Is south-western Western Australia a centre of origin for eastern Australian taxa or is the centre an artefact of a method of analysis? A comment on Hakea and its supposed divergence over the past 12 million years

Lamont et al. (2016) concluded that the Australian sclerophyllous genus Hakea (Proteaceae) arose 18million years ago in the South West of Western Australia (SWA) and dispersed 18 times to eastern (EA) and central Australia (CA) only 12million years ago (mid-Miocene). Their explanation of the biogeographic history of Hakea was based on the following: accepting a fully resolved molecular phylogenetic tree, although ~40% of nodes had posterior probability values below 0.95; using all nodes including geographically paralogous nodes to determine ancestral area probabilities; and applying a strict clock to estimate clade divergence times. Our re-analyses of the same dataset using a relaxed clock model pushes the age of Hakea to 32.4 (21.8–43.7) million years ago relative to its nearest outgroups, and the age of the divergence of two major clades (A and B) to 24.7 (17.2–33.7) million years ago. Calibration based on a new finding of Late Cretaceous fossil Banksia pushes these dates to 48.0 (24.3–75.2) million years ago and 36.6 (18.5–55.4) million years ago respectively. We confirm that each of the two main clades includes lineages in SWA, CA and EA. At the basal node of Clade A, two eastern Australian species form the sister group to three SWA scrub–heath–Eremaean species. These two groups together are sister to a large, mostly unresolved clade of SWA, CA and EA taxa. Similarly, at the base of Clade B is a polytomy of lineages from the SWA, CA and EA, with no resolution of area relationships. There is no evidence of a centre of origin and diversification of the genus is older than the mid-Miocene, being at least Oligocene, and probably older, although calibration points for molecular dating are too far removed from the ingroup to provide any great confidence in the methodology. Consideration should be given to the possibility of vicariance of multiple, widespread ancestral lineages as an explanation for lineages now disjunct between EA and SWA.

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The double odyssey of Madagascan polystome flatworms leads to new insights on the origins of their amphibian hosts

Proceedings of The Royal Society B Biological Sciences ◽

10.1098/rspb.2008.1530 ◽

2009 ◽

Vol 276 (1662) ◽

pp. 1575-1583 ◽

Cited By ~ 13

Author(s):

Olivier Verneau ◽

Louis H Du Preez ◽

Véronique Laurent ◽

Liliane Raharivololoniaina ◽

Frank Glaw ◽

...

Keyword(s):

Molecular Dating ◽

Phylogenetic Position ◽

Late Mesozoic ◽

Biogeographic History ◽

On This Island ◽

The Family ◽

Molecular Phylogenetic ◽

History Of ◽

Recent Origin ◽

High Species Richness

Polystomatid flatworms are parasites of high host specificity, which mainly infect amphibian hosts. Only one polystome species has so far been recorded from Madagascar despite the high species richness and endemicity of amphibians on this island. Out of the 86 screened Malagasy frog species, we recovered polystomes from 25 in the families Ptychadenidae and Mantellidae. Molecular phylogenetic analysis uncovered an unexpected diversity of polystome species belonging to two separate clades: one forming a lineage within the genus Metapolystoma , with one species in Ptychadena and several species in the mantellid host genera Aglyptodactylus and Boophis ; and the second corresponding to an undescribed genus that was found in the species of the subfamily Mantellinae in the family Mantellidae. The phylogenetic position of the undescribed genus along with molecular dating suggests that it may have colonized Madagascar in the Late Mesozoic or Early Cainozoic. By contrast, the more recent origin of Metapolystoma in Madagascar at ca 14–2 Myr ago strongly suggests that the ancestors of Ptychadena mascareniensis colonized Madagascar naturally by overseas dispersal, carrying their Metapolystoma parasites. Our findings provide a striking example of how parasite data can supply novel insights into the biogeographic history of their hosts.

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Taxonomic review of Australian Mecyclothorax Sharp (Coleoptera, Carabidae, Moriomorphini) with special emphasis on the M. lophoides (Chaudoir) species complex

Deutsche Entomologische Zeitschrift ◽

10.3897/dez.65.27424 ◽

2018 ◽

Vol 65 (2) ◽

pp. 177-224 ◽

Cited By ~ 2

Author(s):

James K. Liebherr

Keyword(s):

Western Australia ◽

Species Complex ◽

Sister Group ◽

Late Eocene ◽

Sister Species ◽

Sister Group Relationship ◽

Special Focus ◽

Species Pair ◽

Spermathecal Duct ◽

Biogeographic History

The Australian fauna ofMecyclothoraxSharp (Coleoptera: Carabidae: Moriomorphini) is reviewed, with special focus on species assigned to the monophyletic subgenus Eucyclothorax Liebherr:M.isolatus,sp. n.from Western Australia,M.mooreiBaehr,M.punctatus(Sloane),M.curtus(Sloane),M.blackburni(Sloane);M.eyrensis(Blackburn);M.peryphoides(Blackburn);M.darlingtoni,sp. n.from Queensland;M.jameswalkeri,sp. n.from Western Australia;M.lophoides(Chaudoir); andM.cordicollis(Sloane). The last six species listed above–theM.lophoidesspecies complex–have been the source of long-term confusion for taxonomists, with male genitalic characters providing trouble-free species circumscription. One new subspecies,M.lewisensisestriatus,subsp. n.from Queensland is added to the seven previously described taxa of the monophyletic subgenus Qecyclothorax Liebherr. The balance of the fauna consists of four species in the subgenus Mecyclothorax:1and2, the sister-species pairM.lateralis(Castelnau) andM.minutus(Castelnau);3,M.ambiguus(Erichson); and4,M.punctipennis(MacLeay).Mecyclothoraxfortis(Blackburn),syn. n., is newly synonymized withM.minutus.MecyclothoraxovalisSloane is recombined asNeonomiusovalis(Sloane),comb. n., and a neotype is designated to replace the destroyed holotype. Phylogenetic relationships for the AustralianMecyclothoraxare proposed based on information from 68 terminal taxa and 139 morphological characters. The biogeographic history of AustralianMecyclothoraxis deduced based the sister-group relationship betweenMecyclothoraxand theAmblytelus-related genera, with both groups hypothesized to have originated during the late Eocene. Diversification withinMecyclothoraxhas occurred since then in montane rainforests of tropical Queensland, temperate forest biomes of the southwest and southeast, and in grasslands and riparian habitats adjacent and inland from those forests. Several species presently occupy interior desert regions, though no sister species mutually occupy such climatically harsh habitats. TheM.lophoidesspecies complex exhibits profound male genitalic diversification within the context of conserved external anatomy. This disparity is investigated with regard to the functional interaction of the male internal sac flagellum and female spermathecal duct. Though limited association of flagellar and spermathecal duct configurations can be documented, several factors complicate proposing a general evolutionary mechanism for the observed data. These include:1, the occurrence of derived, elongate spermathecal ducts in three species, two of which exhibit very long male flagella, whereas males of the third exhibit a very short flagellum; and2, a highly derived and exaggerated male flagellar configuration shared across a sister-species pair even though the two species can be robustly diagnosed using external anatomical characters, other significant genitalic differences involving male parameral setation, and biogeographic allopatry associated with differential occupation of desert versus forest biomes.

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Molecular phylogeny of pimoid spiders and the limits of Linyphiidae, with a reassessment of male palpal homologies (Araneae, Pimoidae)

Zootaxa ◽

10.11646/zootaxa.5026.1.3 ◽

2021 ◽

Vol 5026 (1) ◽

pp. 77-107

Author(s):

GUSTAVO HORMIGA ◽

SIDDHARTH KULKARNI ◽

THIAGO DA SILVA MOREIRA ◽

DIMITAR DIMITROV

Keyword(s):

Molecular Phylogeny ◽

Phylogenetic Tree ◽

Phylogenetic Relationships ◽

Target Gene ◽

Sister Group ◽

Biogeographic History ◽

Molecular Phylogenetic Tree ◽

Molecular Phylogenetic ◽

History Of

We address the phylogenetic relationships of pimoid spiders (Pimoidae) using a standard target-gene approach with an extensive taxonomic sample, which includes representatives of the four currently recognized pimoid genera, 26 linyphiid genera, a sample of Physoglenidae, Cyatholipidae and one Tetragnathidae species. We test the monophyly of Pimoidae and Linyphiidae and explore the biogeographic history of the group. Nanoa Hormiga, Buckle and Scharff, 2005 and Pimoa Chamberlin & Ivie, 1943 form a clade which is the sister group of a lineage that includes all Linyphiidae, Weintrauboa Hormiga, 2003 and Putaoa Hormiga and Tu, 2008. Weintrauboa, Putaoa, Pecado and Stemonyphantes form a clade (Stemonyphantinae) sister to all remaining linyphiids. We use the resulting optimal molecular phylogenetic tree to assess hypotheses on the male palp sclerite homologies of pimoids and linyphiids. Pimoidae is redelimited to only include Pimoa and Nanoa. We formalize the transfer from Pimoidae of the genera Weintrauboa and Putaoa to Linyphiidae, re-circumscribe the linyphiid subfamily Stemonyphantinae, and offer revised morphological diagnoses for Pimoidae and Linyphiidae.

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Fungi of entomopathogenic potential in Chytridiomycota and Blastocladiomycota, and in fungal allies of the Oomycota and Microsporidia

IMA Fungus ◽

10.1186/s43008-021-00074-y ◽

2021 ◽

Vol 12 (1) ◽

Author(s):

Agata Kaczmarek ◽

Mieczysława I. Boguś

Keyword(s):

Biological Control Agent ◽

Sister Group ◽

Control Agent ◽

Scale Insects ◽

Black Flies ◽

Larval Stages ◽

Phylogenetic Studies ◽

Lady Beetles ◽

Molecular Phylogenetic ◽

The Relationship

AbstractThe relationship between entomopathogenic fungi and their insect hosts is a classic example of the co-evolutionary arms race between pathogen and target host. The present review describes the entomopathogenic potential of Chytridiomycota and Blastocladiomycota fungi, and two groups of fungal allies: Oomycota and Microsporidia. The Oomycota (water moulds) are considered as a model biological control agent of mosquito larvae. Due to their shared ecological and morphological similarities, they had long been considered a part of the fungal kingdom; however, phylogenetic studies have since placed this group within the Straminipila. The Microsporidia are parasites of economically-important insects, including grasshoppers, lady beetles, bumblebees, colorado potato beetles and honeybees. They have been found to display some fungal characteristics, and phylogenetic studies suggest that they are related to fungi, either as a basal branch or sister group. The Blastocladiomycota and Chytridiomycota, named the lower fungi, historically were described together; however, molecular phylogenetic and ultrastructural research has classified them in their own phylum. They are considered parasites of ants, and of the larval stages of black flies, mosquitoes and scale insects.

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Discovery of a new family of amphibians from northeast India with ancient links to Africa

Proceedings of The Royal Society B Biological Sciences ◽

10.1098/rspb.2012.0150 ◽

2012 ◽

Vol 279 (1737) ◽

pp. 2396-2401 ◽

Cited By ~ 59

Author(s):

Rachunliu G. Kamei ◽

Diego San Mauro ◽

David J. Gower ◽

Ines Van Bocxlaer ◽

Emma Sherratt ◽

...

Keyword(s):

Dna Sequences ◽

Nuclear Dna ◽

Phylogenetic Analyses ◽

Sister Group ◽

Northeast India ◽

Sister Group Relationship ◽

New Family ◽

Ancient Lineage ◽

Molecular Phylogenetic ◽

Threatened Habitats

The limbless, primarily soil-dwelling and tropical caecilian amphibians (Gymnophiona) comprise the least known order of tetrapods. On the basis of unprecedented extensive fieldwork, we report the discovery of a previously overlooked, ancient lineage and radiation of caecilians from threatened habitats in the underexplored states of northeast India. Molecular phylogenetic analyses of mitogenomic and nuclear DNA sequences, and comparative cranial anatomy indicate an unexpected sister-group relationship with the exclusively African family Herpelidae. Relaxed molecular clock analyses indicate that these lineages diverged in the Early Cretaceous, about 140 Ma. The discovery adds a major branch to the amphibian tree of life and sheds light on both the evolution and biogeography of caecilians and the biotic history of northeast India—an area generally interpreted as a gateway between biodiversity hotspots rather than a distinct biogeographic unit with its own ancient endemics. Because of its distinctive morphology, inferred age and phylogenetic relationships, we recognize the newly discovered caecilian radiation as a new family of modern amphibians.

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Leptolejeunea nigra (Lejeuneaceae), a new species with brownish black ocelli based upon morphology and DNA sequences

Phytotaxa ◽

10.11646/phytotaxa.427.1.4 ◽

2019 ◽

Vol 427 (1) ◽

pp. 31-42

Author(s):

LEI SHU ◽

RUI-LIANG ZHU

Keyword(s):

New Species ◽

Molecular Phylogeny ◽

Dna Sequences ◽

Phylogenetic Analyses ◽

Morphological Characters ◽

Time Span ◽

Molecular Dating ◽

Molecular Phylogenetic ◽

Brownish Black ◽

A New Species

Based on molecular phylogenetic analyses and morphological characters, a new species from Bangladesh, northern Vietnam, and southwestern China, Leptolejeunea nigra, is described. It is mostly similar to L. balansae but remarkable for having brownish black ocelli in its leaf lobes. In the molecular phylogeny, the samples of L. nigra are not nested within any clade and form an independent lineage. In particular, the molecular dating suggested that the divergence of L. nigra happened in time span of the formation of the Himalayas.

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Fungia fungites (Linnaeus, 1758) (Scleractinia, Fungiidae) is a species complex that conceals large phenotypic variation and a previously unrecognized genus

Contributions to Zoology ◽

10.1163/18759866-20191421 ◽

2020 ◽

Vol 89 (2) ◽

pp. 188-209

Author(s):

Yutaro Oku ◽

Kenji Iwao ◽

Bert W. Hoeksema ◽

Naoko Dewa ◽

Hiroyuki Tachikawa ◽

...

Keyword(s):

Species Complex ◽

Phylogenetic Analyses ◽

Molecular Data ◽

Scleractinian Corals ◽

Type Specimens ◽

Mitochondrial Coi ◽

Clade B ◽

Unknown Species ◽

Molecular Phylogenetic ◽

Morphological Differences

Recent molecular phylogenetic analyses of scleractinian corals have resulted in the discovery of cryptic lineages. To understand species diversity in corals, these lineages need to be taxonomically defined. In the present study, we report the discovery of a distinct lineage obscured by the traditional morphological variation of Fungia fungites. This taxon exists as two distinct morphs: attached and unattached. Molecular phylogenetic analyses using mitochondrial COI and nuclear ITS markers as well as morphological comparisons were performed to clarify their phylogenetic relationships and taxonomic positions. Molecular data revealed that F. fungites consists of two genetically distinct clades (A and B). Clade A is sister to a lineage including Danafungia scruposa and Halomitra pileus, while clade B formed an independent lineage genetically distant from these three species. The two morphs were also found to be included in both clades, although the attached morph was predominantly found in clade A. Morphologically, both clades were statistically different in density of septal dentation, septal number, and septal teeth shape. These results indicate that F. fungites as presently recognized is actually a species complex including at least two species. After checking type specimens, we conclude that specimens in clade A represent true F. fungites with two morphs (unattached and attached) and that all of those in clade B represent an unknown species and genus comprising an unattached morph with only one exception. These findings suggest that more unrecognized taxa with hitherto unnoticed morphological differences can be present among scleractinian corals.

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Speciation in the genera Anthericum and Chlorophytum (Asparagaceae) in Ethiopia—a molecular phylogenetic approach

Phytotaxa ◽

10.11646/phytotaxa.297.2.2 ◽

2017 ◽

Vol 297 (2) ◽

pp. 139 ◽

Cited By ~ 1

Author(s):

Charlotte Sletten Bjorå ◽

MARTE ELDEN ◽

INGER NORDAL ◽

ANNE K. BRYSTING ◽

TESFAYE AWAS ◽

...

Keyword(s):

Electron Microscopy ◽

Phylogenetic Analyses ◽

Sister Group ◽

Molecular Data ◽

Group Relations ◽

Variation Patterns ◽

Molecular Phylogenetic ◽

Lowland Area ◽

A New Species ◽

Scanning Electron

Sister group relations of Ethiopian species of Anthericum and Chlorophytum and variation patterns in the C. gallabatense and C. comosum complexes were studied using molecular phylogenetic analyses, morphometrics, and scanning electron microscopy of seed surfaces. Results indicate that molecular data largely support previous morphological conclusions, and that speciation has occurred in Ethiopia at least three times in Anthericum and repeatedly within different subclades of Chlorophytum. Areas particularly rich in endemic species are the lowland area around Bale Mountains in SE Ethiopia and in the Beninshangul Gumuz regional state in W Ethiopia near the border to Sudan. A new species, Chlorophytum mamillatum Elden & Nordal, is described, and the names C. tordense and C. tetraphyllum are re-instated.

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Algal Viruses with Distinct Intraspecies Host Specificities Include Identical Intein Elements

Applied and Environmental Microbiology ◽

10.1128/aem.71.7.3599-3607.2005 ◽

2005 ◽

Vol 71 (7) ◽

pp. 3599-3607 ◽

Cited By ~ 50

Author(s):

Keizo Nagasaki ◽

Yoko Shirai ◽

Yuji Tomaru ◽

Kensho Nishida ◽

Shmuel Pietrokovski

Keyword(s):

Dna Polymerase ◽

Homing Endonuclease ◽

Sister Group ◽

Dna Virus ◽

Single Nucleotide Change ◽

Double Stranded Dna ◽

Endonuclease Domain ◽

Algal Viruses ◽

Molecular Phylogenetic ◽

Position Coding

ABSTRACT Heterosigma akashiwo virus (HaV) is a large double-stranded DNA virus infecting the single-cell bloom-forming raphidophyte (golden brown alga) H. akashiwo. A molecular phylogenetic sequence analysis of HaV DNA polymerase showed that it forms a sister group with Phycodnaviridae algal viruses. All 10 examined HaV strains, which had distinct intraspecies host specificities, included an intein (protein intron) in their DNA polymerase genes. The 232-amino-acid inteins differed from each other by no more than a single nucleotide change. All inteins were present at the same conserved position, coding for an active-site motif, which also includes inteins in mimivirus (a very large double-stranded DNA virus of amoebae) and in several archaeal DNA polymerase genes. The HaV intein is closely related to the mimivirus intein, and both are apparently monophyletic to the archaeal inteins. These observations suggest the occurrence of horizontal transfers of inteins between viruses of different families and between archaea and viruses and reveal that viruses might be reservoirs and intermediates in horizontal transmissions of inteins. The homing endonuclease domain of the HaV intein alleles is mostly deleted. The mechanism keeping their sequences basically identical in HaV strains specific for different hosts is yet unknown. One possibility is that rapid and local changes in the HaV genome change its host specificity. This is the first report of inteins found in viruses infecting eukaryotic algae.

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Diversity, complementary distributions and taxonomy of Rhagada land snails (Gastropoda : Camaenidae) on the Burrup Peninsula, Western Australia

Invertebrate Systematics ◽

10.1071/is15046 ◽

2016 ◽

Vol 30 (4) ◽

pp. 323 ◽

Cited By ~ 1

Author(s):

Michael S. Johnson ◽

Sean Stankowski ◽

Peter G. Kendrick ◽

Zoë R. Hamilton ◽

Roy J. Teale

Keyword(s):

Western Australia ◽

Genetic Similarity ◽

Phylogenetic Diversity ◽

Sister Group ◽

Land Snails ◽

Island Species ◽

Local Sampling ◽

Geographic Overlap

Phylogenetic diversity of Rhagada land snails is high on the Burrup Peninsula, Western Australia, with four distinct clades, representing three of the four major clades of the Pilbara region. Detailed sampling indicated little geographic overlap of the four clades, conforming to the general rarity of congeneric sympatry in Australian camaenids. The diversity on the Burrup Peninsula includes three previously unclassified morphotypes. One of these lies within the broad endemic clade of the adjacent Dampier Archipelago, and is provisionally assigned to the island species R. perprima, based on phylogenetic evidence. The two other undescribed morphotypes constitute an endemic clade that is the sister group of the broader Dampier Archipelago clade. All COI p-distances within clades are less than 6%, whereas nearly all distances between clades exceed 10%, the gap corresponding to differences among species of Rhagada generally. One morphotype in the Burrup Peninsula endemic clade has a low spire and a distinctive keel, and is restricted to a single rockpile. Detailed local sampling revealed gradation between this form and the more widely distributed globose morphotype. On the basis of genetic similarity and morphological continuity, we describe the morphologically variable endemic Burrup Peninsula clade as Rhagada ngurrana, sp. nov., which has a distribution spanning only 9 km.

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