval: La Cueva (Junction of Highways 126 and 4; 35°52'N, 106°38.4'W; 2342 m)), Allotrichoma wallowa (Oregon Baker: Goose Creek (35 km E Baker City; 44°49.2'N, 117°27.79'W; 825 m)), Allotrichoma baliops (Florida. Monroe: Key West (Willie Ward Park; 24°32.9'N, 81°47.9'W)), and Allotrichoma insulare (Dominica. Cabrits Swamp (15°35'N, 61°29'W)). Within Allotrichoma, we recognize three subgenera of which one, Neotrichoma (type species: Allotrichoma atrilabre), is newly described. All known species from the New World are described with an emphasis on structures of the male terminalia, which are fully illustrated. Detailed locality data and distribution maps for the New World species are provided. A lectotype is designated for Discocerina simplex Loew and a neotype is designated for Allotrichoma bezzii Becker. Allotrichoma filiforme Becker, Allotrichoma trispinum Becker, and Allotrichoma dahli Beschovski are reported as new synonyms of Allotrichoma simplex (Loew) and Allotrichoma yosemite Cresson is a new synonym of Allotrichoma atrilabre Cresson. We also clarify the status of previously described species, including those with Holarctic distributions. For perspective and to facilitate genus-group and species-group recognition, the tribe Hecamedini is diagnosed and a key to included genera is provided.

Stipa (Poaceae) and allies in the Old World: molecular phylogenetics realigns genus circumscription and gives evidence on the origin of American and Australian lineages

The tribe Stipeae with an estimated number of ca. 600 species is part of the grass subfamily Pooideae and has near worldwide distribution. Its species are often dominant constituents of steppe vegetation and other grasslands, especially in Eurasia, the Americas and Australia. The taxonomy of Old World Stipeae has been studied to date primarily on the basis of morphology and anatomy, while existing molecular phylogenetic investigations have mainly dealt with New World or Australian taxa. We studied 109 new ingroup taxa with a focus on Old World Stipeae (in addition with an extensive outgroup sampling) using chloroplast and nuclear ribosomal DNA sequences (3′trnK region, ITS1–5.8S gene–ITS2), and discuss taxonomic key characters. Five highly supported monophyletic lineages were identified, some of which were rather unexpected: (a) the narrowly defined Stipa core clade, which is primarily Eurasian but extends into Africa north of the Sahara Desert, (b) the majority of Old World Piptatherum, (c) a “Transcontinental Stipeae Clade” encompassing Eurasian, African, American and Australian lineages, (d) a Himalayan to E Asian clade and (e) the single species Achnatherum splendens. The large “Transcontinental Stipeae Clade” contained several lineages of Eurasian Stipeae different from the Stipa core (a), i.e., genera Aristella, Celtica, Oloptum gen. nov., Stipella stat. et. gen. nov., species of Achnatherum, and the species-rich lineages of Nassella/Jarava in America and of Austrostipa in Australia. In our circumscription Ptilagrostis was nested in (d), a clade (which included some species of Achnatherum and poorly studied Himalayan species ascribed to either Stipa or Orthoraphium) and whose internal structure remained unclear. Oloptum, gen. nov., is described, and the following combinations are made: Achnatherum pelliotii, comb. nov., Aristella keniensis, comb. nov., Oloptum miliaceum, comb. nov., Stipella, stat. et. gen. nov., S. capensis, comb. nov., S. nitens, comb. nov., S. parviflora, comb. nov., S. staintonii, comb. nov., and S. tigrensis, comb. nov.

Taxonomic revision and phylogenetic analysis of the flightless Mancallinae (Aves, Pan-Alcidae).

Although flightless alcids from the Miocene and Pliocene of the eastern Pacific Ocean have been known for over 100 years, there is no detailed evaluation of diversity and systematic placement of these taxa. This is the first combined analysis of morphological and molecular data to include all extant alcids, the recently extinct Great Auk Pinguinus impennis, the mancalline auks, and a large outgroup sampling of 29 additional non-alcid charadriiforms. Based on the systematic placement of Mancallinae outside of crown clade Alcidae, the clade name Pan-Alcidae is proposed to include all known alcids. An extensive review of the Mancallinae fossil record resulted in taxonomic revision of the clade, and identification of three new species. In addition to positing the first hypothesis of inter-relationships between Mancallinae species, phylogenetic results support placement of Mancallinae as the sister taxon to all other Alcidae, indicating that flightlessness evolved at least twice in the alcid lineage. Convergent osteological characteristics of Mancallinae, the flightless Great Auk, and Spheniscidae are summarized, and implications of Mancallinae diversity, radiation, and extinction in the context of paleoclimatic changes are discussed.

Maternal inheritance in polyploid fish inferred from mitochondrial ATPase genes analysis

Abstract The sequences of the ATPase8/6 genes for the triploid, tetraploid and pentaploid hybrids as well as for their male parent blunt snout bream were determined. In order to examine mitochondrial maternal inheritance, the sequences were subjected to a comparative sequence analysis with the homologous sequences of red crucian carp, their female parent, and zebrafish as the outgroup. Base composition and variation as well as the divergences based on nucleotide sequences and deduced amino acid sequences were calculated. Phylogenetic trees were also constructed with maximum parsimony (MP), minimum evolution (ME), neighbor joining (NJ) and the unweighted pair group method with arithmetic mean (UPGMA) algorithms in MEGA 3.1. The results showed that most nucleotide substitutions occurred at the third codon position of the two genes and thus represented synonymous mutations. The nucleotide sequence divergences of the ATPase8/6 genes ranged from 0.0% to 21.6% among ingroup samples (three types of polyploids and their parents), and 27.0–28.2% between their ingroup and the outgroup samples. All the polyploids were considerably closer in sequence relationship to the female parent red crucian carp (0.0–3.3%) compared to their male parent blunt snout bream (21.0–21.6%). The phylogenetic trees also showed a similar result. In conclusion, the mitochondrial ATPase8/6 genes of artificial polyploid fish stringently indicated maternal inheritance. Our results also suggested that the ATPase8/6 genes are valuable genetic markers to track genealogies and variations in the progenies of the hybrids.

Contrasting evolution of diversity at two disease-associated chicken genes

There have been significant evolutionary pressures on the chicken during both its speciation and its subsequent domestication by man. Infectious diseases are expected to have exerted strong selective pressures during these processes. Consequently, it is likely that genes associated with disease susceptibility or resistance have been subject to some form of selection. Two genes involved in the immune response (interferon-gamma and interleukin 1-beta) were selected for sequencing in diverse chicken populations from Pakistan, Sri Lanka, Bangladesh, Kenya, Senegal, Burkina Faso and Botswana, as well as six outgroup samples (grey, green, red and Ceylon jungle fowl and grey francolin and bamboo partridge). Haplotype frequencies, tests of neutrality, summary statistics, coalescent simulations and phylogenetic analysis by maximum likelihood were used to determine the population genetic characteristics of the genes. Networks indicate that these chicken genes are most closely related to the red jungle fowl. Interferon-gamma had lower diversity and considerable coding sequence conservation, which is consistent with its function as a key inflammatory cytokine of the immune response. In contrast, the pleiotropic cytokine interleukin 1-beta had higher diversity and showed signals of balancing selection moderated by recombination, yielding high numbers of diverse alleles, possibly reflecting broader functionality and potential roles in more diseases in different environments.

Lack of spatial genetic variation in the edible crab (Cancer pagurus) in the Kattegat–Skagerrak area

Abstract Ungfors, A., McKeown, N. J., Shaw, P. W., and André, C. 2009. Lack of spatial genetic variation in the edible crab (Cancer pagurus) in the Kattegat–Skagerrak area. – ICES Journal of Marine Science, 66: 462–469. The stock structure of the edible crab (Cancer pagurus L.) in the Kattegat and Skagerrak was investigated using eight microsatellite DNA loci. Replicate samples, collected 4–6 years apart, were derived from the Kattegat (Grove Bank, 57°N) and the Skagerrak (Lunneviken, 59°N), plus a geographical outgroup sample from the Norwegian Sea (Midsund, 62°N). Genetic differentiation among samples, estimated as global FST = 0.002, was significant (p = 0.03) when the statistical test was based on allele frequencies, but not when based on genotype frequencies. Moreover, all single- and multilocus pairwise tests between samples were non-significant. An analysis of molecular variance, AMOVA, did not reveal significant differentiation between spatial (Kattegat vs. Skagerrak) or temporal (2001/2002 vs. 2006/2007) groups of samples. Power analysis suggested that the loci and sample sizes employed conferred a power of >90% of detecting even low (true FST = 0.002) levels of population structure. Low spatial and temporal genetic structure might be explained by either or both of (i) high levels of contemporary gene flow in the area attributable to adult migration or larval dispersal or both factors taken together, and (ii) patterns of historical gene flow persisting among recently founded large populations.

The Predominantly South American Clade of Lobeliaceae

Abstract A 3.7 kilobase region of chloroplast DNA that includes atpB, rbcL, and their intergenic spacer was sequenced in 61 samples from 45 species of South American Lobeliaceae plus two outgroup samples from Australia. A clade of four hexaploid Lobelia species from Chile is sister to a clade comprising Lysipomia, Siphocampylus, Centropogon, and Burmeistera. Lysipomia is a monophyletic group of small cushion-forming plants endemic to the high Andes, and is sister to the clade comprising the remaining three shrubby genera, which are most diverse in the Andes, but also extend to Central America, Mexico, and the West Indies. Siphocampylus has capsular fruit and is inferred to be paraphyletic relative to fleshy-fruited Centropogon and Burmeistera, but fleshy fruits have evidently evolved repeatedly, making Centropogon polyphyletiC. Burmeistera is primarily bat-pollinated and monophyletic, having evolved from one group of species in Centropogon. The phylogenetic relationships within Burmeistera indicate that t...

Social kin associations and genetic structuring of striped dolphin populations (Stenella coeruleoalba) in the Mediterranean Sea

We investigated hierarchical patterns of genetic subdivision, and assessed kinship within and between social groups of striped dolphins (Stenella coeruleoalba) in the Tyrrhenian Sea. A total of 165 samples were analysed at eight microsatellite DNA loci, including outgroup samples from the Adriatic, Scotland and Spain for population-level comparisons. We found population genetic structure within the Mediterranean basin, including small but significant differentiation between the Adriatic and Tyrrhenian Seas (FST=0.0047, P=0.008), and between putative 'inshore' and 'offshore' (FST=0.0217, P=0.005) populations in the Tyrrhenian Sea. Assessment of kinship within and among 12 association groups showed higher average kinship for females within than between groups, and smaller groups showed higher average kinship. Comparisons of relatedness for both sexes showed a significant difference between males and females, with females more likely to associate with adult kin. Together these data emphasize the importance of the social cohesion of kin in small groups to the structuring of striped dolphin populations in this environment.