The Phylogeographic Relationships and the Evolution History of Carassius Auratus Complex With a Newborn Homodiploid Crucian Carp-like Fish (2nNCRC)

Abstract Background: One of the important aspects of studying evolution is to understand how new species are formed and their uniqueness maintained. Hybridization can lead to the formation of new species with the reorganization of adaptive system and significant changes in phenotype. It is wondrous that eight stable strains of 2nNCRC derived from the interspecies hybridization have been established in our laboratory. To examine the phylogeographical pattern of the wildly distributed genus Carassius in the Eurasia, and investigate the possible hybrid origin of Carassius auratus lineage, in light of past climatic events, the mitochondrial genome (mtDNA) were used to reconstruct the phylogenetic relationship between the C. auratus complex and the 2nNCRC, and to assess how demographic history, dispersal and barriers to gene flow have led to the current distribution of mtDNA lineages for C. auratus complex. Results: As expected, the 2nNCRC had a very close relationship with the C. auratus complex, which was distinctly separated with other three species of Carassius. The C. auratus lineage possibly originated from China during the Late Pliocene, far postdated the diversification of C. carassius in Europe and C. cuvieri in Japan. The admixture of mtDNA haplotype lineages of C. auratus detected across the whole Eurasia has experienced a rapid diversification since Early PleistoceneConclusion: Combined the molecular dating analyses, species distribution modeling and ancestral area reconstruction, the speciation of C. auratus seemed not to be the processing of lineage diversification from the most recent common ancestor of C. carassius or C. cuvieri. The formation of 2nNCRC in our laboratory could be a good candidate explaining for the hybrid origin species for C. auratus lineage, as well as the paleoclimate oscillation and geological event during Pliocene and Pleistocene in China supplying an opportunity for the distant hybridization. The most wildly distributed C. auratus lineage could be attributed to the dispersal during the glacial period and the recent human-facilitated dispersal.

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Mitogenomics and the genetic differentiation of contemporary Balaena mysticetus (Cetacea) from Svalbard

Zoological Journal of the Linnean Society ◽

10.1093/zoolinnean/zlaa082 ◽

2020 ◽

Author(s):

Lutz Bachmann ◽

Andrea A Cabrera ◽

Mads Peter Heide-Jørgensen ◽

Olga V Shpak ◽

Christian Lydersen ◽

...

Keyword(s):

Genetic Differentiation ◽

High Throughput Sequencing ◽

Demographic History ◽

Bowhead Whale ◽

Recent Common Ancestor ◽

Mitochondrial Genomes ◽

Balaena Mysticetus ◽

Bowhead Whales ◽

Most Recent Common Ancestor ◽

Loop Region

Abstract Full mitochondrial genomes were assembled for 12 recently sampled animals from the Svalbard bowhead whale (Balaena mysticetus) stock via high-throughput sequencing data, facilitating analysis of the demographic history of the population for the first time. The Svalbard population has retained noticeable amounts of mitochondrial genome diversity despite extreme historical harvest levels. Haplotype and nucleotide diversities were similar to those estimated earlier for other bowhead whale populations. The reconstructed demographic history was in accordance with a boom–bust scenario, combining a slight Pleistocene population growth 25 000–35 000 years ago and a Holocene decline. Employing a mutation rate of 3.418 × 10–8 substitutions per site per year, the time to the most recent common ancestor for the mitochondrial genomes of the contemporary Svalbard bowhead whales was estimated to be 68 782 (54 353–83 216) years before the present. Based on 370 bp fragments of the D-loop region, significant genetic differentiation was detected between all extant bowhead whale populations across the circumpolar Arctic. Thus, the Svalbard bowhead whales can be regarded as a population with its own genetic legacy.

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Near-complete phylogeny of extant Crocodylia (Reptilia) using mitogenome-based data

Zoological Journal of the Linnean Society ◽

10.1093/zoolinnean/zlaa074 ◽

2020 ◽

Cited By ~ 2

Author(s):

Tao Pan ◽

Jia-Shun Miao ◽

Hua-Bin Zhang ◽

Peng Yan ◽

Ping-Shin Lee ◽

...

Keyword(s):

Upper Cretaceous ◽

Phylogenetic Analyses ◽

Decisive Role ◽

Late Eocene ◽

Molecular Dating ◽

Recent Common Ancestor ◽

Most Recent Common Ancestor ◽

Late Cretaceous Period ◽

Climate Fluctuation ◽

Cretaceous Period

Abstract Species of the order Crocodylia are mostly large, predatory and semi-aquatic reptiles. Crocodylia, the closest living relatives of birds, first appeared in the Late Cretaceous period. In the present study, the complete mitochondrial (mt) genomes of 19 Crocodylia species, including two species (Melanosuchus niger and Caiman yacare) that have not been previously sequenced for mitogenomes, were processed through Illumina sequencing to offer genetic resources and compare with the mitogenomes of Crocodylia species reported previously. In addition, a high-resolution phylogenetic tree of nearly all current recognized species of Crocodylia is constructed based on mitogenomic data. Phylogenetic analyses support monophyly of three families: Alligatoridae (four genera: Alligator, Caiman, Melanosuchus and Paleosuchus), Crocodylidae (three genera: Crocodylus, Mecistops and Osteolaemus) and Gavialidae (two genera: Gavialis and Tomistoma). The tree topology is generally similar to previous studies. Molecular dating suggests that the first split within Crocodylia date back to the Upper Cretaceous (approx. 86.75 Mya). The estimated time to the most recent common ancestor (TMRCA) of Alligatoridae is 53.33 Mya and that of Crocodylidae and Gavialidae is 50.13 Mya, which might be closely linked to climate changes during the Late Palaeocene and Early Eocene. Additionally, this study proves that the diversification rate within Crocodylia began to increase from the Late Eocene (about 36 Mya) and two diversification peak periods of Crocodylia (0–10 Mya and 10–20 Mya) are disclosed, which is roughly consistent with the estimated crocodylian species richness through time. Combining all these clues, we can suggest that climate fluctuation may have played a decisive role in the speciation of Crocodylia.

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Signatures of human European Paleolithic expansion shown by resequencing of non-recombining X-chromosome segments

10.1101/067835 ◽

2016 ◽

Author(s):

Pierpaolo Maisano Delser ◽

Rita Neumann ◽

Stéphane Ballereau ◽

Pille Hallast ◽

Chiara Batini ◽

...

Keyword(s):

Y Chromosome ◽

X Chromosome ◽

Rare Variants ◽

Demographic History ◽

Recent Common Ancestor ◽

Haplotype Blocks ◽

Most Recent Common Ancestor ◽

Snp Data ◽

Female Bias ◽

Chromosome Segments

AbstractHuman genetic diversity in Europe has been extensively studied using uniparentally-inherited sequences (mitochondrial DNA [mtDNA] and the Y chromosome), which reveal very different patterns indicating sex-specific demographic histories. The X chromosome, haploid in males and inherited twice as often from mothers as from fathers, could provide insights into past female behaviours, but has not been extensively investigated. Here, we use HapMap SNP data to identify segments of the X chromosome in which recombination is historically absent and mutations are likely to be the only source of genetic variation, referring to these as Phylogeographically informative Haplotypes on Autosomes and X chromosome (PHAXs). Three such sequences spanning a total of ~49 kb were resequenced in 240 males from Europe, the Middle East and Africa at an average coverage of 181 ×. PHAXs were confirmed to be essentially non-recombining across European samples. All three loci show highly homogeneous patterns across Europe and are highly differentiated from the African sample. Star-like structures of European-specific haplotypes in median-joining networks indicate past population expansions. Bayesian skyline plots and time-to-most-recent-common-ancestor estimates suggest expansions pre-dating the Neolithic transition, a finding that is more compatible with data on mtDNA than the Y chromosome, and with the female bias of X-chromosomal inheritance. This study demonstrates the potential of the use of X-chromosomal haplotype blocks, and the utility of the accurate ascertainment of rare variants for inferring human demographic history.

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Serpentine mountain uplift in northern Japan triggered the divergence of a narrow endemic from a widespread (sub)arctic Asia-Alaska species complex of Lagotis (Plantaginaceae)

10.1101/857441 ◽

2019 ◽

Author(s):

Atsushi Sugano ◽

Tomoko Fukuda ◽

Yoshinori Murai ◽

Olga A Chernyagina ◽

Suyama Yoshihisa ◽

...

Keyword(s):

Species Complex ◽

Incomplete Lineage Sorting ◽

Nuclear Gene ◽

Volcanic Eruptions ◽

Early Pleistocene ◽

Recent Common Ancestor ◽

Widespread Species ◽

Most Recent Common Ancestor ◽

Narrow Endemics ◽

Northern Japan

AbstractIn the circumboreal region, plants often have extremely-wide species ranges. Lagotis minor-glauca species complex widespread from (sub)arctic Asia to Alaska, however, have two allied narrow endemics in northern Japan: a serpentine plant L. takedana endemic to the Yubari Mountains (Mt. Yubari) and a non-serpentine plant L. yesoensis endemic to the Taisetsu Mountains (Mt. Taisetsu). Elucidating their origins sheds light on drivers for secondary-speciation of widespread circumboreal plants. To infer phylogenetic distinctiveness of two narrow endemics with those related taxa, which contained 25 out of all the 29 species of the genus, chloroplast DNA (cpDNA), nuclear ribosomal (nrITS), two low copy nuclear gene (LCN) markers and genome-wide single-nucleotide polymorphism genotyping (MIG-seq) were used. In the result of cpDNA analyses, the Lagotis minor-glauca species complex formed a clade. Within the clade, L. yesoensis and a portion of L. glauca samples formed a subclade. However, monophyly of each of the four species was not supported. In the results of nrITS and two LCN analyses, L. takedana was monophyletic, while monophyly was not recovered for each L. yesoensis, L. glauca, and L. minor. Based on a Bayesian dating analysis using nrITS data, the age of the most recent common ancestor of L. takedana was Ma (95% confidence interval: 0.05-1.75 Ma). Possible scenario is that an ancestral linage being adapted to serpentine soils migrated into the alpine habitat of Mt. Yubari, that was formed with mountain uplift by the early Pleistocene, and subsequently reproductively isolated from non-serpentine populations and speciated. The contrasting result of L. yesoensis, that was phylogenetically indistinct, is possibly explained by incorrect taxonomy, or alternatively, shallow history and incomplete lineage sorting. In Mt. Taisetsu, massive volcanic eruptions had occurred the Early Pleistocene and even after the last glacial period, suggesting that alpine plants have not migrated into and established populations in Mt. Taisetsu until very recently. To fully resolve the phylogeny of the three species L. yesoensis, L. glauca, and L. minor, further analyses using high resolution molecular markers are needed. The present study illustrated that two narrow endemics in northern Japan diverged from the widespread species include phylogenetically distinctive and indistinctive species, owing to historical orogeny and ecological factors.

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The age of flowering plants is unknown

10.32942/osf.io/n4v6b ◽

2021 ◽

Author(s):

Hervé Sauquet ◽

Santiago Ramírez-Barahona ◽

Susana Magallón

Keyword(s):

Molecular Data ◽

Flowering Plants ◽

Molecular Dating ◽

Flowering Plant ◽

Recent Common Ancestor ◽

Crown Group ◽

Most Recent Common Ancestor ◽

Research Fields ◽

History Of ◽

Future Work

The origin of flowering plants (angiosperms) was one of the most transformative events in the history of our planet. Despite considerable interest from multiple research fields, numerous questions remain, including the age of the group as a whole. Recent studies have reported a perplexing range of estimates for the crown-group age of angiosperms, from ca. 140 Ma (Early Cretaceous) to 270 Ma (Permian). Both ends of the spectrum are now supported by both quantitative analyses of the fossil record and fossil-calibrated molecular dating analyses. Here, we first clarify and distinguish among the three ages of angiosperms: the age of their divergence with acrogymnosperms (stem age), the age(s) of emergence of their unique, distinctive features including flowers (morphological age), and the age of the most recent common ancestor of all their living species (crown age). We then demonstrate, based on recent studies, that fossil-calibrated molecular dating estimates of the crown-group age of angiosperms have little to do with either the amount of molecular data or the number of internal fossil calibrations included. Instead, we argue that this age is almost entirely conditioned by its own prior. Lastly, we discuss which future discoveries or novel types of analyses are most likely to bring more definitive answers. In the meantime, we propose that the age of angiosperms is best described as unknown (140–270 Ma) and that future work that depends on the time scale of flowering plant diversification be designed to integrate over this vexing uncertainty.

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Two new species of Schistonchus (Nematoda: Aphelenchoididae) associated with Ficus hispida in China

Nematology ◽

10.1163/156854107780739135 ◽

2007 ◽

Vol 9 (2) ◽

pp. 169-187 ◽

Cited By ~ 17

Author(s):

Weimin Ye ◽

Yongsan Zeng ◽

Robin Giblin-Davis

Keyword(s):

New Species ◽

Excretory Pore ◽

Large Subunit ◽

Recent Common Ancestor ◽

Rrna Gene ◽

Small Subunit Rrna ◽

Male Tail ◽

Most Recent Common Ancestor ◽

Ficus Hispida ◽

Tail Tip

AbstractTwo new nematode species of the genus Schistonchus were recovered from syconia from a single Ficus hispida caprifig tree in Guangzhou, China. They are described herein as Schistonchus guangzhouensis n. sp. and S. centerae n. sp. Schistonchus guangzhouensis n. sp. is characterised by possessing the longest postuterine sac (PUS) of all currently described females in the genus (84-148 μm or >3.5 vulval body diam. (VBD) long), excretory pore situated near the level of the metacorpus, two pairs of subventral papillae on the male tail, and unique recurved and mitten-shaped spicules. Schistonchus centerae n. sp. is characterised by a unique fusiform tail tip and short PUS (8-20 μm or <1.0 VBD long) in reproductive females, excretory pore located near the head, spicules with an indistinct rostrum, male tail with three pairs of papillae, and broadly truncate tail tip. Both new species were easily differentiated from each other and other members of the genus for which sequences of the D2/D3 expansion segments of the large subunit rRNA gene (LSU) and partial small subunit rRNA gene (SSU) were available. Phylogenetic analysis also supported a monophyletic Schistonchus within a well-supported clade of Aphelenchoididae (sensu Hunt, 1993) and shared a most recent common ancestor with Aphelenchoides and Laimaphelenchus.

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Phylogeny of beech in western Eurasia as inferred by approximate Bayesian computation

Acta Societatis Botanicorum Poloniae ◽

10.5586/asbp.3582 ◽

2018 ◽

Vol 87 (2) ◽

Cited By ~ 4

Author(s):

Dušan Gömöry ◽

Ladislav Paule ◽

Vladimír Mačejovský

Keyword(s):

Species Complex ◽

Approximate Bayesian Computation ◽

Demographic History ◽

Sensu Stricto ◽

Early Pleistocene ◽

Hybrid Origin ◽

Bayesian Computation ◽

Western Asia ◽

Approximate Bayesian ◽

Western Eurasia

The Fagus sylvatica L. species complex in Europe and Western Asia comprises two commonly recognized subspecies, F. sylvatica subsp. sylvatica [= F. sylvatica sensu stricto (s. str.)] and F. sylvatica subsp. orientalis (= F. orientalis), and two putatively hybridogenous or intermediate taxa, “F. moesiaca” and “F. taurica”. The present study aimed to examine the demographic history of this species complex using 12 allelic loci of nine allozymes scored in 279 beech populations in western Eurasia. Three sets of phylogenetic scenarios were tested by approximate Bayesian computation: one dealing with the divergence of subspecies and/or regional populations within the whole taxonomical complex, and two others focusing on the potential hybrid origin of “F. moesiaca” and “F. taurica”. The best-supported scenario within the first set placed the time of divergence of regional populations of F. orientalis in the Early Pleistocene (1.18–1.87 My BP). According to this scenario, the Iranian population was the ancestral lineage, whereas F. sylvatica s. str. was the lineage that diverged most recently. “Fagus taurica” was found to have originated from hybridization between the Caucasian population of F. orientalis and F. sylvatica s. str. at 144 ky BP. In contrast, there was no evidence of a hybrid origin of “F. moesiaca”. The best-supported scenario suggested that the Balkan lineage is a part of F. sylvatica s. str., which diverged early from F. orientalis in Asia Minor (817 ky BP), while both the Italian and Central-European lineages diverged from the Balkan one later, at the beginning of the last (Weichselian) glacial period.

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Phylogenetic revision of the psammophilic Trogloderus LeConte (Coleoptera: Tenebrionidae), with biogeographic implications for the Intermountain Region

PeerJ ◽

10.7717/peerj.8039 ◽

2019 ◽

Vol 7 ◽

pp. e8039 ◽

Cited By ~ 2

Author(s):

M. Andrew Johnston

Keyword(s):

New Species ◽

Great Basin ◽

Colorado Plateau ◽

Recent Common Ancestor ◽

Owens Valley ◽

Most Recent Common Ancestor ◽

Western Colorado ◽

Intermountain Region ◽

Mohave Desert ◽

Phylogenetic Revision

The genus Trogloderus LeConte, 1879, which is restricted to dunes and sandy habitats in the western United States, is revised using morphological and molecular information. Six new species are described from desert regions: Trogloderus arcanus New Species (Lahontan Trough); Trogloderus kandai New Species (Owens Valley); Trogloderus major New Species (Mohave Desert); Trogloderus skillmani New Species (eastern Great Basin and Mohave Desert); Trogloderus verpus New Species (eastern Colorado Plateau); and Trogloderus warneri New Species (western Colorado Plateau). A molecular phylogeny is presented for the genus and used to infer its historical biogeography. The most recent common ancestor of Trogloderus is dated to 5.2 mya and is inferred to have inhabited the Colorado Plateau. Current species most likely arose during the mid-Pleistocene where the geographic features of the Lahontan Trough, Bouse Embayment and Kaibab Plateau were significant factors driving speciation.

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Molecular dating of the emergence of anaerobic rumen fungi and the impact of laterally acquired genes

10.1101/401869 ◽

2018 ◽

Cited By ~ 2

Author(s):

Yan Wang ◽

Noha Youssef ◽

M.B. Couger ◽

Radwa Hanafy ◽

Mostafa Elshahed ◽

...

Keyword(s):

Plant Biomass ◽

Molecular Dating ◽

Recent Common Ancestor ◽

Comparative Genomic ◽

Phylogenomic Analysis ◽

Gene Gain ◽

Plant Materials ◽

Most Recent Common Ancestor ◽

The Impact ◽

Lineage Specific Genes

AbstractThe anaerobic gut fungi (AGF) or Neocallimastigomycota inhabit the rumen and alimentary tract of herbivorous mammals, where they play an important role in the degradation of plant fiber. Comparative genomic and phylogenomic analysis of the AGF has long been hampered by their fastidious growth pattern as well as their large and AT-biased genomes. We sequenced 21 AGF transcriptomes and combined them with 5 available genome sequences of AGF taxa to explore their evolutionary relationships, time their divergence, and characterize patterns of gene gain/loss associated with their evolution. We estimate that the most recent common ancestor of the AGF diverged 66 (±10) million years ago, a timeframe that coincides with the evolution of grasses (Poaceae), as well as the mammalian transition from insectivory to herbivory. The concordance of these independently estimated ages of AGF evolution, grasses evolution, and mammalian transition to herbivory suggest that AGF have been important in shaping the success of mammalian herbivory transition by improving the efficiency of energy acquisition from recalcitrant plant materials. Comparative genomics identified multiple lineage-specific genes and protein domains in the AGF, two of which were acquired from an animal host (galectin) and rumen gut bacteria (carbohydrate-binding domain) via horizontal gene transfer (HGT). Four of the bacterial derived “Cthe_2159” genes in AGF genomes also encode eukaryotic Pfam domains (“Atrophin-1”, “eIF-3_zeta”, “Nop14”, and “TPH”) indicating possible gene fusion events after the acquisition of “Cthe_2159” domain. A third AGF domain, plant-like polysaccharide lyase N-terminal domain (“Rhamnogal_lyase”), represents the first report from fungi that potentially aids AGF to degrade pectin. Analysis of genomic and transcriptomic sequences confirmed the presence and expression of these lineage-specific genes in nearly all AGF clades supporting the hypothesis that these laterally acquired and novel genes in fungi are likely functional. These genetic elements may contribute to the exceptional abilities of AGF to degrade plant biomass and enable metabolism of the rumen microbes and animal hosts.

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Molecular phylogeny of Hiptage (Malpighiaceae) reveals a new species from Southwest China

PhytoKeys ◽

10.3897/phytokeys.135.37011 ◽

2019 ◽

Vol 135 ◽

pp. 91-104 ◽

Cited By ~ 1

Author(s):

Ke Tan ◽

Hai-Lei Zheng ◽

Shu-Peng Dong ◽

Ming-Xun Ren

Keyword(s):

New Species ◽

Molecular Phylogeny ◽

Internal Transcribed Spacer ◽

Southwest China ◽

Common Ancestor ◽

Its Region ◽

Recent Common Ancestor ◽

Most Recent Common Ancestor ◽

First Time ◽

A New Species

Hiptage is an Asia-endemic genus of Malpighiaceae currently placed in the tetrapteroid clade, representing one of the seven inter-continent dispersions from New to Old World. A molecular phylogeny based on sequences of the internal transcribed spacer (ITS) region was recovered for the first time for the genus. Our results showed that the most recent common ancestor of Hiptage probably originated in the South Indo-China Peninsula and diversified in this region. Based on phylogenetic evidence and relevant morphological traits, we propose a new species; Hiptage incurvatum is characterised by mericarps with arcuate anterior lateral wings, two large glands on the dorsal sepals, and small glands on the remaining sepals. The new species is from Mt. Cangshan, Dali City (25°35'N, 100°02'E) in North Yunnan, Southwest China and is notable for its occurrence at high altitude, 1400 m (the highest distribution currently known for the genus). The implications of this unusual species for the dispersal and evolution of the genus are discussed.

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