scholarly journals Population Connectivity and Traces of Mitochondrial Introgression in New Zealand Black-Billed Gulls (Larus bulleri)

Genes ◽  
2018 ◽  
Vol 9 (11) ◽  
pp. 544 ◽  
Author(s):  
Claudia Mischler ◽  
Andrew Veale ◽  
Tracey van Stijn ◽  
Rudiger Brauning ◽  
John McEwan ◽  
...  
Keyword(s):  
Mitochondrial Dna ◽  
Population Structure ◽  
New Zealand ◽  
Nuclear Dna ◽  
Isolation By Distance ◽  
Population Connectivity ◽  
Nucleotide Polymorphisms ◽  
Population Declines ◽  
The South ◽  
Mitochondrial Introgression

Black-billed gulls (Larus bulleri) are endemic to New Zealand and are suspected to be undergoing substantial population declines. They primarily breed on open gravel beds in braided rivers of the South Island—a habitat that is diminishing and becoming increasingly modified. Although management of this species is increasing, little has been published on their movements and demographics. In this study, both mitochondrial DNA (mtDNA) control region domain I and nuclear single nucleotide polymorphisms (SNPs) were examined to help understand the connectivity and population structure of black-billed gulls across the country and to help inform management decisions. Mitochondrial DNA showed no population structure, with high haplotype and low nucleotide diversity, and analyses highlighted mitochondrial introgression with the closely related red-billed gulls (Larus novaehollandiae scopulinus). Nuclear DNA analyses, however, identified two groups, with Rotorua birds in the North Island being distinct from the rest of New Zealand, and isolation-by-distance evident across the South Island populations. Gene flow primarily occurs between nearby colonies with a stepwise movement across the landscape. The importance from a genetic perspective of the more isolated North Island birds (1.6% of total population) needs to be further evaluated. From our results, we infer that the South Island black-billed gull management should focus on maintaining several populations within each region rather than focusing on single specific colonies or river catchments. Future study is needed to investigate the genetic structure of populations at the northern limit of the species’ range, and identify the mechanisms behind, and extent of, the hybridisation between red-billed and black-billed gulls.

scholarly journals Population connectivity predicts vulnerability to white-nose syndrome in the Chilean myotis (Myotis chiloensis) - a genomics approach

2020 ◽  
Author(s):  
Thomas M. Lilley ◽  
Tiina M. Sävilammi TM ◽  
Gonzalo Ossa ◽  
Anna S Blomberg ◽  
Anti Vasemägi ◽  
...  
Keyword(s):  
Population Structure ◽  
Isolation By Distance ◽  
Geographic Distance ◽  
Population Connectivity ◽  
Tierra Del Fuego ◽  
Secondary Contact ◽  
Mountain Range ◽  
Population Declines ◽  
White Nose Syndrome ◽  
The North

ABSTRACTDespite its peculiar distribution, the biology of the southernmost bat species in the world, the Chilean myotis (Myotis chiloensis), has garnered little attention so far. The species has a north-south distribution of c. 2800 km, mostly on the eastern side of the Andes mountain range. Use of extended torpor occurs in the southernmost portion of the range, putting the species at risk of bat white-nose syndrome (WNS), a fungal disease responsible for massive population declines in North American bats. Here, we examined how geographic distance and topology would be reflected in the population structure of M. chiloensis along the majority of its range using a double digestion RAD-tag method. We sampled 66 individuals across the species range and discovered pronounced isolation-by-distance. Furthermore, and surprisingly, we found higher degrees of heterozygosity in the southernmost populations compared to the north. A coalescence analysis revealed that our populations may still not have reached secondary contact after the Last Glacial Maximum. As for the potential spread of pathogens, such as the fungus causing WNS, connectivity among populations was noticeably low, especially between the southern hibernatory populations in the Magallanes and Tierra del Fuego, and more northerly populations. This suggests the probability of geographic spread of the disease from the north through bat-to-bat contact to susceptible populations is low. The study presents a rare case of defined population structure in a bat species and warrants further research on the underlying factors contributing to this.

scholarly journals Population Connectivity Predicts Vulnerability to White-Nose Syndrome in the Chilean Myotis (Myotis chiloensis) - A Genomics Approach

2020 ◽  
Vol 10 (6) ◽  
pp. 2117-2126
Author(s):  
Thomas M. Lilley ◽  
Tiina Sävilammi ◽  
Gonzalo Ossa ◽  
Anna S. Blomberg ◽  
Anti Vasemägi ◽  
...  
Keyword(s):  
Population Structure ◽  
Isolation By Distance ◽  
Geographic Distance ◽  
Population Connectivity ◽  
Tierra Del Fuego ◽  
Secondary Contact ◽  
Mountain Range ◽  
Population Declines ◽  
White Nose Syndrome ◽  
The North

Despite its peculiar distribution, the biology of the southernmost bat species in the world, the Chilean myotis (Myotis chiloensis), has garnered little attention so far. The species has a north-south distribution of c. 2800 km, mostly on the eastern side of the Andes mountain range. Use of extended torpor occurs in the southernmost portion of the range, putting the species at risk of bat white-nose syndrome, a fungal disease responsible for massive population declines in North American bats. Here, we examined how geographic distance and topology would be reflected in the population structure of M. chiloensis along the majority of its range using a double digestion RAD-seq method. We sampled 66 individuals across the species range and discovered pronounced isolation-by-distance. Furthermore, and surprisingly, we found higher degrees of heterozygosity in the southernmost populations compared to the north. A coalescence analysis revealed that our populations may still not have reached secondary contact after the Last Glacial Maximum. As for the potential spread of pathogens, such as the fungus causing WNS, connectivity among populations was noticeably low, especially between the southern hibernatory populations in the Magallanes and Tierra del Fuego, and more northerly populations. This suggests the probability of geographic spread of the disease from the north through bat-to-bat contact to susceptible populations is low. The study presents a rare case of defined population structure in a bat species and warrants further research on the underlying factors contributing to this. See the graphical abstract here. https://doi.org/10.25387/g3.12173385

Evolution of the south-western Pacific genus Melicytus (Violaceae): evidence from DNA sequence data, cytology and sex expression

2009 ◽  
Vol 22 (3) ◽  
pp. 143 ◽  
Author(s):  
A. D. Mitchell ◽  
P. B. Heenan ◽  
B. G. Murray ◽  
B. P. J. Molloy ◽  
P. J. de Lange
Keyword(s):  
New Zealand ◽  
Chromosome Numbers ◽  
Tree Species ◽  
Nuclear Dna ◽  
Sequence Data ◽  
Sex Expression ◽  
The South ◽  
Shrub Species ◽  
Biogeographic Patterns ◽  
Norfolk Island

Phylogenetic analyses of nuclear DNA external transcribed spacer (ETS) and chloroplast DNA trnL–trnF markers were undertaken to reconstruct the evolutionary history of the South Pacific genus Melicytus. Bayesian analyses of the ETS sequence data produced a phylogenetic tree with several well supported groups, including clades comprising: (1) species from Australia, Tasmania and Lord Howe Island; (2) the Norfolk Island M. latifolius and New Zealand off-shore island M. novae-zelandiae subsp. novae-zelandiae; (3) the large-leaved M. ramiflorus complex; (4) M. fasciger and M. micranthus; and (5) M. obovatus and allies from the Cook Strait region. Phylogenetic analysis of trnL–trnF sequence data also retrieved some of these groups although, in general, was not as well resolved. The relationships of M. lanceolatus are equivocal, as in the ETS phylogeny it is sister to a clade comprising the large-leaved tree species M. fasciger and M. ramiflorus complex and the small-leaved M. micranthus, whereas in the trnL–trnF phylogeny it is sister to a clade of small-leaved shrub species such as M. alpinus and M. crassifolius. Several biogeographic patterns are evident, with dispersal to the west from New Zealand, to Australia, involving small-leaved shrub species. Dispersal to the north from New Zealand, to Norfolk Island and Fiji, involves large-leaved tree species. The sex expression is documented for all named species and undescribed entities, with these being either hermaphroditic or dioecious. When sex expression is mapped onto the phylogeny, the hermaphroditic system is inferred to have evolved from the dioecious system. New chromosome counts are presented for M. angustifolius (2n = 64) and M. dentatus (2n = 32), and earlier counts of 2n = 64 are confirmed for M. crassifolius and M. alpinus. An additional 17 counts are provided for two natural hybrids and several undescribed entities from Australia and New Zealand. The polyploid chromosome number of 2n = 64 occurs most frequently in small-leaved divariate plants with hermaphroditic flowers. When chromosome numbers are plotted onto the phylogeny it is inferred that high polyploids (e.g. 2n = 64) and small-leaved shrubs have evolved from large-leaved trees with functional diploid (e.g. 2n = 32) chromosome numbers.

scholarly journals Structure and phylogeography of two tropical predators, spinner ( Stenella longirostris ) and pantropical spotted ( S. attenuata ) dolphins, from SNP data

2018 ◽  
Vol 5 (4) ◽  
pp. 171615 ◽  
Author(s):  
Matthew S. Leslie ◽  
Phillip A. Morin
Keyword(s):  
Population Structure ◽  
Pacific Ocean ◽  
Nuclear Dna ◽  
Population Level ◽  
Genetic Connectivity ◽  
Nucleotide Polymorphisms ◽  
Stenella Longirostris ◽  
Spinner Dolphin ◽  
Spinner Dolphins ◽  
Almost All

Little is known about global patterns of genetic connectivity in pelagic dolphins, including how circumtropical pelagic dolphins spread globally following the rapid and recent radiation of the subfamily delphininae. In this study, we tested phylogeographic hypotheses for two circumtropical species, the spinner dolphin ( Stenella longirostris ) and the pantropical spotted dolphin ( Stenella attenuata ), using more than 3000 nuclear DNA single nucleotide polymorphisms (SNPs) in each species. Analyses for population structure indicated significant genetic differentiation between almost all subspecies and populations in both species. Bayesian phylogeographic analyses of spinner dolphins showed deep divergence between Indo-Pacific, Atlantic and eastern tropical Pacific Ocean (ETP) lineages. Despite high morphological variation, our results show very close relationships between endemic ETP spinner subspecies in relation to global diversity. The dwarf spinner dolphin is a monophyletic subspecies nested within a major clade of pantropical spinner dolphins from the Indian and western Pacific Ocean populations. Population-level division among the dwarf spinner dolphins was detected—with the northern Australia population being very different from that in Indonesia. In contrast to spinner dolphins, the major boundary for spotted dolphins is between offshore and coastal habitats in the ETP, supporting the current subspecies-level taxonomy. Comparing these species underscores the different scale at which population structure can arise, even in species that are similar in habitat (i.e. pelagic) and distribution.

scholarly journals Population structure and dispersal across small and large spatial scales in a direct developing marine isopod

2020 ◽  
Author(s):  
William S. Pearman ◽  
Sarah J. Wells ◽  
Olin K. Silander ◽  
Nikki E. Freed ◽  
James Dale
Keyword(s):  
Population Structure ◽  
Gene Flow ◽  
Population Genetic ◽  
Isolation By Distance ◽  
Spatial Scales ◽  
Population Connectivity ◽  
Clear Pattern ◽  
Small Spatial Scale ◽  
Cook Strait ◽  
Genetic Break

AbstractMarine organisms generally exhibit one of two developmental modes: biphasic, with distinct adult and larval morphology, and direct development, in which larvae resemble adults. Developmental mode is thought to significantly influence dispersal, with direct developers expected to have much lower dispersal potential. However, in contrast to our relatively good understanding of dispersal and population connectivity for biphasic species, comparatively little is known about direct developers. In this study, we use a panel of 8,020 SNPs to investigate population structure and gene flow for a direct developing species, the New Zealand endemic marine isopod Isocladus armatus. On a small spatial scale (20 kms), gene flow between locations is extremely high and suggests an island model of migration. However, over larger spatial scales (600km), populations exhibit a clear pattern of isolation-by-distance. Because our sampling range is intersected by two well-known biogeographic barriers (the East Cape and the Cook Strait), our study provides an opportunity to understand how such barriers influence dispersal in direct developers. Our results indicate that I. armatus exhibits significant migration across these barriers, and suggests that ocean currents associated with these locations do not present a barrier to dispersal. Interestingly, we do find evidence of a north-south population genetic break occurring between Māhia and Wellington, two locations where there are no obvious biogeographic barriers between them. We conclude that developmental life history largely predicts dispersal in intertidal marine isopods. However, localised biogeographic processes can disrupt this expectation.

Nondestructive sampling of mitochondrial DNA from voles (Microtus)

1987 ◽  
Vol 65 (1) ◽  
pp. 175-180 ◽  
Author(s):  
Yves Plante ◽  
Peter T. Boag ◽  
Bradley N. White
Keyword(s):  
Mitochondrial Dna ◽  
Population Structure ◽  
Social Interactions ◽  
Nuclear Dna ◽  
Microtus Pennsylvanicus ◽  
Dna Polymorphisms ◽  
Biochemical Taxonomy ◽  
Meadow Voles ◽  
Blood Samples ◽  
Cellular Dna

We present two techniques for sampling mitochondrial DNA (mtDNA) without killing individual voles. Total cellular DNA was extracted from small blood samples (100–250 μL) and tail segments (2 cm long) collected from meadow voles (Microtus pennsylvanicus). Restriction fragment patterns produced by the restriction endonucleases HindIII, BamH1, and EcoR1 after hybridization with a probe of nick-translated mtDNA compared well with standard mtDNA assays. Both techniques can be used in the field, and should prove useful in biochemical taxonomy as well as in investigations of population structure, dispersal, and social interactions on both micro- and macro-geographic scales. The Southern blots produced by these procedures have the added advantage of being reuseable, so that nuclear DNA polymorphisms can be examined with appropriate probes.

scholarly journals Evidence of hybridization, mitochondrial introgression and biparental inheritance of the kDNA minicircles in Trypanosoma cruzi I

2019 ◽  
Author(s):  
Fanny Rusman ◽  
Noelia Floridia-Yapur ◽  
Paula G. Ragone ◽  
Patricio Diosque ◽  
Nicolás Tomasini
Keyword(s):  
Mitochondrial Dna ◽  
Trypanosoma Cruzi ◽  
Dna Sequences ◽  
Dna Content ◽  
Nuclear Dna ◽  
Genetic Exchange ◽  
Natural Hybridization ◽  
Biparental Inheritance ◽  
Hybrid Strain ◽  
Mitochondrial Introgression

AbstractBackgroundGenetic Exchange in Trypanosoma cruzi is controversial not only in relation to its frequency but also in relation to its mechanism. A mechanism of parasexuality has been proposed based on laboratory hybrids, but population genomics strongly suggests meiosis. In addition, mitochondrial introgression has been reported several times in natural isolates although its mechanism is not clear. Moreover, hybrid DTUs (TcV and TcVI) have inherited at least part of the kinetoplastic DNA (kDNA = mitochondrial DNA) from both parents.Methodology/Principal findingsIn order to address such topics, we sequenced and analyzed fourteen nuclear DNA fragments and three kDNA maxicircle genes in three TcI stocks which are natural clones potentially involved in events of genetic exchange. We also deep-sequenced (a total of 6,146,686 paired-end reads) the hypervariable region of kDNA minicircles (mHVR) in such three strains. In addition, we analyzed the DNA content by flow cytometry to address cell ploidy. We observed that most polymorphic sites in nuclear loci showed a hybrid pattern in one cloned strain and the other two cloned strains were compatible as parental strains (or nearly related to the true parents). The three clones have almost the same ploidy and the DNA content was similar to the reference strain Sylvio (an almost diploid strain). Despite maxicircle genes evolve faster than nuclear housekeeping ones, we did not detect polymorphism in the sequence of three maxicircle genes showing mito-nuclear discordance. In addition, the hybrid stock shared 66% of its mHVR clusters with one putative parental and 47% with the another one. In contrast, the putative parental stocks shared less than 30% of the mHVR clusters among them.Conclusions/significanceThe results suggest a reductive division, a natural hybridization, biparental inheritance of the minicircles in the hybrid and maxicircle introgression. The models including such phenomena and that would explain the relationships between these three clones are discussed.Author summaryChagas disease, an important public health problem in Latin America, is caused by the parasite Trypanosoma cruzi. Despite it is a widely studied parasite, several questions about the biology of genetic exchange remain. Meiosis has not been yet observed in laboratory, although inferred from population genomic studies. In addition, previous results suggest that the mitochondrial DNA (called kDNA) may be inherited from both parents in hybrids. Here, we analyzed a hybrid strain and the potential parents to address about the mechanisms of genetic exchange at nuclear and mitochondrial level. We observed that the hybrid strain has heterozygous patterns and DNA content compatible with an event of meiosis. In addition, we observed that the evolutionary histories of nuclear DNA and maxicircles (a part of the kDNA) were discordant and the three strains share identical DNA sequences. Mitochondrial introgression of maxicircle DNA from one genotype to another may explain this observation. In addition, we detected that the hybrid strain shared minicircles (another part of the kDNA) with both parental strains. Our results suggest that hybridization implied meiosis and biparental inheritance of the kDNA. Further research is required to address such phenomena in detail.

scholarly journals Population structure, temporal stability and seascape genetics of two endemic New Zealand Pleuronectiformes, Rhombosolea plebeia (sand flounder) and R. leporina (yellowbelly flounder)

2021 ◽  
Author(s):  
◽  
Heather B. Constable
Keyword(s):  
Population Structure ◽  
New Zealand ◽  
Coastal Waters ◽  
Population Genetic ◽  
East Coast ◽  
Temporal Stability ◽  
Soft Bottom ◽  
The South ◽  
Management Options ◽  
Genetic Patterns

<p>New Zealand’s coastal waters are an integral part of the social, economic and environmental heritage of this Pacific archipelago. Evolving in isolation for 82 million years under volatile tectonic action and volcanism, the marine biogeography of New Zealand is complex and diverse. Many hypotheses have been proposed to explain the subdivisions of biogeographic areas based on species distributions, habitat and population genetics. In this study, I test whether there is differentiation in coastal population connectivity between northern and southern provinces, the location of the break and what environmental factors may explain the patterns observed.  Sandy, soft bottom and estuarine ecosystems make up a large proportion of the coastline, but are not well-represented in population genetic studies in New Zealand and internationally. I chose Rhombosolea leporina (sand flounder) and Rhombosolea plebeia (yellowbelly flounder) as endemic, commercially and traditionally important inhabitants of the shallow coastal waters and estuaries to explore levels of gene flow among most of the marine biogeographic regions of the New Zealand mainland.  The goal of this thesis research was to (1) develop polymorphic DNA microsatellite markers and (2) investigate the population genetic patterns at multiple spatial scales. Although these species have a relatively long pelagic larval duration (PLD) of ~70 days, I found a significant level of population structure for both species. There was a pattern of isolation by distance and a north to south break in connectivity on the east coast for R. plebeia, but an east to west disjunction in R. leporina. There was no evidence of a north to south genetic break in R. leporina, however populations on the south east coast of the South Island were significantly differentiated in both species.  A test for temporal effects (3) of genetic variation was conducted to determine whether spatial patterns of differentiation were consistent across multiple sampling seasons and age classes. Aspects of the sweepstakes recruitment success (SRS) hypothesis were tested by examining differences in allele frequencies and levels of genetic diversity as a function of time. The analyses found evidence of temporal stability between years and between juveniles and adults.  Lastly, (4) the coastal and estuarine environmental variables were modelled using information from two public GIS datasets and several measures of genetic differentiation. The aim of this chapter was to determine which environmental and geospatial factors showed a significant level of correlation with the spatial genetic patterns reported in the earlier studies. For R. leporina, latitude, sediment and current speeds were significantly correlated with the genetic estimates of FST, F’ST and Jost’s D. In R. plebeia, a correlation was found between latitude, longitude, sediment, current speeds, sea surface temperature and width of the estuary mouth. The results of the modelling study suggest avenues for further research using candidate genes, such as heat shock proteins and rhodopsin.  This was the first study of New Zealand pleuronectids using a multidisciplinary approach with microsatellite DNA markers, GIS, and an array of bioinformatics software to study coastal connectivity on multiple spatial and temporal scales. Significant genetic structuring was found among populations of animals that are potentially well connected through continuous sandy, soft bottom environments and a long PLD. Despite similar life histories and ecologies, the two species were quite divergent in that there was little cross amplification of markers, different patterns of genetic structure and separate outcomes from environmental modelling. These results suggest that managing several species under one management plan may be an oversimplification of the complexities of the population dynamics and evolutionary histories of these species. Conservation and management options for coastal fisheries and possible avenues for future research are proposed.</p>

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