Displaying publications 61 - 80 of 1825 in total

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  1. Zhang W, Liang Y, Zheng K, Gu C, Liu Y, Wang Z, et al.
    BMC Genomics, 2021 Sep 20;22(1):675.
    PMID: 34544379 DOI: 10.1186/s12864-021-07978-4
    BACKGROUND: Marine bacteriophages play key roles in the community structure of microorganisms, biogeochemical cycles, and the mediation of genetic diversity through horizontal gene transfer. Recently, traditional isolation methods, complemented by high-throughput sequencing metagenomics technology, have greatly increased our understanding of the diversity of bacteriophages. Oceanospirillum, within the order Oceanospirillales, are important symbiotic marine bacteria associated with hydrocarbon degradation and algal blooms, especially in polar regions. However, until now there has been no isolate of an Oceanospirillum bacteriophage, and so details of their metagenome has remained unknown.

    RESULTS: Here, we reported the first Oceanospirillum phage, vB_OliS_GJ44, which was assembled into a 33,786 bp linear dsDNA genome, which includes abundant tail-related and recombinant proteins. The recombinant module was highly adapted to the host, according to the tetranucleotides correlations. Genomic and morphological analyses identified vB_OliS_GJ44 as a siphovirus, however, due to the distant evolutionary relationship with any other known siphovirus, it is proposed that this virus could be classified as the type phage of a new Oceanospirivirus genus within the Siphoviridae family. vB_OliS_GJ44 showed synteny with six uncultured phages, which supports its representation in uncultured environmental viral contigs from metagenomics. Homologs of several vB_OliS_GJ44 genes have mostly been found in marine metagenomes, suggesting the prevalence of this phage genus in the oceans.

    CONCLUSIONS: These results describe the first Oceanospirillum phage, vB_OliS_GJ44, that represents a novel viral cluster and exhibits interesting genetic features related to phage-host interactions and evolution. Thus, we propose a new viral genus Oceanospirivirus within the Siphoviridae family to reconcile this cluster, with vB_OliS_GJ44 as a representative member.

    Matched MeSH terms: Phylogeny
  2. Karin BR, Freitas ES, Shonleben S, Grismer LL, Bauer AM, Das I
    Zootaxa, 2018 Jan 12;4370(4):345-362.
    PMID: 29689833 DOI: 10.11646/zootaxa.4370.4.2
    We collected two specimens of an undescribed species of Lygosoma from pitfall traps in an urban rainforest in Kuching and from the base of a forested hill in western Sarawak, East Malaysia. The new species is diagnosable from all south-east Asian congeners by morphological characters, and most closely resembles Lygosoma herberti from the Thai-Malay Peninsula. The new species shows substantial molecular divergence from its closest relatives in two protein-coding genes, one mitochondrial (ND1) and one nuclear (R35) that we sequenced for several south-east Asian congeners. We describe the new species on the basis of this distinct morphology and genetic divergence. It is the third species of Lygosoma known from Borneo, and highlights the continuing rise in lizard species diversity on the island. In addition, the discovery of this species from a small urban rainforest underscores the importance of preserving intact rainforest areas of any size in maintaining species diversity.
    Matched MeSH terms: Phylogeny
  3. Kurita T, Nishikawa K, Matsui M, Hikida T
    Zootaxa, 2017 05 03;4258(6):525-538.
    PMID: 28609895 DOI: 10.11646/zootaxa.4258.6.2
    A new species of Asian rock gecko, genus Cnemaspis, is described from Padawan, western Sarawak, Malaysian Borneo. The new species forms a clade with C. paripari and C. nigridia of the C. nigridia group in a mitochondrial DNA phylogeny and is similar to them morphologically in some characters such as caudal scalation. It differs from the other Asian Cnemaspis species in its unique combination of snout-vent length (up to 62.7 mm), 4-9 precloacal pores in males, keeled subcaudals with an enlarged, smooth, median row, presence of ventrolateral caudal tubercles, and coloration (head and upper flanks dark-yellow; anterior portion of tail black; posterior portion of tail white with black, paravertebral blob). Phylogenetic relationships within the C. nigridia group and the distributional ranges of species within the group suggest allopatric speciation by geographic isolation.
    Matched MeSH terms: Phylogeny
  4. Berčič RL, Bányai K, Růžek D, Fehér E, Domán M, Danielová V, et al.
    Microorganisms, 2019 Oct 13;7(10).
    PMID: 31614950 DOI: 10.3390/microorganisms7100447
    Lednice virus (LEDV) has been detected in Culex modestus mosquitoes in several European countries within the last six decades. In this study, phylogenetic analyses of the complete genome segments confirm that LEDV belongs to the Turlock orthobunyavirus (Orthobunyavirus, Peribunyaviridae) species and is closely related to Umbre, Turlock, and Kedah viruses.
    Matched MeSH terms: Phylogeny
  5. Quah ESH, Grismer LL, Wood PLJ, Mohd Sah SA
    Zootaxa, 2019 Sep 09;4668(1):zootaxa.4668.1.3.
    PMID: 31716638 DOI: 10.11646/zootaxa.4668.1.3
    A new species of limestone karst-adapted gecko of the Cyrtodactylus pulchellus complex, C. dayangbuntingensis sp. nov., is described from Dayang Bunting Island of the Langkawi Archipelago off the northwest coast of Peninsular Malaysia. It is the third species of the group to be described from the archipelago after C. langkawiensis and C. macrotuberculatus. The new species can be distinguished from all other species of Cyrtodactylus based on molecular evidence from the mitochondrial gene ND2 and its flanking tRNAs as well as having unique combinations of morphological and color pattern characteristics. This discovery underscores the need for continued surveys of the many islands in the archipelago to properly ascertain its true herpetological diversity.
    Matched MeSH terms: Phylogeny
  6. Grismer LL, Wood PLJ, Quah ESH, Anuar S, Poyarkov NA, Thy N, et al.
    Zootaxa, 2019 Oct 09;4683(3):zootaxa.4683.3.4.
    PMID: 31715918 DOI: 10.11646/zootaxa.4683.3.4
    Molecular phylogenetic analyses of the sister species Sphenomorphus stellatus and S. praesignis based on the mitochondrial genes 12S and 16S rRNA recover the former as paraphyletic with respect to the latter in that a specimen of S. stellatus from the type locality in Peninsular Malaysia is more closely related to S. praesignis than to Indochinese populations of S. stellatus. Furthermore, the phylogeny indicates that the Indochinese populations represent two species, thus resulting in four major lineages within this clade. These relationships are consistent with multivariate and univariate analyses of morphological and discrete color pattern data which statistically define and diagnose the four lineages and together with the molecular data, provide the foundation for robust, testable, species-level hypotheses. As such, S. stellatus is herein restricted to Peninsular Malaysia; S. annamiticus is resurrected for the circum-continental populations ranging through southeastern Thailand, southern Cambodia, and southern Vietnam; a new species-S. preylangensis sp. nov.-is described from an isolated mountain, Phnom Chi, from the Prey Lang Wildlife Sanctuary in central Cambodia; and the taxonomy of S. praesignis remains unchanged. The description of S. preylangensis sp. nov. underscores the necessity to conserve this remnant of lowland evergreen rainforest in the Prey Lang Wildlife Sanctuary.
    Matched MeSH terms: Phylogeny
  7. Grismer LL, Dzukafly Z, Muin MA, Quah ESH, Karin BR, Anuar S, et al.
    Zootaxa, 2019 May 23;4609(2):zootaxa.4609.2.10.
    PMID: 31717113 DOI: 10.11646/zootaxa.4609.2.10
    An integrative taxonomic analysis of Subdoluseps herberti from southern Thailand and Peninsular Malaysia and S. samajaya from Sarawak, East Malaysia (Borneo) recovers the former as paraphyletic with respect to the latter. The analyses recover the three southernmost populations of S. herberti in Peninsular Malaysia as conspecific and the sister lineage of S. samajaya, whereas S. herberti from Thailand and northern Peninsular Malaysia constitute the sister species to S. samajaya plus the southern three Peninsular Malaysian populations. As such, the southern populations are described herein as S. malayana sp. nov. and all three species are referred to as the S. herberti group. Clade boundaries and breaks within this group on the Thai-Malay Peninsula occurring at the Isthmus of Kra, across the Kangar-Pattani line, and between the Thai-Malay Peninsula and Borneo are consistent with phylogeographic patterns of other Sundaic taxa. The discovery of S. malayana sp. nov. continues to underscore the fact that, despite the well-studied nature of the lizard fauna of Peninsular Malaysia, much of it still remains unrealized and for conservation efforts to move forward, field research followed by expeditiously revised taxonomies must continue.
    Matched MeSH terms: Phylogeny
  8. Ballantyne LA, Lambkin CL, Ho JZ, Jusoh WFA, Nada B, Nak-Eiam S, et al.
    Zootaxa, 2019 Oct 18;4687(1):zootaxa.4687.1.1.
    PMID: 31719466 DOI: 10.11646/zootaxa.4687.1.1
    This overview of the Luciolinae addresses the fauna of S. E. Asia including India, Sri Lanka, China, Japan, Malaysia, Thailand, Laos, Cambodia, Vietnam, Indonesia, the Philippines, the Republic of Palau, Federated States of Micronesia, and the Australopacific area of Australia, Papua New Guinea, Solomon Islands, New Caledonia, Vanuatu and Fiji.Of the 28 genera now recognised in the Luciolinae we address 27 genera from the study area as defined above, including three new genera which are described herein, and 222 species including 13 species newly described herein. Photuroluciola Pic from Madagascar is the only Luciolinae genus not addressed here. A key to genera is presented. Keys to species are either included here or referenced in existing literature. Twelve genera have had no new taxonomic decisions made nor are any new species records listed, and are addressed in an abbreviated fashion, with short diagnoses and plates of features of life stages: Aquatica Fu et al. 2010, Australoluciola Ballantyne 2013, Convexa Ballantyne 2009, Emeia Fu et al. 2012a, Inflata Boontop 2015, Lloydiella Ballantyne 2009, Missimia Ballantyne 2009, Pteroptyx Olivier 1902, Pyrophanes Olivier 1885, Sclerotia Ballantyne 2016, Triangulara Pimpasalee 2016, and Trisinuata Ballantyne 2013.                Abscondita Ballantyne 2013 contains 8 species, and includes new records for Abs. anceyi (Olivier 1883), Abs. chinensis (L.) (which is newly synonymised with Luciola succincta Bourgeois), Abs. terminalis (Olivier 1883) including a first record from both Laos and Thailand, and Abs. perplexa (Walker 1858). Luciola pallescens Gorham 1880 is transferred to Abscondita and the pronotal colour range is addressed from a wide range of localities. Abs. berembun Nada sp. nov. and Abs. jerangau Nada sp. nov. are described from Malaysia. Hooked bursa plates are described for pallescens and berembun.                Aquilonia Ballantyne 2009 is expanded to include 3 species. Gilvainsula Ballantyne 2009, represented by two species from the south eastern coast of New Guinea is synonymised under Aquilonia Ballantyne 2009, which is briefly redescribed and keyed from: Aquil. costata (Lea) from northern Australia, including many new records, Aquil. messoria (Ballantyne) comb. nov. and Aquil. similismessoria (Ballantyne) comb. nov.                Asymmetricata Ballantyne 2009 now includes 4 species. As. bicoloripes (Pic 1927) comb. nov. and As. humeralis (Walker 1858) comb. nov. are transferred from Luciola, with L. doriae Olivier 1885, L. impressa Olivier 1910b and L. notatipennis Olivier 1909a newly synonymised with As. humeralis. Luciola aemula Olivier 1891 is synonymised with As. ovalis (Hope 1831). The variation in the extent of the anterior median emargination of the light organ in ventrite 7, and the possibility of a bipartite light organ in males of As. circumdata (Motsch. 1854) is explored. Females of both As. circumdata and As. ovalis (Hope 1831) are without bursa plates and the distinctively shaped median oviduct plate in each is described. Records from Thailand are recorded for both As. circumdata and As. ovalis.                Atyphella Olliff 1890 now contains 28 species with 4 transferred from other genera, and one new species: Aty. abdominalis (Olivier 1886) comb. nov. and Aty. striata (Fabricius 1801) comb. nov. are transferred from Luciola, with Aty. carolinae Olivier 1911b and Aty. rennellia (Ballantyne 2009) comb. nov. transferred from Magnalata Ballantyne 2009. Atyphella telokdalam Ballantyne sp. nov. from Indonesia is described herein. Atyphella is now known from records in the Philippines and Indonesia as well as Australia and New Guinea.                Colophotia Motschulsky 1853 is considered here from seven species for which intact types can be located for three. An abbreviated revision based on the United States National Museum collection only is presented, with specimens of C. bakeri Pic 1924, C. brevis Olivier 1903a, C. plagiata (Erichson 1834) and C. praeusta (Eschscholtz 1822) redescribed, using where possible features of males, females and larvae. Colophotia particulariventris Pic 1938 is newly synonymised with C. praeusta. Colophotia miranda Olivier 1886 and L. truncata Olivier 1886 are treated as species incertae sedis.                Curtos Motschulsky 1845 includes 19 species with suggestions made, but not yet formalised, for the possible transfer of the following seven species from Luciola: Luciola complanata Gorham 1895, L. costata Pic 1929, L. delauneyi Bourgeois 1890, L. deplanata Pic 1929, L. extricans Walker 1858, L. multicostulata Pic 1927 and L. nigripes Gorham 1903. Curtos is not revised here.                Emarginata Ballantyne gen nov. is described for E. trilucida (Jeng et al. 2003b) comb. nov., transferred from Luciola and characterised by the emarginated elytral apex. An extended range of specimens from Thailand is listed.                Kuantana Ballantyne gen. nov. from Selangor, Malaysia is described from K. menayah gen. et sp. nov. having bipartite light organs in ventrite 7 and an asymmetrical tergite 8 which is not emarginated on its left side. Female has no bursa plates.                Luciola Laporte 1833 s. stricto as defined by a population of the type species Luciola italica (L. 1767) from Pisa, Italy, is further expanded and considered to comprise the following19 species: L. antipodum (Bourgeois 1884), L. aquilaclara Ballantyne 2013, L. chapaensis Pic 1923 which is synonymised with L. atripes Pic 1929, L. curtithorax Pic 1928, L. filiformis Olivier 1913c, L. horni Bourgeois 1905, L. hypocrita Olivier 1888, L. italica (L. 1767), L. kagiana Matsumura 1928, L. oculofissa Ballantyne 2013, L. pallidipes Pic 1928 which is synonymised with L. fletcheri Pic 1935, L. parvula Kiesenwetter 1874, L. satoi Jeng Yang 2003, L. tuberculata Yiu 2017, and two species treated as near L. laticollis Gorham 1883, and near L. nicollieri Bugnion 1922. The following are described as new: L. niah Jusoh sp. nov., L. jengai Nada sp. nov. and L. tiomana Ballantyne sp. nov. Luciola niah sp. nov. female has two wide bursa plates on each side of the bursa.                Luciola s. lato (as defined here) consists of 36 species. Twenty-seven species formerly standing under Luciola have been assigned to other genera or synonymised. Seven species are recommended for transfer to Curtos, and 32 species now stand under species incertae sedis.                Magnalata Ballantyne is reduced to the type species M. limbata and redescribed.                Medeopteryx Ballantyne 2013 is expanded to 20 species with the addition of two new combinations, Med. semimarginata (Olivier 1883) comb. nov. and Med. timida (Olivier 1883) comb. nov., both transferred from Luciola, and one new species, Med. fraseri Nada sp. nov. from Malaysia. The range of this genus now extends from Australia and the island of New Guinea to SE Asia. Medeopteryx semimarginata females have wide paired bursa plates.                Pygoluciola Wittmer 1939 now includes 19 species with 5 new species: P. bangladeshi Ballantyne sp. nov., P. dunguna Nada 2018, P. matalangao Ballantyne sp. nov. (scored by the code name 'Jeng Matalanga' in Ballantyne Lambkin 2013), P. phupan Ballantyne sp. nov. and P. tamarat Jusoh sp. nov. Six species are transferred from Luciola: P. abscondita (Olivier 1891) comb. nov., P. ambita (Olivier 1896) comb. nov., P. calceata (Olivier 1905) comb. nov., P. insularis (Olivier 1883) comb. nov., P. nitescens (Olivier 1903b) comb. nov. and P. vitalisi (Pic 1934) comb. nov., and redescribed from males, and includes female reproductive anatomy for P. nitescens comb. nov. and P. dunguna, both of which have hooked bursa plates.                Serratia Ballantyne gen. nov. is erected for S. subuyania gen. et sp. nov. and characterised by the serrate nature of certain antennal flagellar segments in the male.                The following 37 species listed under species incertae sedis are further explored: Colophotia miranda Olivier 1886, Lampyris serraticornis Boisduval 1835, Luciola angusticollis Olivier 1886, L. antennalis Bourgeois 1905, L. antica (Boisduval 1835), L. apicalis (Eschscholtz 1822), L. aurantiaca Pic 1927, L. bicoloriceps Pic 1924, L. binhana Pic 1927, L. bourgeoisi Olivier 1895, L. dilatata Pic 1929, L. exigua (Gyllenhall 1817), L. exstincta Olivier 1886, L. fissicollis Fairmaire 1891, L. flava Pic 1929, L. flavescens (Boisduval 1835), L. fukiensis Pic 1955, L. immarginata Bourgeois 1890, L. incerta (Boisduval 1835), L. infuscata (Erichson 1834), L. intricata (Walker 1858), L. japonica (Thunberg 1784), L. klapperichi Pic 1955, L. lata Olivier 1883, L. limbalis Fairmaire 1889, L. marginipennis (Boisduval 1835), L. melancholica Olivier 1913a, L. robusticeps Pic 1928, L. ruficollis (Boisduval 1835), L. spectralis Gorham 1880, L. stigmaticollis Fairmaire 1887, L. tincticollis Gorham 1895, L. trivandrensis Raj 1947, L. truncata Olivier 1886, L. vittata (Laporte 1833) Pteroptyx atripennis Pic 1923 and P. curticollis Pic 1923.                While phylogenetic analyses indicate their distinctiveness, no further taxonomic action is taken with Luciola cruciata Motschulsky 1854 and L. owadai Sâtô et Kimura 1994 from Japan given the importance of the former as a national icon. Analyses also indicate that Lampyroidea syriaca Costa 1875 belongs in Luciola s. str. A much wider taxonomic analysis of this genus including all the species is necessary before any further action can be taken.
    Matched MeSH terms: Phylogeny
  9. Haja Maideen, Nor Hazwani A, Nurfarahain Z, Damanhuri A, Noraini T, Qistina L, et al.
    Sains Malaysiana, 2013;42:693-696.
    An anatomical study was carried out on 14 taxa belonging to Selaginellaceae in an attempt to study their stipe anatomical characteristics and to provide anatomical data for the selected taxa in Selaginellaceae. Out of 29 taxa of Selaginellaceae recorded in Peninsular Malaysia, 14 taxa have been selected namely Selaginella alutacia, S. argentea, S. frondosa, S. intermedia var. intermedia, S. intermedia var. dolichocentrus, S. mayeri, S. morganii, S. ornata, S. plana, S. polita, S. roxburghii var. roxburghii, S. stipulata, S. wallichii and S. willdenowii. Method used in this study was sectioning using sliding microtome. Findings in this study have shown that Selaginellaceae species studied can be clustered into two groups based on the stipe stellar systems, which are monostelic and tristelic groups. There are some variations exist in the cross sections of the stipes of the same species due to the presence and absence of the leaf trace. Each species is proved to have distinct stipe anatomical characteristics that can be used to differentiate species in Selaginellaceae.
    Matched MeSH terms: Phylogeny
  10. Zaki S, Merican F, Muangmai N, Convey P, Broady P
    Harmful Algae, 2020 03;93:101800.
    PMID: 32307064 DOI: 10.1016/j.hal.2020.101800
    Microcystins (MCs) are secondary metabolites produced by cyanobacteria and have been well-documented in temperate and tropical regions. However, knowledge of the production of MCs in extremely cold environments is still in its infancy. Recently, examination of 100-year-old Antarctic cyanobacterial mats collected from Ross Island and the McMurdo Ice Shelf during Captain R.F. Scott's Discovery Expedition revealed that the presence of MCs in Antarctica is not a new phenomenon. Here, morphological and molecular phylogenetic analyses are used to identify a new microcystin-producing freshwater cyanobacterium, Anagnostidinema pseudacutissimum. The strain was isolated from a deep-frozen (-15 °C) sample collected from a red-brown cyanobacterial mat in a frozen pond at Cape Crozier (Ross Island, continental Antarctica) in 1984-1985. Amplification of the mcyE gene fragment involved in microcystin biosynthesis from A. pseudacutissimum confirmed that it is identical to the sequence from other known microcystin-producing cyanobacteria. Analysis of extracts from this A. pseudacutissimum strain by HPLC-MS/MS confirmed the presence of MC-LR and -YR at concentrations of 0.60 μg/L and MC-RR at concentrations of 0.20 μg/L. This is the first report of microcystin production from a species of Anagnostidinema from Antarctica.
    Matched MeSH terms: Phylogeny
  11. Liu JW, Li SF, Wu CT, Valdespino IA, Ho JF, Wu YH, et al.
    Am J Bot, 2020 04;107(4):562-576.
    PMID: 32227348 DOI: 10.1002/ajb2.1455
    PREMISE: Unique among vascular plants, some species of Selaginella have single giant chloroplasts in their epidermal or upper mesophyll cells (monoplastidy, M), varying in structure between species. Structural variants include several forms of bizonoplast with unique dimorphic ultrastructure. Better understanding of these structural variants, their prevalence, environmental correlates and phylogenetic association, has the potential to shed new light on chloroplast biology unavailable from any other plant group.

    METHODS: The chloroplast ultrastructure of 76 Selaginella species was studied with various microscopic techniques. Environmental data for selected species and subgeneric relationships were compared against chloroplast traits.

    RESULTS: We delineated five chloroplast categories: ME (monoplastidy in a dorsal epidermal cell), MM (monoplastidy in a mesophyll cell), OL (oligoplastidy), Mu (multiplastidy, present in the most basal species), and RC (reduced or vestigial chloroplasts). Of 44 ME species, 11 have bizonoplasts, cup-shaped (concave upper zone) or bilobed (basal hinge, a new discovery), with upper zones of parallel thylakoid membranes varying subtly between species. Monoplastidy, found in 49 species, is strongly shade associated. Bizonoplasts are only known in deep-shade species (<2.1% full sunlight) of subgenus Stachygynandrum but in both the Old and New Worlds.

    CONCLUSIONS: Multiplastidic chloroplasts are most likely basal, implying that monoplastidy and bizonoplasts are derived traits, with monoplastidy evolving at least twice, potentially as an adaptation to low light. Although there is insufficient information to understand the adaptive significance of the numerous structural variants, they are unmatched in the vascular plants, suggesting unusual evolutionary flexibility in this ancient plant genus.

    Matched MeSH terms: Phylogeny
  12. Kawachi M, Nakayama T, Kayama M, Nomura M, Miyashita H, Bojo O, et al.
    Curr Biol, 2021 06 07;31(11):2395-2403.e4.
    PMID: 33773100 DOI: 10.1016/j.cub.2021.03.012
    Rapidly accumulating genetic data from environmental sequencing approaches have revealed an extraordinary level of unsuspected diversity within marine phytoplankton,1-11 which is responsible for around 50% of global net primary production.12,13 However, the phenotypic identity of many of the organisms distinguished by environmental DNA sequences remains unclear. The rappemonads represent a plastid-bearing protistan lineage that to date has only been identified by environmental plastid 16S rRNA sequences.14-17 The phenotypic identity of this group, which does not confidently cluster in any known algal clades in 16S rRNA phylogenetic reconstructions,15 has remained unknown since the first report of environmental sequences over two decades ago. We show that rappemonads are closely related to a haptophyte microalga, Pavlomulina ranunculiformis gen. nov. et sp. nov., and belong to a new haptophyte class, the Rappephyceae. Organellar phylogenomic analyses provide strong evidence for the inclusion of this lineage within the Haptophyta as a sister group to the Prymnesiophyceae. Members of this new class have a cosmopolitan distribution in coastal and oceanic regions. The relative read abundance of Rappephyceae in a large environmental barcoding dataset was comparable to, or greater than, those of major haptophyte species, such as the bloom-forming Gephyrocapsa huxleyi and Prymnesium parvum, and this result indicates that they likely have a significant impact as primary producers. Detailed characterization of Pavlomulina allowed for reconstruction of the ancient evolutionary history of the Haptophyta, a group that is one of the most important components of extant marine phytoplankton communities.
    Matched MeSH terms: Phylogeny
  13. Gopalakrishnan S, Ebenesersdóttir SS, Lundstrøm IKC, Turner-Walker G, Moore KHS, Luisi P, et al.
    Curr Biol, 2022 Nov 07;32(21):4743-4751.e6.
    PMID: 36182700 DOI: 10.1016/j.cub.2022.09.023
    Human populations have been shaped by catastrophes that may have left long-lasting signatures in their genomes. One notable example is the second plague pandemic that entered Europe in ca. 1,347 CE and repeatedly returned for over 300 years, with typical village and town mortality estimated at 10%-40%.1 It is assumed that this high mortality affected the gene pools of these populations. First, local population crashes reduced genetic diversity. Second, a change in frequency is expected for sequence variants that may have affected survival or susceptibility to the etiologic agent (Yersinia pestis).2 Third, mass mortality might alter the local gene pools through its impact on subsequent migration patterns. We explored these factors using the Norwegian city of Trondheim as a model, by sequencing 54 genomes spanning three time periods: (1) prior to the plague striking Trondheim in 1,349 CE, (2) the 17th-19th century, and (3) the present. We find that the pandemic period shaped the gene pool by reducing long distance immigration, in particular from the British Isles, and inducing a bottleneck that reduced genetic diversity. Although we also observe an excess of large FST values at multiple loci in the genome, these are shaped by reference biases introduced by mapping our relatively low genome coverage degraded DNA to the reference genome. This implies that attempts to detect selection using ancient DNA (aDNA) datasets that vary by read length and depth of sequencing coverage may be particularly challenging until methods have been developed to account for the impact of differential reference bias on test statistics.
    Matched MeSH terms: Phylogeny
  14. Tan CY, Lin CN, Ooi PT
    Transbound Emerg Dis, 2021 Nov;68(6):2915-2935.
    PMID: 34110095 DOI: 10.1111/tbed.14185
    Porcine circovirus 3 (PCV3) was first discovered in 2016, almost concomitantly by two groups of researchers in the United States. The novel case was reported in a group of sows with chronic reproductive problems with clinical presentation alike porcine dermatitis and nephropathy syndrome (PDNS), where metagenomic sequencing revealed a genetically divergent porcine circovirus designated PCV3. The discovery of PCV3 in a PDNS case, which used to be considered as part of PCVAD attributed to PCV2 (porcine circovirus 2), has garnered attention and effort in further research of the novel virus. Just when an infectious molecular DNA clone of PCV3 has been developed and successfully used in an in vivo pathogenicity study, yet another novel PCV strain surfaced, designated PCV4 (porcine circovirus 4). So far, PCV3 has been reported in domestic swine population globally at low to moderate prevalence, from almost all sample types including organ tissues, faecal, semen and colostrum samples. PCV3 has been associated with a myriad of clinical presentations, from PDNS to porcine respiratory disease complex (PRDC). This review paper summarizes the studies on PCV3 to date, with focus on diagnosis.
    Matched MeSH terms: Phylogeny
  15. Sivananthan GD, Shantti P, Kupriyanova EK, Quek ZBR, Yap NWL, Teo SLM
    Zootaxa, 2021 Sep 20;5040(1):33-65.
    PMID: 34811055 DOI: 10.11646/zootaxa.5040.1.2
    The intertidal serpulid polychaete Spirobranchus kraussii was originally described from South Africa and has since been reported in numerous sub (tropical) localities around the world. Recently, however, S. kraussii was uncovered as a complex of morphologically similar and geographically restricted species, raising the need to revise S. cf. kraussii populations. We formally describe S. cf. kraussii from Singapore mangroves as Spirobranchus bakau sp. nov. based on morphological and molecular data. Despite their morphological similarities, Maximum Likelihood and Bayesian Inference analyses of 18S and Cyt b DNA sequence data confirm that S. bakau sp. nov. is genetically distinct from S. kraussii and other known species in the complex. Both analyses recovered S. bakau sp. nov. as part of a strongly supported clade (96% bootstrap, 1 posterior probability), comprising S. sinuspersicus, S. kraussii and S. cf. kraussii from Australia and Hawaii. Additionally, paratypes of S. kraussii var. manilensis, described from Manila Bay in the Philippines, were examined and elevated to the full species S. manilensis. Finally, we tested the hypothesis that fertilisation and embryonic development of S. bakau sp. nov. can occur under the wide range of salinities (19.630.9 psu) and temperatures (2531C) reported in the Johor Strait. Fertilisation success of ≥70% was achieved across a temperature range of 2532C and a salinity range of 2032 psu. Embryonic development, however, had a narrower salinity tolerance range of 2732 psu. Clarifying the taxonomic status of S. cf. kraussii populations reported from localities elsewhere in Singapore and Southeast Asia will be useful in establishing the geographical distribution of S. bakau sp. nov. and other members of the S. kraussii-complex.
    Matched MeSH terms: Phylogeny
  16. Kropachev II, Vassilieva AB, Orlov NL, Rybaltovsky EM, Nguyen TT
    Zootaxa, 2021 Sep 14;5039(1):144-148.
    PMID: 34811091 DOI: 10.11646/zootaxa.5039.1.9
    To date, 20 species of Kurixalus Ye, Fei, and Dubois have been described, and all of these species are distributed throughout South and Southeast Asia, from eastern India, throughout Myanmar and the mountainous regions of southern China, to Indochina, western and northern peninsular Thailand, Malaysia, Sumatra, Borneo, and the Philippines (Frost 2021). Descriptions of the tadpoles of only 6 species have been published: K. berylliniris and K. wangi Wu, Huang, Tsai, Li, Jhang, Wu (Wu et al. 2016); K. eiffingeri (Boettger) (Kuramoto Wang 1987); K. idiootocus (Kuramoto Wang) (Kuramoto Wang 1987); K. cf. verrucosus (Boulenger) (Ziegler Vences 2002), and Kurixalus yangi Yu, Hui, Rao, Yang (Humtsoe et al. 2020). A description of the tadpoles of K. baliogaster (Inger, Orlov, Darevsky) is also given in the species description (Inger et al. 1999), but described larvae are assigned tentatively to this species in the published text. Additional studies on the identification of the conspecificity of the described tadpoles with K. baliogaster have not been conducted. Based on the much larger size of the tadpole body (TL up to 40.3 mm), as well as the labial tooth row formula 6(26)/5(1) given by Inger et al. (1999), we concluded that these described tadpoles cannot be larval K. baliogaster and most likely belong to some other species of rhacophorid frogs.
    Matched MeSH terms: Phylogeny
  17. Takaoka H, Fukuda M, Otsuka Y, Low VL, Ya'cob Z
    Acta Trop, 2022 Jan;225:106207.
    PMID: 34687650 DOI: 10.1016/j.actatropica.2021.106207
    Simulium (Gomphostilbia) omutaense Ogata & Sasa, 1954 is the only named species in the Simulium batoense species-group of the subgenus Gomphostilbia Enderlein recorded from Honshu and Kyushu, Japan. It represents the northernmost distribution of this species-group, of which most members are distributed in the Oriental region. This species, the only member of the Simulium omutaense subgroup, is unique among the seven subgroups of the S. batoense species-group by having the pupal gill with one long filament and seven short filaments, similar to the arrangement of the pupal gill filaments in the S. zonatum subgroup of the S. epistum species-group in the same subgenus. This species is fully redescribed based on adults, pupal exuviae and mature larvae, and is most similar to species of the S. decuplum subgroup, based on adult morphological characteristics, although the pupal gill of the latter subgroup is markedly different by having 10 or 12 short filaments. Its close relationship to the S. decuplum subgroup is supported by a DNA analysis using COI gene sequences, with genetic distances of 9.30-11.02%. On the other hand, genetic distances between S. (G.) omutaense and species of the S. zonatum subgroup were 16.32-16.93%. Our study shows that a similar arrangement of the pupal gills in two different species-groups, which is rarely seen, has evolved independently and its occurrence does not necessarily reflect phylogenetic relationships.
    Matched MeSH terms: Phylogeny
  18. Williams EW, Gardner EM, Harris R, Chaveerach A, Pereira JT, Zerega NJ
    Ann Bot, 2017 03 01;119(4):611-627.
    PMID: 28073771 DOI: 10.1093/aob/mcw249
    Background and Aims: The breadfruit genus ( Artocarpus , Moraceae) includes valuable underutilized fruit tree crops with a centre of diversity in Southeast Asia. It belongs to the monophyletic tribe Artocarpeae, whose only other members include two small neotropical genera. This study aimed to reconstruct the phylogeny, estimate divergence dates and infer ancestral ranges of Artocarpeae, especially Artocarpus , to better understand spatial and temporal evolutionary relationships and dispersal patterns in a geologically complex region.

    Methods: To investigate the phylogeny and biogeography of Artocarpeae, this study used Bayesian and maximum likelihood approaches to analyze DNA sequences from six plastid and two nuclear regions from 75% of Artocarpus species, both neotropical Artocarpeae genera, and members of all other Moraceae tribes. Six fossil-based calibrations within the Moraceae family were used to infer divergence times. Ancestral areas and estimated dispersal events were also inferred.

    Key Results: Artocarpeae, Artocarpus and four monophyletic Artocarpus subgenera were well supported. A late Cretaceous origin of the Artocarpeae tribe in the Americas is inferred, followed by Eocene radiation of Artocarpus in Asia, with the greatest diversification occurring during the Miocene. Borneo is reconstructed as the ancestral range of Artocarpus , with dozens of independent in situ diversification events inferred there, as well as dispersal events to other regions of Southeast Asia. Dispersal pathways of Artocarpus and its ancestors are proposed.

    Conclusions: Borneo was central in the diversification of the genus Artocarpus and probably served as the centre from which species dispersed and diversified in several directions. The greatest amount of diversification is inferred to have occurred during the Miocene, when sea levels fluctuated and land connections frequently existed between Borneo, mainland Asia, Sumatra and Java. Many species found in these areas have extant overlapping ranges, suggesting that sympatric speciation may have occurred. By contrast, Artocarpus diversity east of Borneo (where many of the islands have no historical connections to the landmasses of the Sunda and Sahul shelves) is unique and probably the product of over water long-distance dispersal events and subsequent diversification in allopatry. This work represents the most comprehensive Artocarpus phylogeny and biogeography study to date and supports Borneo as an evolutionary biodiversity hotspot.

    Matched MeSH terms: Phylogeny
  19. Quah ESH, Grismer LL, Wood PLJ, Thura MK, Zin T, Kyaw H, et al.
    Zootaxa, 2017 Mar 06;4238(4):571-582.
    PMID: 28603251 DOI: 10.11646/zootaxa.4238.4.5
    A newly discovered species of homalopsid snake from the genus Gyiophis Murphy & Voris is described from the lowlands of Mawlamyine District in Mon state, southeastern Myanmar. Gyiophis salweenensis sp. nov. is presumed to be closely related to G. maculosa Blanford and G. vorisi Murphy based on the similarities in pholidosis and patterning but can be separated from G. maculosa by the shape of its first three dorsal scale rows that are square, ventral scale pattern that lacks a central spot, and a faint stripe on dorsal scale rows 1-4. It can be further distinguished from G. vorisi by its lower number of ventral scales (129 vs. 142-152), lower number of subcaudals (30/29 vs. 41-58), narrow rostral scale, and having more rows of spots on the dorsum (four vs. three). A preliminary molecular analysis using 1050 base pairs of cytochrome b (cytb) recovered G. salweenensis sp. nov. as the sister species to the Chinese Mud Snake (Myrrophis chinensis). G. maculosa and G. vorisi were unavailable for the analysis. The discovery of G. salweenensis sp. nov. highlights the need for more surveys into the herpetological diversity of eastern Myanmar which remains very much underestimated.
    Matched MeSH terms: Phylogeny
  20. Boyd DA, Nithirojpakdee P, Deein G, Vidthayanon C, Grudpan C, Tangjitjaroen W, et al.
    Zootaxa, 2017 Oct 31;4341(2):151-192.
    PMID: 29245684 DOI: 10.11646/zootaxa.4341.2.1
    Acantopsis (Cobitidae) is revised based on analysis of morphological and molecular data. Four of the six available names, A. dialuzona, A. spectabilis, A. octoactinotos, and A. thiemmedhi, are valid, and three new species, A. rungthipae, A. dinema, and A. ioa, are described. All species are described morphologically, distributions are mapped, and relationships are discussed for those for which molecular data (CO1, RAG1) are available. Labial barbels, color pattern, and meristic counts are the most diagnostic features. Although the long snout of Acantopsis is perhaps the most emblematic attribute of the genus, its relative length increases with growth, reducing its taxonomic value. Species can be difficult to identify on the basis of color pattern alone, as habitat and preservation methods appear to strongly influence the color pattern. Despite interspecific overlap of some highly variable traits, each species has a unique set of morphological characteristics that remain observable even when the color pattern is obscured, and some species are restricted to single drainages, greatly simplifying identification. The phylogenetic analyses revealed high molecular divergence between even the most morphologically similar species, with mean uncorrected CO1 p-distances between species ranging from 12.1-15.4%. Species of Acantopsis exhibit significant genetic structuring consistent with recognized freshwater ecoregions. Acanthopsis lachnostoma Rutter 1897, from Swatow, China, is not assignable to Acantopsis.
    Matched MeSH terms: Phylogeny
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