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Journal articles on the topic 'Cryptic lineage'

Author: Grafiati

Published: 3 June 2025

Last updated: 31 July 2025

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1

Gregory, Devon A., Clayton Rushford, Torin Hunter, et al. "Continued selection on cryptic SARS-CoV-2 observed in Missouri wastewater." PLOS Pathogens 19, no. 12 (2023): e1011688. http://dx.doi.org/10.1371/journal.ppat.1011688.

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Deep sequencing of wastewater to detect SARS-CoV-2 has been used during the COVID-19 pandemic to monitor viral variants as they appear and circulate in communities. SARS-CoV-2 lineages of an unknown source that have not been detected in clinical samples, referred to as cryptic lineages, are sometimes repeatedly detected from specific locations. We have continued to detect one such lineage previously seen in a Missouri site. This cryptic lineage has continued to evolve, indicating continued selective pressure similar to that observed in Omicron lineages.

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2

Puechmaille, Sébastien J., Benjamin Allegrini, Emma S.M. Boston, et al. "Genetic analyses reveal further cryptic lineages within the Myotis nattereri species complex." Mammalian Biology 77, no. 3 (2012): 224–28. https://doi.org/10.5281/zenodo.13415867.

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(Uploaded by Plazi for the Bat Literature Project) In recent years, new cryptic mammalian species have been discovered in Europe, many of which belong to the order Chiroptera. Within this order, some species such as Myotis nattereri contain several cryptic lineages/species, especially in the Mediterranean region. Here we present genetic, phylogenetic and morphological analysis on the Myotis nattereri species complex, focusing on France which is thought to be a contact zone for the different lineages/species. We sequenced the full Cytochrome b gene from individuals from 23 localities and invest

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3

Puechmaille, Sébastien J., Benjamin Allegrini, Emma S.M. Boston, et al. "Genetic analyses reveal further cryptic lineages within the Myotis nattereri species complex." Mammalian Biology 77, no. 3 (2012): 224–28. https://doi.org/10.5281/zenodo.13415867.

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Abstract:

(Uploaded by Plazi for the Bat Literature Project) In recent years, new cryptic mammalian species have been discovered in Europe, many of which belong to the order Chiroptera. Within this order, some species such as Myotis nattereri contain several cryptic lineages/species, especially in the Mediterranean region. Here we present genetic, phylogenetic and morphological analysis on the Myotis nattereri species complex, focusing on France which is thought to be a contact zone for the different lineages/species. We sequenced the full Cytochrome b gene from individuals from 23 localities and invest

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4

Puechmaille, Sébastien J., Benjamin Allegrini, Emma S.M. Boston, et al. "Genetic analyses reveal further cryptic lineages within the Myotis nattereri species complex." Mammalian Biology 77, no. 3 (2012): 224–28. https://doi.org/10.5281/zenodo.13415867.

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Abstract:

(Uploaded by Plazi for the Bat Literature Project) In recent years, new cryptic mammalian species have been discovered in Europe, many of which belong to the order Chiroptera. Within this order, some species such as Myotis nattereri contain several cryptic lineages/species, especially in the Mediterranean region. Here we present genetic, phylogenetic and morphological analysis on the Myotis nattereri species complex, focusing on France which is thought to be a contact zone for the different lineages/species. We sequenced the full Cytochrome b gene from individuals from 23 localities and invest

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5

Puechmaille, Sébastien J., Benjamin Allegrini, Emma S.M. Boston, et al. "Genetic analyses reveal further cryptic lineages within the Myotis nattereri species complex." Mammalian Biology 77, no. 3 (2012): 224–28. https://doi.org/10.5281/zenodo.13415867.

Full text

Abstract:

(Uploaded by Plazi for the Bat Literature Project) In recent years, new cryptic mammalian species have been discovered in Europe, many of which belong to the order Chiroptera. Within this order, some species such as Myotis nattereri contain several cryptic lineages/species, especially in the Mediterranean region. Here we present genetic, phylogenetic and morphological analysis on the Myotis nattereri species complex, focusing on France which is thought to be a contact zone for the different lineages/species. We sequenced the full Cytochrome b gene from individuals from 23 localities and invest

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6

Puechmaille, Sébastien J., Benjamin Allegrini, Emma S.M. Boston, et al. "Genetic analyses reveal further cryptic lineages within the Myotis nattereri species complex." Mammalian Biology 77, no. 3 (2012): 224–28. https://doi.org/10.5281/zenodo.13415867.

Full text

Abstract:

(Uploaded by Plazi for the Bat Literature Project) In recent years, new cryptic mammalian species have been discovered in Europe, many of which belong to the order Chiroptera. Within this order, some species such as Myotis nattereri contain several cryptic lineages/species, especially in the Mediterranean region. Here we present genetic, phylogenetic and morphological analysis on the Myotis nattereri species complex, focusing on France which is thought to be a contact zone for the different lineages/species. We sequenced the full Cytochrome b gene from individuals from 23 localities and invest

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7

Puechmaille, Sébastien J., Benjamin Allegrini, Emma S.M. Boston, et al. "Genetic analyses reveal further cryptic lineages within the Myotis nattereri species complex." Mammalian Biology 77, no. 3 (2012): 224–28. https://doi.org/10.5281/zenodo.13415867.

Full text

Abstract:

(Uploaded by Plazi for the Bat Literature Project) In recent years, new cryptic mammalian species have been discovered in Europe, many of which belong to the order Chiroptera. Within this order, some species such as Myotis nattereri contain several cryptic lineages/species, especially in the Mediterranean region. Here we present genetic, phylogenetic and morphological analysis on the Myotis nattereri species complex, focusing on France which is thought to be a contact zone for the different lineages/species. We sequenced the full Cytochrome b gene from individuals from 23 localities and invest

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8

Parker, Matthew A. "Cryptic species within Amphicarpaea bracteata (Leguminosae): evidence from isozymes, morphology, and pathogen specificity." Canadian Journal of Botany 74, no. 10 (1996): 1640–50. http://dx.doi.org/10.1139/b96-199.

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All North American plants of the genus Amphicarpaea are currently classified into a single variable species (Amphicarpaea bracteata). However, an isozyme analysis of 33 populations from a 1000-km region revealed the presence of two divergent lineages (I, II) that shared no alleles in common at 7 of 18 loci examined. These lineages coexisted on both a local and a regional scale with virtually no hybridization: among nearly 1000 plants analyzed, only a single hybrid individual was found that had alleles from both lineages. A multivariate analysis of seven leaf traits showed that these lineages w

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9

Liebeke, Manuel, Michael W. Bruford, Robert K. Donnelly, et al. "Identifying biochemical phenotypic differences between cryptic species." Biology Letters 10, no. 9 (2014): 20140615. http://dx.doi.org/10.1098/rsbl.2014.0615.

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Molecular genetic methods can distinguish divergent evolutionary lineages in what previously appeared to be single species, but it is not always clear what functional differences exist between such cryptic species. We used a metabolomic approach to profile biochemical phenotype (metabotype) differences between two putative cryptic species of the earthworm Lumbricus rubellus . There were no straightforward metabolite biomarkers of lineage, i.e. no metabolites that were always at higher concentration in one lineage. Multivariate methods, however, identified a small number of metabolites that tog

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10

Karlin, Eric F., Sean C. Robinson, and Peter E. Smouse. "Genetic diversity within and across gametophytic ploidy levels in a Sphagnum cryptic species complex." Australian Journal of Botany 68, no. 1 (2020): 49. http://dx.doi.org/10.1071/bt19143.

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We deploy Shannon analysis of five ancestrally (ANCE) diagnostic microsatellite loci to explore the patterns of ‘deep’ allelic genetic diversity within the peat moss Sphagnum ×australe Mitt. s.l. cryptic species complex across its Australasian distribution. There is both notable divergence among and considerable allelic overlap within the three allopolyploid lineages of this complex, two gametophytically allodiploid (R1S1 and R2S2) and one gametophytically allotriploid (FR1*S1*). Detailed biogeographic patterns reflect historical differences in genetic isolation and interbreeding. Lineage I (R

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11

Suarez, Reinier, Devon A. Gregory, David A. Baker, et al. "Detecting SARS-CoV-2 cryptic lineages using publicly available whole genome wastewater sequencing data." PLOS Pathogens 21, no. 6 (2025): e1012850. https://doi.org/10.1371/journal.ppat.1012850.

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Beginning in early 2021, unique and highly divergent lineages of SARS-CoV-2 were sporadically found in wastewater sewersheds using a sequencing strategy focused on amplifying the most rapidly evolving region of SARS-CoV-2, the receptor binding domain (RBD). Because these RBD sequences did not match known circulating strains and their source was not known, we termed them “cryptic lineages”. To date, more than 20 cryptic lineages have been identified using the RBD-focused sequencing strategy. Here, we identified and characterized additional cryptic lineages from SARS-CoV-2 wastewater sequences s

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12

Byrne, Allison Q., Vance T. Vredenburg, An Martel, et al. "Cryptic diversity of a widespread global pathogen reveals expanded threats to amphibian conservation." Proceedings of the National Academy of Sciences 116, no. 41 (2019): 20382–87. http://dx.doi.org/10.1073/pnas.1908289116.

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Biodiversity loss is one major outcome of human-mediated ecosystem disturbance. One way that humans have triggered wildlife declines is by transporting disease-causing agents to remote areas of the world. Amphibians have been hit particularly hard by disease due in part to a globally distributed pathogenic chytrid fungus (Batrachochytrium dendrobatidis [Bd]). Prior research has revealed important insights into the biology and distribution of Bd; however, there are still many outstanding questions in this system. Although we know that there are multiple divergent lineages of Bd that differ in p

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Trickey, Jennifer S., Martin Thiel, and Jonathan M. Waters. "Transoceanic dispersal and cryptic diversity in a cosmopolitan rafting nudibranch." Invertebrate Systematics 30, no. 3 (2016): 290. http://dx.doi.org/10.1071/is15052.

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The aeolid nudibranch Fiona pinnata (Eschscholtz, 1831) is an obligate rafter that occurs exclusively on macroalgal rafts and other floating substrata, and has a seemingly cosmopolitan marine distribution. Mitochondrial (mtDNA) and nuclear DNA sequence data were generated from specimens collected worldwide to test for global connectivity in this species. Phylogeographic analyses revealed three divergent mtDNA lineages, two of which were abundant and widespread. One of these lineages has an apparent circumequatorial distribution, whereas the other may have an antitropical distribution within th

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14

Loredo Varela, Roberto Carlos, and József Fail. "Host Plant Association and Distribution of the Onion Thrips, Thrips tabaci Cryptic Species Complex." Insects 13, no. 3 (2022): 298. http://dx.doi.org/10.3390/insects13030298.

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Onion thrips, Thrips tabaci Lindeman, 1889 (Thysanoptera: Thripidae) is a pest of economic importance traditionally treated as a polyphagous, cosmopolitan single species. Recent genetic evidence, however, suggests that it is rather a cryptic species complex of three lineages referred to by their host association and displaying different biological and ecological characteristics: leek-associated 1, leek-associated 2 and tobacco-associated. This study reviews host plant associations and distribution of the lineages of this cryptic species complex and discusses its consequences from an agronomica

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15

Addison, Jason A., and Jin-Hong Kim. "Cryptic species diversity and reproductive isolation among sympatric lineages of Strongylocentrotus sea urchins in the northwest Atlantic." FACETS 3, no. 1 (2018): 61–78. http://dx.doi.org/10.1139/facets-2017-0081.

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Distinguishing between intra- and inter-specific variation in genetic studies is critical to understanding evolution because the mechanisms driving change among populations are expected to be different than those that shape reproductive isolation among lineages. Genetic studies of north Atlantic green sea urchins Strongylocentrotus droebachiensis (Müller, 1776) have detected significant population substructure and asymmetric gene flow from Europe to Atlantic Canada and interspecific hybridization between S. droebachiensis and Strongylocentrotus pallidus (Sars, 1871). However, combined with pat

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16

Kabus, Jana, Sarah Cunze, Andrea Dombrowski, Ioannis Karaouzas, Spase Shumka, and Jonas Jourdan. "Uncovering the Grinnellian niche space of the cryptic species complex Gammarus roeselii." PeerJ 11 (August 3, 2023): e15800. http://dx.doi.org/10.7717/peerj.15800.

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Background The discovery of cryptic species complexes within morphologically established species comes with challenges in the classification and handling of these species. We hardly know to what extent species within a species complex differ ecologically. Such knowledge is essential to assess the vulnerability of individual genetic lineages in the face of global change. The abiotic conditions, i.e., the Grinnellian niche that a genetic lineage colonizes, provides insights into how diverse the ecological requirements of each evolutionary lineage are within a species complex. Material and Method

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17

Deng, Zhixiong, Yijun Ni, Jinhui Wang, et al. "Cryptic diversity and gene introgression of Moinidae (Crustacea: Cladocera) in Nigeria." Contributions to Zoology 90, no. 4-5 (2021): 463–86. http://dx.doi.org/10.1163/18759866-bja10022.

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Abstract The distribution and species/lineage diversity of freshwater invertebrate zooplankton is understudied in Sub-Saharan Africa. In the present study, we explored the lineage diversity and regional distribution of Moinidae (Crustacea: Cladocera) species in Southeast Nigeria. Three species of Moinidae were identified, based on morphology, in 11 of 32 Nigerian lakes examined. Their phylogenetic relationships were investigated based on mitochondrial dna sequences (cytochrome oxidase c subunit I gene; coi) and two nuclear internal transcribed spacer regions (its-1 and its-2). Three coi lineag

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18

Porco, David, Anne Zangerlé, Sylvie Hermant, and Guy Colling. "A new cryptic lineage for the earthworm species Aporrectodea caliginosa (Lumbricidae)." Bulletin de la Société des naturalistes luxembourgeois 125 (November 10, 2023): 119–24. http://dx.doi.org/10.59513/snl.2023.125.119.

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A new cryptic lineage of the complex A. caliginosa was found in the grasslands of Luxembourg. Its genetic divergence was of the same level than the one found for the other COI lineages of the complex. The distribution of the pairwise distance comparisons of the DNA barcodes within the complex showed that it could potentially experience gene flow among its components, including this new lineage. This exemplifies that diversity in Lumbricidae can still be uncovered in the well-prospected European zone.

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19

Hoshizaki, S., R. Washimori, S. Kubota, et al. "Two mitochondrial lineages occur in the Asian corn borer, Ostrinia furnacalis (Lepidoptera: Crambidae), in Japan." Bulletin of Entomological Research 98, no. 5 (2008): 519–26. http://dx.doi.org/10.1017/s0007485308005841.

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AbstractThe genealogy and diversity of the mitochondrial cytochrome oxidase subunit II (COII) gene were investigated for Ostrinia furnacalis in Japan. A preliminary examination of mitochondrial lineages in China and the Philippines was also made. Two lineages (A and B) were found in the COII gene. Lineage A was frequent throughout the Japanese main islands (Hokkaido, Honshu, Shikoku and Kyushu), while the frequency of lineage B varied among these islands. No clear patterns of geographical population structure were found. Population genetic features suggested that the O. furnacalis population h

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20

SHIMADA, TOMOHIKO, MASAFUMI MATSUI, PAUL YAMBUN, MAKLARIN LAKIM, and MARYATI MOHAMED. "Detection of two cryptic taxa in Meristogenys amoropalamus (Amphibia, Ranidae) through nuclear and mitochondrial DNA analyses." Zootaxa 1843, no. 1 (2008): 24. http://dx.doi.org/10.11646/zootaxa.1843.1.2.

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We identified three distinct sympatric lineages of frogs among specimens previously considered a single species (Meris- togenys amoropalamus Matsui), based on 909 bp of mitochondrial DNA (12S rRNA and cytochrome b). To seek evidence of reproductive isolation between these lineages, we first analyzed a 249-bp fragment of the nuclear proopiomelanocortin (POMC) gene and found five haplotypes, of which two were limited to lineage 1 and three belonged to lineages 3 and 4. In a subsequent phylogenetic analysis of a 1313-bp fragment of nuclear POMC, Rag-1, and rhodopsin, lineage 1 was again distinct,

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ENGELBRECHT, ADRIAAN, CONRAD A. MATTHEE, EDWARD A. UECKERMANN, and SONJA MATTHEE. "Evidence of cryptic speciation in mesostigmatid mites from South Africa." Parasitology 141, no. 10 (2014): 1322–32. http://dx.doi.org/10.1017/s0031182014000584.

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SUMMARYLaelaps giganteus and Laelaps muricola (Mesostigmata; Laelapidae) are widespread and locally abundant host generalists on small mammals in southern Africa. The large host range and complex life history of these ectoparasites may allude to possible intraspecific cryptic diversity in these taxa. To assess genetic and morphological diversity in L. giganteus and L. muricola, we sampled 228 rodents at eight localities in South Africa. This sample included nine previously recorded host species and on these, L. muricola was only recorded from Mastomys natalensis and Micaelamys namaquensis whil

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22

López-Wilchis, Ricardo, Mayela Flores-Romero, Luis M. Guevara-Chumacero, et al. "Evolutionary scenarios associated with the Pteronotus parnellii cryptic species-complex (Chiroptera: Mormoopidae)." Acta Chiropterologica 18, no. 1 (2016): 91–116. https://doi.org/10.5281/zenodo.13454518.

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(Uploaded by Plazi for the Bat Literature Project) One of the major challenges to understanding the evolution of Neotropical bats concerns our capacity to successfully scrutinize phylogenetic patterns associated with cases of cryptic species complexes. In this study Pteronotus parnellii is examined as a selected example of a known lineage of mormoopid bat that potentially contains several cryptic species. A samples of 452 individuals from 83 different localities, essentially covering its entire mainland distribution, was evaluated using two genetic markers: COI (mitochondrial) and DBY (nuclear

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23

López-Wilchis, Ricardo, Mayela Flores-Romero, Luis M. Guevara-Chumacero, et al. "Evolutionary scenarios associated with the Pteronotus parnellii cryptic species-complex (Chiroptera: Mormoopidae)." Acta Chiropterologica 18, no. 1 (2016): 91–116. https://doi.org/10.5281/zenodo.13454518.

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Abstract:

(Uploaded by Plazi for the Bat Literature Project) One of the major challenges to understanding the evolution of Neotropical bats concerns our capacity to successfully scrutinize phylogenetic patterns associated with cases of cryptic species complexes. In this study Pteronotus parnellii is examined as a selected example of a known lineage of mormoopid bat that potentially contains several cryptic species. A samples of 452 individuals from 83 different localities, essentially covering its entire mainland distribution, was evaluated using two genetic markers: COI (mitochondrial) and DBY (nuclear

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24

López-Wilchis, Ricardo, Mayela Flores-Romero, Luis M. Guevara-Chumacero, et al. "Evolutionary scenarios associated with the Pteronotus parnellii cryptic species-complex (Chiroptera: Mormoopidae)." Acta Chiropterologica 18, no. 1 (2016): 91–116. https://doi.org/10.5281/zenodo.13454518.

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Abstract:

(Uploaded by Plazi for the Bat Literature Project) One of the major challenges to understanding the evolution of Neotropical bats concerns our capacity to successfully scrutinize phylogenetic patterns associated with cases of cryptic species complexes. In this study Pteronotus parnellii is examined as a selected example of a known lineage of mormoopid bat that potentially contains several cryptic species. A samples of 452 individuals from 83 different localities, essentially covering its entire mainland distribution, was evaluated using two genetic markers: COI (mitochondrial) and DBY (nuclear

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25

López-Wilchis, Ricardo, Mayela Flores-Romero, Luis M. Guevara-Chumacero, et al. "Evolutionary scenarios associated with the Pteronotus parnellii cryptic species-complex (Chiroptera: Mormoopidae)." Acta Chiropterologica 18, no. 1 (2016): 91–116. https://doi.org/10.5281/zenodo.13454518.

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Abstract:

(Uploaded by Plazi for the Bat Literature Project) One of the major challenges to understanding the evolution of Neotropical bats concerns our capacity to successfully scrutinize phylogenetic patterns associated with cases of cryptic species complexes. In this study Pteronotus parnellii is examined as a selected example of a known lineage of mormoopid bat that potentially contains several cryptic species. A samples of 452 individuals from 83 different localities, essentially covering its entire mainland distribution, was evaluated using two genetic markers: COI (mitochondrial) and DBY (nuclear

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26

López-Wilchis, Ricardo, Mayela Flores-Romero, Luis M. Guevara-Chumacero, et al. "Evolutionary scenarios associated with the Pteronotus parnellii cryptic species-complex (Chiroptera: Mormoopidae)." Acta Chiropterologica 18, no. 1 (2016): 91–116. https://doi.org/10.5281/zenodo.13454518.

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Abstract:

(Uploaded by Plazi for the Bat Literature Project) One of the major challenges to understanding the evolution of Neotropical bats concerns our capacity to successfully scrutinize phylogenetic patterns associated with cases of cryptic species complexes. In this study Pteronotus parnellii is examined as a selected example of a known lineage of mormoopid bat that potentially contains several cryptic species. A samples of 452 individuals from 83 different localities, essentially covering its entire mainland distribution, was evaluated using two genetic markers: COI (mitochondrial) and DBY (nuclear

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27

KONDAKOV, ALEXANDER V., DMITRY M. PALATOV, ZAKIR P. RAJABOV, et al. "DNA analysis of a non-native lineage of Sinanodonta woodiana species complex (Bivalvia: Unionidae) from Middle Asia supports the Chinese origin of the European invaders." Zootaxa 4462, no. 4 (2018): 511. http://dx.doi.org/10.11646/zootaxa.4462.4.4.

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The Sinanodonta woodiana species complex includes several cryptic species-level phylogenetic lineages, the taxonomic placement of which is unclear. Here, we present the results of molecular analyses of a Sinanodonta sample from Middle Asia (Uzbekistan). The COI haplotype of the Uzbekistan lineage is similar to those of invasive Sinanodonta populations from Europe, Russia and Myanmar. We show that the non-native Sinanodonta flocks in Europe and Middle Asia originated from a single source population in China. Our results reveal that the Sinanodonta woodiana species complex comprises at least six

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28

Singhal, Sonal, and Craig Moritz. "Reproductive isolation between phylogeographic lineages scales with divergence." Proceedings of the Royal Society B: Biological Sciences 280, no. 1772 (2013): 20132246. http://dx.doi.org/10.1098/rspb.2013.2246.

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Phylogeographic studies frequently reveal multiple morphologically cryptic lineages within species. What is not yet clear is whether such lineages represent nascent species or evolutionary ephemera. To address this question, we compare five contact zones, each of which occurs between ecomorphologically cryptic lineages of skinks from the rainforests of the Australian Wet Tropics. Although the contacts probably formed concurrently in response to Holocene expansion from glacial refugia, we estimate that the divergence times ( τ ) of the lineage pairs range from 3.1 to 11.5 Ma. Multi-locus analys

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HAMIDY, AMIR, MISBAHUL MUNIR, MUMPUNI MUMPUNI, MILA RAHMANIA, and AZIS ABDUL KHOLIK. "Detection of Cryptic taxa in the genus Leptophryne (Fitzinger, 1843) (Amphibia; Bufonidae) and the description of a new species from Java, Indonesia." Zootaxa 4450, no. 4 (2018): 427. http://dx.doi.org/10.11646/zootaxa.4450.4.2.

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We investigated phylogenetic relationships among populations of two species within the genus Leptophryne, L. cruentata and L. borbonica, using the mitochondrial 16S rRNA gene. As a result, we identified two distinct lineages within populations currently considered Leptophryne cruentata: 1) a lineage containing L. cruentata from the type locality, and 2) a lineage from Mt. Slamet and Mt. Ciremai. On the basis of genetic and morphological differences, we describe the Mt. Slamet and Mt. Ciremai populations as a new species, L. javanica sp. nov. The new species is distinguished from L. cruentata a

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Vallo, Peter, Antonio Guillén-Servent, Petr Benda, Debra B. Pires, and Petr Koubek. "Variation of mitochondrial DNA in the Hipposideros caffer complex (Chiroptera: Hipposideridae) and its taxonomic implications." Acta Chiropterologica 10, no. 2 (2008): 193–206. https://doi.org/10.5281/zenodo.13504373.

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(Uploaded by Plazi for the Bat Literature Project) The Afrotropical leaf-nosed bat Hipposideros caffer has been traditionally regarded as a complex of populations, currently pertaining to two recognized cryptic species, H. caffer and H. ruber. Extent of distribution and morphological variation of these bats has raised concerns over whether the current perception of the complex reflects true phylogenetic relationships and taxonomic diversity. Our phylogenetic analysis of nucleotide sequences of the mitochondrial cytochrome b gene challenged the hypothesis of two cryptic species. Instead of the

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31

Vallo, Peter, Antonio Guillén-Servent, Petr Benda, Debra B. Pires, and Petr Koubek. "Variation of mitochondrial DNA in the Hipposideros caffer complex (Chiroptera: Hipposideridae) and its taxonomic implications." Acta Chiropterologica 10, no. 2 (2008): 193–206. https://doi.org/10.5281/zenodo.13504373.

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(Uploaded by Plazi for the Bat Literature Project) The Afrotropical leaf-nosed bat Hipposideros caffer has been traditionally regarded as a complex of populations, currently pertaining to two recognized cryptic species, H. caffer and H. ruber. Extent of distribution and morphological variation of these bats has raised concerns over whether the current perception of the complex reflects true phylogenetic relationships and taxonomic diversity. Our phylogenetic analysis of nucleotide sequences of the mitochondrial cytochrome b gene challenged the hypothesis of two cryptic species. Instead of the

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32

Vallo, Peter, Antonio Guillén-Servent, Petr Benda, Debra B. Pires, and Petr Koubek. "Variation of mitochondrial DNA in the Hipposideros caffer complex (Chiroptera: Hipposideridae) and its taxonomic implications." Acta Chiropterologica 10, no. 2 (2008): 193–206. https://doi.org/10.5281/zenodo.14821764.

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(Uploaded by Plazi for the Bat Literature Project) The Afrotropical leaf-nosed bat Hipposideros caffer has been traditionally regarded as a complex of populations, currently pertaining to two recognized cryptic species, H. caffer and H. ruber. Extent of distribution and morphological variation of these bats has raised concerns over whether the current perception of the complex reflects true phylogenetic relationships and taxonomic diversity. Our phylogenetic analysis of nucleotide sequences of the mitochondrial cytochrome b gene challenged the hypothesis of two cryptic species. Instead of the

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33

Vallo, Peter, Antonio Guillén-Servent, Petr Benda, Debra B. Pires, and Petr Koubek. "Variation of mitochondrial DNA in the Hipposideros caffer complex (Chiroptera: Hipposideridae) and its taxonomic implications." Acta Chiropterologica 10, no. 2 (2008): 193–206. https://doi.org/10.5281/zenodo.13504373.

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Abstract:

(Uploaded by Plazi for the Bat Literature Project) The Afrotropical leaf-nosed bat Hipposideros caffer has been traditionally regarded as a complex of populations, currently pertaining to two recognized cryptic species, H. caffer and H. ruber. Extent of distribution and morphological variation of these bats has raised concerns over whether the current perception of the complex reflects true phylogenetic relationships and taxonomic diversity. Our phylogenetic analysis of nucleotide sequences of the mitochondrial cytochrome b gene challenged the hypothesis of two cryptic species. Instead of the

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Vallo, Peter, Antonio Guillén-Servent, Petr Benda, Debra B. Pires, and Petr Koubek. "Variation of mitochondrial DNA in the Hipposideros caffer complex (Chiroptera: Hipposideridae) and its taxonomic implications." Acta Chiropterologica 10, no. 2 (2008): 193–206. https://doi.org/10.5281/zenodo.13504373.

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(Uploaded by Plazi for the Bat Literature Project) The Afrotropical leaf-nosed bat Hipposideros caffer has been traditionally regarded as a complex of populations, currently pertaining to two recognized cryptic species, H. caffer and H. ruber. Extent of distribution and morphological variation of these bats has raised concerns over whether the current perception of the complex reflects true phylogenetic relationships and taxonomic diversity. Our phylogenetic analysis of nucleotide sequences of the mitochondrial cytochrome b gene challenged the hypothesis of two cryptic species. Instead of the

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Yoshida, Ai, Shintaro Yabu, and Joji M. Otaki. "The Plastic Larval Body Color of the Pale Grass Blue Butterfly Zizeeria maha (Lepidoptera: Lycaenidae) in Response to the Host Plant Color: The Maternal Effect on Crypsis." Insects 14, no. 2 (2023): 202. http://dx.doi.org/10.3390/insects14020202.

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Many lepidopteran larvae show body color polyphenism, and their colors may be cryptic on the host plant leaves. To elucidate the effect of the host plant color on the plastic larval body color, we focused on the lycaenid butterfly Zizeeria maha, which shows various larval body colors ranging from green to red, even within a sibling group. We showed that oviposition was normally performed on both green and red leaves, despite a green preference and the fact that the larvae grew equally by consuming either green or red leaves. The number of red larvae decreased from the second instar stage to th

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Santamaria, Carlos A., Joanna K. Bluemel, Nancy Bunbury, and Melinda Curran. "Cryptic biodiversity and phylogeographic patterns of Seychellois Ligia isopods." PeerJ 5 (October 6, 2017): e3894. http://dx.doi.org/10.7717/peerj.3894.

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Ligia isopods are conspicuous inhabitants of rocky intertidal habitats exhibiting several biological traits that severely limit their dispersal potential. Their presence in patchy habitats and low vagility may lead to long term isolation, allopatric isolation and possible cryptic speciation. Indeed, various species of Ligia have been suggested to represent instead cryptic species complexes. Past studies; however, have largely focused in Eastern Pacific and Atlantic species of Ligia, leaving in doubt whether cryptic diversity occurs in other highly biodiverse areas. The Seychelles consists of 1

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Dong, Yan, Jibao Jiang, Zhu Yuan, Qi Zhao, and Jiangping Qiu. "Population Genetic Structure Reveals Two Lineages of Amynthas triastriatus (Oligochaeta: Megascolecidae) in China, with Notes on a New Subspecies of Amynthas triastriatus." International Journal of Environmental Research and Public Health 17, no. 5 (2020): 1538. http://dx.doi.org/10.3390/ijerph17051538.

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Amynthas triastriatus (Oligochaete: Megascolecidae) is a widely distributed endemic species in Southern China. To shed light on the population genetic diversity and to elucidate the population differentiation and dispersal of A. triastriatus, a population genetic structure study was undertaken based on samples from 35 locations collected from 2010 to 2016. Two exclusive lineages within A. triastriatus—lineage A and lineage B—were revealed. Lineage A was mainly distributed at high altitudes while lineage B was mainly distributed at low altitudes in Southeast China. The genetic diversity indices

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Makhov, Ilia A., Yelizaveta Y. U. Gorodilova, and Vladimir A. Lukhtanov. "Sympatric occurrence of deeply diverged mitochondrial DNA lineages in Siberian geometrid moths (Lepidoptera: Geometridae): cryptic speciation, mitochondrial introgression, secondary admixture or effect of Wolbachia?" Biological Journal of the Linnean Society 134, no. 2 (2021): 342–65. http://dx.doi.org/10.1093/biolinnean/blab089.

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Abstract The divergent sympatric mitochondrial lineages within traditionally recognized species present a challenge regularly faced by taxonomists and evolutionary biologists. We encountered this problem when studying the Siberian geometrid moths, Alcis deversata and Thalera chlorosaria. Within each of these species we found two deeply diverged mitochondrial lineages that demonstrated a level of genetic differentiation exceeding the standard interspecific DNA barcode threshold. Using analyses of nuclear genes, morphology, ecological preferences and Wolbachia endosymbionts, we tested five hypot

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Nirchio, Mauro, Claudio Oliveira, Zoila R. Siccha-Ramirez, et al. "The Mugil curema species complex (Pisces, Mugilidae): a new karyotype for the Pacific white mullet mitochondrial lineage." Comparative Cytogenetics 11, no. (2) (2017): 225–37. https://doi.org/10.3897/CompCytogen.v11i2.11579.

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Recent molecular phylogenetic analyses have shown that the Mugil curema Valenciennes, 1836 species complex includes M. incilis Hancock, 1830, M. thoburni (Jordan & Starks, 1896) and at least four "M. curema" mitochondrial lineages, considered as cryptic species. The cytogenetic data on some representatives of the species complex have shown a high cytogenetic diversity. This research reports the results of cytogenetic and molecular analyses of white mullet collected in Ecuador. The analyzed specimens were molecularly assigned to the Mugil sp. O, the putative cryptic species present in the P

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McKeague, Sean J., Kacey O’Rourke, Stephen Fanning, et al. "Cryptic switch – acute leukaemia with cytogenetically cryptic FGFR1 rearrangement and lineage switch during therapy." Pathology 55 (February 2023): S23. http://dx.doi.org/10.1016/j.pathol.2022.12.078.

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Hart, Michael W., Maria Byrne, and Sheri L. Johnson. "Patiriella pseudoexigua (Asteroidea: Asterinidae): a cryptic species complex revealed by molecular and embryological analyses." Journal of the Marine Biological Association of the United Kingdom 83, no. 5 (2003): 1109–16. http://dx.doi.org/10.1017/s002531540300835xh.

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Cryptic lineages were identified within a morphologically uniform group of sea stars distributed from Australia to Japan. Among eight populations, all of which have been referred to Patiriella pseudoexigua, we found seven unique mitochondrial DNA sequences clustered into four distinct lineages. These four lineages formed a monophyletic group in which sister clades were separated by small genetic distances but could be differentiated from each other on the basis of reproductive differences. The four lineages thus appear to be separate but very closely related species. Examination of reproductio

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Norman, Victoria, Hugo Darras, Christopher Tranter, Serge Aron, and William O. H. Hughes. "Cryptic lineages hybridize for worker production in the harvester ant Messor barbarus." Biology Letters 12, no. 11 (2016): 20160542. http://dx.doi.org/10.1098/rsbl.2016.0542.

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The reproductive division of labour between queen and worker castes in social insects is a defining characteristic of eusociality and a classic example of phenotypic plasticity. Whether social insect larvae develop into queens or workers has long been thought to be determined by environmental cues, i.e. larvae are developmentally totipotent. Contrary to this paradigm, several recent studies have revealed that caste is determined by genotype in some ant species, but whether this is restricted to just a few exceptional species is still unclear. Here, we show that the Mediterranean harvester ant

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Batsleer, Femke, Elena Portelli, John J. Borg, Andreas Kiefer, Michael Veith, and Daan Dekeukeleire. "Maltese bats show phylogeographic affiliation with North-Africa: implications for conservation." Hystrix, the Italian Journal of Mammalogy 30, no. 2 (2019): 172–77. https://doi.org/10.5281/zenodo.13472192.

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(Uploaded by Plazi for the Bat Literature Project) In the Mediterranean region, cryptic diversity of bats is common. As distinct genetic lineages should be managed independently for conservation, insight into bat phylogeography is important. The Maltese islands are located in the centre of the Mediterranean between North Africa and Sicily and are densely populated. At present, it is thought that at least seven species of bats are native, but phylogeographic affiliations remain largely unexplored. Therefore, we sequenced a ca. 540 bp fragment of the mitochondrial 16S rRNA gene from 23 bats, whi

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Batsleer, Femke, Elena Portelli, John J. Borg, Andreas Kiefer, Michael Veith, and Daan Dekeukeleire. "Maltese bats show phylogeographic affiliation with North-Africa: implications for conservation." Hystrix, the Italian Journal of Mammalogy 30, no. 2 (2019): 172–77. https://doi.org/10.5281/zenodo.13472192.

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(Uploaded by Plazi for the Bat Literature Project) In the Mediterranean region, cryptic diversity of bats is common. As distinct genetic lineages should be managed independently for conservation, insight into bat phylogeography is important. The Maltese islands are located in the centre of the Mediterranean between North Africa and Sicily and are densely populated. At present, it is thought that at least seven species of bats are native, but phylogeographic affiliations remain largely unexplored. Therefore, we sequenced a ca. 540 bp fragment of the mitochondrial 16S rRNA gene from 23 bats, whi

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Batsleer, Femke, Elena Portelli, John J. Borg, Andreas Kiefer, Michael Veith, and Daan Dekeukeleire. "Maltese bats show phylogeographic affiliation with North-Africa: implications for conservation." Hystrix, the Italian Journal of Mammalogy 30, no. 2 (2019): 172–77. https://doi.org/10.5281/zenodo.13472192.

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Abstract:

(Uploaded by Plazi for the Bat Literature Project) In the Mediterranean region, cryptic diversity of bats is common. As distinct genetic lineages should be managed independently for conservation, insight into bat phylogeography is important. The Maltese islands are located in the centre of the Mediterranean between North Africa and Sicily and are densely populated. At present, it is thought that at least seven species of bats are native, but phylogeographic affiliations remain largely unexplored. Therefore, we sequenced a ca. 540 bp fragment of the mitochondrial 16S rRNA gene from 23 bats, whi

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46

Batsleer, Femke, Elena Portelli, John J. Borg, Andreas Kiefer, Michael Veith, and Daan Dekeukeleire. "Maltese bats show phylogeographic affiliation with North-Africa: implications for conservation." Hystrix, the Italian Journal of Mammalogy 30, no. 2 (2019): 172–77. https://doi.org/10.5281/zenodo.13472192.

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Abstract:

(Uploaded by Plazi for the Bat Literature Project) In the Mediterranean region, cryptic diversity of bats is common. As distinct genetic lineages should be managed independently for conservation, insight into bat phylogeography is important. The Maltese islands are located in the centre of the Mediterranean between North Africa and Sicily and are densely populated. At present, it is thought that at least seven species of bats are native, but phylogeographic affiliations remain largely unexplored. Therefore, we sequenced a ca. 540 bp fragment of the mitochondrial 16S rRNA gene from 23 bats, whi

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47

Batsleer, Femke, Elena Portelli, John J. Borg, Andreas Kiefer, Michael Veith, and Daan Dekeukeleire. "Maltese bats show phylogeographic affiliation with North-Africa: implications for conservation." Hystrix, the Italian Journal of Mammalogy 30, no. 2 (2019): 172–77. https://doi.org/10.5281/zenodo.13472192.

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Abstract:

(Uploaded by Plazi for the Bat Literature Project) In the Mediterranean region, cryptic diversity of bats is common. As distinct genetic lineages should be managed independently for conservation, insight into bat phylogeography is important. The Maltese islands are located in the centre of the Mediterranean between North Africa and Sicily and are densely populated. At present, it is thought that at least seven species of bats are native, but phylogeographic affiliations remain largely unexplored. Therefore, we sequenced a ca. 540 bp fragment of the mitochondrial 16S rRNA gene from 23 bats, whi

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48

Chiarini, Franco E., Marisel A. Scaldaferro, Gabriel Bernardello, and M. Cristina Acosta. "Cryptic genetic diversity in Solanum elaeagnifolium (Solanaceae) from South America." Australian Journal of Botany 66, no. 7 (2018): 531. http://dx.doi.org/10.1071/bt17245.

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Solanum elaeagnifolium is a global invasive weed that is polyploid in the South American range. Our aim was to establish the origin and distribution of these polyploid lineages, together with their relationship with the invasion of new habitats. Ploidy level was determined in 26 natural populations using chromosomal counts, and two non-coding plastid regions trnL-trnF and rpl32F-trnL were sequenced. Relationships among haplotypes were examined by a median-joining network, and groups of populations were identified by employing a spatial analysis of molecular variance. Phylogenetic relationships

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Pieńkowska, Joanna R., Giuseppe Manganelli, Folco Giusti, Alessandro Hallgass, and Andrzej Lesicki. "Exploring Monacha cantiana (Montagu, 1803) phylogeography: cryptic lineages and new insights into the origin of the English populations (Eupulmonata, Stylommatophora, Hygromiidae)." ZooKeys 765 (June 6, 2018): 1–41. http://dx.doi.org/10.3897/zookeys.765.24386.

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Molecular analysis of nucleotide sequences of mitochondrial cytochrome oxidase subunit 1 (COI) and 16S ribosomal DNA (16SrDNA) as well as nuclear histone 3 (H3) and internal transcribed spacer 2 of rDNA (ITS2) gene fragments together with morphological analysis of shell and genitalia features showed that English, French and Italian populations usually assigned to Monachacantiana consist of four distinct lineages (CAN-1, CAN-2, CAN-3, CAN-4). One of these lineages (CAN-1) included most of the UK (five sites) and Italian (five sites) populations examined. Three other lineages represented populat

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Titus, Robert. "Cryptic variation and its manifestation in the Lower Trentonian Rafinesquina lineage (Ordovician, New York State)." Paleontological Society Special Publications 6 (1992): 292. http://dx.doi.org/10.1017/s2475262200008522.

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Species populations commonly carry a great deal of genetic variation which is not expressed in individual phenotypes. Cryptic variation can be carried in recessive alleles, in cases of heterosis, or where modifier genes inhibit expression of the hidden trait. Other genetic and ecological factors also allow cryptic variation. Stabilizing selection prevents the expression of hidden traits; normalizing selection weeds out the deviants and canalizing selection suppresses their traits. Together the two keep the species near the top of the adaptive peak. Cryptic variation balances a species' need to

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