Cryptic species complexes in manipulative echinostomatid trematodes: when two become six

SUMMARYRecent studies have shown that some digenean trematodes previously identified as single species due to the lack of distinguishing morphological characteristics actually consist of a number of genetically distinct cryptic species. We obtained mitochondrial 16S and nuclear ITS1 sequences for the redial stages of Acanthoparyphium sp. and Curtuteria australis collected from snails and whelks at various locations around Otago Peninsula, New Zealand. These two echinostomes are well-known host manipulators whose impact extends to the entire intertidal community. Using phylogenetic analyses, we found that Acanthoparyphium sp. is actually composed of at least 4 genetically distinct species, and that a cryptic species of Curtuteria occurs in addition to C. australis. Molecular data obtained for metacercariae dissected from cockle second intermediate hosts matched sequences obtained for Acanthoparyphium sp. A and C. australis rediae, respectively, but no other species. The various cryptic species of both Acanthoparyphium and Curtuteria also showed an extremely localized pattern of distribution: some species were either absent or very rare in Otago Harbour, but reached far higher prevalence in nearby sheltered inlets. This small-scale spatial segregation is unexpected as shorebird definitive hosts can disperse trematode eggs across wide geographical areas, which should result in a homogeneous mixing of the species on small geographical scales. Possible explanations for this spatial segregation of the species include sampling artefacts, local adaptation by first intermediate hosts, environmental conditions, and site fidelity of the definitive hosts.

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Molecular, chromosomal and morphological characters reveal a new diploid species in the Smilax china complex (Smilacaceae)

Phytotaxa ◽

10.11646/phytotaxa.212.3.2 ◽

2015 ◽

Vol 212 (3) ◽

pp. 199 ◽

Cited By ~ 1

Author(s):

Yunpeng Zhao ◽

Zhongshuai Sun ◽

Yihan Wang ◽

Chengxin Fu

Keyword(s):

Species Complex ◽

Phylogenetic Analyses ◽

Diploid Species ◽

Distinct Species ◽

Morphological Characters ◽

Molecular Data ◽

Eastern Asia ◽

Diploid Population ◽

Species Complexes ◽

Molecular Phylogenetic

The Smilax china complex (Smilacaceae) is a typical mixoploid species complex including five extant diploid taxa with a widespread distribution across eastern Asia. The diploid population (mHB, 2n = 32), which was originally considered to be diploid S. china, together with two newly discovered diploid populations (mZZ and mYXS) is supported here as a distinct species by morphological, karyotypic and molecular data. These three populations present consistent morphological characters of sub-erect stems, rudimentary tendrils and minutely serrulate leaf margins, in which they differ from S. china. Molecular phylogenetic analyses also confirm its monophyly with a closer relationship to the other two erect species S. biflora and S. trinervula in the complex. These three populations are thus proposed to be a clear new diploid species and described with the name of Smilax microdontus Z. S. Sun & C.X. Fu, sp. nov. The discovery of this new species highlights the importance of closer examinations on species complexes by integrating multiple evidence.

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Updating species diversity of Colletotrichum, with a phylogenomic overview

Studies in Mycology ◽

10.3114/sim.2022.101.01 ◽

2022 ◽

Author(s):

F. Liu ◽

Z.Y. Ma ◽

L.W. Hou ◽

Y.Z. Diao ◽

W.P. Wu ◽

...

Keyword(s):

Species Diversity ◽

Plant Pathogens ◽

Phylogenetic Analyses ◽

Morphological Characteristics ◽

Single Copy ◽

Molecular Data ◽

Human Pathogens ◽

Species Complexes ◽

Backbone Tree ◽

The Uk

The genus Colletotrichum includes important plant pathogens, endophytes, saprobes and human pathogens. Even though the polyphasic approach has facilitated Colletotrichum species identification, knowledge of the overall species diversity and host distribution is largely incomplete. To address this, we examined 952 Colletotrichum strains isolated from plants representing 322 species from 248 genera, or air and soil samples, from 87 locations in China, as well as 56 strains from Saudi Arabia, Thailand, Turkey, and the UK. Based on morphological characteristics and multi-locus phylogenetic analyses, the strains were assigned to 107 species, including 30 new species described in this paper and 18 new records for China. The currently most comprehensive backbone tree of Colletotrichum, comprising 16 species complexes (including a newly introduced C. bambusicola species complex) and 15 singleton species, is provided. Based on these analyses, 280 species with available molecular data are accepted in this genus, of which 139 have been reported in China, accounting for 49.6 % of the species. Colletotrichum siamense, C. karsti, C. fructicola, C. truncatum, C. fioriniae, and C. gloeosporioides were the most commonly detected species in China, as well as the species with the broadest host range. By contrast, 76 species were currently found to be associated with a single plant species or genus in China. To date, 33 Colletotrichum species have been exclusively reported as endophytes. Furthermore, we generated and assembled whole-genome sequences of the 30 new and a further 18 known species. The most comprehensive genome tree comprising 94 Colletotrichum species based on 1 893 single-copy orthologous genes was hence generated, with all nodes, except four, supported by 100 % bootstrap values. Collectively, this study represents the most comprehensive investigation of Colletotrichum diversity and host occurrence to date, and greatly enhances our understanding of the diversity and phylogenetic relationships in this genus.

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On the status of Rossmaessleria scherzeri scherzeri (Zelebor in Pfeiffer & Zelebor, 1867) (Gastropoda: Pulmonata: Helicidae)

Zootaxa ◽

10.11646/zootaxa.4286.1.7 ◽

2017 ◽

Vol 4286 (1) ◽

pp. 116

Author(s):

MARCO T. NEIBER

Keyword(s):

Species Delimitation ◽

Type Species ◽

Phylogenetic Analyses ◽

Single Species ◽

Distinct Species ◽

Molecular Data ◽

Land Snails ◽

North African ◽

The Status ◽

Mitochondrial Sequences

The genus Rossmaessleria Hesse, 1907, belonging to a mainly North African radiation of land snails assigned to the tribe Otalini (Helicidae: Helicinae, see Razkin et al. 2015 and Neiber & Hausdorf 2015) has recently been subject to two independent revisions (Walther et al. 2016; Torres Alba et al. 2016). Torres Alba et al. (2016) provided a detailed re-description of the type species of Rossmaessleria, R. scherzeri (Zelebor in Pfeiffer & Zelebor, 1867), including an anatomical investigation. Additionally, Torres Alba et al. (2016) provided new data on several Moroccan taxa belonging to the genus, e.g. R. tetuanensis (Kobelt, 1881) and R. olcesei (Pallary, 1899). Walther et al. (2016) revised the taxa included in Rossmaessleria on the basis of an examination of all available type material and newly collected specimens and described several, conchologically distinct new taxa. These authors also examined genital anatomy, conducted phylogenetic analyses on the basis of mitochondrial sequences and used species delimitation approaches based on their molecular data, concluding that several conchologically distinct lineages can be recognized in Rossmaessleria, but that anatomical and genetic differentiation does not support the recognition of distinct species in the genus. This result was further corroborated by the presence, although infrequent, of conchologically intermediate forms between some of the Rossmaessleria taxa. Accordingly, Walther et al. (2016) recognized only a single species, R. scherzeri, with 11 subspecies, which are geographically restricted to isolated limestone ranges or outcrops in the western parts of the Rif Mountains in northern Morocco (ten subspecies) and to the Rock of Gibraltar, from where the nominotypical subspecies was described (Zelebor in Pfeiffer & Zelebor 1867).

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Linking morphological and molecular sources to disentangle the case of Xylodon australis

Scientific Reports ◽

10.1038/s41598-020-78399-8 ◽

2020 ◽

Vol 10 (1) ◽

Author(s):

Javier Fernández-López ◽

M. Teresa Telleria ◽

Margarita Dueñas ◽

Mara Laguna-Castro ◽

Klaus Schliep ◽

...

Keyword(s):

New Zealand ◽

Phylogenetic Analyses ◽

Single Species ◽

R Package ◽

Molecular Data ◽

Historical Collections ◽

Close Relationship ◽

Kinship Relations ◽

History Of ◽

Different Sources

AbstractThe use of different sources of evidence has been recommended in order to conduct species delimitation analyses to solve taxonomic issues. In this study, we use a maximum likelihood framework to combine morphological and molecular traits to study the case of Xylodon australis (Hymenochaetales, Basidiomycota) using the locate.yeti function from the phytools R package. Xylodon australis has been considered a single species distributed across Australia, New Zealand and Patagonia. Multi-locus phylogenetic analyses were conducted to unmask the actual diversity under X. australis as well as the kinship relations respect their relatives. To assess the taxonomic position of each clade, locate.yeti function was used to locate in a molecular phylogeny the X. australis type material for which no molecular data was available using morphological continuous traits. Two different species were distinguished under the X. australis name, one from Australia–New Zealand and other from Patagonia. In addition, a close relationship with Xylodon lenis, a species from the South East of Asia, was confirmed for the Patagonian clade. We discuss the implications of our results for the biogeographical history of this genus and we evaluate the potential of this method to be used with historical collections for which molecular data is not available.

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Co-occurring cryptic species pose challenges for conservation: a case study of the African dwarf crocodile (Osteolaemusspp.) in Cameroon

Oryx ◽

10.1017/s0030605314000647 ◽

2014 ◽

Vol 49 (4) ◽

pp. 584-590 ◽

Cited By ~ 3

Author(s):

Nicole L. Smolensky

Keyword(s):

Cryptic Species ◽

Conservation Status ◽

Taxonomic Revision ◽

Single Species ◽

Conservation Strategies ◽

Encounter Rates ◽

Distribution Maps ◽

Species Complexes ◽

Threatened Taxa ◽

Population Structures

AbstractThe conservation status of threatened taxa may be obfuscated by the detection of cryptic species complexes, in both vertebrate and invertebrate species. African dwarf crocodiles (Osteolaemusspp.) are hunted throughout their range but their conservation status is unknown. Few population assessments have been carried out and there has been a taxonomic revision of the number of species in the genus. The similar morphologies ofOsteolaemus tetraspisandOsteolaemus osbornipose a challenge for conservation in Cameroon, where they are still managed as a single species. Nocturnal spotlight surveys were conducted in three regions during August–November 2010 and December 2011–February 2012 to provide population assessments ofO. tetraspisandO. osborniand raise awareness of the two species in Cameroon. The mean encounter rates ofO. tetraspisandO. osborniwere 1.02 ± SD 1.34 (65 individuals in 39 surveys) and 0.61 ± SD 0.38 (three in four surveys) crocodiles per km, respectively. TheO. tetraspispopulation comprised juveniles predominantly and had a male-biased sex ratio. The fewO. osbornidetected comprised both adults and juveniles. Both species are threatened in Cameroon, based on low encounter rates, young population structures and the threats of habitat loss and hunting pressure. This study provides distribution maps and serves as a baseline to quantify population trends and inform conservation strategies.

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A re-examination of the molecular systematics and phylogeography of taxa of the Peromyscus aztecus species group, with comments on the distribution of P. winkelmanni

Therya ◽

10.12933/therya-21-1115 ◽

2021 ◽

Vol 12 (2) ◽

pp. 331-346

Author(s):

C. William Kilpatrick ◽

Nelish Pradhan ◽

Ryan W Norris

Keyword(s):

Phylogenetic Analyses ◽

Distinct Species ◽

Molecular Study ◽

Molecular Data ◽

Species Group ◽

Cytb Sequence ◽

Voucher Specimen ◽

Cranial Measurements ◽

Mitochondrial Cytochrome B ◽

Isthmus Of Tehuantepec

The objectives of this study are to examine the available molecular data from the mitochondrial cytochrome-b gene (Cytb) and a concatenated dataset with this gene and two nuclear introns (Adh-1-I2 and Fgb-I7) to reexamine the systematic and phylogeographic conclusions reached by Sullivan et al. (1997) concerning the Peromyscus aztecus species group. The divergence of samples of P. aztecus oaxacensis across the Isthmus of Tehuantepec are further examined and taxonomic revisions are suggested. In addition, this study reviews the sources of data that lead to the conclusion that P. winkelmanni occurred in the Sierra Madre del Sur in Guerrero including a morphometric examination of a reported voucher. Bayesian and maximum likelihood analyses were conducted on a dataset of 31 Cytb sequences of all taxa in the P. aztecus group except for P. a. cordillerae and a concatenated dataset including five individuals of this group. Representative taxa of the P. boylii, P. mexicanus, and P. truei groups were included in both analyses. Body and cranial measurements of the voucher of the P. winkelmanni from Guerrero from which a Cytb sequence is reported to have been obtained was compared with measurements from specimens taken from the vicinity of Dos Aguas, Michoacán, including the type locality. We identified seven instances involving problematic identifications in GenBank. Once these issues were addressed, well-supported monophyletic sister clades of the P. aztecus and P. boylii species groups were recovered from phylogenetic analyses of Cytb sequences (Fig 1). Phylogenetic analyses of the Cytb and the concatenated datasets recover similar topologies that support the relationships of taxa of the aztecus group proposed by an earlier molecular study. Populations of P. a. oaxacensis southeast of the Isthmus of Tehuantepec represent a distinct species. Measurements of the voucher from Guerrero identified as the source of a P. winkelmanni Cytb sequence are smaller than P. winkelmanni for several characters. The divergent populations of P. a. oaxacensis from southeast of the Isthmus of Tehuantepec are recognized as two subspecies of P. cordillerae, P. c. cordillerae and P. c. hondurensis, whereas those northwest of the Isthmus are retained as P. a. oaxacensis. The lack of genetic divergence observed between P. a. evides and P. a. oaxacensis questions whether these two taxa should continue to be recognized as separate subspecies. Northern and southern populations of P. spicilegus demonstrate moderate divergence and additional examination of morphological and molecular differentiation within this taxon is warranted. The distribution of P. winkelmanni should be restricted to the vicinity of Dos Aguas, Michoacán, due to the lack of a voucher specimen that would confirm its reported occurrence in Guerrero.

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A revision of the Leptogium saturninum group in North America

The Lichenologist ◽

10.1017/s0024282916000323 ◽

2016 ◽

Vol 48 (5) ◽

pp. 387-421 ◽

Cited By ~ 6

Author(s):

Daphne F. STONE ◽

James W. HINDS ◽

Frances L. ANDERSON ◽

James C. LENDEMER

Keyword(s):

North American ◽

Morphological Study ◽

Sequence Data ◽

Phylogenetic Analyses ◽

Morphological Characteristics ◽

Lower Surface ◽

Molecular Data ◽

The North ◽

Molecular Phylogenetic ◽

Nrits Sequence

AbstractA revision of the North American members of the Leptogium saturninum group (i.e. species with long lower-surface hairs, isidia, and usually smooth upper surface) is presented based on molecular phylogenetic analyses of mtSSU and nrITS sequence data, together with an extensive morphological study. Three species supported by both molecular and morphological characteristics are recognized: L. acadiense sp. nov. (distinguished by granular saturninum-type isidia, medulla composed of irregularly arranged or perpendicular hyphae), L. cookii sp. nov. (distinguished by cylindrical saturninum-type isidia) and L. hirsutum (distinguished by hirsutum-type isidia and medulla composed of loosely intertwined hyphae). One species supported by morphological characteristics, but for which no molecular data could be generated, is also recognized: L. compactum sp. nov. (distinguished by hirsutum-type isidia and medulla composed of tightly packed hyphae). Finally, L. saturninum (distinguished by granular saturninum-type isidia and medulla composed of perpendicular and parallel hyphae) is supported by morphological characteristics but molecular data from geographically diverse populations, including those near the type locality, indicate that the morphologically defined species is paraphyletic. Leptogium burnetiae is excluded from North American based on morphological study of the type. The species are described and illustrated in detail, and are distinguished morphologically by their isidium development, morphology of mature isidia, and pattern of hyphae in the medulla in transverse sections near lobe margins. A key to the members of the L. saturninum group and related species is also presented.

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Global classification and evolution of brushlegged mayflies (Insecta: Ephemeroptera: Oligoneuriidae): phylogenetic analyses of morphological and molecular data and dated historical biogeography

Zoological Journal of the Linnean Society ◽

10.1093/zoolinnean/zlz031 ◽

2019 ◽

Vol 187 (2) ◽

pp. 378-412 ◽

Cited By ~ 3

Author(s):

Fabiana Criste Massariol ◽

Daniela Maeda Takiya ◽

Frederico Falcão Salles

Keyword(s):

Phylogenetic Analyses ◽

Divergence Time ◽

Time Estimation ◽

Single Species ◽

Molecular Data ◽

Neotropical Region ◽

Fossil Species ◽

Divergence Time Estimation ◽

The Family ◽

Family Based

AbstractOligoneuriidae is a Pantropical family of Ephemeroptera, with 68 species described in 12 genera. Three subfamilies are recognized: Chromarcyinae, with a single species from East Asia; Colocrurinae, with two fossil species from Brazil; and Oligoneuriinae, with the remaining species distributed in the Neotropical, Nearctic, Afrotropical and Palaearctic regions. Phylogenetic and biogeographical analyses were performed for the family based on 2762 characters [73 morphological and 2689 molecular (COI, 16S, 18S and 28S)]. Four major groups were recovered in all analyses (parsimony, maximum likelihood and Bayesian inference), and they were assigned to tribal level, namely Oligoneuriini, Homoeoneuriini trib. nov., Oligoneuriellini trib. nov. and Elassoneuriini trib. nov. In addition, Yawari and Madeconeuria were elevated to genus level. According to Statistical Dispersal-Vicariance (S-DIVA), Dispersal Extinction Cladogenesis (DEC) and divergence time estimation analyses, Oligoneuriidae originated ~150 Mya in the Gondwanan supercontinent, but was probably restricted to the currently delimited Neotropical region. The initial divergence of Oligoneuriidae involved a range expansion to Oriental and Afrotropical areas, sometime between 150 and 118 Mya. At ~118 Mya, the family started its diversification, reaching the Nearctic through dispersal from the Neotropical region and the Palaearctic and Madagascar from the Afrotropical region.

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Two species of Agaricus subg. Minoriopsis from Mexico

Phytotaxa ◽

10.11646/phytotaxa.404.3.1 ◽

2019 ◽

Vol 404 (3) ◽

pp. 91

Author(s):

JIE CHEN ◽

PHILIPPE CALLAC ◽

RÉGULO CARLOS LLARENA-HERNÁNDEZ ◽

GERARDO GERARDO MATA

Keyword(s):

New Species ◽

New Record ◽

Phylogenetic Analyses ◽

Morphological Characteristics ◽

Molecular Data ◽

Edible Fungi ◽

The World ◽

Wild Edible Fungi ◽

A New Species ◽

Taxonomic System

Agaricus is a species-rich genus with more than 500 species over the world. Recent studies on tropical Agaricus revealed new tropical clades and a revised taxonomic system was consequently developed. Agaricus subg. Minoriopsis, a sixth subgenus was recently added, comprising species exclusively from the Americas. The diversity of Agaricus is little studied in Mexico, despite this country has a long history in the consumption of wild edible fungi. In this paper, we introduce a new species A. guzmanii and a new record for A. globocystidiatus from Mexico based on morphological characteristics and molecular data. Phylogenetic analyses indicate that they belong to A. subg. Minoriopsis.

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A new species of Physaloptera (Nematoda: Spirurida) from Proechimys gardneri (Rodentia: Echimyidae) from the Amazon rainforest and molecular phylogenetic analyses of the genus

Journal of Helminthology ◽

10.1017/s0022149x19000610 ◽

2019 ◽

Vol 94 ◽

Cited By ~ 1

Author(s):

A. Maldonado ◽

R.O. Simões ◽

J. São Luiz ◽

S.F. Costa-Neto ◽

R.V. Vilela

Keyword(s):

New Species ◽

Phylogenetic Analyses ◽

Molecular Data ◽

Amazon Rainforest ◽

Ancestral State ◽

Intermediate Hosts ◽

The Status ◽

Molecular Phylogenetic ◽

History Of ◽

A New Species

Abstract Nematodes of the genus Physaloptera are globally distributed and more than 100 species are known. Their life cycle involves insects, including beetles, cockroaches and crickets, as intermediate hosts. This study describes a new species of Physaloptera and reports molecular phylogenetic analyses to determine its relationships within the family Physalopteridae. Physaloptera amazonica n. sp. is described from the stomach of the caviomorph rodent Proechimys gardneri collected in the Amazon rainforest in the state of Acre, Brazil. The species is characterized by the male having the first and second pair of sessile papillae asymmetrically placed, lacking a median papilla-like protuberance between the third pairs of sessile papillae, differentiated by size and shape of the spicules, while females have four uterine branches. For both nuclear 18S rRNA and MT-CO1 gene-based phylogenies, we recovered Turgida sequences forming a clade nested within Physaloptera, thus making Physaloptera paraphyletic to the exclusion of Turgida, suggesting that the latter may have evolved from the former monodelphic ancestral state to a derived polydelphic state, or that some species of Physaloptera may belong to different genera. Relationships between most taxa within Physaloptera were poorly resolved in our phylogenies, producing multifurcations or a star phylogeny. The star-like pattern may be attributed to evolutionary processes where past simultaneous species diversification events took place. Physaloptera amazonica n. sp. formed an independent lineage, separately from the other species of Physaloptera, thus supporting the status of a new species. However, all molecular data suggested a closer relationship with other Neotropical species. In conclusion, we added a new species to this already largely diverse genus Physaloptera, bringing new insights to its phylogenetic relationships. Further analyses, adding more species and markers, should provide a better understanding of the evolutionary history of physalopterids.

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