Who’s your daddy? On the identity and distribution of the paternal hybrid ancestor of the parthenogenetic gecko Lepidodactylus lugubris (Reptilia: Squamata: Gekkonidae)

The widespread parthenogenetic gecko Lepidodactylus lugubris is comprised of several clonal lineages, at least one of which has been known for some time to have originated from hybridization between its maternal ancestor, Lepidodactylus moestus, and a putatively undescribed paternal ancestor previously known only from remote islands in the Central Pacific. By integrating new genetic sequences from multiple studies on Lepidodactylus and incorporating new genetic sequences from previously sampled populations, we recovered a phylogenetic tree that shows a close genetic similarity between the generally hypothesized paternal hybrid ancestor and a recently described species from Maluku (Indonesia), Lepidodactylus pantai. Our results suggest that the paternal hybrid ancestor of at least one parthenogenetic clone of L. lugubris is conspecific with L. pantai and that the range of this species extends to Palau, the Caroline Islands, the Kei Islands, Wagabu, and potentially other small islands near New Guinea. Deeper genetic structure in the western (Palau, Maluku) versus eastern (eastern Melanesia, Micronesia, Polynesia) part of this species’ range suggests that the western populations likely dispersed via natural colonization, whereas the eastern populations may be the result of human-mediated dispersal. The potential taxonomic affinities and biogeographic history should be confirmed with further morphological and genetic analyses, including research on L. woodfordi from its type locality, which would have nomenclatural priority if found to be conspecific with L. pantai. We recommend referring to the wide-ranging sexual species as Lepidodactylus pantai until such a comparison can be made.

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Genetic variability in physic nuts cultivated in Northeastern Brazil

Ciência Rural ◽

10.1590/s0103-84782013005000060 ◽

2013 ◽

Vol 43 (6) ◽

pp. 978-984 ◽

Cited By ~ 3

Author(s):

Vanice Dias Oliveira ◽

Allivia Rouse Carregosa Rabbani ◽

Ana Veruska Cruz da Silva ◽

Ana da Silva Lédo

Keyword(s):

Molecular Markers ◽

Genetic Structure ◽

Genetic Variability ◽

Genetic Similarity ◽

Rapd Markers ◽

Dna Amplification ◽

Northeastern Brazil ◽

Jaccard Coefficient ◽

Physic Nut ◽

Genetic Structure And Diversity

This research had as objective to characterize genetically individuals of physic nut cultivated in experimental areas in Sergipe, Brazil by means of RAPD molecular markers. Leaves of 40 individuals were collected and DNA was isolated using CTAB 2% method. Were used 30 primers RAPD for DNA amplification, and this data was used to estimate the genetic similarity among the pairs of individuals, using Jaccard coefficient, and group them out for the UPGMA method. Also, the genetic structure and diversity of the populations were assessed using AMOVA. Of the 100 fragments generated, 29 of were polymorphic. A similarity average of 0.54 among the individuals was found and the amplitude similarities varied from 0.18 to 1.00. One of them (U5) was unit clusters and formed by the most divergent individuals. AMOVA indicated that there is more variation within (63%) the population. In conclusion, it was possible verify genetic variability in physic nut using RAPD markers at these experimental areas.

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The role of Central American barriers in shaping the evolutionary history of the northernmost glassfrog,Hyalinobatrachium fleischmanni(Anura: Centrolenidae)

PeerJ ◽

10.7717/peerj.6115 ◽

2019 ◽

Vol 7 ◽

pp. e6115 ◽

Cited By ~ 4

Author(s):

Angela M. Mendoza ◽

Wilmar Bolívar-García ◽

Ella Vázquez-Domínguez ◽

Roberto Ibáñez ◽

Gabriela Parra Olea

Keyword(s):

Genetic Structure ◽

Central America ◽

Population Expansion ◽

Central American ◽

Fault System ◽

Mountain Range ◽

Amphibian Species ◽

Biogeographic History ◽

History Of ◽

The Impact

The complex geological history of Central America has been useful for understanding the processes influencing the distribution and diversity of multiple groups of organisms. Anurans are an excellent choice for such studies because they typically exhibit site fidelity and reduced movement. The objective of this work was to identify the impact of recognized geographic barriers on the genetic structure, phylogeographic patterns and divergence times of a wide-ranging amphibian species,Hyalinobatrachium fleischmanni. We amplified three mitochondrial regions, two coding (COI and ND1) and one ribosomal (16S), in samples collected from the coasts of Veracruz and Guerrero in Mexico to the humid forests of Chocó in Ecuador. We examined the biogeographic history of the species through spatial clustering analyses (Geneland and sPCA), Bayesian and maximum likelihood reconstructions, and spatiotemporal diffusion analysis. Our data suggest a Central American origin ofH. fleischmanniand two posterior independent dispersals towards North and South American regions. The first clade comprises individuals from Colombia, Ecuador, Panama and the sister speciesHyalinobatrachium tatayoi; this clade shows little structure, despite the presence of the Andes mountain range and the long distances between sampling sites. The second clade consists of individuals from Costa Rica, Nicaragua, and eastern Honduras with no apparent structure. The third clade includes individuals from western Honduras, Guatemala, and Mexico and displays deep population structure. Herein, we synthesize the impact of known geographic areas that act as barriers to glassfrog dispersal and demonstrated their effect of differentiatingH. fleischmanniinto three markedly isolated clades. The observed genetic structure is associated with an initial dispersal event from Central America followed by vicariance that likely occurred during the Pliocene. The southern samples are characterized by a very recent population expansion, likely related to sea-level and climatic oscillations during the Pleistocene, whereas the structure of the northern clade has probably been driven by dispersal through the Isthmus of Tehuantepec and isolation by the Motagua–Polochic–Jocotán fault system and the Mexican highlands.

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Genetic structure and biogeographic history of the Bicknell’s Thrush/ Gray-cheeked Thrush species complex

The Auk ◽

10.1093/auk/ukz066 ◽

2019 ◽

Vol 137 (1) ◽

Cited By ~ 1

Author(s):

Alyssa M Fitzgerald ◽

Jason Weir ◽

Joel Ralston ◽

Ian G Warkentin ◽

Darroch M Whitaker ◽

...

Keyword(s):

Genetic Structure ◽

Late Pleistocene ◽

Species Complex ◽

Extended Period ◽

Genetic Data ◽

Distribution Models ◽

Biogeographic History ◽

History Of ◽

Low Levels ◽

Bicknell's Thrush

Abstract We examined species limits, admixture, and genetic structure among populations in the Bicknell’s Thrush (Catharus bicknelli)–Gray-cheeked Thrush (C. minimus) species complex to establish the geographic and temporal context of speciation in this group, which is a model system in ecology and a high conservation priority. We obtained mitochondrial ND2 sequences from 186 Bicknell’s Thrushes, 77 Gray-cheeked Thrushes, and 55 individuals of their closest relative, the Veery (C. fuscescens), and genotyped a subset of individuals (n = 72) at 5,633 anonymous single nucleotide polymorphic (SNP) loci. Between-species sequence divergence was an order of magnitude greater than divergence within each species, divergence was dated to the late Pleistocene (420 kbp) based on Bayesian coalescence estimation, and a coalescent model (IMa) revealed almost no gene flow between species based on ND2. SNP data were consistent with mitochondrial results and revealed low levels of admixture among species (3 of 37 Bicknell’s Thrushes, no Gray-cheeked Thrushes, and no Veeries were >2% admixed). Species distribution models projected to the Last Glacial Maximum suggest that Bicknell’s Thrush and Gray-cheeked Thrush resided in primarily allopatric refugia in the late Pleistocene, consistent with the genetic data that support reproductive isolation over an extended period of time. Our genetic data suggest that both species underwent demographic expansions, possibly as they expanded out of Pleistocene refugia into their current ranges. We conclude that Bicknell’s Thrush and Gray-cheeked Thrush are 2 distinct species-level lineages despite low levels of Gray-cheeked Thrush introgression in Bicknell’s Thrushes, and divergence has been maintained by a long history of allopatry in subtly different habitats. Their unique phylogeography among boreal forest birds indicates that either cryptic species breaks in eastern North America are still undiscovered, or another factor, such as divergent natural selection, high migratory connectivity, or interspecific competition, played a role in their divergence.

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New Insights into the Occurrence and Toxin Profile of Ciguatoxins in Selvagens Islands (Madeira, Portugal)

Toxins ◽

10.3390/toxins10120524 ◽

2018 ◽

Vol 10 (12) ◽

pp. 524 ◽

Cited By ~ 14

Author(s):

Pedro Costa ◽

Pablo Estevez ◽

David Castro ◽

Lucía Soliño ◽

Neide Gouveia ◽

...

Keyword(s):

Trophic Levels ◽

Small Islands ◽

Mass Spectrometry Detection ◽

Natural Reserve ◽

The Pacific ◽

Fish Samples ◽

Biological Sampling ◽

The Caribbean ◽

Remote Islands ◽

High Fish

Ciguatoxins (CTXs), endemic from tropical and subtropical regions of the Pacific and Indian Ocean and the Caribbean Sea, have caused several human poisonings during the last decade in Europe. Ciguatera fish poisonings (CFP) in Madeira and Canary Islands appear to be particularly related with consumption of fish caught close to Selvagens Islands, a Portuguese natural reserve composed of three small islands that harbor high fish biomass. In this study, fish specimens considered as potential vectors of CTXs were caught in Madeira and Selvagens archipelagos for toxins determination via sensitive liquid chromatography with tandem mass spectrometry detection (LC–MS/MS). CTXs were found in most of the fish samples from Selvagens and none from Madeira. Caribbean ciguatoxin-1 (C-CTX1) was the only toxin congener determined, reaching the highest value of 0.25 µg C-CTX1 kg−1 in a 4.6 kg island grouper (Mycteroperca fusca). This study indicates that a diversity of fish from different trophic levels contains CTXs, Selvagens appear to be one of the most favorable locations for CTXs food web transfer and finally, this study highlights the need of further research based on intensive environmental and biological sampling on these remote islands.

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Some leptothecate hydroids (Cnidaria, Hydrozoa) from Hawaii, mostly from inshore and nearshore waters

Zootaxa ◽

10.11646/zootaxa.4830.2.1 ◽

2020 ◽

Vol 4830 (2) ◽

pp. 201-246

Author(s):

DALE R. CALDER

Keyword(s):

Pacific Ocean ◽

Shallow Water ◽

Marine Species ◽

Pacific Region ◽

Bishop Museum ◽

Central Pacific ◽

Central Pacific Ocean ◽

Small Collection ◽

Remote Islands ◽

First Time

This report is based on a small collection of hydroids from the Hawaiian Islands, in the central Pacific Ocean. Most of the examined material was obtained by staff of the Bernice Pauahi Bishop Museum, Honolulu, during surveys for nonindigenous marine species in shallow, sheltered, inshore or nearshore waters, and especially in harbours, bays, and lagoons. In all, 34 species of leptothecate hydroids, assigned to 14 families and 20 genera, were identified and are discussed. One of them, based on a single infertile colony with a damaged hydrotheca, was identified provisionally only to the rank of suborder. Given the limited geographic and bathymetric focus of the surveys, only four of the species, Clytia thornelyi, Halecium sibogae, Macrorhynchia balei, and M. hawaiensis, were collected at depths greater than 25 m. Seven species, Cirrholovenia tetranema Kramp, 1959, Orthopyxis crenata (Hartlaub, 1901), Clytia elongata Marktanner-Turneretscher, 1890, C. paulensis (Vanhöffen, 1910), Tridentata maldivensis (Borradaile, 1905), Monotheca flexuosa (Bale, 1894), and a hydroid identified only as Eirenida (undetermined), are recorded from Hawaii for the first time. Three others, Lytocarpia nigra (Nutting, 1905) Macrorhynchia balei (Nutting, 1905), and M. hawaiensis (Nutting, 1905), have their type localities in Hawaii, with the last of these being known to date only from the Hawaiian archipelago. Most of the species are well-known from shallow water areas across the tropical and subtropical Indo-Pacific region, and over half of them have been reported as well from warm waters in the Atlantic Ocean. Their existence in the remote islands of Hawaii is attributed to long-range dispersal by both natural and human-mediated means, including shipping.

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Phylogeography and genetic structure of the slow worms Anguis cephallonica and Anguis graeca (Squamata: Anguidae) from the southern Balkan Peninsula

Amphibia-Reptilia ◽

10.1163/15685381-00002947 ◽

2014 ◽

Vol 35 (2) ◽

pp. 263-269 ◽

Cited By ~ 9

Author(s):

Evanthia Thanou ◽

Sinos Giokas ◽

Panagiotis Kornilios

Keyword(s):

Genetic Diversity ◽

Genetic Variation ◽

Genetic Structure ◽

Genetic Similarity ◽

Morphological Study ◽

Phylogenetic Analyses ◽

Morphological Characteristics ◽

Balkan Peninsula ◽

Intraspecific Genetic Diversity ◽

Well Differentiated

Two slow worm species are distributed at the southernmost part of the Balkan Peninsula: Anguis cephallonica, an endemic of the Peloponnese and the islands Zakynthos, Ithaki and Kephallonia, and A. graeca. Here, we investigate the intraspecific genetic diversity of A. cephallonica from the Peloponnese and Kephallonia and analyse A. graeca, from the northern Peloponnese, where it is found in sympatry with A. cephallonica. MtDNA and nDNA phylogenetic analyses confirm the genetic similarity of Peloponnesian and Kephallonian populations of A. cephallonica and reveal significant mtDNA genetic variation within it, probably related to the occurrence of multiple subrefugia in the Peloponnese. Peloponnesian A. graeca populations are genetically similar to non-Peloponnesian conspecifics implying recent dispersal to the Peloponnese. In contrast to the genetic markers, morphological characteristics (such as the number of mid-body scale-rows) failed to distinguish between Peloponnesian A. cephallonica and A. graeca. Although the former species is believed to be well-differentiated from its congeneric taxa, a thorough morphological study is needed.

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Crossing the impassable: genetic connections in 20 reef fishes across the eastern Pacific barrier

Proceedings of The Royal Society B Biological Sciences ◽

10.1098/rspb.2006.3543 ◽

2006 ◽

Vol 273 (1598) ◽

pp. 2201-2208 ◽

Cited By ~ 160

Author(s):

H.A Lessios ◽

D.R Robertson

Keyword(s):

Gene Flow ◽

Genetic Similarity ◽

Reef Fishes ◽

Eastern Pacific ◽

Cryptic Speciation ◽

Central Pacific ◽

Species Migration ◽

Initial Separation ◽

Haplotype Networks ◽

Biogeographic Barrier

The ‘impassable’ Eastern Pacific Barrier (EPB), ca 5000 km of deep water separating the eastern from the central Pacific, is the World's widest marine biogeographic barrier. Sequencing of mitochondrial DNA in 20 reef fish morphospecies encountered on both sides of the barrier revealed cryptic speciation in two. Among the other 18 species only two showed significant differentiation (as revealed by haplotype networks and F ST statistics) between the eastern and the central Pacific. Coalescence analyses indicated that genetic similarity in the 18 truly transpacific species resulted from different combinations of ages of most recent invasion and of levels of recurrent gene flow, with estimated times of initial separation ranging from approximately 30 000 to 1 Myr (ago). There is no suggestion of simultaneous interruptions of gene flow among the species. Migration across the EPB was previously thought to be exclusively eastward, but our evidence showed two invasions from east to west and eight cases in which subsequent gene flow possibly proceeded in the same direction. Thus, the EPB is sporadically permeable to propagules originating on either side.

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Spatial genetic structure of lowbush blueberry, Vaccinium angustifolium, in four fields in Maine

Botany ◽

10.1139/b09-058 ◽

2009 ◽

Vol 87 (10) ◽

pp. 932-946 ◽

Cited By ~ 25

Author(s):

Daniel J. Bell ◽

Lisa J. Rowland ◽

Dapeng Zhang ◽

Frank A. Drummond

Keyword(s):

Genetic Structure ◽

Genetic Similarity ◽

Seedling Recruitment ◽

Expressed Sequence Tag ◽

Spatial Genetic Structure ◽

Spatial Scales ◽

Principal Component ◽

Physical Distance ◽

Vaccinium Angustifolium ◽

Lowbush Blueberry

Expressed sequence tag – polymerase chain reaction (EST-PCR) molecular markers were used to infer spatial genetic structure of four lowbush blueberry ( Vaccinium angustifolium Ait.) fields in Maine. Genetic structure was quantified at three spatial scales: (1) within apparent clones (intrapatch), (2) among clones within a field, and (3) among fields separated by as much as 65 km. Of five “clones” or putative individuals examined in the intrapatch study, two showed complete genetic homogeneity within the patch, while three showed some band differences at their edges compared with their interiors. These differences at the edges, however, matched adjacent clones (so-called “intruders”), from which it was concluded that lowbush blueberry exhibits a fairly tight, phalanx clonal architecture with no evidence of invasive seedling establishment within clones. No significant correlation between genetic and physical distance was found among clones within fields via several statistical approaches. Significant among-field genetic differentiation was found via AMOVA (ΦPT = 8.4%; p ≤ 0.01) based upon transect samples across four fields ranging from 12.5 to 65 km apart. Principal component analysis and spatial autocorrelation (SA) corroborated these findings. Significant positive SA was found at the within-field distance class of <350 m, but SA decreased to an insignificant value by the first interfield distance of 12.5 km. A special form of SA analysis was employed to detect “hotspots” of genetic similarity between pairs of adjacent clones in two fields. Results indicated that 5 of 23 pairs of clones (21.7%) were genetically similar to each other, while the majority of pairs (18 of 23; 78.3%) showed random, decreasing patterns of genetic similarity. Results are discussed in terms of clonal dynamics including architecture, seedling recruitment, and inferred pollen or seed dispersal distances.

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Evidence of the interplay of genetics and culture in Ethiopia

Nature Communications ◽

10.1038/s41467-021-23712-w ◽

2021 ◽

Vol 12 (1) ◽

Author(s):

Saioa López ◽

Ayele Tarekegn ◽

Gavin Band ◽

Lucy van Dorp ◽

Nancy Bird ◽

...

Keyword(s):

Genetic Structure ◽

Genetic Similarity ◽

Cultural Practices ◽

Geographic Distance ◽

Human Populations ◽

Genetic Studies ◽

Sampling Protocols ◽

Show Evidence ◽

History Of ◽

The Rich

AbstractThe rich linguistic, ethnic and cultural diversity of Ethiopia provides an unprecedented opportunity to understand the level to which cultural factors correlate with–and shape–genetic structure in human populations. Using primarily new genetic variation data covering 1,214 Ethiopians representing 68 different ethnic groups, together with information on individuals’ birthplaces, linguistic/religious practices and 31 cultural practices, we disentangle the effects of geographic distance, elevation, and social factors on the genetic structure of Ethiopians today. We provide evidence of associations between social behaviours and genetic differences among present-day peoples. We show that genetic similarity is broadly associated with linguistic affiliation, but also identify pronounced genetic similarity among groups from disparate language classifications that may in part be attributable to recent intermixing. We also illustrate how groups reporting the same culture traits are more genetically similar on average and show evidence of recent intermixing, suggesting that shared cultural traits may promote admixture. In addition to providing insights into the genetic structure and history of Ethiopia, we identify the most important cultural and geographic predictors of genetic differentiation and provide a resource for designing sampling protocols for future genetic studies involving Ethiopians.

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Competition for hosts modulates vast antigenic diversity to generate persistent strain structure in Plasmodium falciparum

10.1101/406546 ◽

2018 ◽

Author(s):

Shai Pilosof ◽

Qixin He ◽

Kathryn E. Tiedje ◽

Shazia Ruybal-Pesántez ◽

Karen P. Day ◽

...

Keyword(s):

Plasmodium Falciparum ◽

Genetic Structure ◽

Genetic Similarity ◽

Antigenic Variation ◽

Host Immunity ◽

Modular Structure ◽

Immune Selection ◽

Frequency Dependent Selection ◽

Antigenic Diversity ◽

Human Immune

AbstractIn their competition for hosts, parasites with antigens that are novel to host immunity will be at a competitive advantage. The resulting frequency-dependent selection can structure parasite populations into strains of limited genetic overlap. For Plasmodium falciparum–the causative agent of malaria–in endemic regions, the high recombination rates and associated vast diversity of its highly antigenic and multicopy var genes preclude such clear clustering; this undermines the definition of strains as specific, temporally-persisting gene variant combinations. We use temporal multilayer networks to analyze the genetic similarity of parasites in both simulated data and in an extensively and longitudinally sampled population in Ghana. When viewed over time, populations are structured into modules (i.e., groups) of parasite genomes whose var gene combinations are more similar within, than between, the modules, and whose persistence is much longer than that of the individual genomes that compose them. Comparison to neutral models that retain parasite population dynamics but lack competition reveals that the selection imposed by host immunity promotes the persistence of these modules. The modular structure is in turn associated with a slower acquisition of immunity by individual hosts. Modules thus represent dynamically generated niches in host immune space, which can be interpreted as strains. Negative frequency-dependent selection therefore shapes the organization of the var diversity into parasite genomes, leaving a persistence signature over ecological time scales. Multilayer networks extend the scope of phylodynamics analyses by allowing quantification of temporal genetic structure in organisms that generate variation via recombination or other non-bifurcating processes. A strain structure similar to the one described here should apply to other pathogens with large antigenic spaces that evolve via recombination. For malaria, the temporal modular structure should enable the formulation of tractable epidemiological models that account for parasite antigenic diversity and its influence on intervention outcomes.SignificanceMany pathogens, including the causative agent of malaria Plasmodium falciparum, use antigenic variation, obtained via recombination, as a strategy to evade the human immune system. The vast diversity and multiplicity of genes encoding antigenic variation in high transmission regions challenge the notion of the existence of distinct strains: temporally-persistent and specific combinations of genes relevant to epidemiology. We examine the role of human immune selection in generating such genetic population structure in the major blood-stage antigen of Plasmodium falciparum. We show, using simulated and empirical data, that immune selection generates and maintains ‘modules’ of genomes with higher genetic similarity within, than between, these groups. Selection further promotes the persistence of these modules for much longer times than those of their constituent genomes. Simulations show that the temporal modular structure reduces the speed at which hosts acquire immunity to the parasite. We argue that in P. falciparum modules can be viewed as dynamic strains occupying different niches in human immune space; they are thus relevant to formulating transmission models that encompass the antigenic diversity of the parasite. Our analyses may prove useful to understand the interplay between temporal genetic structure and epidemiology in other pathogens of human and wildlife importance.

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