Historical biogeography, systematics, and integrative taxonomy of the non-Ethiopian speckled pelage brush-furred rats (Lophuromys flavopunctatus group)

Abstract Background The speckled-pelage brush-furred rats (Lophuromys flavopunctatus group) have been difficult to define given conflicting genetic, morphological, and distributional records that combine to obscure meaningful accounts of its taxonomic diversity and evolution. In this study, we inferred the systematics, phylogeography, and evolutionary history of the L. flavopunctatus group using maximum likelihood and Bayesian phylogenetic inference, divergence times, historical biogeographic reconstruction, and morphometric discriminant tests. We compiled comprehensive datasets of three loci (two mitochondrial [mtDNA] and one nuclear) and two morphometric datasets (linear and geometric) from across the known range of the genus Lophuromys. Results The mtDNA phylogeny supported the division of the genus Lophuromys into three primary groups with nearly equidistant pairwise differentiation: one group corresponding to the subgenus Kivumys (Kivumys group) and two groups corresponding to the subgenus Lophuromys (L. sikapusi group and L. flavopunctatus group). The L. flavopunctatus group comprised the speckled-pelage brush-furred Lophuromys endemic to Ethiopia (Ethiopian L. flavopunctatus members [ETHFLAVO]) and the non-Ethiopian ones (non-Ethiopian L. flavopunctatus members [NONETHFLAVO]) in deeply nested relationships. There were distinctly geographically structured mtDNA clades among the NONETHFLAVO, which were incongruous with the nuclear tree where several clades were unresolved. The morphometric datasets did not systematically assign samples to meaningful taxonomic units or agree with the mtDNA clades. The divergence dating and ancestral range reconstructions showed the NONETHFLAVO colonized the current ranges over two independent dispersal events out of Ethiopia in the early Pleistocene. Conclusion The phylogenetic associations and divergence times of the L. flavopunctatus group support the hypothesis that paleoclimatic impacts and ecosystem refugia during the Pleistocene impacted the evolutionary radiation of these rodents. The overlap in craniodental variation between distinct mtDNA clades among the NONETHFLAVO suggests unraveling underlying ecomorphological drivers is key to reconciling taxonomically informative morphological characters. The genus Lophuromys requires a taxonomic reassessment based on extensive genomic evidence to elucidate the patterns and impacts of genetic isolation at clade contact zones.

Download Full-text

Systematics and Phylogeography of The Non-Ethiopian Speckled-Pelage Brush-Furred Rats (Lophuromys Flavopunctatus Group) Inferred From Integrative Genetics and Morphometry

10.21203/rs.3.rs-157741/v1 ◽

2021 ◽

Author(s):

Kenneth Onditi ◽

Julian Kerbis Peterhans ◽

Chen Zhongzheng ◽

Terrence Demos ◽

Josef Bryja ◽

...

Keyword(s):

Taxonomic Diversity ◽

Morphological Characters ◽

Early Pleistocene ◽

Divergence Times ◽

Mtdna Phylogeny ◽

Divergence Dating ◽

History Of ◽

Primary Groups ◽

Bayesian Phylogenetic Inference ◽

Dispersal Events

Abstract Background: The speckled-pelage brush-furred rats (Lophuromys flavopunctatus group) has been difficult to define given conflicting genetic, morphological, and distributional records that combine to obscure meaningful accounts of its taxonomic diversity. In this study, we inferred the systematics, phylogeography, and evolutionary history of the L. flavopunctatus group using maximum likelihood and Bayesian phylogenetic inference, divergence times, historical biogeographic reconstruction, and morphometric discriminant tests. We compiled comprehensive datasets of three loci (two mitochondrial [mtDNA] and one nuclear) and two morphometric datasets (linear and geometric) from across the known range of the genus Lophuromys.Results: The mtDNA phylogeny supported the division of the genus Lophuromys into three primary groups with nearly equidistant pairwise differentiation: one group corresponding to the subgenus Kivumys (Kivumys group) and two groups corresponding to the subgenus Lophuromys (L. sikapusi group and L. flavopunctatus group). The L. flavopunctatus group comprised the speckled-pelage brush-furred Lophuromys endemic to Ethiopia (Ethiopian L. flavopunctatus members [ETHFLAVO]) and the non-Ethiopian ones (non-Ethiopian L. flavopunctatus members [NONETHFLAVO]) in deeply nested relationships. There were distinctly geographically structured mtDNA clades among the NONETHFLAVO, which were incongruous with the nuclear tree where several clades were unresolved. The morphometric datasets did not systematically assign samples to meaningful taxonomic units or agreed with the mtDNA clades. The divergence dating and ancestral range reconstructions showed the NONETHFLAVO colonized the current ranges over two independent dispersal events out of Ethiopia in the early Pleistocene.Conclusion: The phylogenetic associations and divergence times of the L. flavopunctatus group conform to demonstrated hypotheses surrounding the paleoclimatic and ecosystem refugium impacts on the evolutionary radiation of rodents dependent on stably humid conditions in the East Africa region. The overlap in craniodental variation between distinct mtDNA clades among the NONETHFLAVO suggests unraveling underlying ecomorphological drivers is key to reconciling taxonomically informative morphological characters. The genus Lophuromys requires a taxonomic reassessment based on extensive genomic evidence to elucidate the patterns and impacts of genetic isolation at clade contact zones.

Download Full-text

First endemic freshwaterGammarusfrom Crete and its evolutionary history—an integrative taxonomy approach

PeerJ ◽

10.7717/peerj.4457 ◽

2018 ◽

Vol 6 ◽

pp. e4457 ◽

Cited By ~ 6

Author(s):

Kamil Hupało ◽

Tomasz Mamos ◽

Weronika Wrzesińska ◽

Michał Grabowski

Keyword(s):

Morphological Characters ◽

Integrative Taxonomy ◽

16S Rrna Genes ◽

Rrna Genes ◽

Mediterranean Islands ◽

Marine Fauna ◽

Strongly Connected ◽

History Of ◽

The Mediterranean ◽

High Level

The Mediterranean islands are known as natural laboratories of evolution with a high level of endemic biodiversity. However, most biodiversity assessments have focused mainly on terrestrial and marine fauna, leaving the freshwater animals aside. Crete is one of the largest islands in the Mediterranean Basin, with a long history of isolation from the continental mainland. Gammarid amphipods are often dominant in macrozoobenthic communities in European inland waters. They are widely used in biomonitoring and exotoxicological studies. Herein, we describeGammarus plaitisisp. nov., endemic to Cretan streams, based on morphological characters and a set of molecular species delimitation methods using mitochondrial cytochrome oxidase subunit I and 16S rRNA genes as well as nuclear 28S rDNA, ITS1 and EF1-alpha genes. The divergence of the new species is strongly connected with the geological history of the island supporting its continental origin.

Download Full-text

The Botanical, Chemical and Ethnobotanical Diversity of Southern African Lamiaceae

Molecules ◽

10.3390/molecules26123712 ◽

2021 ◽

Vol 26 (12) ◽

pp. 3712

Author(s):

Ryan D. Rattray ◽

Ben-Erik Van Wyk

Keyword(s):

Southern Africa ◽

Folk Medicine ◽

Taxonomic Diversity ◽

Volatile Oils ◽

Edible Plant ◽

Flora Of Southern Africa ◽

Traditional Uses ◽

History Of ◽

Pharmaceutical Industries ◽

History Of Use

The Lamiaceae is undoubtedly an important plant family, having a rich history of use that spans the globe with many species being used in folk medicine and modern industries alike. Their ability to produce aromatic volatile oils has made them valuable sources of materials in the cosmetic, culinary, and pharmaceutical industries. A thorough account of the taxonomic diversity, chemistry and ethnobotany is lacking for southern African Lamiaceae, which feature some of the region’s most notable medicinal and edible plant species. We provide a comprehensive insight into the Lamiaceae flora of southern Africa, comprising 297 species in 42 genera, 105 of which are endemic to the subcontinent. We further explore the medicinal and traditional uses, where all genera with documented uses are covered for the region. A broad review of the chemistry of southern African Lamiaceae is presented, noting that only 101 species (34%) have been investigated chemically (either their volatile oils or phytochemical characterization of secondary metabolites), thus presenting many and varied opportunities for further studies. The main aim of our study was therefore to present an up-to-date account of the botany, chemistry and traditional uses of the family in southern Africa, and to identify obvious knowledge gaps.

Download Full-text

Beyond Wallace: a new lineage of Chrysorthenches (Lepidoptera: Yponomeutoidea: Glyphipterigidae) reveals a journey tracking its host-plants, Podocarpus (Pinopsida: Podocarpaceae)

Zoological Journal of the Linnean Society ◽

10.1093/zoolinnean/zlaa009 ◽

2020 ◽

Vol 190 (2) ◽

pp. 709-736

Author(s):

Jae-Cheon Sohn ◽

Shigeki Kobayashi ◽

Yutaka Yoshiyasu

Keyword(s):

Maximum Likelihood ◽

East Asia ◽

Host Plants ◽

Morphological Characters ◽

Species Group ◽

Geological History ◽

Dna Barcodes ◽

History Of ◽

Species Groups ◽

Maximum Likelihood Phylogeny

Abstract A northward trans-Wallacean radiation is demonstrated for Chrysorthenches, a member of the Orthenches group. Here we review Chrysorthenches and allied genera resulting in a generic transfer of Diathryptica callibrya to Chrysorthenches and two new congeners: C. muraseaeSohn & Kobayashisp. nov. from Japan and C. smaragdinaSohnsp. nov. from Thailand. We review morphological characters of Chrysorthenches and allied genera, and find polyphyly of Diathryptica and the association of the Orthenches-group with Glyphipterigidae. These findings were supported in a maximum likelihood phylogeny of DNA barcodes from ten yponomeutoids. We analysed 30 morphological characters for 12 species of Chrysorthenches, plus one outgroup, via a cladistic approach. The resulting cladogram redefined two pre-existing Chrysorthenches species-groups and identified one novel lineage: the C. callibrya species-group. We review the host associations between Chrysorthenches and Podocarpaceae, based on mapping the working phylogenies. Our review suggests that ancestral Chrysorthenches colonized Podocarpus and later shifted to other podocarp genera. Biogeographical patterns of Chrysorthenches show that they evolved long after the Podocarpaceae radiation. Disjunctive trans-Wallacean distribution of the C. callibrya species-group is possibly related to the tracking of their host-plants and the complicated geological history of the island-arc system connecting Australia and East Asia.

Download Full-text

Evolutionary Relationship between Two Firefly Species,Curtos costipennisandC. okinawanus(Coleoptera, Lampyridae), in the Ryukyu Islands of Japan Revealed by the Mitochondrial and Nuclear DNA Sequences

The Scientific World JOURNAL ◽

10.1100/2012/653013 ◽

2012 ◽

Vol 2012 ◽

pp. 1-9 ◽

Cited By ~ 2

Author(s):

Masahiko Muraji ◽

Norio Arakaki ◽

Shigeo Tanizaki

Keyword(s):

Dna Sequences ◽

Evolutionary History ◽

Nuclear Dna ◽

Evolutionary Relationship ◽

Early Pleistocene ◽

Ryukyu Islands ◽

Mtdna Sequences ◽

Northern Half ◽

The Ryukyu Islands ◽

History Of

The phylogenetic relationship, biogeography, and evolutionary history of closely related two firefly species,Curtos costipennisandC. okinawanus, distributed in the Ryukyu Islands of Japan were examined based on nucleotide sequences of mitochondrial (2.2 kb long) and nuclear (1.1-1.2 kb long) DNAs. In these analyses, individuals were divided among three genetically distinct local groups,C. costipennisin the Amami region,C. okinawanusin the Okinawa region, andC. costipennisin the Sakishima region. Their mtDNA sequences suggested that ancestralC. costipennispopulation was first separated between the Central and Southern Ryukyu areas, and the northern half was then subdivided betweenC. costipennisin the Amami andC. okinawanusin the Okinawa. The application of the molecular evolutionary clocks of coleopteran insects indicated that their vicariance occurred 1.0–1.4 million years ago, suggesting the influence of submergence and subdivision of a paleopeninsula extending between the Ryukyu Islands and continental China through Taiwan in the early Pleistocene.

Download Full-text

Morphological and molecular phylogenetic analyses of Zepedanulus ishikawai (Arachnida: Opiliones: Laniatores: Epedanidae) in the southern part of the Ryukyu Archipelago

The Canadian Entomologist ◽

10.4039/tce.2021.42 ◽

2021 ◽

pp. 1-28

Author(s):

Yoshimasa Kumekawa ◽

Haruka Fujimoto ◽

Osamu Miura ◽

Ryo Arakawa ◽

Jun Yokoyama ◽

...

Keyword(s):

Phylogenetic Tree ◽

Phylogenetic Analyses ◽

Divergence Time ◽

Morphological Characters ◽

Ryukyu Archipelago ◽

Divergence Time Estimates ◽

Time Estimates ◽

Molecular Phylogenetic ◽

History Of ◽

Polymerase Chain

Abstract Harvestmen (Arachnida: Opiliones) are soil animals with extremely low dispersal abilities that experienced allopatric differentiation. To clarify the morphological and phylogenetic differentiation of the endemic harvestman Zepedanulus ishikawai (Suzuki, 1971) (Laniatores: Epedanidae) in the southern part of the Ryukyu Archipelago, we conducted molecular phylogenetic analyses and divergence time estimates based on CO1 and 16S rRNA sequences of mtDNA, the 28S rRNA sequence of nrDNA, and the external morphology. A phylogenetic tree based on mtDNA sequences indicated that individuals of Z. ishikawai were monophyletic and were divided into clade I and clade II. This was supported by the nrDNA phylogenetic tree. Although clades I and II were distributed sympatrically on all three islands examined (Ishigaki, Iriomote, and Yonaguni), heterogeneity could not be detected by polymerase chain reaction–restriction fragment length polymorphism of nrDNA, indicating that clades I and II do not have a history of hybridisation. Also, several morphological characters differed significantly between individuals of clade I and clade II. The longstanding isolation of the southern Ryukyus from the surrounding islands enabled estimation of the original morphological characters of both clades of Z. ishikawai.

Download Full-text

Cosmogenic burial dating of in cave-deposited alluvium: unravelling long-term incision rates and complex speleogenesis in multi-level cave systems

10.5194/egusphere-egu2020-19598 ◽

2020 ◽

Author(s):

Gilles Rixhon ◽

Didier L. Bourlès ◽

Régis Braucher ◽

Alexandre Peeters ◽

Alain Demoulin

Keyword(s):

Early Pleistocene ◽

Middle Pleistocene ◽

Fluvial Terrace ◽

Base Level ◽

Cave System ◽

River Incision ◽

Order Of Magnitude ◽

History Of ◽

Multi Level

Multi-level cave systems record the history of regional river incision in abandoned alluvium-filled phreatic passages which, mimicking fluvial terrace sequences, represent former phases of fluvial base-level stability. In this respect, cosmogenic burial dating of in cave-deposited alluvium (usually via the nuclide pair 26Al/10Be) represents a suitable method to quantify the pace of long-term river incision. Here, we present a dataset of fifteen 26Al/10Be burial ages measured in fluvial pebbles washed into a multi-level cave system developed in Devonian limestone of the uplifted Ardenne massif (eastern Belgium). The large and well-documented Chawresse system is located along the lower Ourthe valley (i.e. the main Ardennian tributary of the Meuse river) and spans altogether an elevation difference exceeding 120 m.The depleted 26Al/10Be ratios measured in four individual caves show two main outcomes. Firstly, computed burial ages ranging from ~0.2 to 3.3 Ma allows highlighting an acceleration by almost one order of magnitude of the incision rates during the first half of the Middle Pleistocene (from ~25 to ~160 m/Ma). Secondly, according to the relative elevation above the present-day floodplain of the sampled material in the Manants cave (<35 m), the four internally-consistent Early Pleistocene burial ages highlight an &#8220;anomalous&#8221; old speleogenesis in the framework of a gradual base-level lowering. They instead point to intra-karsting reworking of the sampled material in the topographically complex Manants cave. This in turn suggests an independent, long-lasting speleogenetic evolution of this specific cave, which differs from the per descensum model of speleogenesis generally acknowledged for the regional multi-level cave systems and their abandoned phreatic galleries. In addition to its classical use for inferring long-term incision rates, cosmogenic burial dating can thus contribute to better understand specific and complex speleogenetic evolution.

Download Full-text

The incredible diversity of Labiobaetis Novikova & Kluge in New Guinea revealed by integrative taxonomy (Ephemeroptera, Baetidae)

ZooKeys ◽

10.3897/zookeys.804.28988 ◽

2018 ◽

Vol 804 ◽

pp. 1-136 ◽

Cited By ~ 8

Author(s):

Thomas Kaltenbach ◽

Jean-Luc Gattolliat

Keyword(s):

New Species ◽

Genetic Distance ◽

Papua New Guinea ◽

New Guinea ◽

Morphological Characters ◽

Integrative Taxonomy ◽

On This Island

Material collected between 1999 and 2011 in Papua New Guinea and the Papua Province of Indonesia unveiled the enormous diversity ofLabiobaetison this island. Twenty-six new species were identified and delimited by integrative taxonomy using genetic distance (COI, Kimura-2-parameter) and morphology. These new species are described and illustrated based on larvae, augmenting the total number ofLabiobaetisspecies on the island of New Guinea to 32. Seven morpho-groups of species are proposed based on morphological characters and a key to all New Guinea species is provided. The generic attributes of the larvae are summarised and slightly modified based on the examinations of the new species. Results on the genetics of most species (COI) are also provided. The interspecific K2P distances are between 13% and 32%, the intraspecific distances usually between 0% and 2%. Possible reasons for the remarkable richness of this genus in New Guinea are discussed.

Download Full-text

Synanthedon mesiaeformis (Herrich-Schäffer) new to the Czech Republic and to Spain (Lepidoptera: Sesiidae)

Acta Universitatis Agriculturae et Silviculturae Mendelianae Brunensis ◽

10.11118/actaun200856050141 ◽

2008 ◽

Vol 56 (5) ◽

pp. 141-146 ◽

Cited By ~ 1

Author(s):

Zdeněk Laštůvka ◽

Aleš Laštůvka

Keyword(s):

Czech Republic ◽

Close Contact ◽

Morphological Characters ◽

Habitat Requirements ◽

Specific Population ◽

The Czech Republic ◽

Southern France ◽

History Of ◽

First Time ◽

The Town

Synanthedon mesiaeformis (Herrich-Schäffer, 1846) has been found in the Czech Republic and in Spain for the first time. The species was found in the south-easternmost part of the Czech Republic, near the town of Břeclav (faunistic quadrat 7267) in May 2008. The holes and pupae were found only in one, solitary growing group of trees about 20 years old. This finding place lies at a distance of more than 250 km from the localities in SW Hungary and about 550 km from the localities in eastern Poland. In June 2008, the species was found also in alders growing in the flat river alluvium on gravel sands between La Jonquera and Figueres in northern Catalonia. This locality is in a close contact with the finding places near Perpignan and Beziers in southern France. The diagnostic morphological characters and bionomics of this species are briefly summarized and figured. The history of its distribution research is recapitulated and the causes of its disjunct range are discussed as follows. The present disjunct range represents a residual of the former distribution over the warmer and moister postglacial period; landscape modifications and elimination of solitary alder trees as „weeds“ from the 18th up to the mid-20th century in large areas of Europe; narrow and partly unknown habitat requirements and specific population ethology; an insufficient level of faunistic investigations in several parts of southern and eastern Europe.

Download Full-text

Diversity of tree frogs (Amphibia: Anura: Rhacophoridae) from Lai Chau Province, Vietnam

VNU Journal of Science Natural Sciences and Technology ◽

10.25073/2588-1140/vnunst.4880 ◽

2019 ◽

Vol 35 (2) ◽

Author(s):

Anh Van Pham

Keyword(s):

Additional Data ◽

Morphological Characters ◽

Iucn Red List ◽

Red List ◽

Red Data Book ◽

The Family ◽

History Of ◽

Data Book ◽

Tree Frogs ◽

First Time

We report 13 species of treefrogs belonging to six genera of the family Rhacophoridae from Lai Chau Province on the basis of new amphibian collection from Sin Ho District. Four of them, Kurixalus bisacculus, Polypedates mutus, Rhacophorus kio, and Theloderma bicolor are recorded for the first time from this province. We also provide additional data of morphological characters and natural history of the afore mentioned species. Among 13 recorded species of rhacophorids from Lai Chau Province, two species is listed in the IUCN Red List (2018) and two are listed in the Red Data Book of Vietnam (2007).

Download Full-text