Putative Relatives Research Articles

Likelihood evaluation using 15 common short tandem repeat loci: a practical and simulated approach to establishing personal identification via sibling/parental assessments

In individual identification, often the only way to circumvent the lack of personal reference materials is to resort to a kinship analysis between the unidentified party (UP) and putative relatives. Genotypes of 15 short tandem repeat loci in 20,000 families were simulated and the likelihood ratios (LRs) were calculated based on the frequencies of alleles in the Japanese population. These LR values illustrate the likelihood of whether an alleged kin is related to a UP. First, three sets of kinship were assessed: UP and one parent (or child); UP and two children; and UP and both parents. Next, an UP was compared with one to three alleged siblings (ASs). In the end, these calculations were applied to 21 actual cases where the identity of an individual lay in dispute. When comparisons were made between a UP and both parents, or two children, the LR median dramatically increased (6.68 x 10(11) and 1.10 x 10(8), respectively) in comparison to assessments involving an UP and one parent or child (48,900). Similarly, when two or three true siblings were made available for comparison, the LR was far greater (7.32 x 10(6) and 4.50 x 10(8), respectively) than in cases where only one sibling was available (9,250). Of the 21 actual cases these calculations were applied to, 1 case ended in exclusion with absolute certainty and the remaining 20 cases obtained high LRs. As demonstrated, this system is extremely effective in cases of personal identification where both parents, two or more children, or two or more ASs are available for comparison.

A new species of Orthomus Chaudoir, 1838 (Coleoptera: Carabidae) from Madeira island (Macaronesia) and notes on related species

The present study describes a new ground-beetle species (Coleoptera, Carabidae) from Madeira island (type localities: FANAL and RIBEIRO BONITO), Orthomus (Nesorthomus) susanae Serrano & Borges, n. sp. Adults were sampled by means of pitfall traps. This work provides diagnostic characters, in particular the structure of male genitalia, and the distribution of this new species. Affinities to putative relatives and a key for the identification of males of the eight Orthomus (Nesorthomus) species of the Madeira island are also given.

Two new species of <i>Typhlocharis</i> Dieck, 1869 (Coleoptera, Carabidae) from Portugal: description and notes on the related species

The present study describes two endogean carabid species of Typhlocharis Dieck, Typhlocharis rochapitei n. sp. and Typhlocharis crespoi n. sp., belonging to the T. diecki species group and to the T. outereloi species group, respectively. The work provides diagnostic characters and in particular, the structure of male genitalia. Affinities to putative relatives and keys for the identification of the diecki (all species) and outereloi (Portugal) species groups are also given.

Enzootic Rabies Elimination from Dogs and Reemergence in Wild Terrestrial Carnivores, United States

To provide molecular and virologic evidence that domestic dog rabies is no longer enzootic to the United States and to identify putative relatives of dog-related rabies viruses (RVs) circulating in other carnivores, we studied RVs associated with recent and historic dog rabies enzootics worldwide. Molecular, phylogenetic, and epizootiologic evidence shows that domestic dog rabies is no longer enzootic to the United States. Nonetheless, our data suggest that independent rabies enzootics are now established in wild terrestrial carnivores (skunks in California and north-central United States, gray foxes in Texas and Arizona, and mongooses in Puerto Rico), as a consequence of different spillover events from long-term rabies enzootics associated with dogs. These preliminary results highlight the key role of dog RVs and human-dog demographics as operative factors for host shifts and disease reemergence into other important carnivore populations and highlight the need for the elimination of dog-related RVs worldwide.

Phylogeny of the avian genus Pitohui and the evolution of toxicity in birds

Bird species in the avian genus Pitohui contain potent neurotoxic alkaloids that may be used for defense. The genus comprises multiple species that are endemic to New Guinea and were presumed to belong to the family Pachycephalidae or Colluricinclidae, within the core corvoidea, an ancient Australasian radiation of crow-like birds. In order to understand the evolution of toxicity within the genus Pitohui, we sequenced three mitochondrial and two nuclear gene segments and reconstructed a phylogeny of the genus Pitohui and its putative relatives. We show that the genus Pitohui is polyphyletic, and consists of five different lineages. Using Bayesian ancestral state reconstruction, we estimate that toxicity likely evolved multiple times within this group. Furthermore, because the morphological and behavioral similarity among these poisonous birds appears to have evolved convergently, we hypothesize that this may be a possible example of Müllerian mimicry in birds. The Morningbird of Palau, Micronesia, that has often been included in the genus Pitohui, actually belongs in the genus Pachycephala and offers an intriguing case of pronounced evolution on a remote oceanic island.

In search of monophyletic taxa in the family Desmidiaceae (Zygnematophyceae, Viridiplantae): the genus Cosmarium

Nuclear-encoded small subunit (SSU) rDNA, 1506 group I introns, and chloroplast rbcL genes were sequenced from 97 strains representing the largest desmid genus Cosmarium (45 spp.), its putative relatives Actinotaenium (5 spp.), Xanthidium (4 spp.), Euastrum (9 spp.), Staurodesmus (13 spp.), and other Desmidiaceae (Zygnematophyceae, Streptophyta) and used to assess phylogenetic relationships in the family. Analyses of single genes and of a concatenated data set (3260 nt) established 10 well-supported clades in the family with Cosmarium species distributed in six clades and one nonsupported assemblage. Most of the clades contained representatives of at least two genera highlighting the polyphyletic nature of the genera Cosmarium, Euastrum, Staurodesmus, and Actinotaenium. To enhance resolution between clades, we extended the data set by sequencing the slowly evolving chloroplast-encoded large subunit (LSU) rRNA gene from 40 taxa. Phylogenetic analyses of a concatenated data set (5509 nt) suggested a sister relationship between two clades that consisted mainly of Cosmarium species and included C. undulatum, the type species of the genus. We describe molecular signatures in the SSU rRNA for two clades and conclude that more studies involving new isolates, additional molecular markers, and reanalyses of morphological traits are necessary before the taxonomic revision of the genus Cosmarium can be attempted.

A new species of Lotononis section Oxydium (Fabaceae, Crotalarieae)

A new species, Lotononis macroloba B-E. Van Wyk and H. Kolberg, is described. It is similar to L. rabenaviana Dinter and Harms but differs in its greatly expanded sepals, larger leaves with short petioles, differently shaped petals and the silky rather than strigillose vestiture. The new species appears to be endemic to north-western Namibia, while the putative relatives, L. rabenaviana and L. sparsiflora (E. Mey.) B-E. Van Wyk, are restricted to the southern parts of Namibia and the adjoining dry western region of South Africa.

Molecular, morphological, and biogeographic resolution of cryptic taxa in the Greenside Darter Etheostoma blennioides complex

The systematic identity and genetic divergence of cryptic taxa and morphological subspecies in the Greenside Darter Etheostoma blennioides complex are analyzed from mitochondrial and nuclear DNA sequence data, along with morphological characters. We sequenced the mtDNA cytochrome b gene and control region and is the nuclear S7 intron 1 for 345 Greenside Darters from 19 locations across their distribution including areas of sympatry and allopatry, in comparison to putative sister species and relatives. Results provide the first genetic evidence that E. gutselli is a separate species and is the sister species of E. blennius, which together with E. rupestre comprise the sister group to the Greenside Darter complex; separating ∼4.0 mya. MtDNA results show that the complex comprises 6 clades and supports only the morphological subspecies Etheostoma blennioides blennioides, distinguished by θ ST = 0.94, ∼1.7 my, scale counts, and ventral squamation. The former E. b. pholidotum and E. b. newmanii are polyphyletic and are invalid taxa, together comprising 5 differentiated clades that diverged ∼0.90–1.7 mya. Nuclear DNA results recover some of the mtDNA clades, which are distinguished morphologically by subtle meristic count differences. Populations of E. b. blennioides genetically diverge, with diversity increasing to the southwest; attributed to restricted gene flow and genetic isolation with geographic distance. Samples of the former E. b. pholidotum from the Great Lakes/Wabash River clade are less divergent, with diversity increasing to the southwest, reflecting allopatric fragmentation and isolation by distance.

A Phylogenomic Investigation into the Origin of Metazoa

The evolution of multicellular animals (Metazoa) from their unicellular ancestors was a key transition that was accompanied by the emergence and diversification of gene families associated with multicellularity. To clarify the timing and order of specific events in this transition, we conducted expressed sequence tag surveys on 4 putative protistan relatives of Metazoa including the choanoflagellate Monosiga ovata, the ichthyosporeans Sphaeroforma arctica and Amoebidium parasiticum, and the amoeba Capsaspora owczarzaki, and 2 members of Amoebozoa, Acanthamoeba castellanii and Mastigamoeba balamuthi. We find that homologs of genes involved in metazoan multicellularity exist in several of these unicellular organisms, including 1 encoding a membrane-associated guanylate kinase with an inverted arrangement of protein-protein interaction domains (MAGI) in Capsaspora. In Metazoa, MAGI regulates tight junctions involved in cell-cell communication. By phylogenomic analyses of genes encoded in nuclear and mitochondrial genomes, we show that the choanoflagellates are the closest relatives of the Metazoa, followed by the Capsaspora and Ichthyosporea lineages, although the branching order between the latter 2 groups remains unclear. Understanding the function of "metazoan-specific" proteins we have identified in these protists will clarify the evolutionary steps that led to the emergence of the Metazoa.

Critical taxonomic analysis of Dichoropetalum, Johrenia, Zeravschania and related genera of Umbelliferae-Apioideae-Peucedaneae

Pimenov, M. G., Kljuykov, E. V. & Ostroumova, T. A.: Critical taxonomic analysis of Dichoropetalum, Johrenia, Zeravschania and related genera of Umbelliferae-Apioideae-Peucedaneae. — Willdenowia 37: 465–502. — ISSN 0511-9618; © 2007 BGBM Berlin-Dahlem. doi:10.3372/wi.37.37208 (available via http://dx.doi.org/)During critical investigation of the Umbelliferae in the Near East, N Africa and Europe some additional species were found to be putative relatives of Johrenia and the Peucedanum segregate Johreniopsis. A comparative multivariate analysis of 41 species, based on 32 morphological diagnostic characters, revealed a revised taxonomic grouping of the species. The forgotten generic name Dichoropetalum, typified by D. alpinum, is restored to accommodate a group of 26 SW Asian and Mediterranean species, including species of the former genera Johreniopsis and Holandrea (now regarded as sections), as well as some Peucedanum and Johrenia species. We recognize six sections in Dichoropetalum, of which three are described as new. Two species of Johreniopsis, poorly known before, are transferred to Zeravschania. Johrenia, on the contrary, is regarded as a genus with five species only. Johrenia westii, which requires further investigation, belongs most probably to the genus Ferulago. 28 new nomenclatural combinations are validated and lectotypes are designated for several names.

Monophyly and phylogenetic relationships of Minthostachys (Labiatae, Nepetoideae) examined using morphological and nrITS data

Minthostachys (Benth.) Spach (Labiatae) from Andean South America was long held to be closely related to Macaronesian Bystropogon L’Her. or to North American Pycnanthemum Michx. The possibility of a close relationship to elements of South American Satureja/Clinopodium s.l. is here proposed for the first time, and a phylogenetic analysis of nrITS data is employed to test the competing hypotheses. For Minthostachys and its putative closest relatives, the possible evolution of morphological characters is investigated with a cladistic analysis. The results suggest that Minthostachys is nested in a clade of South American Mentheae, and probably in the former genus Xenopoma Willd., a group of small-flowered, bee-pollinated species currently included in Clinopodium L.. Minthostachys is considered monophyletic based on nrITS data and its scandent habit.

DNA based association and description of the larval stage of Drusus melanchaetes McLachlan, 1876 (Trichoptera: Limnephilidae: Drusinae) with notes on ecology and zoogeography

At three alpine locations in Switzerland adults of Drusus melanchaetes and unknown Drusinae larvae which could not be identified with existing keys were sampled. Based on DNA association with adults, we identified the unknown larvae as D. melanchaetes. To further support the association of specimens a phylogeny was estimated with the putative closest relatives of D. melanchaetes – D. monticola and D. nigrescens – and five other species of Drusus ( D. chrysotus, destitutus, discolor, muelleri and romanicus). A highly supported monophyletic clade groups unknown larvae and D. melanchaetes specimens from the central Alps and Austria (Vorarlberg), confirming the association. Based on morphology, larvae of D. melanchaetes key out together with D. destitutus in existing keys. D. melanchaetes is separated from the latter species by the shape of the lateral head profile which is almost straight and shows a small step at the height of the antenna, whereas in D. destitutus the lateral head profile is evenly rounded. In addition, in frontal view, the shape of the lateral head outline is straight in D. melanchaetes and rounded in D. destititus. There are also differences in the shape of the pronotum and in the number of the posterodorsal setae at the eighth abdominal dorsum.

Chaetal arrangement provides no support for a close relationship of Sabellidae and Sabellariidae (Annelida)

Sabellid and sabellariid polychaetes are regarded as sister groups in a number of recent phylogenetic analyses. This is based mainly on a shared specific arrangement of chaetae referred to as chaetal inversion. Remarkably, the uncini have a notopodial position in the abdomen, whereas capillary chaetae occur in the neuropodia in both taxa in contrast to the situation in putative relatives. However, in sabellids uncini and capillary chaetae change their position completely at the border between thorax and abdomen, whereas uncini are missing in the parathorax of Sabellariidae. Due to this difference the significance of the chaetal inversion for systematics has been subject to discussion for years. Serial semithin sections of parapodia of the Sabellidae Sabella pavonina, Branchiomma bombyx, Fabricia stellaris, and of the Sabellariidae Sabellaria alveolata were studied in order to obtain detailed information on their chaetal arrangement and sites of chaetal origin. SEM investigations and computer-aided 3D-reconstructions provide deep insight into the spatial organization of the rami. Though differing externally, the principal chaetal arrangement and the location of the formative sites turned out to be almost identical within the species of Sabellidae. Most chaetae are aligned in straight transverse rows with a dorsal site of origin within neuropodia and a ventral one in notopodia as is common in sedentary polychaetes. Semicircular and spiral arrangements are revealed to be modified transverse rows. Only in thoracic notopodia does an additional dorsocaudal formative site form distinct rows. The chaetal inversion in Sabellidae is additionally characterized by an abrupt change of capillary chaetae and uncini along with a sudden change of the parapodial morphology at the border between thorax and abdomen. All chaetae of S. alveolata are aligned in transverse rows with the same location of the formative sites as in sabellids and other sedentary polychaetes. However, in contrast to sabellids the chaetae are not inverted across a parathoracic abdominal border. Moreover, there is no inversion of the parapodial structure from parathorax to abdomen and the neuropodial chaetal composition changes gradually from parathorax to abdomen. The chaetal arrangement in Sabellariidae thus cannot be described as inverted along the body-axis as in Sabellidae. Evolutionary steps implied by the assumption of an inverted chaetal pattern in a supposed common ancestor are discussed. It is concluded that the specific chaetal arrangement of Sabellidae and Sabellariidae arose independently and therefore provides no support for a sistergroup relationship of sabellids and sabellariids.

Molecular evidence for phylogenetic relationships of Jacquemontia reclinata House (Convolvulaceae) – a critically endangered species from south Florida

Jacquemontia reclinata House (Convolvulaceae) is a federally listed endangered species endemic to coastal strand habitat of south-eastern Florida. In order to identify the closest relatives of J. reclinata, a phylogenetic reconstruction was performed based on nucleotide sequence data from the internal transcribed spacer region of nuclear ribosomal DNA and from the trnH-psbA intergenic spacer of chloroplast DNA. The three putative relatives of J. reclinata and the majority of Jacquemontia Choicy species known to occur in the Caribbean Islands were included. The strict consensus tree concurs with previous morphological studies, indicating that J. reclinata is closely related to the Caribbean species J. cayensis Britton, J. curtisii Hallier f., and J. havanensis (Jacq.) Urb. These three species and J. reclinata form an unresolved clade. Nucleotide divergence within this clade is low, suggesting that the group is recent, perhaps diversifying after the latest glacial period. These taxa need to be studied further using population-level DNA markers. Most species endemic to the Caribbean Basin form a strongly supported clade. Our phylogeny supports Convolvulus nodiflorus Desr. as part of Jacquemontia. In addition, J. ovalifolia (West) Hallier f. ssp. sandwicensis (A. Gray) K.R. Robertson is sister to the Antillean endemic J. solanifolia (L.) Hallier f. © 2007 The Linnean Society of London, Botanical Journal of the Linnean Society, 2007, 154, 443-454.

Mitochondrial cox1 and plastid rbcL genes of Gracilaria vermiculophylla (Gracilariaceae, Rhodophyta)

The mitochondrial cytochrome c oxidase subunit I gene sequence was recently developed for DNA barcoding of red algal species. We determined the 1245 base pairs of the gene from 27 taxa of an agar-producing species, Gracilaria vermiculophylla, and putative relatives and compared the results with rbcL data from the same species. A total of 392 positions (31.5%) were variable, 282 positions (22.6%) were parsimoniously informative, and average sequence divergence was 13% in an ingroup. Within G. vermiculophylla, pairwise divergence of the gene was variable up to 11 bp (0.9%). Seven recognized haplotypes of cox1 tended to be geographically related. In the aligned 1386 bp of rbcL, three haplotypes were recognized. These results suggest that cox1 is a valuable molecular marker within species and will be very useful in haplotype analyses.

Phylogenetic Relationships of the Cultivated Neotropical Palm Bactris gasipaes (Arecaceae) with its Wild Relatives Inferred from Chloroplast and Nuclear DNA Polymorphisms

Peach palm (Bactris gasipaes Kunth.) is the only Neotropical palm domesticated since pre-Columbian times. It plays an important role not only at the local level due to its very nutritious fruits, but also in the international market for its gourmet palm heart. Phylogenetic relationships of the peach palm with wild Bactris taxa are still in doubt, and have never been addressed using molecular sequence data. We generated a chloroplast DNA phylogeny using intergenic spacers from a sampling of cultivars of Bactris gasipaes as well as putative wild relatives and other members of the genus Bactris. We estimated phylogenetic relationships using maximum parsimony (MP), maximum likelihood (ML), and Bayesian analysis. Our results indicated a close affinity between three taxa: Bactris gasipaes var. gasipaes, B. gasipaes var. chichagui, and B. riparia. There was no clear differentiation between these three taxa at the level of chloroplast sequences, and they shared a unique inversion that we characterized in this paper. Bactris setulosa, a species potentially related to the Bactris gasipaes complex, appeared highly divergent, and seemed to be a composite taxon with affinities outside the complex. We also investigated nuclear microsatellite polymorphisms at 8 loci within Bactris gasipaes, B. riparia, and B. setulosa, finding a pattern of relationships in agreement with the cpDNA data. The results presented here are important for future studies on domestication and crop improvement of Bactris gasipaes.

Three New Species in Salvia Subgenus Calosphace (Lamiaceae) from Mesoamerica

Three new Salvia L. (Lamiaceae) species, S. colonica Standley & Williams ex Klitgaard, S. univerticillata Ramamoorthy ex Klitgaard, and S. whitefoordiae Klitgaard, were revealed during the study of Salvia for the Flora Mesoamericana in which 69 Salvia species in total are recognized for the Flora region. The three species belong to Salvia subg. Calosphace (Bentham) Epling, and they are endemic to Mesoamerica. In this paper the species are described and illustrated, and their morphological affinities and putative relatives are discussed.

THE RECLASSIFICATION OF LESSONIA LAMINARIOIDES (LAMINARIALES, PHAEOPHYCEAE): PSEUDOLESSONIA GEN. NOV.1

A new genus, Pseudolessonia, is proposed for the kelp Lessonia laminarioides Postels et Ruprecht (Laminariales, Phaeophyceae), which occurs on the northwest side of the Sea of Okhotsk, in the northwest Pacific Ocean. Pseudolessonia is monotypic and differs from Lessonia in its short primary stipes and its corrugated, unilaterally arranged blades with entire margins. This species is transferred on the basis of morphology and plastid gene sequence comparisons. We determined psaA and rbcL gene sequences from 17 taxa of Pseudolessonia, Lessonia, and putative relatives. Analyses of individual and combined data sets resulted in congruent trees showing a clear separation of Pseudolessonia laminarioides from Lessonia, but suggesting its sister relationships with the clade of Nereocystis, Macrocystis, Pelagophycus, and Postelsia in the North Pacific Ocean. On the other hand, Lessonia species from the South Pacific Ocean formed a strongly supported clade. The results indicate that the basal splitting of the blade, which has been considered a diagnostic character for the family Lessoniaceae, is a result of convergent evolution.

Two new species ofTyphlocharis Dieck, 1869 (Coleoptera, Carabidae) from Portugal and notes on the related species

The present study describes two endogean carabid species of Typhlocharis Dieck, Typhlocharis bivari sp. n. and Typhlocharis lunai sp. n., belonging to the T. gomezi species group and to the T. diecki species group, respectively. The work provides diagnostic characters and in particular, the structure of male genitalia. Affinities to putative relatives and keys for the identification of males and females of the gomezi and diecki species groups are also given. (© 2006 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim)

Taxonomy and phylogeny of flattened species of Gracilaria (Gracilariceae, Rhodophyta) from Korea based on morphology and protein-coding plastid rbcL and psbA sequences

M.-S. Kim, E.C. Yang and S.M. Boo. 2006. Taxonomy and phylogeny of flattened species of Gracilaria (Gracilariceae, Rhodophyta) from Korea based on morphology and protein-coding plastid rbcL and psbA sequences. Phycologia 45: 520–528. DOI: 10.2216/05-38.1Despite extensive studies on cylindrical Gracilaria species, the taxonomy and phylogeny of the flattened species of the genus has received little attention. We studied the morphology and molecular phylogeny of three flattened species of Gracilaria, hitherto reported from Korea. Gracilaria textorii is characterized by having a wider blade relative to other species, margins entire or proliferous, coriaceous thallus texture, one to three large cells in the medulla, and shallow male conceptacles. Gracilaria cuneifolia is membranous in texture, and has shallow spermatangial conceptacles (approximately 10 µm in depth). We generated psbA and rbcL sequences from 32 specimens of G. textorii, G. cuneifolia and its putative relatives in Korea and surrounding waters. Twenty-three specimens of G. textorii from Korea, including two from Japan, were almost identical in both rbcL and psbA regions, except for some specimens that were different by one to four nucleotides. Three specimens of G. cuneifolia were identical in both rbcL and psbA. However, we found no evidence for the occurrence of G. incurvata in Korea. In all analyses of rbcL, psbA, and rbcL + psbA data sets, G. textorii was determined to be a unique species, with G. incurvata from Japan as a sister species. Gracilaria cuneifolia is more closely related to the G. tikvahiae group from the Atlantic than G. textorii and G. incurvata.