Unheeded biodiversity: perspectives of DNA barcoding of Trichoptera in Bosnia and Herzegovina

Bosnia and Herzegovina has valuable natural resources with a high percentage of endemic and autochthonous species (Kučinić et al. 2008, Đug and Drešković 2012). The freshwater fauna of Trichoptera in this area is under-investigated, with a lack of morphological description of different life stages and DNA barcode data. Public data show 58,993 barcode entries for Trichoptera in the Barcode of Life Data Systems (BOLD) submitted from 92 countries, and none from Bosnia and Herzegovina (B&H) (BOLD 2021). Previous research in Bosnia and Herzegovina has provided the first DNA barcode for the endemic species Rhyacophila bosnica, stored in GeneBank, under accession number MK211322 by a domestic institution (Kalamujić Stroil et al. 2018). A few DNA barcodes of adult individuals of Trichoptera from Bosnia and Herzegovina were found in BOLD. However, these specimens were collected on B&H territory, but analyzed, processed, and stored by foreign institutions. To change the current state of DNA barcoding of Trichoptera in Bosnia and Herzegovina, we aimed to employ this approach in investigating caddisflies in selected habitats in the Sarajevo Canton. Our fieldwork was done in all five protected areas (spring of the Bosna River, Bijambare, Trebević, Skakavac, and Bentbaša) in which larvae samples were collected according to the AQEM sampling methodology. The standard animal DNA barcode was successfully obtained using degenerated primers LCO1490- JJ and HCO2198-JJ (Astrin and Stüben 2008). Out of 684 collected individuals (313 Trebević, 130 spring of the Bosna River, 117 Bijambare, 71 Bentbaša, 53 Skakavac), a subset of specimens were sequenced. We uncovered 14 different taxa, 11 genera and six families (Limnephilidae, Glossosomatidae, Rhyacophilidae, Goeridae, Hydropsychidae, Polycentropodidae). The preliminary data of Trichoptera composition in the Sarajevo Canton indicated species richness. Based on our sequential data, a new subspecies was discovered in two investigated areas (Valladolid et al. 2020), proving that Trichoptera species diversity in our country is far from entirely uncovered. The benefit and power of the DNA barcoding approach are that it can pinpoint the areas of vast and unknown species diversity more economically, both financially and temporarily, than the morphological approach. Therefore, we believe that it is critical to support the development of DNA barcoding for the bioassessment of freshwater ecosystems in Bosnia and Herzegovina. Several problems prevented us from exploiting sequential data to the fullest. Despite a general notion among scientists that European Trichoptera species are well covered in the BOLD database, most of the sequences we obtained were absent from the database. Secondly, we recognized that morphological data about the larval developmental stage of B&H Trichoptera species are largely missing. The unified, updated, and complete data on this order of insects is urgently needed. However, insufficient financial support by governmental institutions and lack of systematic approach to barcoding the wildlife of Bosnia and Herzegovina hampers this process. Further attempts to collaborate with the stakeholders can be crucial with profound and substantial implications for biomonitoring of aquatic macroinvertebrates in general. New approaches, such as novel DNA barcoding-based methodology can fill an important gap in our knowledge of Balkan caddisflies haplotypes, lineages, and their diversification and distribution patterns.

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A DNA barcode examination of the red algal family Dumontiaceae in Canadian waters reveals substantial cryptic species diversity. 1. The foliose Dilsea–Neodilsea complex and WeeksiaThis paper is one of a selection of papers published in the Special Issue on Systematics Research.

Botany ◽

10.1139/b08-001 ◽

2008 ◽

Vol 86 (7) ◽

pp. 773-789 ◽

Cited By ~ 122

Author(s):

Gary W. Saunders

Keyword(s):

Species Diversity ◽

Dna Barcoding ◽

Life Histories ◽

Dna Barcode ◽

Genetic System ◽

Marine Macroalgae ◽

Accurate Identification ◽

Additional Species ◽

Large Numbers ◽

Red Algal

The field of DNA barcoding is working towards generating a genetic system for the quick and accurate identification of eukaryotic species. For the more systematic minded, however, DNA barcoding offers a new approach towards screening and uniting large numbers of biological specimens in genetic groups as a first step towards assigning them to species and genera in an approach best termed “molecular-assisted alpha taxonomy”. This approach is particularly amenable in organisms with simple morphologies, a propensity for convergence, extensive phenotypic plasticity, and life histories with an alternation of heteromorphic generations. It is hard to imagine a group of organisms better defined by all of these traits than the marine macroalgae. In an effort to assess the utility of the DNA barcode (COI-5′) for testing the current concepts of biodiversity of marine macroalgae in Canada, a study to assess species diversity in the red algal family, Dumontiaceae, was initiated. Through this work I confirm the presence in Canadian waters of Dilsea californica (J. Agardh) Kuntze, Dilsea integra (Kjellman) Rosenvinge, and Neodilsea borealis (I.A. Abbott) Lindstrom of the Dilsea–Neodilsea complex, and Weeksia coccinea (Harvey) Lindstrom for the genus Weeksia . However, our work has uncovered two additional species of the former complex, Dilsea lindstromiae Saunders sp. nov. and Dilsea pygmaea (Setchell) Setchell, and an additional species of the latter, Weeksia reticulata Setchell, effectively doubling representation of these foliose dumontiacean genera in Canadian waters.

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DNA Barcoding of Mullets (Family Mugilidae) from Pakistan Reveals Surprisingly High Number of Unknown Candidate Species

Diversity ◽

10.3390/d13060232 ◽

2021 ◽

Vol 13 (6) ◽

pp. 232

Author(s):

Ariba Hasan ◽

Pirzada Jamal Ahmed Siddiqui ◽

Shabir Ali Amir ◽

Jean-Dominique Durand

Keyword(s):

Species Diversity ◽

Cryptic Species ◽

Dna Barcoding ◽

Dna Barcode ◽

Morphological Examination ◽

Operational Taxonomic Units ◽

Phylogenetic Studies ◽

Management Measures ◽

Morphological Criteria ◽

Candidate Species

The mullets are a widespread group of ecologically and economically important fishes of disputed taxonomy due to their uniform external morphology. Barcoding and phylogenetic studies from various locations around the world largely highlighted the species diversity underestimation using morphological criteria used to establish the taxonomy of the family. Here, we investigated the mullet species diversity from Pakistan, a biogeographic area where nearly no mullet species were genetically characterized. Morphological examination of 40 mullets reveals 6 known species (Planiliza macrolepis, P. klunzingeri, P. subviridis, Crenimugil seheli, Ellochelon vaigiensis, and Mugil cephalus). Using a references DNA barcode library, the DNA barcode-based species identification flagged eight molecular operational taxonomic units (MOTUs) belonging to five genera (Crenimugil, Ellochelon, Mugil, Osteomugil, and Planiliza). Among these MOTUs, only one was already present in Barcode of Life Data system, all other representing new Barcode Index Numbers (BIN). These results emphasize the importance of the recognition of cryptic species and the necessity to re-evaluate the overall diversity by the genetic characterization of different species of this family. DNA barcoding is an effective tool to reveal cryptic species that need to be considered in conservation and management measures of fisheries in Pakistan.

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A revision of European species of the genus Tetrastichus Haliday (Hymenoptera: Eulophidae) using integrative taxonomy

Biodiversity Data Journal ◽

10.3897/bdj.8.e59177 ◽

2020 ◽

Vol 8 ◽

Author(s):

Christer Hansson ◽

Stefan Schmidt

Keyword(s):

Dna Barcoding ◽

Dna Barcode ◽

Host Record ◽

Current Data ◽

Biological Information ◽

Morphological Data ◽

Integrative Approach ◽

Similar Species ◽

European Species ◽

Wide Range

The European species of the genus Tetrastichus (Insecta, Hymenoptera, Eulophidae, Tetrastichinae) are revised with 93 species, including 50 species described as new. The revision was conducted using an integrative taxonomic approach, based on DNA barcoding in combination with morphological characters. The Tetrastichinae are a biologically diverse and species-rich group of parasitoid wasps with numerous complexes of morphologically often very similar species that attack a wide range of hosts in over 100 insect families in 10 different orders. The genus Tetrastichus is, with almost 500 described species, the third largest genus of Tetrastichinae. Although biological information is lacking for most species, current data indicate that Tetrastichus species are gregarious koinobiont endoparasitoids developing on juvenile stages of mainly holometabolous insects. Due to their host specificity, several species of Tetrastichus are used as biological control agents. The European species of Tetrastichus Haliday (Hymenoptera: Eulophidae) are revised using a combination of externo-morphological and DNA barcoding data. This is the first integrative approach for any of the large genera of the Tetrastichinae. A total of 93 species are included, of which 50 are described as new: T. agonus sp. n., T. antonjanssoni sp. n., T. argei sp. n., T. argutus sp. n., T. asilis sp. n., T. ballotus sp. n., T. bledius sp. n., T. broncus sp. n., T. calcarius sp. n., T. calmius sp. n., T. clisius sp. n., T. cosidis sp. n., T. cumulus sp. n., T. cyprus sp. n., T. delvarei sp. n., T. doczkali sp. n., T. elanus sp. n., T. elodius sp. n., T. ennis sp. n., T. enodis sp. n., T. erinus sp. n., T. evexus sp. n., T. fadus sp. n., T. fenrisi sp. n., T. flaccius sp. n., T. gredius sp. n., T. iasi sp. n., T. illydris sp. n., T. incanus sp. n., T. inscitus sp. n., T. intruitus sp. n., T. johnnoyesi sp. n., T. lacustrinus sp. n., T. ladrus sp. n., T. lanius sp. n., T. lazius sp. n., T. lixalius sp. n., T. lycus sp. n., T. marcusgrahami sp. n., T. minius sp. n., T. mixtus sp. n., T. nataliedaleskeyae sp. n., T. nymphae sp. n., T. pixius sp. n., T. scardiae sp. n., T. splendens sp. n., T. sti sp. n., T. suecus sp. n., T. tacitus sp. n. and T. tartus sp. n. Two keys for the identification of species are presented, one for females and one for males. Based on DNA barcode sequences for 70 of the species, a Maximum Likelihood tree to assess phylogenetic relationships within the genus is presented. These 70 species are also characterised by a combination of CO1 and morphological data. The remaining 23 species, without a DNA barcode, are characterised by morphological data. Using a combination of data from the morphology and CO1 or morphological data only, the species are separated into three species groups (clito-, hylotomarum-, murcia-groups) with 41 unplaced species outside these groups. Hosts are known for 27 of the species and they are gregarious, koinobiont endoparasitoids on a wide range of immature stages of holometabolous insects and appear to be very host specific. The first host record for Lepidoptera (Tineidae) in Europe is included.

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Beyond Bycatch: The Species Diversity of Tonguesole (Pleuronectiformes: Cynoglossidae) in Coastal Fisheries of the Tanintharyi Region, Southern Myanmar

Asian Fisheries Science ◽

10.33997/j.afs.2021.34.1.003 ◽

2021 ◽

Vol 34 (1) ◽

Author(s):

IRIS SEGURA-GARCIA ◽

SABAI SOE ◽

NYO-NYO TUN ◽

STEPHEN BOX

Keyword(s):

Species Diversity ◽

Dna Barcoding ◽

Life Histories ◽

Dna Barcode ◽

Common Species ◽

Small Scale ◽

New Information ◽

The Family ◽

Management Plans ◽

Species Specific

Flatfishes in the family Cynoglossidae are an important coastal fishery in Myanmar. Due to the overlapping morphologies of multiple tonguesole species, caught both as bycatch from trawl fisheries and targeted specifically by small scale fishers, they are all marketed under a single local name, “khwayshar”. This presents a management challenge given the potential differences in the species-specific life-histories, population dynamics, fishing vulnerability and harvest rates. This study investigated the species diversity of tonguesole landings from coastal communities of the Tanintharyi Region of southern Myanmar. DNA barcoding was used to distinguish potentially 10 different species, of which five were identified to species level and five at the genus level. Unconfirmed genetic identifications were based on external morphology. The poor efficacy of DNA barcoding for tonguesole species identification resulted from the limited DNA barcode reference sequences available for the family Cynoglossidae in public databases. An asymmetric occurrence and relative abundance of the identified species in landing sites where samples were collected suggested that the most common species was Cynoglossus oligolepis (Bleeker, 1855), a new species record for Myanmar, followed by Cynoglossus lingua Hamilton, 1822. The results of the present study provide new information to characterise the tonguesole fishery as a first step in the development of management plans for the coastal fishery in Myanmar.

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The first DNA barcode record for Rhyacophila bosnica Schmid, 1970 and pairing of adult and larval life stages

Genetics & Applications ◽

10.31383/ga.vol2iss2pp20-27 ◽

2018 ◽

Vol 2 (2) ◽

pp. 20

Author(s):

Belma Kalamujić Stroil ◽

Lejla Lasić ◽

Jasna Hanjalić ◽

Sonja Mačar ◽

Adi Vesnić

Keyword(s):

Dna Barcoding ◽

Bosnia And Herzegovina ◽

Endemic Species ◽

Developmental Stages ◽

Dna Barcode ◽

Balkan Peninsula ◽

Life Stages ◽

Larval Life ◽

Globally Distributed ◽

Locus Typicus

Rhyacophila Pictet 1834 is globally distributed and highly diverse genus of caddisflies (Trichoptera), characterized by numerous regionally endemic species. In the Balkan Peninsula, the highest number of Rhyacophila species (23) was recorded for Bosnia and Herzegovina. Rhyacophila bosnica Schmid, 1970 is found only in the Balkan Dinaric region, with a locus typicus in Vučja Luka, Bosnia and Herzegovina. Like with many species of Trichoptera, the morphology of its larva is still unknown. Therefore, DNA barcoding approach was used to link two developmental stages. In this paper, we report on the first DNA barcode record for this species.

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Establishing the first DNA barcode reference library for freshwater decapod species (Crustacea: Decapoda) in Republic of North Macedonia

ARPHA Conference Abstracts ◽

10.3897/aca.4.e65138 ◽

2021 ◽

Vol 4 ◽

Author(s):

Valentina Slavevska Stamenkovic ◽

Jelena Hinic ◽

Michal Grabowski ◽

Tomasz Mamos ◽

Leona Lovrenčić ◽

...

Keyword(s):

Dna Barcoding ◽

Dna Barcode ◽

Morphological Characters ◽

Freshwater Ecosystems ◽

Aquatic Biota ◽

Reference Library ◽

Irreversible Loss ◽

The Republic ◽

Different Parts ◽

Comprehensive Study

The freshwater ecosystems in the Republic of North Macedonia are considered as biodiversity hotspot on the European level since they provide diverse habitats that correspond with the complex of ecological preferences that many species require. This specially applies to the freshwater crustaceans that, unfortunately, have never been in the focus of a continuous research. In R. North Macedonia, freshwater crustaceans usually inhabit ecosystems exposed to negative anthropogenic impact. Thus, some species may become extinct presenting an irreversible loss for the Macedonian natural heritage. Although DNA barcoding, as a highly effective tool for fast species detection, is already a routine protocol in many taxonomical studies all over the world, there is still no official national DNA barcoding initiative in Republic of North Macedonia. This study employs DNA barcoding based on the ca. 650-bp long standard fragment of the mt COI gene of Astacus astacus, Austropotamobius torrentium, Potamon fluviatile and Potamon ibericum previously identified based on morphological characters, collected from different parts in R. North Macedonia. The ability of the DNA barcoding to rapidly identify all species has been proven. Our research presents the first comprehensive study that employs DNA barcoding as a molecular tool in decapod taxonomy in Republic of North Macedonia, giving the first attempt to establish DNA barcode reference library for freshwater decapod species in the country. We hope that further application of this approach will lead to the construction of DNA barcode reference library for different aquatic biota in the country. Such a library will find purpose in effective and modern bioassessment protocols as well as in phylogenetic research detecting interpopulation genetic variability.

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Differentiation of Mitragyna speciosa, a narcotic plant, from allied Mitragyna species using DNA barcoding-high-resolution melting (Bar-HRM) analysis

Scientific Reports ◽

10.1038/s41598-021-86228-9 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Chayapol Tungphatthong ◽

Santhosh Kumar J. Urumarudappa ◽

Supita Awachai ◽

Thongchai Sooksawate ◽

Suchada Sukrong

Keyword(s):

High Resolution ◽

Dna Barcoding ◽

High Resolution Melting ◽

Dna Barcode ◽

Herbal Medicines ◽

Efficient Tool ◽

Hrm Analysis ◽

Mitragyna Speciosa ◽

Leaf Powder

AbstractMitragyna speciosa (Korth.) Havil. [MS], or “kratom” in Thai, is the only narcotic species among the four species of Mitragyna in Thailand, which also include Mitragyna diversifolia (Wall. ex G. Don) Havil. [MD], Mitragyna hirsuta Havil. [MH], and Mitragyna rotundifolia (Roxb.) O. Kuntze [MR]. M. speciosa is a tropical tree belonging to the Rubiaceae family and has been prohibited by law in Thailand. However, it has been extensively covered in national and international news, as its abuse has become more popular. M. speciosa is a narcotic plant and has been used as an opium substitute and traditionally used for the treatment of chronic pain and various illnesses. Due to morphological disparities in the genus, the identification of plants in various forms, including fresh leaves, dried leaf powder, and finished products, is difficult. In this study, DNA barcoding combined with high-resolution melting (Bar-HRM) analysis was performed to differentiate M. speciosa from allied Mitragyna and to assess the capability of Bar-HRM assays to identify M. speciosa in suspected kratom or M. speciosa-containing samples. Bar-HRM analysis of PCR amplicons was based on the ITS2, rbcL, trnH-psbA, and matK DNA barcode regions. The melting profiles of ITS2 amplicons were clearly distinct, which enabled the authentication and differentiation of Mitragyna species from allied species. This study reveals that DNA barcoding coupled with HRM is an efficient tool with which to identify M. speciosa and M. speciosa-containing samples and ensure the safety and quality of traditional Thai herbal medicines.

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Research Paper DNA barcode identification of fish products from Guiyang markets in southwest China

Journal of Food Protection ◽

10.4315/jfp-21-258 ◽

2022 ◽

Author(s):

Qian Tang ◽

Qi Luo ◽

Qian Duan ◽

Lei Deng ◽

Renyi Zhang

Keyword(s):

Dna Barcoding ◽

Molecular Identification ◽

Fish Consumption ◽

Southwest China ◽

Dna Barcode ◽

Guizhou Province ◽

Accurate Identification ◽

Continuous Growth ◽

Fish Products ◽

Fresh Frozen

Nowadays, the global fish consumption continues to rise along with the continuous growth of the population, which has led to the dilemma of overfishing of fishery resources. Especially high-value fish that are overfished are often replaced by other fish. Therefore, the accurate identification of fish products in the market is a problem worthy of attention. In this study, full-DNA barcoding (FDB) and mini-DNA barcoding (MDB) used to detect the fraud of fish products in Guiyang, Guizhou province in China. The molecular identification results showed that 39 of the 191 samples were not consistent with the labels. The mislabelling of fish products for fresh, frozen, cooked and canned were 11.70%, 20.00%, 34.09% and 50.00%, respectively. The average kimura 2 parameter distances of MDB within species and genera were 0.27% and 5.41%, respectively; while average distances of FDB were 0.17% within species and 6.17% within genera. In this study, commercial fraud is noticeable, most of the high-priced fish were replaced of low-priced fish with a similar feature. Our study indicated that DNA barcoding is a valid tool for the identification of fish products and that it allows an idea of conservation and monitoring efforts, while confirming the MDB as a reliable tool for fish products.

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Phylogenetic Analysis of Black Peper (Piper Spp.) Population Collected in Different Locations of Vietnam Based on the ITSU1-4 Gene Region

10.21203/rs.3.rs-844711/v1 ◽

2021 ◽

Author(s):

Sonexay Rasphone ◽

Long Thanh Dang ◽

Hoan Nguyen ◽

Ngoc Quang Nguyen ◽

Oanh Thi Duong ◽

...

Keyword(s):

Dna Barcoding ◽

Ribosomal Dna ◽

Maximum Likelihood Method ◽

Dna Barcode ◽

Population Expansion ◽

Nuclear Ribosomal Dna ◽

Likelihood Method ◽

Gene Region ◽

Universal Primers ◽

Intraspecific Distance

Abstract Background: The internal transcribed spacer (ITS) of nuclear ribosomal DNA is one of the most commonly used DNA markers in plant phylogenetic and DNA barcoding analyses, and it has been recommended as a core plant DNA barcode. To compare and find out the analysis genetic diversity difference some pepper individuals collected in different localities in Vietnam when using the ITS of nuclear ribosomal DNA. The ITS gene region from the nuclear genomes were tested for their suitability as DNA barcoding regions of thirty-nine pepper individuals. Universal primers were used, and sequenced products were analyzed using the Maximum Likelihood method and Tamura-Nei model in the MEGA X program.Results: We did not observe high variability in intraspecific distance within the ITSu1-4 gene region between individuals, ranged from 0.000 to 0.155 (mean = 0.033). The size of the gene region has fluctuated from 667 to 685 bp between different individuals with the percentage (G + C) contained in the ITSu1-4 gene region was ranged from 54.776% to 60.805%, mean = 60.174%. The values of Fu’s Fs, D, Fu and Li’s D* and F* were negative as well (Fs = -0.209, D = -1.824; P < 0.05, D* = -1.205; not significant, P > 0.10 and F* = -1.699; not significant, 0.10 > P > 0.05), indicating an excess of recently derived haplotypes and suggesting that either population expansion or background selection has occurred. The value Strobeck’s S the obtained between individuals in a population is high (S = 0.684). The results of evolutionary relationships of taxa obtained 3 groups with the highest value of Fst is shown in the pairs of groups II and III (Fst = 0.151), and the lowest is in groups II and I (Fst = 0.015). All of the new sequences have been deposited in GeneBank under the following accession numbers MZ636718 to MZ636756.Conclusions: This database is an important resource for researchers working on Species of pepper in Vietnam and also provides a tool to create ITSu1-4 databases for any given taxonomy.

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Three new Cenomanian conifers from El Chango (Chiapas, Mexico) offer a snapshot of the geographic mosaic of the Mesozoic conifer decline

10.1101/2021.09.01.458614 ◽

2021 ◽

Author(s):

Ixchel Gonzalez-Ramirez ◽

Sergio RS Cevallos-Ferriz ◽

Carl Rothfels

Keyword(s):

Evolutionary History ◽

Mixed Forest ◽

Freshwater Ecosystems ◽

Total Evidence ◽

Morphological Data ◽

Phylogenetic Position ◽

Dominant Group ◽

Geographic Mosaic ◽

History Of ◽

Rare Opportunity

Premise of study: El Chango is a recently discovered quarry that contains extremely well preserved fossils. The Cenomanian age of the locality corresponds to a time when the global flora was transitioning from gymnosperm- to angiosperm-dominated, yet conifers predominate in this locality. These fossils thus provide a rare opportunity to understand the replacement of conifers by angiosperms as the dominant group of plants. Methods: We collected material from El Chango in annual expeditions (2010 to 2014). We selected the three most abundant and best preserved conifer morphotypes and conducted a total-evidence (i.e., including molecular and morphological data) phylogenetic analysis of a sample of 72 extant conifer species plus the three fossils. We use these results to inform our taxonomic decisions. Results: We obtained four equally most-parsimonious trees (consistency index = 44.1%, retention index = 78.8%). Despite ambiguous relationships among some extant taxa, the three fossil conifers had the same phylogenetic position in all four most parsimonious trees; we describe these species as new: Sequoiadendron helicalancifolium sp. nov. (Cupressaceae), and Microcachrys rhomboidea sp. nov. and Dacrydium bifoliosus sp. nov (Podocarpaceae). The ecosystem is interpreted as a coastal humid mixed forest. Conclusions: Our findings contribute to the understanding of Cenomanian equatorialregions, and support the hypothesis of a geographically and ecologically structured rise of angiosperms, with conifers remaining dominant in brackish-water and angiosperms becoming dominant in freshwater-ecosystems. These fossils fill in gaps in the evolutionary history of lineages like Microcachrys, which we demonstrate occurred in the Northern hemisphere before becoming restricted to its current range (Tasmania).

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