cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.25442/hku.24786792
title: Compiled dataset for the mix designs of geopolymer used in soil stabilization.

description: The dataset was compiled from 16 peer-reviewed literature and includes 990 mix design of geopolymer used in soil stabilization. For each mix design, the dataset provides the detailed information on soil properties, chemical composition of geopolymer, curing time, and the measured unconfined compressive strength. The compiled dataset was used to develop our machine learning model for mix design of geopolymer, which is introduced in our manuscript entitled "New Generic Framework for Mix Design of Geopolymer for Soil Stabilization: Composition-informed Machine Learning Model"
DOI: 10.25442/hku.24786792.v1
title: Compiled dataset for the mix designs of geopolymer used in soil stabilization.

description: The dataset was compiled from 16 peer-reviewed literature and includes 990 mix design of geopolymer used in soil stabilization. For each mix design, the dataset provides the detailed information on soil properties, chemical composition of geopolymer, curing time, and the measured unconfined compressive strength. The compiled dataset was used to develop our machine learning model for mix design of geopolymer, which is introduced in our manuscript entitled "New Generic Framework for Mix Design of Geopolymer for Soil Stabilization: Composition-informed Machine Learning Model"
DOI: 10.57967/hf/1448
title: code-commerce
DOI: 10.6084/m9.figshare.24791268
title: streptococcus thermophilus-transcriptome annotation

description: Transcriptome data of wild strains of <i>Streptococcus thermophilus</i> ST222 and mutant strains of CovRst.
DOI: 10.6084/m9.figshare.24791268.v1
title: streptococcus thermophilus-transcriptome annotation

description: Transcriptome data of wild strains of <i>Streptococcus thermophilus</i> ST222 and mutant strains of CovRst.
DOI: 10.6084/m9.figshare.22300879.v1
title: A new species of <i>Mukupirna</i> (Diprotodontia, Mukupirnidae) from the Oligocene of Central Australia sheds light on basal vombatoid interrelationships

description: The late Oligocene taxa <i>Marada arcanum</i> and <i>Mukupirna nambensis</i> (Diprotodontia, Vombatiformes) are the only known representatives of the families Maradidae and Mukupirnidae, respectively. <i>Mukupirna nambensis</i> was described from a partial skeleton, including a cranium but no dentary, and reconstructed as the sister taxon to Vombatidae (wombats). By contrast, <i>Ma. arcanum</i> is known only from a single dentary, preventing direct comparison between the two. Here, we describe a new species, <i>Mu. fortidentata</i> sp. nov., based on craniodental and postcranial specimens from the Oligocene Pwerte Marnte Marnte Local Fauna, Northern Territory, Australia. Phylogenetic analysis of Vombatiformes, using 124 craniodental and 20 postcranial characters, places these three species within Vombatoidea, wherein <i>Marada arcanum</i> is sister to species of <i>Mukupirna +</i> Vombatidae. <i>Mukupirna fortidentata</i> sp. nov. does not share any robust synapomorphies of the dentary with <i>Ma. arcanum</i> that would support placing them together in a clade to the exclusion of Vombatidae. We therefore maintain separation of the families Mukupirnidae and Maradidae. From a functional perspective, the craniodental specimens of <i>Mu. fortidentata</i> sp. nov. reveal a suite of morphological traits that are unusual among vombatiforms, which we interpret as adaptations for acquiring and processing hard plant material. These include: a short, broad rostrum; large, robust, steeply upturned incisors; and a steep, anteroposteriorly decreasing gradient in cheek tooth size. The dental specimens of <i>Mu. fortidentata</i> sp. nov. also assist in the identification of two further allied taxa: an early vombatid from the younger late Oligocene Tarkarooloo Local Fauna, South Australia; and a possible vombatoid from the earliest Miocene Geilston Bay Local Fauna, Tasmania. The Tarkarooloo Local Fauna taxon indicates that vombatids diverged from other vombatoids prior to 24 million years ago. <i>Arthur I. Crichton [arthur.crichton@flinders.edu.au], College of Science and Engineering, Flinders University, Bedford Park, Adelaide, 5042, South Australia;</i> <i>Trevor H. Worthy [trevor.worthy@flinders.edu.au], Aaron B. Camens [aaron.camens@flinders.edu.au], Adam Yates [Adamm.Yates@magnt.net.au] Museum and Art Gallery of the Northern Territory, Alice Springs 0870, Northern Territory, Alice Springs, 0870 Australia;</i> <i>Aidan M. C. Couzens [acouzens@ucla.edu], Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA 90095, USA;</i> <i>Gavin J. Prideaux [gavin.prideaux@flinders.edu.au], Flinders University School of Biological Sciences, Palaeontology, Adelaide, 5001 Australia.</i>
DOI: 10.6084/m9.figshare.22223604.v1
title: First fossil record of <i>Perameles fasciata</i> from New South Wales and Queensland: reassessment of <i>Perameles sobbei</i>

description: The first fossil record of the Liverpool Plains striped bandicoot, <i>Perameles fasciata</i>, is presented. Since this species was split from its west coast counterpart, <i>Perameles bougainville</i>, no fossil record had been reported. <i>Perameles fasciata</i> is found in five fossil sites in Queensland and New South Wales, all Pleistocene in age. <i>Perameles sobbei</i>, described from the Darling Downs in Queensland, is found to be a junior synonym of <i>P. fasciata</i>, based on morphometrics and diagnostic morphological features. A morphological phylogeny finds that <i>P. fasciata</i> is more closely related to <i>Perameles nasuta</i>, <i>Perameles pallescens</i> and <i>Perameles gunnii</i> than <i>P. bougainville. Perameles fasciata</i> was likely more widespread in the Pleistocene, but by the Holocene had only survived on the Liverpool Plains in New South Wales until its extinction in the 1860s, probably as a result of land clearing and the introduction of foxes. While <i>P. bougainville</i> has been translocated in New South Wales, <i>P. gunnii</i>, which co-occurred with <i>P. fasciata</i>, is a better ecological analogue because of it is similar size, morphology and phylogenetic affinity. <i>Kenny J. Travouillon [</i>Kenny.Travouillon@museum.wa.gov.au<i>], Collections and Research Centre, Western Australian Museum, 49 Kew Street, Welshpool, WA 6106, Australia.</i>
DOI: 10.6084/m9.figshare.22300879
title: A new species of <i>Mukupirna</i> (Diprotodontia, Mukupirnidae) from the Oligocene of Central Australia sheds light on basal vombatoid interrelationships

description: The late Oligocene taxa <i>Marada arcanum</i> and <i>Mukupirna nambensis</i> (Diprotodontia, Vombatiformes) are the only known representatives of the families Maradidae and Mukupirnidae, respectively. <i>Mukupirna nambensis</i> was described from a partial skeleton, including a cranium but no dentary, and reconstructed as the sister taxon to Vombatidae (wombats). By contrast, <i>Ma. arcanum</i> is known only from a single dentary, preventing direct comparison between the two. Here, we describe a new species, <i>Mu. fortidentata</i> sp. nov., based on craniodental and postcranial specimens from the Oligocene Pwerte Marnte Marnte Local Fauna, Northern Territory, Australia. Phylogenetic analysis of Vombatiformes, using 124 craniodental and 20 postcranial characters, places these three species within Vombatoidea, wherein <i>Marada arcanum</i> is sister to species of <i>Mukupirna +</i> Vombatidae. <i>Mukupirna fortidentata</i> sp. nov. does not share any robust synapomorphies of the dentary with <i>Ma. arcanum</i> that would support placing them together in a clade to the exclusion of Vombatidae. We therefore maintain separation of the families Mukupirnidae and Maradidae. From a functional perspective, the craniodental specimens of <i>Mu. fortidentata</i> sp. nov. reveal a suite of morphological traits that are unusual among vombatiforms, which we interpret as adaptations for acquiring and processing hard plant material. These include: a short, broad rostrum; large, robust, steeply upturned incisors; and a steep, anteroposteriorly decreasing gradient in cheek tooth size. The dental specimens of <i>Mu. fortidentata</i> sp. nov. also assist in the identification of two further allied taxa: an early vombatid from the younger late Oligocene Tarkarooloo Local Fauna, South Australia; and a possible vombatoid from the earliest Miocene Geilston Bay Local Fauna, Tasmania. The Tarkarooloo Local Fauna taxon indicates that vombatids diverged from other vombatoids prior to 24 million years ago. <i>Arthur I. Crichton [arthur.crichton@flinders.edu.au], College of Science and Engineering, Flinders University, Bedford Park, Adelaide, 5042, South Australia;</i> <i>Trevor H. Worthy [trevor.worthy@flinders.edu.au], Aaron B. Camens [aaron.camens@flinders.edu.au], Adam Yates [Adamm.Yates@magnt.net.au] Museum and Art Gallery of the Northern Territory, Alice Springs 0870, Northern Territory, Alice Springs, 0870 Australia;</i> <i>Aidan M. C. Couzens [acouzens@ucla.edu], Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA 90095, USA;</i> <i>Gavin J. Prideaux [gavin.prideaux@flinders.edu.au], Flinders University School of Biological Sciences, Palaeontology, Adelaide, 5001 Australia.</i>
DOI: 10.6084/m9.figshare.22680706
title: <i>Urrayira whitei</i> gen. et sp. nov.: a dasyuromorphian (Mammalia: Marsupialia) with incipient zalambdodonty from the Middle Pleistocene of Queensland, Australia

description: <i>Urrayira whitei</i> gen. et sp. nov. is described based on dental remains from middle Pleistocene cave sites at Mount Etna, Queensland. Its higher-level systematic affinities are unclear but it appears to be a dasyuromorphian. It is unusual in having a specialized reduced dentition characterized by reduction of the stylar cusps, protocone and talonid, resulting in an incipiently zalambdodont morphology that emphasizes the shearing crests. In addition, only two upper premolars are present, and we assume that it is P3 that has been suppressed, as has occurred multiple times within Dasyuridae. Maximum parsimony and undated Bayesian analyses of a 174 morphological character matrix intended to resolve relationships within Dasyuromorphia, with a molecular scaffold enforced, suggest that <i>Urrayira</i> is a dasyurid. In the maximum parsimony analysis, <i>Urrayira</i> is sister to <i>Planigale gilesi</i> (which also lacks P3), whereas in the undated Bayesian analysis, <i>Urrayira</i> resolves as part of a trichotomy at the base of Dasyuridae, together with Sminthopsinae and Dasyurinae; however, support values are generally low throughout the tree. While the majority of rainforest-adapted taxa in the Mount Etna sites became either extinct or were locally extirpated at, or soon after, 280 ka, there is no evidence that <i>U. whitei</i> gen. et sp. nov. even persisted until that time. <i>Urrayira whitei</i> was likely a rainforest-specialist, thus may have been particularly vulnerable to incipient effects of the Mid-Brunhes climatic shift towards aridity that eventually drove the disappearance of the Mount Etna rainforest and its associated fauna. <i>Jonathan Cramb* [jonathan.cramb@qm.qld.gov.au], Queensland Museum, PO Box 3300, South Brisbane BC, Queensland 4101, Australia; Scott Hocknull [scott.hocknull@qm.qld.gov.au], Queensland Museum, PO Box 3300, South Brisbane BC, Queensland 4101, Australia; Robin M. D. Beck [r.m.d.beck@salford.ac.uk], School of Science, Engineering and Environment, University of Salford, Manchester M5 4WT, UK; Shimona Kealy [shimona.kealy@anu.edu.au], Archaeology and Natural History, College of Asia and the Pacific, The Australian National University, Canberra, ACT, 2601, Australia; Gilbert J. Price [g.price1@uq.edu.au], School of Earth and Environmental Sciences, The University of Queensland, Brisbane, Queensland 4072, Australia.</i>
DOI: 10.6084/m9.figshare.24790991
title: Taxonomic review of the genus <i>Dasycercus</i> (Dasyuromorphia: Dasyuridae) using modern and subfossil material; and the description of three new species

description: The genus <i>Dasycercus</i> (Dasyuridae: Dasyuromorphia) has a long and ongoing history of taxonomic uncertainty. Currently two species are recognized: <i>Dasycercus cristicauda</i> and <i>Dasycercus blythi</i>, with the previously named <i>Dasycercus hillieri</i> considered a junior synonym of <i>D. cristicauda</i>. This investigation integrates modern, historical and subfossil material from across Australia to provide the most comprehensive review of the genus to date. Cranial and dental morphological characters that enable phylogenetic and morphometric analysis of taxa are established. Linear discriminant analysis (LDA) and principal component analysis (PCA) of craniodental measurements, including from the type specimens of named taxa (<i>D. cristicauda</i>, <i>D. hillieri</i> and <i>D. blythi</i>), are used to assess the validity of each taxon. The results confirm the validity of <i>D. cristicauda</i> and <i>D. blythi</i> as species, but also reconfirm the validity of <i>D. hillieri</i>. As a result, much of the modern ‘<i>D. cristicauda</i>’ material is reassigned to <i>D. hillieri</i>. Three new taxa are proposed: <i>Dasycercus woolleyae</i> sp. nov., <i>Dasycercus archeri</i> sp. nov. and <i>Dasycercus marlowi</i> sp. nov. These six <i>Dasycercus</i> species are distributed across Australia’s arid zone and beyond. Based on prior investigations and the results of this taxonomic review, it is likely that only <i>D. hillieri</i> and <i>D. blythi</i> are extant. The identification of four likely extinct taxa marks the first recorded instance of modern extinction within the family Dasyuridae. <i>Jake Newman-Martin [</i>jake.newman-martin@student.curtin.edu.au<i>], School of Earth and Planetary Sciences, Curtin University Kent St, Bentley, WA, 6102 Australia;</i> <i>Kenny J. Travouillon [</i>Kenny.Travouillon@museum.wa.gov.au<i>], Western Australian Museum, Collections and Research, Locked Bag 49, Welshpool DC, WA, 6986 Australia;</i> <i>Natalie Warburton [</i>N.Warburton@murdoch.edu.au<i>], Harry Butler Institute, Murdoch University, 90 South Street, Murdoch Western Australia 6150 Australia;</i> <i>Milo Barham [</i>Milo.Barham@curtin.edu.au<i>], School of Earth and Planetary Sciences, Curtin University Kent St, Bentley, WA, 6102 Australia;</i> <i>Alison J. Blyth [</i>Alison.Blyth@curtin.edu.au<i>], School of Earth and Planetary Sciences, Curtin University Kent St, Bentley, WA, 6102 Australia.</i>
DOI: 10.6084/m9.figshare.24790991.v1
title: Taxonomic review of the genus <i>Dasycercus</i> (Dasyuromorphia: Dasyuridae) using modern and subfossil material; and the description of three new species

description: The genus <i>Dasycercus</i> (Dasyuridae: Dasyuromorphia) has a long and ongoing history of taxonomic uncertainty. Currently two species are recognized: <i>Dasycercus cristicauda</i> and <i>Dasycercus blythi</i>, with the previously named <i>Dasycercus hillieri</i> considered a junior synonym of <i>D. cristicauda</i>. This investigation integrates modern, historical and subfossil material from across Australia to provide the most comprehensive review of the genus to date. Cranial and dental morphological characters that enable phylogenetic and morphometric analysis of taxa are established. Linear discriminant analysis (LDA) and principal component analysis (PCA) of craniodental measurements, including from the type specimens of named taxa (<i>D. cristicauda</i>, <i>D. hillieri</i> and <i>D. blythi</i>), are used to assess the validity of each taxon. The results confirm the validity of <i>D. cristicauda</i> and <i>D. blythi</i> as species, but also reconfirm the validity of <i>D. hillieri</i>. As a result, much of the modern ‘<i>D. cristicauda</i>’ material is reassigned to <i>D. hillieri</i>. Three new taxa are proposed: <i>Dasycercus woolleyae</i> sp. nov., <i>Dasycercus archeri</i> sp. nov. and <i>Dasycercus marlowi</i> sp. nov. These six <i>Dasycercus</i> species are distributed across Australia’s arid zone and beyond. Based on prior investigations and the results of this taxonomic review, it is likely that only <i>D. hillieri</i> and <i>D. blythi</i> are extant. The identification of four likely extinct taxa marks the first recorded instance of modern extinction within the family Dasyuridae. <i>Jake Newman-Martin [</i>jake.newman-martin@student.curtin.edu.au<i>], School of Earth and Planetary Sciences, Curtin University Kent St, Bentley, WA, 6102 Australia;</i> <i>Kenny J. Travouillon [</i>Kenny.Travouillon@museum.wa.gov.au<i>], Western Australian Museum, Collections and Research, Locked Bag 49, Welshpool DC, WA, 6986 Australia;</i> <i>Natalie Warburton [</i>N.Warburton@murdoch.edu.au<i>], Harry Butler Institute, Murdoch University, 90 South Street, Murdoch Western Australia 6150 Australia;</i> <i>Milo Barham [</i>Milo.Barham@curtin.edu.au<i>], School of Earth and Planetary Sciences, Curtin University Kent St, Bentley, WA, 6102 Australia;</i> <i>Alison J. Blyth [</i>Alison.Blyth@curtin.edu.au<i>], School of Earth and Planetary Sciences, Curtin University Kent St, Bentley, WA, 6102 Australia.</i>
DOI: 10.6084/m9.figshare.22300878.v1
title: The evolutionary relationships of Diprotodontia and improving the accuracy of phylogenetic inference from morphological data

description: Large-scale molecular datasets have generally outperformed morphological data for inferring phylogeny, and sources of error in the latter are poorly understood. The morphologically and ecologically diverse marsupial order Diprotodontia (kangaroos and their relatives, the koala, wombats and possums) is well suited to considering these issues. Recent molecular results provide a phylogenetic benchmark for comparing previous molecular and morphological studies, encompassing all of the major phylogenetic data sources and methods that have been employed over the past 50 years. We show here that most molecular methodologies and ‘informal-comparative’ morphological studies have inferred diprotodontian relationships that closely resemble the recent molecular consensus. However, and perhaps surprisingly, algorithmic morphology, such as maximum parsimony analysis of morphological matrices, has inferred markedly inaccurate phylogenies, and is not improved by re-analysis with more recently developed, model-based (e.g., likelihood and Bayesian) methods. This is particularly concerning because algorithmic morphology is the primary approach for integrating fossils into the tree of life, and hence, for both calibrating molecular timescales and extending phylogenetic inferences of evolutionary processes beyond the snapshot provided by modern species. A novel simulation study presented here suggests that the inaccuracies in the marsupial algorithmic morphology studies partly stem from functional and body-size correlations among taxa that over-ride phylogenetic signals. We use the results to trial a reverse engineered phylogeny approach to correcting for such functional and developmental correlations among morphological data. In addition, we interrogated a newly published, densely taxon-sampled morphological matrix. Deeper level phylogeny reconstruction was improved by including fossils alongside extant taxa and counterintuitively, by increased effort to resolve relationships among shallow taxa. <i>Matthew J. Phillips [m9.phillips@qut.edu.au]; Mélina A. Celik [melina.celik@gmail.com] School of Biology and Environmental Science, Queensland University of Technology, 2 George Street, Brisbane, Qld, 4000, Australia; Robin M.D Beck [r.m.d.beck@salford.ac.uk] Ecosystems and Environment Research Centre, School of Science, Engineering and Environment, University of Salford, Manchester, UK</i>.
DOI: 10.6084/m9.figshare.22223604
title: First fossil record of <i>Perameles fasciata</i> from New South Wales and Queensland: reassessment of <i>Perameles sobbei</i>

description: The first fossil record of the Liverpool Plains striped bandicoot, <i>Perameles fasciata</i>, is presented. Since this species was split from its west coast counterpart, <i>Perameles bougainville</i>, no fossil record had been reported. <i>Perameles fasciata</i> is found in five fossil sites in Queensland and New South Wales, all Pleistocene in age. <i>Perameles sobbei</i>, described from the Darling Downs in Queensland, is found to be a junior synonym of <i>P. fasciata</i>, based on morphometrics and diagnostic morphological features. A morphological phylogeny finds that <i>P. fasciata</i> is more closely related to <i>Perameles nasuta</i>, <i>Perameles pallescens</i> and <i>Perameles gunnii</i> than <i>P. bougainville. Perameles fasciata</i> was likely more widespread in the Pleistocene, but by the Holocene had only survived on the Liverpool Plains in New South Wales until its extinction in the 1860s, probably as a result of land clearing and the introduction of foxes. While <i>P. bougainville</i> has been translocated in New South Wales, <i>P. gunnii</i>, which co-occurred with <i>P. fasciata</i>, is a better ecological analogue because of it is similar size, morphology and phylogenetic affinity. <i>Kenny J. Travouillon [</i>Kenny.Travouillon@museum.wa.gov.au<i>], Collections and Research Centre, Western Australian Museum, 49 Kew Street, Welshpool, WA 6106, Australia.</i>
DOI: 10.6084/m9.figshare.22300878
title: The evolutionary relationships of Diprotodontia and improving the accuracy of phylogenetic inference from morphological data

description: Large-scale molecular datasets have generally outperformed morphological data for inferring phylogeny, and sources of error in the latter are poorly understood. The morphologically and ecologically diverse marsupial order Diprotodontia (kangaroos and their relatives, the koala, wombats and possums) is well suited to considering these issues. Recent molecular results provide a phylogenetic benchmark for comparing previous molecular and morphological studies, encompassing all of the major phylogenetic data sources and methods that have been employed over the past 50 years. We show here that most molecular methodologies and ‘informal-comparative’ morphological studies have inferred diprotodontian relationships that closely resemble the recent molecular consensus. However, and perhaps surprisingly, algorithmic morphology, such as maximum parsimony analysis of morphological matrices, has inferred markedly inaccurate phylogenies, and is not improved by re-analysis with more recently developed, model-based (e.g., likelihood and Bayesian) methods. This is particularly concerning because algorithmic morphology is the primary approach for integrating fossils into the tree of life, and hence, for both calibrating molecular timescales and extending phylogenetic inferences of evolutionary processes beyond the snapshot provided by modern species. A novel simulation study presented here suggests that the inaccuracies in the marsupial algorithmic morphology studies partly stem from functional and body-size correlations among taxa that over-ride phylogenetic signals. We use the results to trial a reverse engineered phylogeny approach to correcting for such functional and developmental correlations among morphological data. In addition, we interrogated a newly published, densely taxon-sampled morphological matrix. Deeper level phylogeny reconstruction was improved by including fossils alongside extant taxa and counterintuitively, by increased effort to resolve relationships among shallow taxa. <i>Matthew J. Phillips [m9.phillips@qut.edu.au]; Mélina A. Celik [melina.celik@gmail.com] School of Biology and Environmental Science, Queensland University of Technology, 2 George Street, Brisbane, Qld, 4000, Australia; Robin M.D Beck [r.m.d.beck@salford.ac.uk] Ecosystems and Environment Research Centre, School of Science, Engineering and Environment, University of Salford, Manchester, UK</i>.