Cryptic speciation in populations of the genus Aphyocharax (Characiformes: Characidae) from eastern Amazon coastal river drainages and surroundings revealed by single locus species delimitation methods

Abstract Recent studies in eastern Amazon coastal drainages and their surroundings have revealed new fish species that sometimes exhibit little morphological differentiation (cryptic species). Thus, we used a DNA-based species delimitation approach to test if populations showing the morphotype and typical character states of the Aphyocharax avary holotype correspond either to A. avary or A. brevicaudatus, two known species from the region, or if they form independent lineages, indicating cryptic speciation. WP and GMYC analyses recovered five lineages (species) in the ingroup, while a bPTP analysis delimited three lineages. ABGD analyses produced two possible results: one corroborating the WP and GMYC methods and another corroborating the bPTP method. All methods indicate undescribed cryptic species in the region and show variation from at least 1 to 4 species in the ingroup, depending on the approach, corroborating previous studies, and revealing this region as a possible hotspot for discovering undescribed fish species.

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Molecular taxonomy of endemic coastal Ligia isopods from the Hawaiian Islands: re-description of L. hawaiensis and description of seven novel cryptic species

PeerJ ◽

10.7717/peerj.7531 ◽

2019 ◽

Vol 7 ◽

pp. e7531

Author(s):

Carlos A. Santamaria

Keyword(s):

Cryptic Species ◽

Species Delimitation ◽

Molecular Taxonomy ◽

Hawaiian Islands ◽

Nuclear Gene ◽

Morphological Differentiation ◽

Taxonomic Revision ◽

Hawaiian Archipelago ◽

Genetic Lineages ◽

Molecular Characters

Past phylogeographic work has shown Ligia hawaiensis, a coastal isopod species endemic to the Hawaiian Islands, to be a paraphyletic complex of several highly genetically divergent yet morphologically cryptic lineages. Despite the need for a taxonomic revision of this species, the lack of morphological differentiation has proven an impediment to formally describe new Ligia species in the region. Molecular characters and species delimitation approaches have been successfully used to formally describe cryptic species in other crustacean taxa, suggesting they may aid taxonomic revisions of L. hawaiensis. Herein, various distance- and tree-based molecular species delimitation approaches are applied on a concatenated dataset comprised of both mitochondrial and nuclear gene sequences of L. hawaiensis and L. perkinsi, a terrestrial species endemic to the Hawaiian archipelago. Results of these analyses informed a taxonomic revision leading to the redescription of L. hawaiensis and the description of seven new cryptic species on the basis of molecular characters: L. dante, L. eleluensis, L. honu, L. kamehameha, L. mauinuiensis, L. pele, and L. rolliensis. These coastal Ligia species from the Hawaiian archipelago appear to be largely limited to single islands, where they appear largely constrained to volcanic rift zones suggesting allopatric events at local scales may drive diversification for poorly dispersing organisms in the Hawaiian coastlines. Additional work remains needed to fully assess the role of said events; however, the description of these novel species underscore their potential to aid in studies of local diversification of marine organisms in Hawai‘i. Lastly, this represents the first application of molecular taxonomic approaches to formally describe genetic lineages found in Ligia isopods as species, underscoring the promise these methods hold to taxonomic revisions in other species in the genus shown to harbor cryptic genetic lineages.

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Bipartite molecular approach for species delimitation and resolving cryptic speciation of Exobasidium vexans within the Exobasidium genus

Computational Biology and Chemistry ◽

10.1016/j.compbiolchem.2021.107496 ◽

2021 ◽

Vol 92 ◽

pp. 107496

Author(s):

Chayanika Chaliha ◽

V. Chandra Kaladhar ◽

Robin Doley ◽

Praveen Kumar Verma ◽

Aditya Kumar ◽

...

Keyword(s):

Species Delimitation ◽

Cryptic Speciation ◽

Molecular Approach

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Species delimitation of colour polymorphic Cladophorus (Coleoptera: Lycidae) from New Guinea

Zootaxa ◽

10.11646/zootaxa.4320.3.6 ◽

2017 ◽

Vol 4320 (3) ◽

pp. 505 ◽

Cited By ~ 4

Author(s):

ROMANA KALOUSOVA ◽

LADISLAV BOCAK

Keyword(s):

Phylogenetic Analysis ◽

Mitochondrial Dna ◽

Related Species ◽

Species Delimitation ◽

Morphological Differentiation ◽

Morphological Characters ◽

Molecular Data ◽

Closely Related Species ◽

Dna Fragment ◽

Colour Patterns

Cladophorus Guérin-Méneville, 1830 are endemic Papuan net-winged beetles which take part in highly diverse Müllerian mimicry rings. Available specimens were sequenced for cox1–tRNA-Leu–cox2 mitochondrial DNA fragment and the species delimitations were based on the genetic distance, phylogenetic analysis, and morphology. Three earlier described species were identified in the recently collected material and further 10 species are described: C. pallescens sp. nov., C. bicolor sp. nov., C. craterensis sp. nov., C. motykai sp. nov., C. mindikensis sp. nov., C. kailakiensis sp. nov., C. manokwarensis sp. nov., C. haiaensis sp. nov., C. humeralis sp. nov., and C. boceki sp. nov. DNA-based identifications provided some ambiguous results and closely related species could not be robustly delimited using solely molecular data. Additionally, the species limits were based on clearly defined morphological characters and the morphological differentiation was found unlinked from the genetic divergence. Colour patterns cannot be used for identification because all species available in more specimens were polymorphic and followed various local co-mimics. The Papuan fauna of Cladophorus is very diverse and the closely related species regularly occur in limited regions. Differentiation within restricted ranges is therefore considered as the main speciation mode.

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A hyper-diverse genus of acanthocephalans revealed by tree-based and non-tree-based species delimitation methods: Ten cryptic species of Neoechinorhynchus in Middle American freshwater fishes

Molecular Phylogenetics and Evolution ◽

10.1016/j.ympev.2018.05.023 ◽

2018 ◽

Vol 127 ◽

pp. 30-45 ◽

Cited By ~ 17

Author(s):

Carlos Daniel Pinacho-Pinacho ◽

Martín García-Varela ◽

Ana L. Sereno-Uribe ◽

Gerardo Pérez-Ponce de León

Keyword(s):

Cryptic Species ◽

Species Delimitation ◽

Freshwater Fishes

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A next generation approach to species delimitation reveals the role of hybridization in a cryptic species complex of corals

BMC Evolutionary Biology ◽

10.1186/s12862-019-1427-y ◽

2019 ◽

Vol 19 (1) ◽

Cited By ~ 8

Author(s):

Andrea M. Quattrini ◽

Tiana Wu ◽

Keryea Soong ◽

Ming-Shiou Jeng ◽

Yehuda Benayahu ◽

...

Keyword(s):

Cryptic Species ◽

Species Delimitation ◽

Species Complex ◽

Next Generation ◽

Cryptic Species Complex

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Evidence of cryptic species in the blenniid Cirripectes alboapicalis species complex, with zoogeographic implications for the South Pacific

ZooKeys ◽

10.3897/zookeys.810.28887 ◽

2018 ◽

Vol 810 ◽

pp. 127-138 ◽

Cited By ~ 4

Author(s):

Erwan Delrieu-Trottin ◽

Libby Liggins ◽

Thomas Trnski ◽

Jeffrey T. Williams ◽

Valentina Neglia ◽

...

Keyword(s):

Cryptic Species ◽

Geographic Distribution ◽

Fish Species ◽

Species Complex ◽

Genetic Relationships ◽

South Pacific ◽

The South ◽

Rapa Nui ◽

Distribution Ranges ◽

Geographic Distributions

Rapa Nui, commonly known as Easter Island (Chile), is one of the most isolated tropical islands of the Pacific Ocean. The island location of Rapa Nui makes it the easternmost point of the geographic ranges for many western Pacific fish species that are restricted to the subtropical islands south of 20°S latitude. The blenniid fish speciesCirripectesalboapicalishas been thought to have one of the most extensive geographic distribution ranges among these southern subtropical fish species, extending from the southern Great Barrier Reef to Rapa Nui. A phylogenetic analysis was conducted to determine the taxonomic status of the species. The results provide genetic evidence that suggests that this formerly South Pacific-wide species comprises at least three cryptic species with allopatric geographic distributions. The analyses reveal the geographic distributions of these clades and their genetic relationships with each other, and with other species within the genusCirripectes. The processes that culminated in the current geographic distribution of this species complex and the zoogeographic implications of this finding for the South Pacific region are discussed.

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