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Bernhard A Huber - One of the best experts on this subject based on the ideXlab platform.

  • Inferring global species richness from megatransect data and undetected species estimates
    Contributions to Zoology, 2019
    Co-Authors: Bernhard A Huber, Anne Chao
    Abstract:

    Ratio-like approaches for estimating global species richness have been criticised for their unjustified extrapolation from regional to global patterns. Here we explore the use of cumulative percentages of ‘new’ (i.e., not formally described) species over large geographic areas (‘megatransects’) as a means to overcome this problem. In addition, we take into account undetected species and illustrate these combined methods by applying them to a family of spiders (Pholcidae) that currently contains some 1,700 described species. The raw global cumulative percentage of new species (‘new’ as of the end of 2008, when 1,001 species were formally described) is 75.1%, and is relatively constant across large biogeographic regions. Undetected species are estimated using the Chao2 estimator based on species incidence data (date by species and locality by species matrices). The estimated percentage of new species based on the date by species matrices is 76.0% with an estimated standard error (s.e.) of 2.6%. This leads to an estimated global species richness of about 4,200 with a 95% confidence interval of (3,300, 5,000). The corresponding values based on locality by species matrices are 84.2% (s.e. 3.0%) and 6,300 with a 95% confidence interval of (4,000, 8,600). Our results suggest that the currently known 1,700 species of Pholcidae may represent no more than about 25–40% of the total species richness. The impact of further biasing factors like geography, species size and distribution, cryptic species, and model assumptions needs to be explored.

  • Filling the gaps: descriptions of unnamed species included in the latest molecular phylogeny of Pholcidae (Araneae)
    Zootaxa, 2019
    Co-Authors: Bernhard A Huber, Leonardo S. Carvalho
    Abstract:

    This paper provides formal descriptions of some of the unnamed taxa that were included in the most recent molecular phylogeny of pholcid spiders (Eberle et al. 2018, BMC Evolutionary Biology, 18, 141). The focus is on new genera and on species that belong to recently revised genera. Eight new genera and 25 new species are formally described. In Arteminae, three new species are described in Artema Walckenaer, 1837: A. bahla sp. n., A. ghubrat sp. n., and A. dhofar sp. n. (all from Oman); five new species in Arnapa gen. n. (eastern Indonesia and New Guinea): A. arfak sp. n., A. tinoor sp. n., A. manokwari sp. n., A. meja sp. n., A. tolire sp. n.; and one new species in Chisosa Huber, 2000: C. caquetio sp. n. (Netherlands Antilles). In Ninetinae, three new monotypic genera are described: Pemona gen. n., with the type species P. sapo sp. n. (Venezuela); Pinocchio gen. n., with the type species P. barauna sp. n. (Brazil); and Magana gen. n., with the type species M. velox sp. n. (Oman). In Modisiminae, three new species are described in Chibchea Huber, 2000 (all from Brazil): C. amapa sp. n., C. santosi sp. n., and C. hamadae sp. n.; one new species in Psilochorus Simon, 1893: P. bromelicolus sp. n. (Brazil); and three new monotypic genera, all from Brazil: Arenita gen. n., with the type species A. fazendinha sp. n.; Kairona gen. n., with the type species K. selva sp. n.; and Saciperere gen. n., with the type species S. catuaba sp. n. In Pholcinae, a new monotypic genus is described: Giloloa gen. n., with the type species G. sofifi sp. n. (Indonesia); three new species in the genus Aetana Huber, 2005 (all from Indonesia): A. ternate sp. n.; A. mokwam sp. n.; A. ondawamei sp. n.; and two new species in the genus Panjange Deeleman-Reinhold & Deeleman, 1983 (both from Indonesia): P. thomi sp. n., and P. togutil sp. n.        Artema ghubrat is a cave-dwelling species and the only (slightly) troglomorphic representative of Arteminae; A. dhofar is presumably the closest known relative of the pantropical and synanthropic A. atlanta. The new genus Arnapa is probably species rich in eastern Indonesia and New Guinea but poorly collected; its morphological delimitation from other Australasian Arteminae (Wugigarra Huber, 2001; Holocneminus Berland, 1942; Trichocyclus Simon, 1908) needs further study. Arnapa nigromaculatus (Kulczyński, 1911) comb. n. is newly transferred from Psilochorus. Pemona sapo is the first representative of Ninetinae from Venezuela. The genus Chibchea, previously known from the Andes only, is for the first time recorded from Brazil/lowland Amazonia. Arenita fazendinha is among the few species in Pholcidae with extremely reduced procursus and barely modified male chelicerae. Kairona selva is unique among Pholcidae for its brush of strong hairs on a median horn anteriorly on the ocular area. Saciperere catuaba is one of only four pholcid species currently known to occur both in the Amazon and in the Atlantic Forest; however, variation indicates that more than one species might be included. It is among the few spiders known to have asymmetric genitalia (antisymmetric female internal genitalia). The Brazilian Psilochorus bromelicolus is the first South American Psilochorus of which both sexes are adequately described; however, the assignment to Psilochorus is tentative. Aetana ternate has extremely elongated procursi and accordingly elongated female internal genitalia. Aetana ondawamei and A. mokwam have almost identical male pedipalps and chelicerae (except for size) but differ clearly in the female genitalia. 

  • Inferring global species richness from megatransect data and undetected species estimates: supplementary material
    2019
    Co-Authors: Bernhard A Huber, Anne Chao
    Abstract:

    Ratio-like approaches for estimating global species richness have been criticised for their unjustified extrapolation from regional to global patterns. Here we explore the use of cumulative percentages of ‘new’ (i.e., not formally described) species over large geographic areas (‘megatransects’) as a means to overcome this problem. In addition, we take into account undetected species and illustrate these combined methods by applying them to a family of spiders (Pholcidae) that currently contains some 1,700 described species. The raw global cumulative percentage of new species (‘new’ as of the end of 2008, when 1,001 species were formally described) is 75.1%, and is relatively constant across large biogeographic regions. Undetected species are estimated using the Chao2 estimator based on species incidence data (date by species and locality by species matrices). The estimated percentage of new species based on the date by species matrices is 76.0% with an estimated standard error (s.e.) of 2.6%. This leads to an estimated global species richness of about 4,200 with a 95% confidence interval of (3,300, 5,000). The corresponding values based on locality by species matrices are 84.2% (s.e. 3.0%) and 6,300 with a 95% confidence interval of (4,000, 8,600). Our results suggest that the currently known 1,700 species of Pholcidae may represent no more than about 25–40% of the total species richness. The impact of further biasing factors like geography, species size and distribution, cryptic species, and model assumptions needs to be explored.

  • New species of Idris Förster (Hymenoptera, Platygastroidea) from southeast Asia, parasitoids of the eggs of pholcid spiders (Araneae, Pholcidae).
    ZooKeys, 2018
    Co-Authors: Norman F. Johnson, Hua-yan Chen, Bernhard A Huber
    Abstract:

    Four new species of the genus Idris Forster (Hymenoptera: Platygastroidea), reared from the eggs of pholcid spiders (Araneae: Pholcidae) in southeast Asia are described on the basis of external morphology and the barcode region of the mitochondrial COI gene. The new species and their hosts are: I.badius Johnson & Chen, sp. n. (ex Nipisaphyllicola (Deeleman-Reinhold), Panjangehamiguitan Huber), I.balteus Johnson & Chen, sp. n. (ex Panjangecamiguin Huber), I.curtus Johnson & Chen, sp. n. (ex Calapnitanunezae Huber, Panjangecamiguin Huber, Tissahamiabukittimah (Huber), Uthinaluzonica Simon), and I.fusciceps (ex Belisanakhaosok Huber).

  • The phylogeny of pholcid spiders: a critical evaluation of relationships suggested by molecular data (Araneae, Pholcidae).
    ZooKeys, 2018
    Co-Authors: Bernhard A Huber, Jonas Eberle, Dimitar Dimitrov
    Abstract:

    With almost 600 species, the latest molecular phylogeny of pholcid spiders (Eberle et al. 2018, BMC Evolutionary Biology) more than triples the largest previously available molecular phylogeny of the family. At the level of genera, the coverage is high (86%, i.e., 75 of the 87 named genera), and at the level of subfamilies it is complete. The present paper is an effort to critically evaluate the implications of this phylogeny for pholcid systematics. The analyses largely support the division of Pholcidae into five subfamilies: Ninetinae, Arteminae, Modisiminae, Smeringopinae, and Pholcinae. Their compositions are largely unchanged except that Chisosa Huber, 2000 is moved from Ninetinae to Arteminae. The positions of Artema Walckenaer, 1837 and Priscula Simon, 1893 in this system remain dubious. Relationships among subfamilies remain weakly supported, except for the sister group relationship between Smeringopinae and Pholcinae. Several major clades within subfamilies are separated from each other along geographical boundaries; for example within Modisiminae a South American clade and a Central + North American + Caribbean clade, and within Smeringopinae a Sub-Saharan clade and a clade ranging from the Mediterranean to Central Asia. Central + North American + Caribbean clades in both Ninetinae and Modisiminae may originate from South American ancestors. Many taxonomic changes are suggested by the data, some of which are formally implemented herein. Two new genera result from the splitting of Calapnita Simon, 1892 and Panjange Deeleman-Reinhold & Deeleman, 1983, respectively: Nipisa Huber, gen. n.; and Apokayana Huber, gen. n. Nine new genera result from splitting of Pholcus: Cantikus Huber, gen. n.; Kelabita Huber, gen. n.; Kintaqa Huber, gen. n.; Muruta Huber, gen. n.; Meraha Huber, gen. n.; Paiwana Huber, gen. n.; Pribumia Huber, gen. n.; Teranga Huber, gen. n.; and Tissahamia Huber, gen. n. Two genera are newly synonymized: Platnicknia Ozdikmen & Demir, 2009 is synonymized with Modisimus Simon, 1893; Sihala Huber, 2011 is synonymized with Pholcus Walckenaer, 1805. Pholcusagadir Huber, 2011 is moved to Micropholcus Deeleman-Reinhold & Prinsen, 1987, resulting in the new combination Micropholcusagadir (Huber, 2011).

Kailash Chandra - One of the best experts on this subject based on the ideXlab platform.

  • the complete mitochondrial genome of endemic giant tarantula lyrognathus crotalus araneae theraphosidae and comparative analysis
    Scientific Reports, 2020
    Co-Authors: Vikas Kumar, Kaomud Tyagi, Rajasree Chakraborty, Priya Prasad, Shantanu Kundu, Inderjeet Tyagi, Kailash Chandra
    Abstract:

    The complete mitochondrial genome of Lyrognathus crotalus is sequenced, annotated and compared with other spider mitogenomes. It is 13,865 bp long and featured by 22 transfer RNA genes (tRNAs), and two ribosomal RNA genes (rRNAs), 13 protein-coding genes (PCGs), and a control region (CR). Most of the PCGs used ATN start codon except cox3, and nad4 with TTG. Comparative studies indicated the use of TTG, TTA, TTT, GTG, CTG, CTA as start codons by few PCGs. Most of the tRNAs were truncated and do not fold into the typical cloverleaf structure. Further, the motif (CATATA) was detected in CR of nine species including L. crotalus. The gene arrangement of L. crotalus compared with ancestral arthropod showed the transposition of five tRNAs and one tandem duplication random loss (TDRL) event. Five plesiomophic gene blocks (A-E) were identified, of which, four (A, B, D, E) retained in all taxa except family Salticidae. However, block C was retained in Mygalomorphae and two families of Araneomorphae (Hypochilidae and Pholcidae). Out of 146 derived gene boundaries in all taxa, 15 synapomorphic gene boundaries were identified. TreeREx analysis also revealed the transposition of trnI, which makes three derived boundaries and congruent with the result of the gene boundary mapping. Maximum likelihood and Bayesian inference showed similar topologies and congruent with morphology, and previously reported multi-gene phylogeny. However, the Gene-Order based phylogeny showed sister relationship of L. crotalus with two Araneomorphae family members (Hypochilidae and Pholcidae) and other Mygalomorphae species.

  • The Complete Mitochondrial Genome of endemic giant tarantula, Lyrognathus crotalus (Araneae: Theraphosidae) and comparative analysis.
    Scientific reports, 2020
    Co-Authors: Vikas Kumar, Kaomud Tyagi, Rajasree Chakraborty, Priya Prasad, Shantanu Kundu, Inderjeet Tyagi, Kailash Chandra
    Abstract:

    The complete mitochondrial genome of Lyrognathus crotalus is sequenced, annotated and compared with other spider mitogenomes. It is 13,865 bp long and featured by 22 transfer RNA genes (tRNAs), and two ribosomal RNA genes (rRNAs), 13 protein-coding genes (PCGs), and a control region (CR). Most of the PCGs used ATN start codon except cox3, and nad4 with TTG. Comparative studies indicated the use of TTG, TTA, TTT, GTG, CTG, CTA as start codons by few PCGs. Most of the tRNAs were truncated and do not fold into the typical cloverleaf structure. Further, the motif (CATATA) was detected in CR of nine species including L. crotalus. The gene arrangement of L. crotalus compared with ancestral arthropod showed the transposition of five tRNAs and one tandem duplication random loss (TDRL) event. Five plesiomophic gene blocks (A-E) were identified, of which, four (A, B, D, E) retained in all taxa except family Salticidae. However, block C was retained in Mygalomorphae and two families of Araneomorphae (Hypochilidae and Pholcidae). Out of 146 derived gene boundaries in all taxa, 15 synapomorphic gene boundaries were identified. TreeREx analysis also revealed the transposition of trnI, which makes three derived boundaries and congruent with the result of the gene boundary mapping. Maximum likelihood and Bayesian inference showed similar topologies and congruent with morphology, and previously reported multi-gene phylogeny. However, the Gene-Order based phylogeny showed sister relationship of L. crotalus with two Araneomorphae family members (Hypochilidae and Pholcidae) and other Mygalomorphae species.

Li Shuqiang - One of the best experts on this subject based on the ideXlab platform.

Vikas Kumar - One of the best experts on this subject based on the ideXlab platform.

  • the complete mitochondrial genome of endemic giant tarantula lyrognathus crotalus araneae theraphosidae and comparative analysis
    Scientific Reports, 2020
    Co-Authors: Vikas Kumar, Kaomud Tyagi, Rajasree Chakraborty, Priya Prasad, Shantanu Kundu, Inderjeet Tyagi, Kailash Chandra
    Abstract:

    The complete mitochondrial genome of Lyrognathus crotalus is sequenced, annotated and compared with other spider mitogenomes. It is 13,865 bp long and featured by 22 transfer RNA genes (tRNAs), and two ribosomal RNA genes (rRNAs), 13 protein-coding genes (PCGs), and a control region (CR). Most of the PCGs used ATN start codon except cox3, and nad4 with TTG. Comparative studies indicated the use of TTG, TTA, TTT, GTG, CTG, CTA as start codons by few PCGs. Most of the tRNAs were truncated and do not fold into the typical cloverleaf structure. Further, the motif (CATATA) was detected in CR of nine species including L. crotalus. The gene arrangement of L. crotalus compared with ancestral arthropod showed the transposition of five tRNAs and one tandem duplication random loss (TDRL) event. Five plesiomophic gene blocks (A-E) were identified, of which, four (A, B, D, E) retained in all taxa except family Salticidae. However, block C was retained in Mygalomorphae and two families of Araneomorphae (Hypochilidae and Pholcidae). Out of 146 derived gene boundaries in all taxa, 15 synapomorphic gene boundaries were identified. TreeREx analysis also revealed the transposition of trnI, which makes three derived boundaries and congruent with the result of the gene boundary mapping. Maximum likelihood and Bayesian inference showed similar topologies and congruent with morphology, and previously reported multi-gene phylogeny. However, the Gene-Order based phylogeny showed sister relationship of L. crotalus with two Araneomorphae family members (Hypochilidae and Pholcidae) and other Mygalomorphae species.

  • The Complete Mitochondrial Genome of endemic giant tarantula, Lyrognathus crotalus (Araneae: Theraphosidae) and comparative analysis.
    Scientific reports, 2020
    Co-Authors: Vikas Kumar, Kaomud Tyagi, Rajasree Chakraborty, Priya Prasad, Shantanu Kundu, Inderjeet Tyagi, Kailash Chandra
    Abstract:

    The complete mitochondrial genome of Lyrognathus crotalus is sequenced, annotated and compared with other spider mitogenomes. It is 13,865 bp long and featured by 22 transfer RNA genes (tRNAs), and two ribosomal RNA genes (rRNAs), 13 protein-coding genes (PCGs), and a control region (CR). Most of the PCGs used ATN start codon except cox3, and nad4 with TTG. Comparative studies indicated the use of TTG, TTA, TTT, GTG, CTG, CTA as start codons by few PCGs. Most of the tRNAs were truncated and do not fold into the typical cloverleaf structure. Further, the motif (CATATA) was detected in CR of nine species including L. crotalus. The gene arrangement of L. crotalus compared with ancestral arthropod showed the transposition of five tRNAs and one tandem duplication random loss (TDRL) event. Five plesiomophic gene blocks (A-E) were identified, of which, four (A, B, D, E) retained in all taxa except family Salticidae. However, block C was retained in Mygalomorphae and two families of Araneomorphae (Hypochilidae and Pholcidae). Out of 146 derived gene boundaries in all taxa, 15 synapomorphic gene boundaries were identified. TreeREx analysis also revealed the transposition of trnI, which makes three derived boundaries and congruent with the result of the gene boundary mapping. Maximum likelihood and Bayesian inference showed similar topologies and congruent with morphology, and previously reported multi-gene phylogeny. However, the Gene-Order based phylogeny showed sister relationship of L. crotalus with two Araneomorphae family members (Hypochilidae and Pholcidae) and other Mygalomorphae species.

Kaomud Tyagi - One of the best experts on this subject based on the ideXlab platform.

  • the complete mitochondrial genome of endemic giant tarantula lyrognathus crotalus araneae theraphosidae and comparative analysis
    Scientific Reports, 2020
    Co-Authors: Vikas Kumar, Kaomud Tyagi, Rajasree Chakraborty, Priya Prasad, Shantanu Kundu, Inderjeet Tyagi, Kailash Chandra
    Abstract:

    The complete mitochondrial genome of Lyrognathus crotalus is sequenced, annotated and compared with other spider mitogenomes. It is 13,865 bp long and featured by 22 transfer RNA genes (tRNAs), and two ribosomal RNA genes (rRNAs), 13 protein-coding genes (PCGs), and a control region (CR). Most of the PCGs used ATN start codon except cox3, and nad4 with TTG. Comparative studies indicated the use of TTG, TTA, TTT, GTG, CTG, CTA as start codons by few PCGs. Most of the tRNAs were truncated and do not fold into the typical cloverleaf structure. Further, the motif (CATATA) was detected in CR of nine species including L. crotalus. The gene arrangement of L. crotalus compared with ancestral arthropod showed the transposition of five tRNAs and one tandem duplication random loss (TDRL) event. Five plesiomophic gene blocks (A-E) were identified, of which, four (A, B, D, E) retained in all taxa except family Salticidae. However, block C was retained in Mygalomorphae and two families of Araneomorphae (Hypochilidae and Pholcidae). Out of 146 derived gene boundaries in all taxa, 15 synapomorphic gene boundaries were identified. TreeREx analysis also revealed the transposition of trnI, which makes three derived boundaries and congruent with the result of the gene boundary mapping. Maximum likelihood and Bayesian inference showed similar topologies and congruent with morphology, and previously reported multi-gene phylogeny. However, the Gene-Order based phylogeny showed sister relationship of L. crotalus with two Araneomorphae family members (Hypochilidae and Pholcidae) and other Mygalomorphae species.

  • The Complete Mitochondrial Genome of endemic giant tarantula, Lyrognathus crotalus (Araneae: Theraphosidae) and comparative analysis.
    Scientific reports, 2020
    Co-Authors: Vikas Kumar, Kaomud Tyagi, Rajasree Chakraborty, Priya Prasad, Shantanu Kundu, Inderjeet Tyagi, Kailash Chandra
    Abstract:

    The complete mitochondrial genome of Lyrognathus crotalus is sequenced, annotated and compared with other spider mitogenomes. It is 13,865 bp long and featured by 22 transfer RNA genes (tRNAs), and two ribosomal RNA genes (rRNAs), 13 protein-coding genes (PCGs), and a control region (CR). Most of the PCGs used ATN start codon except cox3, and nad4 with TTG. Comparative studies indicated the use of TTG, TTA, TTT, GTG, CTG, CTA as start codons by few PCGs. Most of the tRNAs were truncated and do not fold into the typical cloverleaf structure. Further, the motif (CATATA) was detected in CR of nine species including L. crotalus. The gene arrangement of L. crotalus compared with ancestral arthropod showed the transposition of five tRNAs and one tandem duplication random loss (TDRL) event. Five plesiomophic gene blocks (A-E) were identified, of which, four (A, B, D, E) retained in all taxa except family Salticidae. However, block C was retained in Mygalomorphae and two families of Araneomorphae (Hypochilidae and Pholcidae). Out of 146 derived gene boundaries in all taxa, 15 synapomorphic gene boundaries were identified. TreeREx analysis also revealed the transposition of trnI, which makes three derived boundaries and congruent with the result of the gene boundary mapping. Maximum likelihood and Bayesian inference showed similar topologies and congruent with morphology, and previously reported multi-gene phylogeny. However, the Gene-Order based phylogeny showed sister relationship of L. crotalus with two Araneomorphae family members (Hypochilidae and Pholcidae) and other Mygalomorphae species.