Putative Relatives Research Articles

CORRECTING MODEL MISSPECIFICATION IN RELATIONSHIP ESTIMATES.

The datasets of large genotyping biobanks and direct-to-consumer genetic testing companies contain many related individuals. Until now, it has been widely accepted that the most distant relationships that can be detected are around fifteen degrees (approximately 8 th cousins) and that practical relationship estimates have a ceiling around ten degrees (approximately 5 th cousins). However, we show that these assumptions are incorrect and that they are due to a misapplication of relationship estimators. In particular, relationship estimators are applied almost exclusively to putative relatives who have been identified because they share detectable tracts of DNA identically by descent (IBD). However, no existing relationship estimator conditions on the event that two individuals share at least one detectable segment of IBD anywhere in the genome. As a result, the relationship estimates obtained using existing estimators are dramatically biased for distant relationships, inferring all sufficiently distant relationships to be around ten degrees regardless of the depth of the true relationship. Existing relationship estimators are derived under a model that assumes that each pair of related individuals shares a single common ancestor (or mating pair of ancestors). This model breaks down for relationships beyond 10 generations in the past because individuals share many thousands of cryptic common ancestors due to pedigree collapse. We first derive a corrected likelihood that conditions on the event that at least one segment is observed between a pair of putative relatives and we demonstrate that the corrected likelihood largely eliminates the bias in estimates of pairwise relationships and provides a more accurate characterization of the uncertainty in these estimates. We then reformulate the relationship inference problem to account for the fact that individuals share many common ancestors, not just one. We demonstrate that the most distant relationship that can be inferred using IBD may be 200 degrees or more, rather than ten, extending the time-to-common ancestor from approximately 300 years in the past to approximately 3,000 years in the past or more. This dramatic increase in the range of relationship estimators makes it possible to infer relationships whose common ancestors lived before historical events such as European settlement of the Americas, the Transatlantic Slave Trade, and the rise and fall of the Roman Empire.

Isodonxiaoluzhiensis (Lamiaceae, Nepetoideae), a new species from Yunnan, southwest China.

Isodonxiaoluzhiensis, a new species of the tribe Ocimeae in family Lamiaceae, is described and illustrated. The new species is known only from the type locality, Xiaoluzhi village in Luzhijang dry-hot valley of Yimen County, central Yunnan, southwest China. It is characterized by having a procumbent habit, gracile stems and branches, relatively small leaves and flowers, and the phenology of flowering in winter. The morphological comparisons with its putative closest relatives (I.adenanthus and I.hsiwenii) are also presented.

Castaways: the Leeward Antilles endemic spider genus Papiamenta (Araneae: Pholcidae).

Ninetinae is a group of small to tiny short-legged spiders largely restricted to arid habitats. Among daddy-long-legs spiders (Pholcidae) this is by far the least diverse subfamily but this may partly be a result of inadequate collecting, poor representation in collections or scientific neglect. We build on a large recent collection of the ninetine genus Papiamenta Huber, 2000 from the Leeward Antilles and use cytochrome oxidase 1 (COI ) sequences, extensive scanning electron microscopy data, transmission electron microscopy data and karyotyping to analyse this geographically isolated and poorly known island genus. COI sequences support the split between the two morphologically distinct species on Curaçao but genetic distances between these are surprisingly low (7.4-9.8%; mean 8.6%). The type species P. levii (Gertsch, 1982) may include more than one species but COI and morphology suggest conflicting clade limits. A third species, P. bonay Huber sp. nov. is newly described from Bonaire. Our data on sperm ultrastructure and karyology are puzzling as these suggest different phylogenetic affinities of Papiamenta to other genera. Males transfer sperm as individual sperm (cleistosperm), agreeing with the putative closest relatives as suggested by molecular data, the North American genera Pholcophora and Tolteca . The sex chromosome system (X 1 X 2 X 3 Y ) of P. levii , however, is as in the South American Ninetinae genera Gertschiola and Nerudia but different from the putative closest relatives. ZooBank: urn:lsid:zoobank.org:pub:7A6A2E84-3A61-4637-AF6F-0E31A9FA79A8.

New Species of Paussus, Subgenus Scaphipaussus (Coleoptera: Carabidae: Paussinae), from Southeast Asia Reveal Ambiguities in Species Group Limits and High Species Diversity in the Oriental Region.

Paussus, commonly known as ant nest beetles, is the most diverse genus of Paussinae (Coleoptera: Carabidae) with a very complex taxonomic history. Biodiversity research in Southeast and South Asia yields new species that can contribute to a better understanding of the morphological disparity and species-group or subgenus delimitation. Here, we describe nine new species from Southeast Asia and China: Paussus (Scaphipaussus) fencli sp. nov. (China), P. (S.) mawdsleyi sp. nov. (Borneo), P. (S.) bakeri sp. nov. (Philippines), P. (S.) jendeki sp. nov. (Laos), P. (S.) saueri sp. nov. (India), P. (S.) annamensis sp. nov. (Vietnam), P. (S.) phoupanensis sp. nov. (Laos, Vietnam), P. (S.) bilyi sp. nov. (Thailand), and P. (S.) haucki sp. nov. (Thailand). We also bring new data on P. (S.) corporaali Reichensperger, 1927 (Java) and P. (S.) madurensis Wasmann, 1913 (India). Besides formal descriptions, we provide photographs of the habitus in the dorsal and dorsolateral view, antennal club, head crest, and male genitalia if the male is available. Based on the comparison of new and earlier described species, we show that the antennae are highly diverse within the Scaphipaussus. Considering other characters, some species are placed in Scaphipaussus, but they differ from putative relatives in the antennal morphology. The presence of the frontal protuberances and crests is a more reliable character. Additional species show that Scaphipaussus is most diverse in southeastern Asia, especially in Indo-Burma. Concerning its supposed late Miocene origin, the group underwent rapid radiation. The species diversity of Scaphipaussus almost doubled in the last decade, and it is highly probable that further species will be described in the future.

Microlicia crenatifolia (Melastomatacae), a new species from the westernmost limits of the Diamantina Plateau, Minas Gerais, Brazil

Microlicia crenatifolia is described from the Diamantina Plateau, a well-known hotspot of plant endemism in southeastern Brazil. It can be recognized by its small leaves (up to 8.3 mm long) that are conspicuously crenulate to slightly serrate, short floral pedicels (0.7–1.0 mm long), and linear calyx lobes that are externally glandular-punctate and covered with short gland-tipped trichomes 0.1–0.3 mm long. We provide line drawings, SEM photos of leaves, seeds and indumentum, a distribution map, and an identification key to M. crenatifolia and putative relatives (M. canastrensis, M. pabstii, M. serratifolia, and M. thomazii).

A new species of Schlegelia (Schlegeliaceae) from wet montane forest of Colombia and a key for the species of the genus.

In this paper we describe and illustrate Schlegelialongirachis a new species from montane forest remnants (1200--1900 m) in the Western slope of the Eastern Cordillera of Colombia ("Serranía de Las Quinchas" and Virolín county) in the Departments of Boyacá and Santander. A root-climbing liana, the new species is contrasted to S.fuscata, S.monachinoi and S.parviflora, the three most morphologically similar species of Schlegelia. This new species is differentiated from its putative close relatives by vegetative (texture, colour, pubescence and shape in leaves, bracts, bracteoles pedicel, calyx and corolla), inflorescences as well as floral characters (staminode absent). We provide an updated key to 24 known species of Schlegelia. For the identification key, S.fuscata and S.roseiflora are regarded here as different from S.parviflora. S.urbaniana is considered a synonym of S.axillaris, whereas S.fastigiata is separated from S.sulphurea as a recognizable species. Schlegelia has its center of distribution in Colombia, where 17 of the species are known to occur.

Phylogenetic and taxonomic relationships between morphotypes related to Elymus caninus (Poaceae) based on sequence of a nuclear gene GBSS1 (waxy) and sexual hybridization

AbstractWe represent a comparative analysis of GBSS1 gene fragment sequences for a number of species related to Elymus caninus: Elymus prokudinii, Elymus viridiglumis, Elymus goloskokovii, as well as a number of morphologically deviating biotypes, inhabiting Russia and Kazakhstan. Microevolutionary relationships between species were assessed from dendrograms derived from sequences of exons and introns. In all taxa, the St subgenome was represented by St2 variants, rather typical of the North American ancestral line of Pseudoroegneria spicata than of the Asian line descending from Pseudoroegneria strigosa. All putative relatives of E. caninus had H1 subgenome variants linked around the Asian diploid carrier of the H genome from Hordeum jubatum and were divided into two subclades. One of them (H1‐1) contained most of the closely related E. caninus clones, including Elymus uralensis. Another subclade (H1‐2) consisted of five variants phylogenetically related to Elymus mutabilis. We have also studied reproductive relationships between species E. goloskokovii, E. prokudinii, and E. viridiglumis and the degree of their integration into the E. caninus complex. Biotypes included in sexual hybridization formed a single recombination gene pool, within which slight differences in reproductive compatibility were observed. A comprehensive study of microevolutionary differentiation of taxa showed the expediency of taxonomic revision. The species mentioned should probably be relegated to the infraspecific rank within E. caninus s. l.

A deep dive into cryptic taxonomic diversity in the rare endemic mustard Draba maguirei.

Previously published evidence suggests that Draba maguirei, a mustard endemic to a few localities in the Bear River, Wellsville, and Wasatch Mountains of northern Utah, may represent a cryptic species complex rather than a single species. Conservation concerns prompted an in-depth systematic study of this taxon and its putative relatives. Sampling most known populations of D. maguirei s.l. (D. maguirei var. maguirei and D. maguirei var. burkei), we integrate data from geography, ecology, morphology, cytogenetics and pollen, enzyme electrophoresis, and the phylogenetic analysis of nuclear ITS sequences to explore potential taxonomic diversity in the species complex. Draba maguirei var. burkei is shown here to be a distinct species (D. burkei) most closely related to D. globosa, rather than to D. maguirei. Within D. maguirei s.s., the northern (high elevation) and southern (low elevation) population clusters are genetically isolated and morphologically distinguishable, leading to the recognition here of the southern taxon as D. maguirei subsp. stonei. Our study reveals that plants traditionally assigned to D. maguirei comprise three genetically divergent lineages (D. burkei and two newly recognized subspecies of D. maguirei), each exhibiting a different chromosome number and occupying a discrete portion of the geographic range. Although previously overlooked and underappreciated taxonomically, the three taxa are morphologically recognizable based on the distribution and types of trichomes present on the leaves, stems, and fruit. Our clarification of the diversity and distribution of these taxa provides an improved framework for conservation efforts. This article is protected by copyright. All rights reserved.

Relational interdependencies and the intra-EU mobility of African European Citizens

How can we better understand the puzzle of low-skilled migrants who have acquired citizenship in a European Union country, often with generous social security provision, choosing to relocate to the United Kingdom? Drawing on Elias’s figurational theory as a lens, we explore how relational interdependencies foster the mobility of low-skilled African European Citizens from European Union states to the United Kingdom. We found that African European Citizens rely on ‘piblings networks’, loose affiliations of putative relatives, to compensate for deficits in their situated social capital, facilitating relocation. The temporary stability afforded by impermanent bonds and transient associations, in constant flux in migrant communities, does not preclude integration but paradoxically promotes it by enabling an ease of connection and disconnection. Our study elucidates how these relational networks offer African European Citizens opportunities to achieve labour market integration, exercise self-efficacy, and realize desired futures; anchoring individuals in existing communities even when they are perpetually transforming.

Argostemmaehuangzhangense (Rubiaceae), a new species from Guangdong, China.

Argostemmaehuangzhangense, a new Rubiaceae species from E'huangzhang Nature Reserve, Guangdong Province, China, is here described and illustrated. A morphological comparison between the new species and its putative relatives, A.lamxayanum, A.laotica and A.verticillatum, is presented. The new species is mostly similar to A.laotica, but they can be distinguished from each other since Argostemmaehuangzhangense presents solitary flower (vs. 2-flowered inflorescences), flower lobes 4 (vs. 5) and anthers opening by longitudinal slits (vs. apical pores). In a preliminary IUCN Red List status of Argostemmaehuangzhangense this species is assigned as Vulnerable (VU).

Phylogeny of the amphibamiform temnospondyls: the relationship of taxa known by adults, larvae and neotenes

The Amphibamiformes, small temnospondyls from late Palaeozoic rocks, have been increasingly considered as the stem-group of some or all extant amphibians (Lissamphibia). Their relationships have become intensely studied after the discovery of new taxa and the revision of poorly known ones, but understanding is hampered by the fact that amphibamiforms fall into two very distinct groups: (a) terrestrial taxa known by adults only (Amphibamidae, Micropholidae) and (b) aquatic taxa known by larvae and neotenic adults (Branchiosauridae). The Branchiosauridae were recognized as a clade supported by a suite of larval synapomorphies, but the unknown larval morphology of the terrestrial clades leaves the question open to whether some branchiosaurid apomorphies might have been more widely distributed. Recently, some branchiosaurid specimens from Nýřany (Czech Republic) were proposed to be larvae of olsoniforms and amphibamids, and together with a revision of ancient branchiosaurid-like taxa from the United States and France prompt a re-analysis of this issue. In a phylogenetic analysis of 48 taxa and 113 characters, the Branchiosauridae were found to be monophyletic and nest in an unresolved trichotomy with Amphibamidae and the putative relatives of Lissamphibia. The present analysis finds the hypothesized olsoniform larvae from Nýřany to be adults of Branchiosaurus salamandroides, whereas some of the larvae from Mazon Creek (Illinois, USA) are not branchiosaurids, but immature specimens of the amphibamid Amphibamus grandiceps. Within branchiosaurids, four clades have been identified: (a) the Carboniferous Anthracobamus clade (Anthracobamus, Montceaubatrachus), (b) the mostly Carboniferous Branchiosaurinae (Branchiosaurus, Milnererpeton) and two largely Permian clades, the newly defined Apateoninae (genus Apateon) and Leptorophinae (Melanerpeton, Leptorophus, Schoenfelderpeton) clade. Branchiosaurid evolution involved a trend towards an enhanced paedomorphosis, a modification of branchial teeth, and successive reduction of bone in the scales and pectoral girdle.

Transitional morphology and Afrotropical affinity of a bythinoplectine rove beetle from the early Eocene of India (Coleoptera: Staphylinidae: Pselaphinae)

Recently discovered Ypresian-age amber from Cambay, India, reveals an ancient arthropod assemblage on the Indian subcontinent during its collision with Asia. Despite the tectonic history of India, limited connections have been found between the Cambay palaeofauna and present-day Madagascan and mainland African faunas. Here, I describe a new fossil pselaphine rove beetle (Staphylinidae: Pselaphinae) recovered from the Cambay deposit that shows closest apparent phylogenetic affinity to modern Afrotropical genera. Yprezethinus grimaldii gen. et sp. nov. is placed in Bythinoplectini, subtribe Bythinoplectina. Based on antennal and maxillary palp morphology, Yprezethinus is a putative transitional stem lineage of the Zethinus-group of genera—an extant clade distributed across equatorial African rainforests. Although Yprezethinus shares with this clade the derived feature of ovoid antennal clubs formed by tight appression of the apical two segments, it differs from its putative extant relatives in its possession of the plesiomorphic complement of 11 antennomeres, without any fusions of segments. The fossil taxon signifies a biotic link between early Eocene India and continental Africa, and marks the Cenozoic emergence of a tropical leaf litter arthropod fauna approaching that of contemporary, ant-dominated rainforests.

Molecular Phylogenetic Analysis of Salt-Tolerance-Related Genes in Root-Nodule Bacteria Species Sinorhizobium meliloti

A molecular phylogenetic analysis of salt-tolerance-related genes was carried out using complete genome sequencing data available for 26 Sinorhizobium meliloti strains and for 25 bacterial strains belonging to 17 genera. It was revealed that the genes of the first and the second stages of the response to salt stress (aqpZ, trkH, and trkA, and betICBA) have copies of many of the above- indicated genes on pSymA. Data obtained can provide evidence that this replicon, known to be essential for nitrogen fixation rhizobia activity, also has a significant role in the formation of a stress-related gene pool. The closest putative phylogenetic relatives were identified for all 14 tested genes and these are the first insights into the evolutionary pathways for the formation of a stress-related gene pool in root nodule nitrogen-fixing bacteria.

Dead migrants in the Mediterranean: genetic analysis of bone samples exposed to seawater

In April 2015, a fishing boat that departed from Libya with about 1,000 migrants on board sank in the Mediterranean Sea. Most of the migrants were packed in the hull of the boat and drowned in the shipwreck. After fifteen months, the ship was recovered from the seabed and brought to a Sicilian naval area for forensic investigations. Skeletal remains belonging to more than 700 people were retrieved. A selected sample composed of 80 victims was considered in order to evaluate the possibility of achieving genetic profiles useful for a positive identification from these challenging specimens. The molecular features of the DNA recovered from a significant number of real casework samples exposed to seawater for long periods of time were described for the first time. Three different DNA extraction protocols and three different commercial kits were employed in order to generate genetic profiles based on the characterization of 21 autosomal STR loci. The combination of multiple DNA extractions and the cross-checking of multiple PCR amplifications with different kits allowed to obtain reliable genetic profiles characterized by at least 16 STR markers in more than 70% of the samples. The factors that could have affected the different quality of the genetic profiles were investigated and the bone preservation was examined through microscopic and macroscopic analyses. The approach presented in this study could be useful in the management of the genetic analysis of bone samples collected in other similar DVI scenarios. The genetic profiles recovered from the bone samples will be compared in kinship analysis to putative relatives of the victims collected in Africa in order to obtain positive identifications.

Unseeing and Unseen: On the Distribution, Morphology, and Larva of One of North America's Rarest Histerid Beetles, Geocolus caecus Wenzel (Coleoptera: Histeridae)

We have revealed a surprisingly wide distribution for the blind, subterranean histerid species, Geocolus caecus Wenzel, largely through the use of buried “pipe” traps. This species is now known from Georgia, Alabama, South Carolina, and Kentucky, and we also describe its newly discovered larva, associated by DNA sequences. The phylogenetic position of this unusual genus has received little attention, but its continued placement in Dendrophilinae, though not in any specific tribe, appears justified. Morphological similarities to other putative relatives, especially the Mediterranean Triballodes Schmidt, less so New Zealand's Brounister Leschen and Ôhara, are suggestive, though at least some are likely to be symplesiomorphies.

A new species of Microlicia (Melastomataceae) endemic to Serra das Confusões expands the range of the genus to Piauí, Brazil

Microlicia piauiensis is described as a new species from Serra das Confusões, a mountainous region located in a transition zone between the Cerrado (Brazilian savanna) and the Caatinga (deciduous bushland in semi-arid areas) domains. Microlicia piauiensis can be recognized by its branchlets, leaves and hypanthia that are glandular-punctate and covered with gland-tipped trichomes, leaves on short petioles, revolute leaf margins, oblong calyx lobes, magenta petals that are yellow at the base, and isomorphic stamens with small but discernible appendages at the ventral base of the pedoconnectives. Microlicia piauiensis has a distribution that is more than 400 kms distant from all areas of endemism previously identified for the tribe Lavoisiereae. It is the first species of Melastomataceae reported as endemic to Piauí. Photos of living and dried specimens are provided, as well as a distribution map, and morphological comparisons with putative relatives. A conservation status of Endangered is suggested for M. piauiensis.

Two new species of Microlicia (Melastomataceae) from Chapada Diamantina, Bahia, Northeastern Brazil

Microlicia is a Neotropical genus with about 245 species centered in central-eastern Brazil, in areas of campo rupestre and Cerrado. The majority of species occur in the states of Minas Gerais, Bahia, and Goiás. Based on specimens from the herbaria ALCB, HUEFS, MBM, SPF, HUFU, and US, we here describe two new species from the Chapada Diamantina region, Microlicia decumbens and Microlicia macaubensis. Microlicia decumbens is apparently endemic to Abaíra municipality, whereas M. macaubensis is known only from Brotas de Macaúbas municipality. We provide morphological descriptions, line drawings, a distribution map, and comparisons with putative relatives for both species.

Phylogenetics of Serjania (Sapindaceae-Paullinieae), with emphasis on fruit evolution and the description of a new species from Michoacán, Mexico

Serjania is among the largest Neotropical genera of Sapindaceae and comprises ∼240 species. Traditionally, the genus has been defined by its schizocarpic fruits separating into three distally winged mericarps. However, recent phylogenetic studies have revealed that fruit type is not consistent within the genus and that it also includes a few species having capsular fruits that were previously placed in other genera. A phylogenetic analysis is presented based on nuclear ITS and chloroplast trnL-F sequences. The ingroup consisted of 48 species broadly sampled from across the geographic range and taxonomic spectrum of Serjania and focusing on species with atypical fruits. An ancestral character state reconstruction of fruit type was performed and demonstrated that the ancestral fruit type of the genus is strongly supported to be a schizocarp, but there are at least five independent derivations to capsular fruits and at least one transition back from capsules to schizocarps. Also, transitions from winged to wingless mericarps have occurred at least twice. Infrageneric classification is problematic and all of the sections that were represented by more than one species come out as poly- or paraphyletic. Our limited sample of taxa precludes the possibility of a new classification at present and a broader phylogenetic sample of the genus will be needed to understand relationships and determine which lineages warrant formal recognition. In addition to the phylogenetic study, Serjania frutescens, a new capsular-fruited species from Michoacán, Mexico, is described, illustrated, and compared with its putative closest relatives. A key is provided to differentiate this species from other Mexican Serjania with capsular fruits, and new synonymies and lectotypifications associated with capsular-fruited Serjania tortuosa and S. sonorensis are established. Phylogenetic results suggest that these two are cryptic species and at least superficially indistinguishable by morphology.

Morphological and molecular variability of Peridinium volzii Lemmerm. (Peridiniaceae, Dinophyceae) and its relevance for infraspecific taxonomy

Contemporary delimitation of species and populations in the microbial domain relies on an integrative approach combining molecular and morphological techniques. In case of the dinophyte Peridinium volzii, a considerable number of infraspecific taxonomic entities have been reported, but it is unclear at present whether the corresponding traits are stable within reproductively isolated units or refer to intraspecific variability. We established 26 monoclonal strains from Central Europe with a morphology that is consistent for P. volzii and characterised them by sequences gained from the rRNA operon. Ten of such strains, representative for the entire diversity observed, were investigated in detail morphologically using light and electron microscopy. In the molecular tree, P. volzii was monophyletic, sister group of Peridinium willei, and three ITS ribotypes could be distinguished. Some traits corresponding to previously described varieties and forms were found in individual cells across the strains under investigation, but not as stable characters correlating to certain ribotypes. We also observed new morphological variability (e.g., unusual shape of plate 4″). Cell size and displacement of the cingulum were significantly different between certain ribotypes but in turn, such diagnostic traits are impossible to assign to already described taxa due to their ambiguity. Based on the small first apical plate as diagnostic trait and putative apomorphy, P. volzii is a characteristic species but the present data given, we are reserved to accept more than a single reproductive unit. Thus, more research is necessary, including a focus on species delimitation to putative close relatives such as Peridinium maeandricum.

The version of microevolutionary relationships between biotypes close to Elymus caninus (Poaceae) according to the sequencing of the nuclear gene GBSS1 (waxy)

A comparative study of the sequences of the GBSS1 gene fragment in accessions of species close to Elymus caninus:E. prokudinii, E. viridiglumis, E. goloskokovii, as well as a number of morphologically deviating forms (MDF) from the territoryof Russia and Kazakhstan was carried out. The StH-genomic constitution was established or confirmed in all studied taxa andMDF, and the microevolutionary relationships between species were assessed by constructing separate NJ dendrograms based onexons and introns together and exons only. Differences in the location of Y subgenomes in reference StY-genomic species on twotypes of constructed dendrograms were noted. Possible evolutionary reasons for these differences are discussed. A characteristicfeature of all taxa close to E. caninus is the presence of only St2clones of the St subgenome, which are closer in composition tothe North American ancestral line Pseudoroegneria spicata than to the Asiatic line ascending to P. strigosa. The reference Polishaccession E. caninus can_5274 is farthest from the Asian accessions in the St2subgenome, but closer to the diploid carrier ofthe St genome P. spicata. According to the levels of differentiation of the H subgenome, all putative relatives of E. caninus havevariants of the H1subgenome around the Asian diploid host Hordeum jubatum, while being divided into two distinct subgroups.Only the accessions of four reference species gravitate towards the North American species Hordeum californicum – the carrierof the H2gene variant. It should be noted that the gene variants of the Ural endemic E. uralensis are close to the main group ofE. caninus accessions in both subgenomes. Together with the results of sexual hybridization, this fact gives grounds to considerE. uralensis as closely related to the main group of taxa deserving the intraspecific rank of E. caninus s. l.