Evolving in the darkness: phylogenomics of Sinocyclocheilus cavefishes highlights recent diversification and cryptic diversity

Troglomorphism-morphological adaptation enabling life in constant darkness of caves, such as loss of pigment, reduced eyesight or blindness, over-developed tactile and olfactory organs has long intrigued biologists. However, inferring the proximate and ultimate mechanisms driving the evolution of troglomorphism in freshwater fish requires a sound understanding of the evolutionary relationships among surface, troglomorphic, and intermediate lineages. We use Restriction Site Associated DNA Sequencing (RADseq) to probe deeper into the evolution of the Sinocyclocheilus fishes of China. They comprise the largest cavefish diversification in the world with a remarkable array of derived troglomorphic traits, and are currently considered as an emerging multi-species model system to study evolutionary novelty. We sequenced a total of 120 individuals from throughout the Sinocyclocheilus distribution. The data comprised a total of 646,497 bp per individual, including 4378 loci and 67,983 SNPs (61,023 parsimony-informative) shared across more than at least 114 individuals at a given locus. Phylogenetic analyses using either the concatenated RAD loci (RAxML) or the SNPs only under a coalescent model (SVDquartets) showed a high degree of congruence and high node support (> 95) for most nodes in the phylogeny. The major clades we recovered conform to a pattern established previously using Sanger-based mt-DNA sequences, however, with a few notable exceptions. With an increased representation of the genome sequenced, we now recognize 6 major clades in this group, two additional clades than before. The blind cavefish S. tianlinensis and the micro-eyed S. microphthalmus are now recognized as distinct clades due to their deep divergence from other clades. A Bayes factor delimitation (BFD) analysis showed support for 21 species, recognizing 19 previously described species and two putative new cryptic ones. Two species whose identity were previously disputed, S. furcodorsalis and S. tianeensis, are supported here as distinct species. Our multi-species calibrated tree in SNAPP suggests that the genus Sinocyclocheilus originated around 10.5 Mya, but most speciation events happened in the last 2 Mya, likely favored by the uplift of Qinghai-Tibetan Plateau and a climate driven aridification event forcing cave occupation during this period. These results provide a firm basis for future comparative studies on the evolution of Sinocyclocheilus and its adaptations to cave life.

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Differential patterns of ophiostomatoid fungal communities associated with three sympatric Tomicus species infesting pines in south-western China, with a description of four new species

MycoKeys ◽

10.3897/mycokeys.50.32653 ◽

2019 ◽

Vol 50 ◽

pp. 93-133 ◽

Cited By ~ 9

Author(s):

Wang HuiMin ◽

Zheng Wang ◽

Fu Liu ◽

Cheng Xu Wu ◽

Su Fang Zhang ◽

...

Keyword(s):

Dna Sequences ◽

Bark Beetles ◽

Phylogenetic Analyses ◽

Large Subunit ◽

Forest Health ◽

Elongation Factor ◽

Distinct Species ◽

Western China ◽

Ophiostomatoid Fungi ◽

Additional Species

Bark beetles and their associated fungi, which cause forest decline and sometimes high mortality in large areas around the world, are of increasing concern in terms of forest health. ThreeTomicusspp. (T.brevipilosus,T.minorandT.yunnanensis) infect branches and trunks ofPinusyunnanensisandP.kesiyain Yunnan Province, in south-western China.Tomicusspp. are well known as vectors of ophiostomatoid fungi and their co-occurrence could result in serious ecological and economic impact on local forest ecosystems. Nonetheless, knowledge about their diversity, ecology, including pathogenicity and potential economic importance is still quite rudimentary. Therefore, an extensive survey of ophiostomatoid fungi associated with theseTomicusspecies infestingP.yunnanensisandP.kesiyawas carried out in Yunnan. Seven hundred and seventy-two strains of ophiostomatoid fungi were isolated from the adult beetles and their galleries. The strains were identified based on comparisons of multiple DNA sequences, including the nuclear ribosomal large subunit (LSU) region, the internal transcribed spacer regions 1 and 2, together with the intervening 5.8S gene (ITS) and the partial genes of β-tubulin (TUB2), elongation factor 1α (TEF1-α) and calmodulin (CAL). Phylogenetic analyses were performed using maximum parsimony (MP) as well as maximum likelihood (ML). Combinations of culture features, morphological characters and temperature-dependent growth rates were also employed for species identification. Eleven species belonging to five genera were identified. These included six known species,Esteyavermicola,Leptographiumyunnanense,Ophiostomabrevipilosi,O.canum,O.minusandO.tingensand four novel taxa, described asGraphilbumanningense,O.aggregatum,SporothrixpseudoabietinaandS.macroconidia. A residual strain was left unidentified asOphiostomasp. 1. The overall ophiostomatoid community was by far dominated by three species, representing 87.3% of the total isolates; in decreasing order, these wereO.canum,O.brevipilosiandO.minus. Furthermore, the ophiostomatoid community of each beetle, although harbouring a diversity of ophiostomatoid species, was differentially dominated by a single fungal species;Ophiostomacanumwas preferentially associated with and dominated the ophiostomatoid community ofT.minor, whereasO.brevipilosiandO.minuswere exclusively associated with and dominated the ophiostomatoid communities ofT.brevipilosusandT.yunnanensis, respectively. Eight additional species, representing the remaining 12.7% of the total isolates, were marginal or sporadic. These results suggested that sympatricTomicuspopulations are dominated by distinct species showing some level of specificity or even exclusivity.

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Detection of hybrid Pyganodon grandis and P. lacustris (Bivalvia: Unionidae) using F- and M-type mitochondrial DNA sequences and geometric morphometrics

Journal of Molluscan Studies ◽

10.1093/mollus/eyaa013 ◽

2020 ◽

Vol 86 (3) ◽

pp. 233-239 ◽

Cited By ~ 1

Author(s):

Kate C Beauchamp ◽

Tyler W Beyett ◽

Mariah W Scott ◽

David T Zanatta

Keyword(s):

Dna Sequences ◽

Lake Michigan ◽

Morphological Variability ◽

Distinct Species ◽

Shell Shape ◽

Species Identity ◽

Mt Dna ◽

Pyganodon Grandis ◽

Coi Sequences ◽

Putative Hybrids

ABSTRACT Pyganodon grandis and P. lacustris, widespread and common species in North America, are known to co-occur across parts of their distributions. These mussels are genetically distinguishable with a sequence divergence between 9% and 13% for the mitochondrial (mt) DNA barcoding region, cytochrome c oxidase subunit I (COI), which is well beyond thresholds for distinct species. The objectives of this study were to (1) confirm the presence of two genetically distinct species (P. grandis and P. lacustris) in Font Lake and Lake Geneserath on Beaver Island in northern Lake Michigan, (2) identify hybrids using mitogenotype mismatch and (3) compare species and populations morphometrically. Of the 212 specimens sequenced, 146 (68.9%) were found to be heteroplasmic, with successful amplifications of both maternally (F-type, from mantle tissue) and paternally (M-type, from gonad tissue) inherited mt DNA sequences. Mismatches in species identity of the F- and M-type COI sequences were found in 22 specimens (15.1% of heteroplasmic specimens), with these being considered putative hybrids. Geometric morphometric analyses of shell shape reliably differentiated specimens by species (identified using COI sequences) and between lakes, correctly assigning 97.4% of homoplasmic and heteroplasmic specimens with matching mitogenomes to both species and lake of origin. The shape of putative hybrids generally resembled those of the F-type mt DNA sequence that was recovered. This study confirms that hybridization does occur between sympatric Pyganodon species. Additionally, our results reemphasize the value of modern morphometric techniques for distinguishing among species and populations with overlapping morphological variability.

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Molecular systematics of New Zealand Cyanoramphus parakeets: conservation of Orange-fronted and Forbes' Parakeets

Bird Conservation International ◽

10.1017/s0959270900000198 ◽

2000 ◽

Vol 10 (3) ◽

pp. 211-239 ◽

Cited By ~ 10

Author(s):

W. M. Boon ◽

J. C. Kearvell ◽

C. H. Daugherty ◽

G. K. Chambers

Keyword(s):

Dna Sequences ◽

Sequence Data ◽

Phylogenetic Analyses ◽

Distinct Species ◽

Biological Species ◽

Biological Species Concept ◽

Allozyme Data ◽

Dna Sequence Data ◽

Data Support ◽

High Conservation

The controversy that presently surrounds the taxonomy of the Orange-fronted Cyanoramphus malherbi and Forbes' C. forbesi Parakeets has important implications for the conservation of both birds. Both taxa are critically endangered, but consensus regarding their specific status has not yet been achieved. We present mitochondrial DNA sequences for the cytochrome b gene and the control region from 17 Cyanoramphus parakeets representing nine populations and six taxa together with field observations of courtship and breeding behaviour in a sympatric population of Orange-fronted and Yellow-crowned Parakeets C. auriceps. Field data support species status of the Orange-fronted Parakeet under the Biological Species Concept. Phylogenetic analyses of our DNA sequence data support earlier hypotheses based on allozyme data that both Orange-fronted and Forbes' Parakeets represent distinct species under four species concepts and indicate that high conservation priority is warranted for both taxa.

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Morphological, Molecular, and Biogeographic Evidence for Specific Recognition of Euthamia hirtipes and Euthamia scabra (Asteraceae, Astereae)

Systematic Botany ◽

10.1600/036364420x15935294613446 ◽

2020 ◽

Vol 45 (3) ◽

pp. 658-667

Author(s):

Marisa B. Szubryt ◽

Lowell E. Urbatsch ◽

Yalma L. Vargas-Rodriguez ◽

David Barfknecht ◽

Kurt M. Neubig

Keyword(s):

Dna Sequences ◽

Ecological Niche Modeling ◽

Gulf Coast ◽

Phylogenetic Analyses ◽

Atlantic Coast ◽

Distinct Species ◽

Eastern United States ◽

Intermediate Morphology ◽

Specific Rank ◽

Florida Panhandle

Abstract—The number and identity of species within Euthamia (Asteraceae, Astereae) have varied considerably among taxonomic treatments. Euthamia graminifolia (L.) Nutt. is often treated broadly, including plants from the northern and eastern United States and Canada, including the Atlantic and Gulf Coasts. Broad-leaved, largely glabrous plants from New Jersey to the Florida Panhandle have been inconsistently treated as E. graminifolia, E. graminifolia var. hirtipes (Fernald) C.E.S. Taylor & R.J. Taylor, E. hirtipes (Fernald) Sieren, or a hybrid between E graminifolia and E. caroliniana (L.) Greene ex Porter & Britton. Similarly, plants from the Florida Panhandle to eastern Louisiana have been incorporated into E. graminifolia or E. graminifolia var. hirtipes with only Greene in 1902 recognizing these plants as a distinct species, E. scabra Greene. To determine the identity and proper rank of these entities, morphological and phylogenetic analyses were performed to evaluate relationships within Euthamia. Plants from the Atlantic Coast most morphologically resemble Gulf Coast plants which similarly resemble E. gymnospermoides Greene. The Gulf Coast plants and E. gymnospermoides share similar DNA sequences while the Atlantic Coast plants represent a unique clade. Neither Gulf Coast nor Atlantic Coast plants contain highly polymorphic sequences, indicating that they are not hybrids. Occasional plants found within southernmost Alabama and the Florida Panhandle have polymorphic sequences and intermediate morphology however, suggesting that putative hybrids exist between Gulf and Atlantic Coast plants. This study concludes that both entities deserve specific rank as E. scabra Greene for scabrous plants along the central Gulf Coast and E. hirtipes (Fernald) Sieren for largely glabrous plants mostly along the Atlantic Coast. Ecological niche modeling indicates that precipitation, especially during summer months, and soils, namely coarse fragments and sand content, drive the distribution of these organisms, largely restricted to either side of the Apalachicola River serving as a distributional barrier.

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Relationships of North American members of Rhodiola (Crassulaceae)

Botany ◽

10.1139/cjb-2014-0009 ◽

2014 ◽

Vol 92 (12) ◽

pp. 901-910 ◽

Cited By ~ 3

Author(s):

Joel P. Olfelt ◽

William A. Freyman

Keyword(s):

Dna Sequences ◽

North American ◽

Phylogenetic Analyses ◽

Black Hills ◽

Trnl Intron ◽

The North ◽

Alpine Habitats ◽

Rare And Endangered ◽

Chloroplast Dna Sequences ◽

Rhodiola Integrifolia

Taxa of Rhodiola L. (Crassulaceae) generally grow in arctic or alpine habitats. Some Rhodiola species are used medicinally, one taxon, Rhodiola integrifolia Raf. subsp. leedyi (Rosend. & J.W.Moore) Moran, (Leedy’s roseroot), is rare and endangered, and the group’s biogeography in North America is intriguing because of distributional disjunctions and the possibility that Rhodiola rhodantha (A.Gray) H.Jacobsen (2n = 7II) and Rhodiola rosea L. (2n = 11II) hybridized to form Rhodiola integrifolia Raf. (2n = 18II). Recent studies of the North American Rhodiola suggest that the group’s current taxonomy is misleading. We analyzed nuclear and chloroplast DNA sequences (internal transcribed spacer (ITS), trnL intron, trnL–trnF spacer, trnS–trnG spacer) from the North American Rhodiola taxa. We combined our data with GenBank sequences from Asian Rhodiola species, performed parsimony, maximum likelihood (ML), and Bayesian phylogenetic analyses, and applied a Bayesian clock model to the ITS data. Our analyses reveal two major Rhodiola clades, suggest that hybridization between R. rhodantha and R. rosea lineages was possible, show two distinct clades within R. integrifolia, and demonstrate that a Black Hills, South Dakota, Rhodiola population should be reclassified as Leedy’s roseroot. We recommend that R. integrifolia be revised, and that the Black Hills Leedy’s roseroot population be managed as part of that rare and endangered taxon.

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A rapid loss of stripes: the evolutionary history of the extinct quagga

Biology Letters ◽

10.1098/rsbl.2005.0323 ◽

2005 ◽

Vol 1 (3) ◽

pp. 291-295 ◽

Cited By ~ 34

Author(s):

Jennifer A Leonard ◽

Nadin Rohland ◽

Scott Glaberman ◽

Robert C Fleischer ◽

Adalgisa Caccone ◽

...

Keyword(s):

South African ◽

Dna Sequences ◽

Evolutionary History ◽

Climate Changes ◽

Rapid Loss ◽

Mt Dna ◽

Pleistocene Climate ◽

Equus Burchelli ◽

History Of ◽

Plains Zebra

Twenty years ago, the field of ancient DNA was launched with the publication of two short mitochondrial (mt) DNA sequences from a single quagga ( Equus quagga ) museum skin, an extinct South African equid ( Higuchi et al . 1984 Nature 312 , 282–284). This was the first extinct species from which genetic information was retrieved. The DNA sequences of the quagga showed that it was more closely related to zebras than to horses. However, quagga evolutionary history is far from clear. We have isolated DNA from eight quaggas and a plains zebra (subspecies or phenotype Equus burchelli burchelli ). We show that the quagga displayed little genetic diversity and very recently diverged from the plains zebra, probably during the penultimate glacial maximum. This emphasizes the importance of Pleistocene climate changes for phylogeographic patterns in African as well as Holarctic fauna.

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Systematic status of Campydora Cobb, 1920 (Nematoda: Campydorina)

Nematology ◽

10.1163/156854103322746878 ◽

2003 ◽

Vol 5 (5) ◽

pp. 699-711 ◽

Cited By ~ 6

Author(s):

Peter Mullin ◽

Timothy Harris ◽

Thomas Powers

Keyword(s):

Maximum Likelihood ◽

Ribosomal Dna ◽

Dna Sequences ◽

Maximum Parsimony ◽

Phylogenetic Analyses ◽

Small Subunit ◽

Systematic Position ◽

Nominal Species ◽

Competing Hypotheses ◽

Small Subunit Ribosomal Dna

AbstractThe systematic position of Campydora Cobb, 1920, which possesses many unique morphological features, especially in pharyngeal structure and stomatal armature, has long been a matter of uncertainty with the 'position of the Campydorinae' (containing only Campydora) being questionable. A review of the morphology of C. demonstrans, the only nominal species of Campydora concluded that the species warranted placement as the sole member of a monotypic suborder, Campydorina, in the order Dorylaimida. Others placed Campydorina in the order Enoplida. We conducted phylogenetic analyses, using 18s small subunit ribosomal DNA sequences generated from a number of taxa in the subclasses Enoplia and Dorylaimia, to evaluate these competing hypotheses. Although precise taxonomic placement of the genus Campydora and the identity of its closest living relatives is in need of further investigation, our analyses, under maximum parsimony, distance, and maximum likelihood criteria, unambiguously indicate that Campydora shares a common, more recent, ancestry with genera such as Alaimus, Pontonema, Tripyla and Ironus (Enoplida), rather than with any members of Dorylaimida, Mononchida or Triplonchida.

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A new species of Chlorociboria (Helotiales, Ascomycota) on herbaceous stems from China

Phytotaxa ◽

10.11646/phytotaxa.312.1.9 ◽

2017 ◽

Vol 312 (1) ◽

pp. 111

Author(s):

HUAN-DI ZHENG ◽

WEN-YING ZHUANG

Keyword(s):

New Species ◽

Dna Sequences ◽

Internal Transcribed Spacer ◽

Phylogenetic Analyses ◽

Large Subunit ◽

Central China ◽

Nuclear Ribosomal Dna ◽

Light Blue ◽

Ectal Excipulum ◽

A New Species

A new species, namely Chlorociboria herbicola, is discovered on herbaceous stems in central China. Morphologically, the new fungus is distinctive by the combination of light blue-green apothecia, rectangular cells in ectal excipulum, and elongate-ellipsoidal ascospores with rounded ends. Phylogenetic analyses of the internal transcribed spacer and large subunit of nuclear ribosomal DNA sequences confirm its ascription in Chlorociboria and distinction from the known species of the genus.

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A reassessment of apheloriine millipede phylogeny: additional taxa, Bayesian inference, and direct optimization (Polydesmida: Xystodesmidae)

Zootaxa ◽

10.11646/zootaxa.1610.1.2 ◽

2007 ◽

Vol 1610 (1) ◽

pp. 27-39 ◽

Cited By ~ 12

Author(s):

PAUL E. MAREK ◽

JASON E. BOND

Keyword(s):

Maximum Likelihood ◽

Dna Sequences ◽

Bayes Factor ◽

Appalachian Mountains ◽

Deciduous Forests ◽

Eastern United States ◽

Undescribed Species ◽

Direct Optimization ◽

Species List ◽

Phylogenetic Hypotheses

Millipedes in the tribe Apheloriini occur throughout the eastern United States, predominately in the deciduous forests of the Appalachian Mountains. Herein we present a reassessment of apheloriine millipede phylogeny using mitochondrial DNA sequences and an additional 29 exemplar taxa (including 15 undescribed species and all of the species in the genus Brachoria, except one). In this study, first we check the results of the previous phylogeny of the tribe (Marek and Bond, 2006) with different alignment and phylogenetic techniques (direct optimization and maximum likelihood), and second reconstruct a new phylogeny evaluating it in the same way with Bayesian, maximum likelihood, and direct optimization. Using this updated and expanded phylogeny, we tested historical classifications with Bayes factor and Shimodaira-Hasegawa hypothesis testing, consistently finding very strong evidence against their implied phylogenetic hypotheses. Lastly, using the new phylogeny as a foundation, we make taxonomic modifications and provide an updated species list of Apheloriini (106 species/17 genera).

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Audiological Features and Mitochondrial DNA Sequence in a Large Family Carrying Mitochondrial A1555G Mutation without Use of Aminoglycoside

Annals of Otology Rhinology & Laryngology ◽

10.1177/000348940511400213 ◽

2005 ◽

Vol 114 (2) ◽

pp. 153-160 ◽

Cited By ~ 12

Author(s):

Tatsuo Matsunaga ◽

Hiroshi Kumanomido ◽

Yu-ichi Goto ◽

Masae Shiroma ◽

Shin-ichi Usami

Keyword(s):

Hearing Loss ◽

Mitochondrial Dna ◽

Dna Sequences ◽

Large Family ◽

Outer Hair Cells ◽

Japanese Family ◽

A1555g Mutation ◽

Genetic Mechanisms ◽

High Degree ◽

Sibling Group

To elucidate the pathophysiological and genetic mechanisms of hearing loss associated with the homoplasmic mitochondrial A1555G mutation in the absence of aminoglycoside exposure, we conducted audiological and genetic analyses on 67 maternally related members of a large Japanese family carrying this mutation. A consistent pattern was evident in the audiograms, with features of sensory presbycusis, cochlear origin at all levels of hearing loss, and a high degree of vulnerability of outer hair cells. That the degree of hearing loss was similar in affected subjects within the same sibling group but differed between sibling groups suggests the involvement of nuclear modifier genes. Total mitochondrial DNA sequences were completely identical among subjects with various levels of hearing loss, and lacked additional pathogenic mutations. For the diagnosis of sensorineural hearing loss, the mitochondrial A1555G mutation should be considered when these features are present even in the absence of aminoglycoside exposure.

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