The Experts below are selected from a list of 189 Experts worldwide ranked by ideXlab platform
Michael Westerman - One of the best experts on this subject based on the ideXlab platform.
-
Molecular evidence for the pattern and timing of cladogenesis in dasyurid marsupials
Zoological Journal of the Linnean Society, 2020Co-Authors: Carey Krajewski, Stephen Wroe, Michael WestermanAbstract:Abstract Recent molecular studies have provided estimates of phylogeny for nearly all living and recently extinct species in the Order Dasyuromorphia, the dominant clade of insectivorous-carnivorous marsupials in Australasia. We review these studies along with morphology-based ones, and present an analysis of all cytochrome b , 12S rRNA, and protamine P1 gene sequences available. In light of these results, we provide a revised suprageneric classification and assess the implications of molecular and paleontological data for dasyurid cladogenesis. Molecular results divide extant dasyurids (Dasyuridae) into four major clades apart from the numbat (Myrmecobiidae) and thylacines (Thylacinidae). We recognize these clades as tribes Dasyurini ( Dasyurus, Phascolosorex , and allied genera) and Phascogalini ( Antechinus, Murexia, Phascogale ) in the Subfamily Dasyurinae, and tribes Sminthopsini ( Sminthopsis, Ningaui, Antechinomys ) and Planigalini ( Planigale ) in the Subfamily Sminthopsinae. Each tribe shows a basal radiation of lineages corresponding to genera or species groups. Our results concur with the most recent previous synthesis of dasyurid phylogeny in many respects, but subsumption of New Guinean «phascolosoricines» and «muricines» within Dasyurini and Phascogalini, respectively, constitute significant differences. In particular, the sister-pairing of «phascolosoricines» with a Dasyurus–Sarcophilus clade implied by molecular data is difficult to reconcile with anatomy. Divergence rates of mitochondrial sequences are calibrated approximately by comparing thylacine-to-dasyurid distances with the age of the oldest thylacinid ( Badjcinus , latest Oligocene). Estimated cladogenic dates suggest that extant subfamilies shared a common ancestor around 24 Mya and that major radiations began late in the mid-Miocene, consistent with the results of previous paleontological studies. The late-middle and late Miocene corresponds to an episode of faunal turnover in Australian marsupials (including the decline of thylacinid and bandicoot genera, as well as the rise of dasyurids) and to a time when uplift of the New Guinean highlands accelerated the transition from rainforest to drier habitats. Our findings are consistent with the hypothesis that continent-wide climate changes modulated macroevolution across these independent marsupial clades.
-
phylogenetic relationships within dasyurus Dasyuromorphia dasyuridae quoll systematics based on molecular evidence and male characteristics
Journal of Mammalogy, 2015Co-Authors: Patricia Ann Woolley, Carey Krajewski, Michael WestermanAbstract:Phylogenetic relationships among the 6 species of quolls (Dasyurus) are resolved using DNA sequences from 4 mitochondrial and 5 nuclear loci (approximately 15 kb) sampled from 1 to 29 individuals per species. Our estimate of quoll phylogeny concurs with previous DNA-based estimates in placing Dasyurus hallucatus as sister to the remaining species, and D. maculatus as sister to a clade containing D. viverrinus, D. albopunctatus, D. geoffroii + D. spartacus. We also provide the first formal description of penis anatomy in the northern quoll (D. hallucatus), documenting it as the only species of Dasyurus lacking an appendage to the penis. This appendage thus appears to constitute a morphological synapomorphy for the clade of 5 species that excludes D. hallucatus. The sequence from our single specimen of bronze quoll (D. spartacus) nested within a clade of 3 western quoll (D. geoffroii) sequences, suggesting that the species boundary between these groups (if it exists) is not yet reflected in reciprocal monop...
-
A Phylogeny and Timescale for Marsupial Evolution Based on Sequences for Five Nuclear Genes
Journal of Mammalian Evolution, 2008Co-Authors: Robert W. Meredith, Michael Westerman, Judd A. Case, Mark S. SpringerAbstract:Even though marsupials are taxonomically less diverse than placentals, they exhibit comparable morphological and ecological diversity. However, much of their fossil record is thought to be missing, particularly for the Australasian groups. The more than 330 living species of marsupials are grouped into three American (Didelphimorphia, Microbiotheria, and Paucituberculata) and four Australasian (Dasyuromorphia, Diprotodontia, Notoryctemorphia, and Peramelemorphia) orders. Interordinal relationships have been investigated using a wide range of methods that have often yielded contradictory results. Much of the controversy has focused on the placement of Dromiciops gliroides (Microbiotheria). Studies either support a sister-taxon relationship to a monophyletic Australasian clade or a nested position within the Australasian radiation. Familial relationships within the Diprotodontia have also proved difficult to resolve. Here, we examine higher-level marsupial relationships using a nuclear multigene molecular data set representing all living orders. Protein-coding portions of ApoB, BRCA1, IRBP, Rag1, and vWF were analyzed using maximum parsimony, maximum likelihood, and Bayesian methods. Two different Bayesian relaxed molecular clock methods were employed to construct a timescale for marsupial evolution and estimate the unrepresented basal branch length (UBBL). Maximum likelihood and Bayesian results suggest that the root of the marsupial tree is between Didelphimorphia and all other marsupials. All methods provide strong support for the monophyly of Australidelphia. Within Australidelphia, Dromiciops is the sister-taxon to a monophyletic Australasian clade. Within the Australasian clade, Diprotodontia is the sister taxon to a Notoryctemorphia + Dasyuromorphia + Peramelemorphia clade. Within the Diprotodontia, Vombatiformes (wombat + koala) is the sister taxon to a paraphyletic possum group (Phalangeriformes) with kangaroos nested inside. Molecular dating analyses suggest Late Cretaceous/Paleocene dates for all interordinal divergences. All intraordinal divergences were placed in the mid to late Cenozoic except for the deepest splits within the Diprotodontia. Our UBBL estimates of the marsupial fossil record indicate that the South American record is approximately as complete as the Australasian record.
-
interspecific affinities within the genus sminthopsis Dasyuromorphia dasyuridae based on morphology of the penis congruence with other anatomical and molecular data
Journal of Mammalogy, 2007Co-Authors: P A Woolley, Carey Krajewski, Michael WestermanAbstract:Among the 19 currently recognized species of Sminthopsis, differences in the morphology of the free portion of the penis can be seen in the tip, which may be bifid, blunt, knoblike, or have a terminal median process, and which may have a subterminal skin fold; and the urethral opening and terminal passage (urethral grooves or urethral chamber). The urethra may open dorsally or ventrally, and the urethral grooves may lie mesially or ventrally on the bifid portion of the tip. Ten forms can be recognized and interspecific affinities based on penis morphology have been examined for congruence with species groupings based on other independent character sets including external, cranial, and dental characters and molecular data. Penis forms showed the greatest congruence with phylogenetic groups delineated by molecular data.
-
Nuclear gene sequences provide evidence for the monophyly of australidelphian marsupials
Molecular Phylogenetics and Evolution, 2003Co-Authors: Heather Amrine-madsen, Carey Krajewski, Michael Westerman, Mark Scally, Michael J. Stanhope, Mark S. SpringerAbstract:Abstract Relationships among the seven extant orders of marsupials remain poorly understood. Most classifications recognize a fundamental split between Ameridelphia, which contains the American orders Didelphimorphia and Paucituberculata, and Australidelphia, which contains four Australasian orders (Dasyuromorphia, Diprotodontia, Notoryctemorphia, and Peramelina) and the South American order Microbiotheria, represented by Dromiciops gliroides. Ameridelphia and Australidelphia are each supported by key morphological characters with dichotomous character states. To date, molecular studies indexing all marsupial orders have reported inconclusive results. However, several studies have suggested that Dromiciops is nested within Australidelphia. This result has important implications for understanding the biogeographic history of living marsupials. To address questions in higher-level marsupial systematics, we sequenced portions of five nuclear genes (Apolipoprotein B gene; Breast and Ovarian cancer susceptibility gene 1; Recombination activating gene 1; Interphotoreceptor retinoid binding protein gene; and von Willebrand factor gene) for representatives of all orders of marsupials, as well as placental outgroups. The resulting 6.4 kb concatenation was analyzed using maximum parsimony, distance methods, maximum likelihood, and Bayesian methods. Kishino and Hasegawa (1989) tests were used to examine a priori hypotheses. All analyses provided robust support for the monophyly of Australidelphia (bootstrap support=99–100%; posterior probability=1.00). Ameridelphia received much lower support, although this clade was not rejected in statistical tests. Within Diprotodontia, both Vombatiformes and Phalangeriformes were supported at the 100% bootstrap level and with posterior probabilities of 1.00.
Robin M D Beck - One of the best experts on this subject based on the ideXlab platform.
-
total evidence phylogeny and evolutionary timescale for australian faunivorous marsupials Dasyuromorphia
BMC Evolutionary Biology, 2017Co-Authors: Shimona Kealy, Robin M D BeckAbstract:The order Dasyuromorphia is a diverse radiation of faunivorous marsupials, comprising >80 modern species in Australia and New Guinea. It includes dasyurids, the numbat (the myrmecobiid Myrmecobius fasciatus) and the recently extinct thylacine (the thylacinid Thylacinus cyncocephalus). There is also a diverse fossil record of Dasyuromorphians and “Dasyuromorphian-like” taxa known from Australia. We present the first total evidence phylogenetic analyses of the order, based on combined morphological and molecular data (including a novel set of 115 postcranial characters), to resolve relationships and calculate divergence dates. We use this information to analyse the diversification dynamics of modern Dasyuromorphians. Our morphology-only analyses are poorly resolved, but our molecular and total evidence analyses confidently resolve most relationships within the order, and are strongly congruent with recent molecular studies. Thylacinidae is the first family to diverge within the order, and there is strong support for four tribes within Dasyuridae (Dasyurini, Phascogalini, Planigalini and Sminthopsini). Among fossil taxa, Ankotarinja and Keeuna do not appear to be members of Dasyuromorphia, whilst Barinya and Mutpuracinus are of uncertain relationships within the order. Divergence dates calculated using total evidence tip-and-node dating are younger than both molecular node-dating and total evidence tip-dating, but appear more congruent with the fossil record and are relatively insensitive to calibration strategy. The tip-and-node divergence dates indicate that Dasyurini, Phascogalini and Sminthopsini began to radiate almost simultaneously during the middle-to-late Miocene (11.5–13.1 MYA; composite 95% HPD: 9.5–15.9 MYA); the median estimates for these divergences are shortly after a drop in global temperatures (the middle Miocene Climatic Transition), and coincide with a faunal turnover event in the mammalian fossil record of Australia. Planigalini radiated much later, during the latest Miocene to earliest Pliocene (6.5 MYA; composite 95% HPD: 4.4–8.9 MYA); the median estimates for these divergences coincide with an increase in grass pollen in the Australian palynological record that suggests the development of more open habitats, which are preferred by modern planigale species. Our results provide a phylogenetic and temporal framework for interpreting the evolution of modern and fossil Dasyuromorphians, but future progress will require a much improved fossil record.
-
additional file 1 table s1 of total evidence phylogeny and evolutionary timescale for australian faunivorous marsupials Dasyuromorphia
2017Co-Authors: Shimona Kealy, Robin M D BeckAbstract:Table of taxa, indicating whether or not they have been scored for morphological characters, percentage completeness (if scored for morphological characters) and Genbank accession numbers for molecular sequences. (XLSX 18 kb)
-
The Osteology and Systematics of the Enigmatic Australian Oligo-Miocene Metatherian Yalkaparidon (Yalkaparidontidae; Yalkaparidontia; ?Australidelphia; Marsupialia)
Journal of Mammalian Evolution, 2014Co-Authors: Robin M D Beck, Henk Godthelp, Kenny J. Travouillon, Ken P. Aplin, Michael ArcherAbstract:We provide the first detailed description of the osteology of the enigmatic Oligo-Miocene Australian metatherian Yalkaparidon . This taxon exhibits a number of unusual craniodental apomorphies but appears to be plesiomorphic within Metatheria in retaining four molars, rather than three as previously reported. We demonstrate that the only known skull of Yalkaparidon almost certainly represents a single individual. We also tentatively refer a number of isolated tarsals to the genus. Maximum parsimony analyses of a 258 character morphological matrix (with information from the tarsals described here either included or excluded) place Yalkaparidon within the superordinal clade Australidelphia, but Bayesian analyses of the same matrix are less well resolved, placing Yalkaparidon within Marsupialia but without unequivocally supporting australidelphian affinities. Bayesian analyses of a total evidence matrix that combines the morphological data with 9 kb of sequence data from five nuclear protein-coding genes (APOB, BRCA1, IRBP, RAG1 and VWF), 78 indels, and 53 retroposon insertion characters are similarly poorly resolved and do not clarify the supraordinal relationships of Yalkaparidon beyond suggesting that it is probably a member of Marsupialia. However, if the tarsal remains are correctly attributed to Yalkaparidon , then membership of Australidelphia seems likely, as these specimens exhibit characteristic australidelphian apomorphies. We conclude that the ordinal status of Yalkaparidon remains justified based on current evidence, and we present a revised diagnosis for Yalkaparidontia. We maintain the two currently recognized species, Y. coheni and Y. jonesi , but present revised specific diagnoses. We suggest a revised phylogenetic definition for Marsupialia, and provide phylogenetic definitions for Eomarsupialia (the clade comprising all extant Australian marsupial orders) and for the clade comprising Dasyuromorphia, Peramelemorphia, and Notoryctemorphia to the exclusion of Diprotodontia; we propose the name Agreodontia for the latter clade.
-
A Peculiar Faunivorous Metatherian from the Early Eocene of Australia
Acta Palaeontologica Polonica, 2013Co-Authors: Robin M D BeckAbstract:I describe Archaeonothos henkgodthelpi gen. et. sp. nov., a small (estimated body mass ∼40–80 g) tribosphenic metatherian from the early Eocene Tingamarra Fauna of southeastern Queensland, Australia. This taxon, known only from a single isolated upper molar (M2 or M3) is characterised by a very distinctive combination of dental features that, collectively, probably represent faunivorous adaptations. These include: a straight, elevated centrocrista; a metacone considerably taller than the paracone; a wide stylar shelf (∼50% of the total labiolingual width of the tooth); reduced stylar cusps; a long postmetacrista; a small and anteroposteriorly narrow protocone; an unbasined trigon; and the absence of conules. Some of these features are seen in Dasyuromorphians, but detailed comparisons reveal key differences between A. henkgodthelpi and all known members of this clade. A. henkgodthelpi also predates recent molecular estimates for the divergence of crown-group Dasyuromorphia. Similar dental features are see...
-
A Dated Phylogeny of Marsupials Using a Molecular Supermatrix and Multiple Fossil Constraints
Journal of Mammalogy, 2008Co-Authors: Robin M D BeckAbstract:Phylogenetic relationships within marsupials were investigated based on a 20.1-kilobase molecular supermatrix comprising 7 nuclear and 15 mitochondrial genes analyzed using both maximum likelihood and Bayesian approaches and 3 different partitioning strategies. The study revealed that base composition bias in the 3rd codon positions of mitochondrial genes misled even the partitioned maximum-likelihood analyses, whereas Bayesian analyses were less affected. After correcting for base composition bias, monophyly of the currently recognized marsupial orders, of Australidelphia, and of a clade comprising Dasyuromorphia, Notoryctes ,a nd Peramelemorphia, were supported strongly by both Bayesian posterior probabilities and maximum-likelihood bootstrap values. Monophyly of the Australasian marsupials, of Notoryctes þ Dasyuromorphia, and of Caenolestes þ Australidelphia were less well supported. Within Diprotodontia, Burramyidae þ Phalangeridae received relatively strong support. Divergence dates calculated using a Bayesian relaxed molecular clock and multiple age constraints suggested at least 3 independent dispersals of marsupials from North to South America during the Late Cretaceous or early Paleocene. Within the Australasian clade, the macropodine radiation, the divergence of phascogaline and dasyurine dasyurids, and the divergence of perameline and peroryctine peramelemorphians all coincided with periods of significant environmental change during the Miocene. An analysis of ‘‘unrepresented basal branch lengths’’ suggests that the fossil record is particularly poor for didelphids and most groups within the Australasian radiation.
Shimona Kealy - One of the best experts on this subject based on the ideXlab platform.
-
Total evidence phylogeny and evolutionary timescale for Australian faunivorous marsupials (Dasyuromorphia)
BMC Evolutionary Biology, 2017Co-Authors: Shimona Kealy, Robin BeckAbstract:Background The order Dasyuromorphia is a diverse radiation of faunivorous marsupials, comprising >80 modern species in Australia and New Guinea. It includes dasyurids, the numbat (the myrmecobiid Myrmecobius fasciatus ) and the recently extinct thylacine (the thylacinid Thylacinus cyncocephalus ). There is also a diverse fossil record of Dasyuromorphians and “Dasyuromorphian-like” taxa known from Australia. We present the first total evidence phylogenetic analyses of the order, based on combined morphological and molecular data (including a novel set of 115 postcranial characters), to resolve relationships and calculate divergence dates. We use this information to analyse the diversification dynamics of modern Dasyuromorphians. Results Our morphology-only analyses are poorly resolved, but our molecular and total evidence analyses confidently resolve most relationships within the order, and are strongly congruent with recent molecular studies. Thylacinidae is the first family to diverge within the order, and there is strong support for four tribes within Dasyuridae (Dasyurini, Phascogalini, Planigalini and Sminthopsini). Among fossil taxa, Ankotarinja and Keeuna do not appear to be members of Dasyuromorphia, whilst Barinya and Mutpuracinus are of uncertain relationships within the order. Divergence dates calculated using total evidence tip-and-node dating are younger than both molecular node-dating and total evidence tip-dating, but appear more congruent with the fossil record and are relatively insensitive to calibration strategy. The tip-and-node divergence dates indicate that Dasyurini, Phascogalini and Sminthopsini began to radiate almost simultaneously during the middle-to-late Miocene (11.5–13.1 MYA; composite 95% HPD: 9.5–15.9 MYA); the median estimates for these divergences are shortly after a drop in global temperatures (the middle Miocene Climatic Transition), and coincide with a faunal turnover event in the mammalian fossil record of Australia. Planigalini radiated much later, during the latest Miocene to earliest Pliocene (6.5 MYA; composite 95% HPD: 4.4–8.9 MYA); the median estimates for these divergences coincide with an increase in grass pollen in the Australian palynological record that suggests the development of more open habitats, which are preferred by modern planigale species. Conclusions Our results provide a phylogenetic and temporal framework for interpreting the evolution of modern and fossil Dasyuromorphians, but future progress will require a much improved fossil record.
-
total evidence phylogeny and evolutionary timescale for australian faunivorous marsupials Dasyuromorphia
BMC Evolutionary Biology, 2017Co-Authors: Shimona Kealy, Robin M D BeckAbstract:The order Dasyuromorphia is a diverse radiation of faunivorous marsupials, comprising >80 modern species in Australia and New Guinea. It includes dasyurids, the numbat (the myrmecobiid Myrmecobius fasciatus) and the recently extinct thylacine (the thylacinid Thylacinus cyncocephalus). There is also a diverse fossil record of Dasyuromorphians and “Dasyuromorphian-like” taxa known from Australia. We present the first total evidence phylogenetic analyses of the order, based on combined morphological and molecular data (including a novel set of 115 postcranial characters), to resolve relationships and calculate divergence dates. We use this information to analyse the diversification dynamics of modern Dasyuromorphians. Our morphology-only analyses are poorly resolved, but our molecular and total evidence analyses confidently resolve most relationships within the order, and are strongly congruent with recent molecular studies. Thylacinidae is the first family to diverge within the order, and there is strong support for four tribes within Dasyuridae (Dasyurini, Phascogalini, Planigalini and Sminthopsini). Among fossil taxa, Ankotarinja and Keeuna do not appear to be members of Dasyuromorphia, whilst Barinya and Mutpuracinus are of uncertain relationships within the order. Divergence dates calculated using total evidence tip-and-node dating are younger than both molecular node-dating and total evidence tip-dating, but appear more congruent with the fossil record and are relatively insensitive to calibration strategy. The tip-and-node divergence dates indicate that Dasyurini, Phascogalini and Sminthopsini began to radiate almost simultaneously during the middle-to-late Miocene (11.5–13.1 MYA; composite 95% HPD: 9.5–15.9 MYA); the median estimates for these divergences are shortly after a drop in global temperatures (the middle Miocene Climatic Transition), and coincide with a faunal turnover event in the mammalian fossil record of Australia. Planigalini radiated much later, during the latest Miocene to earliest Pliocene (6.5 MYA; composite 95% HPD: 4.4–8.9 MYA); the median estimates for these divergences coincide with an increase in grass pollen in the Australian palynological record that suggests the development of more open habitats, which are preferred by modern planigale species. Our results provide a phylogenetic and temporal framework for interpreting the evolution of modern and fossil Dasyuromorphians, but future progress will require a much improved fossil record.
-
additional file 1 table s1 of total evidence phylogeny and evolutionary timescale for australian faunivorous marsupials Dasyuromorphia
2017Co-Authors: Shimona Kealy, Robin M D BeckAbstract:Table of taxa, indicating whether or not they have been scored for morphological characters, percentage completeness (if scored for morphological characters) and Genbank accession numbers for molecular sequences. (XLSX 18 kb)
Björn M Hallström - One of the best experts on this subject based on the ideXlab platform.
-
Evolutionary Histories of Transposable Elements in the Genome of the Largest Living Marsupial Carnivore, the Tasmanian Devil
Molecular Biology and Evolution, 2015Co-Authors: Susanne Gallus, Axel Janke, Björn M Hallström, Vikas Kumar, William G. Dodt, Gerald G. Schumann, Maria A NilssonAbstract:The largest living carnivorous marsupial, the Tasmanian devil (Sarcophilus harrisii), is the sole survivor of a lineage originating about 12 Ma. We set out to investigate the spectrum of transposable elements found in the Tasmanian devil genome, the first high-coverage genome of an Australian marsupial. Marsupial genomes have been shown to have the highest amount of transposable elements among vertebrates. We analyzed the horizontally transmitted DNA transposons OC1 and hAT-1_MEu in the Tasmanian devil genome. OC1 is present in all carnivorous marsupials, while having a very limited distribution among the remaining Australian marsupial orders. In contrast, hAT-1_MEu is present in all Australian marsupial orders, and has so far only been identified in a few placental mammals. We screened 158 introns for phylogenetically informative retrotransposons in the order Dasyuromorphia, and found that the youngest SINE (Short INterspersed Element), WSINE1, is no longer active in the subfamily Dasyuridae. The lack of detectable WSINE1 activity in this group may be due to a retrotransposon inactivation event approximately 30 Ma. We found that the Tasmanian devil genome contains a relatively low number of continuous full-length LINE-1 (Long INterspersed Element 1, L1) retrotransposons compared with the opossum genome. Furthermore, all L1 elements in the Tasmanian devil appeared to be nonfunctional. Hidden Markov Model approaches suggested that other potential sources of functional reverse transcriptase are absent from the genome. We discuss the issues associated with assembling long, highly similar L1 copies from short read Illumina data and describe how assembly artifacts can potentially lead to erroneous conclusions.
-
Expansion of CORE-SINEs in the genome of the Tasmanian devil
BMC Genomics, 2012Co-Authors: Maria A Nilsson, Axel Janke, Elizabeth P Murchison, Zemin Ning, Björn M HallströmAbstract:Background The genome of the carnivorous marsupial, the Tasmanian devil ( Sarcophilus harrisii , Order: Dasyuromorphia), was sequenced in the hopes of finding a cure for or gaining a better understanding of the contagious devil facial tumor disease that is threatening the species’ survival. To better understand the Tasmanian devil genome, we screened it for transposable elements and investigated the dynamics of short interspersed e lement (SINE) retroposons. Results The temporal history of Tasmanian devil SINEs, elucidated using a transposition in transposition analysis, indicates that WSINE1, a CORE-SINE present in around 200,000 copies, is the most recently active element. Moreover, we discovered a new subtype of WSINE1 (WSINE1b) that comprises at least 90% of all Tasmanian devil WSINE1s. The frequencies of WSINE1 subtypes differ in the genomes of two of the other Australian marsupial orders. A co-segregation analysis indicated that at least 66 subfamilies of WSINE1 evolved during the evolution of Dasyuromorphia. Using a substitution rate derived from WSINE1 insertions, the ages of the subfamilies were estimated and correlated with a newly established phylogeny of Dasyuromorphia. Phylogenetic analyses and divergence time estimates of mitochondrial genome data indicate a rapid radiation of the Tasmanian devil and the closest relative the quolls ( Dasyurus ) around 14 million years ago. Conclusions The radiation and abundance of CORE-SINEs in marsupial genomes indicates that they may be a major player in the evolution of marsupials. It is evident that the early phases of evolution of the carnivorous marsupial order Dasyuromorphia was characterized by a burst of SINE activity. A correlation between a speciation event and a major burst of retroposon activity is for the first time shown in a marsupial genome.
-
Expansion of CORE-SINEs in the genome of the Tasmanian devil
BMC Genomics, 2012Co-Authors: Maria A Nilsson, Axel Janke, Elizabeth P Murchison, Zemin Ning, Björn M HallströmAbstract:The genome of the carnivorous marsupial, the Tasmanian devil (Sarcophilus harrisii, Order: Dasyuromorphia), was sequenced in the hopes of finding a cure for or gaining a better understanding of the contagious devil facial tumor disease that is threatening the species’ survival. To better understand the Tasmanian devil genome, we screened it for transposable elements and investigated the dynamics of short interspersed element (SINE) retroposons.
Carey Krajewski - One of the best experts on this subject based on the ideXlab platform.
-
Molecular evidence for the pattern and timing of cladogenesis in dasyurid marsupials
Zoological Journal of the Linnean Society, 2020Co-Authors: Carey Krajewski, Stephen Wroe, Michael WestermanAbstract:Abstract Recent molecular studies have provided estimates of phylogeny for nearly all living and recently extinct species in the Order Dasyuromorphia, the dominant clade of insectivorous-carnivorous marsupials in Australasia. We review these studies along with morphology-based ones, and present an analysis of all cytochrome b , 12S rRNA, and protamine P1 gene sequences available. In light of these results, we provide a revised suprageneric classification and assess the implications of molecular and paleontological data for dasyurid cladogenesis. Molecular results divide extant dasyurids (Dasyuridae) into four major clades apart from the numbat (Myrmecobiidae) and thylacines (Thylacinidae). We recognize these clades as tribes Dasyurini ( Dasyurus, Phascolosorex , and allied genera) and Phascogalini ( Antechinus, Murexia, Phascogale ) in the Subfamily Dasyurinae, and tribes Sminthopsini ( Sminthopsis, Ningaui, Antechinomys ) and Planigalini ( Planigale ) in the Subfamily Sminthopsinae. Each tribe shows a basal radiation of lineages corresponding to genera or species groups. Our results concur with the most recent previous synthesis of dasyurid phylogeny in many respects, but subsumption of New Guinean «phascolosoricines» and «muricines» within Dasyurini and Phascogalini, respectively, constitute significant differences. In particular, the sister-pairing of «phascolosoricines» with a Dasyurus–Sarcophilus clade implied by molecular data is difficult to reconcile with anatomy. Divergence rates of mitochondrial sequences are calibrated approximately by comparing thylacine-to-dasyurid distances with the age of the oldest thylacinid ( Badjcinus , latest Oligocene). Estimated cladogenic dates suggest that extant subfamilies shared a common ancestor around 24 Mya and that major radiations began late in the mid-Miocene, consistent with the results of previous paleontological studies. The late-middle and late Miocene corresponds to an episode of faunal turnover in Australian marsupials (including the decline of thylacinid and bandicoot genera, as well as the rise of dasyurids) and to a time when uplift of the New Guinean highlands accelerated the transition from rainforest to drier habitats. Our findings are consistent with the hypothesis that continent-wide climate changes modulated macroevolution across these independent marsupial clades.
-
phylogenetic relationships within dasyurus Dasyuromorphia dasyuridae quoll systematics based on molecular evidence and male characteristics
Journal of Mammalogy, 2015Co-Authors: Patricia Ann Woolley, Carey Krajewski, Michael WestermanAbstract:Phylogenetic relationships among the 6 species of quolls (Dasyurus) are resolved using DNA sequences from 4 mitochondrial and 5 nuclear loci (approximately 15 kb) sampled from 1 to 29 individuals per species. Our estimate of quoll phylogeny concurs with previous DNA-based estimates in placing Dasyurus hallucatus as sister to the remaining species, and D. maculatus as sister to a clade containing D. viverrinus, D. albopunctatus, D. geoffroii + D. spartacus. We also provide the first formal description of penis anatomy in the northern quoll (D. hallucatus), documenting it as the only species of Dasyurus lacking an appendage to the penis. This appendage thus appears to constitute a morphological synapomorphy for the clade of 5 species that excludes D. hallucatus. The sequence from our single specimen of bronze quoll (D. spartacus) nested within a clade of 3 western quoll (D. geoffroii) sequences, suggesting that the species boundary between these groups (if it exists) is not yet reflected in reciprocal monop...
-
interspecific affinities within the genus sminthopsis Dasyuromorphia dasyuridae based on morphology of the penis congruence with other anatomical and molecular data
Journal of Mammalogy, 2007Co-Authors: P A Woolley, Carey Krajewski, Michael WestermanAbstract:Among the 19 currently recognized species of Sminthopsis, differences in the morphology of the free portion of the penis can be seen in the tip, which may be bifid, blunt, knoblike, or have a terminal median process, and which may have a subterminal skin fold; and the urethral opening and terminal passage (urethral grooves or urethral chamber). The urethra may open dorsally or ventrally, and the urethral grooves may lie mesially or ventrally on the bifid portion of the tip. Ten forms can be recognized and interspecific affinities based on penis morphology have been examined for congruence with species groupings based on other independent character sets including external, cranial, and dental characters and molecular data. Penis forms showed the greatest congruence with phylogenetic groups delineated by molecular data.
-
Nuclear gene sequences provide evidence for the monophyly of australidelphian marsupials
Molecular Phylogenetics and Evolution, 2003Co-Authors: Heather Amrine-madsen, Carey Krajewski, Michael Westerman, Mark Scally, Michael J. Stanhope, Mark S. SpringerAbstract:Abstract Relationships among the seven extant orders of marsupials remain poorly understood. Most classifications recognize a fundamental split between Ameridelphia, which contains the American orders Didelphimorphia and Paucituberculata, and Australidelphia, which contains four Australasian orders (Dasyuromorphia, Diprotodontia, Notoryctemorphia, and Peramelina) and the South American order Microbiotheria, represented by Dromiciops gliroides. Ameridelphia and Australidelphia are each supported by key morphological characters with dichotomous character states. To date, molecular studies indexing all marsupial orders have reported inconclusive results. However, several studies have suggested that Dromiciops is nested within Australidelphia. This result has important implications for understanding the biogeographic history of living marsupials. To address questions in higher-level marsupial systematics, we sequenced portions of five nuclear genes (Apolipoprotein B gene; Breast and Ovarian cancer susceptibility gene 1; Recombination activating gene 1; Interphotoreceptor retinoid binding protein gene; and von Willebrand factor gene) for representatives of all orders of marsupials, as well as placental outgroups. The resulting 6.4 kb concatenation was analyzed using maximum parsimony, distance methods, maximum likelihood, and Bayesian methods. Kishino and Hasegawa (1989) tests were used to examine a priori hypotheses. All analyses provided robust support for the monophyly of Australidelphia (bootstrap support=99–100%; posterior probability=1.00). Ameridelphia received much lower support, although this clade was not rejected in statistical tests. Within Diprotodontia, both Vombatiformes and Phalangeriformes were supported at the 100% bootstrap level and with posterior probabilities of 1.00.
-
DNA Sequence Analysis of Familial Relationships Among Dasyuromorphian Marsupials
Journal of Mammalian Evolution, 2000Co-Authors: Carey Krajewski, Mark J. Blacket, Michael WestermanAbstract:Although modern morphological and molecular analyses support the monophyly of the Australasian marsupial order Dasyuromorphia, there is much less certainty about relationships among its constituent families (Dasyuridae, Myrmecobiidae, and Thylacinidae). While most authors regard Dasyuridae as monophyletic, a few have suggested that thylacines, numbats, or both have their closest relatives among dasyurids. Recent morphocladistic studies have identified several basicranial characters as putative synapomorphies of dasyurids, but no features that clearly implicate thylacinids, myrmecobiids, or both, as the sister group of Dasyuridae. Only two previous DNA studies have included both thylacine and numbat sequences along with dasyurids, and neither provided strong resolution of interfamilial relationships. In this study, we report a more thorough analytical treatment of complete cytochrome b , 12S rRNA, and protamine P1 gene sequences from Dasyuromorphians than has heretofore been attempted. Our results concur with previous morphological studies in showing that Dasyuridae is monophyletic and with immunological findings that thylacinids and dasyurids are sister groups, apart from myrmecobiids. However, the level of support for nodes is highly dependent on the method of phylogenetic analysis employed. Our results also suggest that partitioning of sequence data sets to account for substitutional heterogeneity within and among genes does not necessarily lead to a major reduction in the precision of estimated phylogenies.
