Strong population structure and limited gene flow between Yellow-billed Ducks and Mallards in southern Africa

The Condor ◽  
2019 ◽  
Author(s):  
Joshua I Brown ◽  
Philip Lavretsky ◽  
Graeme S Cumming ◽  
Jeffrey L Peters
Keyword(s):  
Mitochondrial Dna ◽  
Gene Flow ◽  
Southern Africa ◽  
Secondary Contact ◽  
Nuclear Markers ◽  
Nuclear Introns ◽  
Contemporary Gene Flow ◽  
Limited Gene Flow ◽  
Genetic Swamping ◽  
Evolutionary Consequences

AbstractSecondary contact and hybridization between recently diverged taxa have been increasing due to anthropogenic changes to the environment. Determining whether secondary contact leads to gene flow between species is important for understanding both the evolutionary consequences of such events (i.e. genetic swamping, speciation reversal, hybrid speciation) and for establishing proper conservation measures. Mallards (Anas platyrhynchos), which natively have a Holarctic distribution, have been introduced nearly worldwide due to game-farm and domestic pet releases. Their expanding range has resulted in secondary contact and increased incidences of hybridization with many closely related Mallard-like ducks that comprise the Mallard complex. Here, we assay molecular diversity for 19 nuclear introns and the mitochondrial DNA for wild Mallards (n = 50) across their Holarctic range and Yellow-billed Ducks (n = 30–75; Anas undulata) from southern Africa to determine population genetic structure and test for evidence of Mallard introgression into Yellow-billed Ducks. While we found limited support for contemporary gene flow across nuclear markers, we provide evidence from mitochondrial DNA that best supports ancient gene flow between Yellow-billed Ducks and Mallards. Yellow-billed Ducks best fit a single population at nuclear markers but show some location-specific mtDNA structure that suggests recent founder or bottleneck events. Although we find that introgression from Mallards into Yellow-billed Duck is limited, Yellow-billed Duck populations should be monitored to determine if expanding feral Mallard populations in southern Africa are increasing introgression.

Genetic variation of microsatellite and mitochondrial DNA markers in broad whitefish (Coregonus nasus) in the Colville and Sagavanirktok rivers in northern Alaska

1997 ◽  
Vol 54 (7) ◽  
pp. 1548-1556 ◽  
Author(s):  
J C Patton ◽  
B J Gallaway ◽  
R G Fechhelm ◽  
M A Cronin
Keyword(s):  
Mitochondrial Dna ◽  
Genetic Variation ◽  
Gene Flow ◽  
Microsatellite Loci ◽  
Genetic Relationships ◽  
Nuclear Genome ◽  
Pcr Amplification ◽  
Colville River ◽  
Limited Gene Flow ◽  
Northern Alaska

There has been concern that a causeway leading to oil production facilities in the Alaskan Beaufort Sea could affect the extent of emigration from, and immigration into, a population of broad whitefish (Coregonus nasus) in the Sagavanirktok River. To assess this, we analyzed the genetic relationships of the broad whitefish populations in the Sagavanirktok River, and the nearest adjacent population, in the Colville River. Three microsatellite loci from the nuclear genome, and the NADH-1 gene of mitochondrial DNA (mtDNA), were analyzed. Diploid genotypes were determined with PCR amplification of the microsatellite loci, and mtDNA genotypes were identified with PCR amplification followed by sequencing of 798 nucleotides. Several alleles were identified at each locus and both populations had high levels of genetic variation. There is significant differentiation of the Sagavanirktok River and Colville River broad whitefish stocks for the three microsatellite loci (FST = 0.031) but not mtDNA (FST < 0.001). Possible explanations for the lower level of differentiation of mtDNA than microsatellites include female-mediated gene flow between populations, skewed sex ratios, natural selection, or mutation. The results indicate that there is limited gene flow between the Colville and Sagavanirktok rivers, which represent semi-isolated spawning populations.

Mitochondrial DNA Variation Indicates Gene Flow across a Zone of Known Secondary Contact between Two Subspecies of the Brown-Headed Cowbird

The Condor ◽  
1991 ◽  
Vol 93 (1) ◽  
pp. 185-189 ◽  
Author(s):  
Robert C. Fleischer ◽  
Stephen I. Rothstein ◽  
Linda S. Miller
Keyword(s):  
Mitochondrial Dna ◽  
Gene Flow ◽  
Secondary Contact ◽  
Dna Variation

Geographic distribution and seasonal variation of mitochondrial DNA haplotypes in the aphid Rhopalosiphum padi (Hemiptera: Aphididae)

1997 ◽  
Vol 87 (2) ◽  
pp. 161-167 ◽  
Author(s):  
D. Martinez-Torres ◽  
A. Moya ◽  
P.D.N. Hebert ◽  
J.-C. Simon
Keyword(s):  
Mitochondrial Dna ◽  
Seasonal Variation ◽  
Gene Flow ◽  
Temperature Regime ◽  
Rhopalosiphum Padi ◽  
Nuclear Gene ◽  
Selective Advantage ◽  
Nuclear Markers ◽  
Host Alternation ◽  
Dna Diversity

AbstractThis study examines the spatial and seasonal patterning of mitochondrial DNA diversity in French populations of the bird cherry-oat aphid, Rhopalosiphum padi (Linnaeus), on both its primary and secondary hosts. Our results confirm the presence of two major mitochondrial lineages that are generally associated with the breeding system variation (cyclic and obligate parthenogenesis) shown by this species. The strength of this relationship varies regionally, being most evident in the south and west. Cyclically parthenogenetic populations show no significant regional or seasonal genetic divergence reflecting high levels of gene flow, possibly promoted by their obligate host-alternation. However, obligately parthenogenetic populations show a north-south cline in the distribution of the dominant haplotypes. This pattern might result from a selective advantage of some obligately parthenogenetic lineages under cold temperature regime. Alternatively, this cline might be established by a gradient in the intensity of nuclear gene flow between cyclically and obligately parthenogenetic populations mediated by androcyclic males. The discrimination between these possible explanations will require extending analysis to include hypervariable nuclear markers.

scholarly journals Limited gene flow and partial isolation phylogeography of Himalayan snowcock Tetraogallus himalayensis based on part mitochondrial D-loop sequences

2011 ◽  
Vol 57 (6) ◽  
pp. 758-767 ◽  
Author(s):  
Xiaoli Wang ◽  
Jiangyong Qu ◽  
Naifa Liu ◽  
Xinkang Bao ◽  
Sen Song
Keyword(s):  
Mitochondrial Dna ◽  
Gene Flow ◽  
Control Region ◽  
Divergence Time ◽  
Population Expansion ◽  
Middle Pleistocene ◽  
Distribution Analysis ◽  
D Loop ◽  
Limited Gene Flow ◽  
Partial Isolation

Abstract Himalayan snowcock Tetraogallus himalayensis are distributed in alpine and subalpine areas in China. We used mitochondrial DNA control-region data to investigate the origin and past demographic change in sixty-seven Himalayan snowcock T. himalayensis. The fragments of 1155 nucleotides from the control region of mitochondrial DNA were sequenced, and 57 polymorphic positions defined 37 haplotypes. A high level of genetic diversity was detected in all populations sampled and may be associated isolation of the mountains and habitat fragmentation and deterioration from Quaternary glaciations. In the phylogenetic tree, all haplotypes grouped into four groups: clade A (Kunlun Mountains clade), clade B (Northern Qinghai-Tibetan Plateau clade), clade C (Tianshan Mountains clade) and clade D (Kalakunlun Mountains clade). We found a low level of gene flow and significant genetic differentiation among all populations. Based on divergence time we suggest that the divergence of Himalayan snowcock occurred in the middle Pleistocene inter-glaciation, and expansion occurred in the glaciation. Analysis of mtDNA D-loop sequences confirmed demographic population expansion, as did our non-significant mismatch distribution analysis. In conclusion, limited gene flow and a pattern of partial isolation phylogeographic was found in geographic populations of T. himalayansis based on the analysis on mtDNA D-loop sequences.

scholarly journals Genomic signatures of sympatric speciation with historical and contemporary gene flow in a tropical anthozoan

2018 ◽  
Author(s):  
Benjamin M. Titus ◽  
Paul D. Blischak ◽  
Marymegan Daly
Keyword(s):  
Gene Flow ◽  
Cryptic Species ◽  
Species Complex ◽  
Sympatric Speciation ◽  
Sea Anemone ◽  
Secondary Contact ◽  
Marine Habitats ◽  
Contemporary Gene Flow ◽  
Cryptic Species Complex ◽  
Tropical Sea

AbstractSympatric diversification is increasingly thought to have played an important role in the evolution of biodiversity around the globe. However, an in situ sympatric origin for co-distributed taxa is difficult to demonstrate empirically because different evolutionary processes can lead to similar biogeographic outcomes-especially in ecosystems with few hard barriers to dispersal that can facilitate allopatric speciation followed by secondary contact (e.g. marine habitats). Here we use a genomic (ddRADseq), model-based approach to delimit a cryptic species complex of tropical sea anemones that are co-distributed on coral reefs throughout the Tropical Western Atlantic. We use coalescent simulations in fastsimcoal2 to test competing diversification scenarios that span the allopatric-sympatric continuum. We recover support that the corkscrew sea anemone Bartholomea annulata (Le Sueur, 1817) is a cryptic species complex, co-distributed throughout its range. Simulation and model selection analyses suggest these lineages arose in the face of historical and contemporary gene flow, supporting a sympatric origin, but an alternative secondary contact model also receives appreciable model support. Leveraging the genome of Exaiptasia pallida we identify five loci under divergent selection between cryptic B. annulata lineages that fall within mRNA transcripts or CDS regions. Our study provides a rare empirical, genomic example of sympatric speciation in a tropical anthozoan-a group that includes reef-building corals. Finally, these data represent the first range-wide molecular study of any tropical sea anemone, underscoring that anemone diversity is under described in the tropics, and highlighting the need for additional systematic studies into these ecologically and economically important species.

High levels of mitochondrial DNA divergence within short-eared rock-wallaby (Petrogale brachyotis) populations in northern Australia

2010 ◽  
Vol 58 (2) ◽  
pp. 104 ◽  
Author(s):  
Wendy R. Telfer ◽  
Mark D. B. Eldridge
Keyword(s):  
Mitochondrial Dna ◽  
Gene Flow ◽  
Control Region ◽  
National Park ◽  
Sequence Divergence ◽  
Mtdna Control Region ◽  
Secondary Contact ◽  
Interspecific Hybridisation ◽  
Secondary Contact Zone

Most population genetics studies of rock-wallabies conducted to date have examined remnant colonies of threatened species inhabiting southern Australia. In this study we examined the natural pattern of contemporary and long-term gene flow among colonies of the widespread and abundant short-eared rock-wallaby, Petrogale brachyotis, in the relatively unmodified landscapes of Australia’s tropical north. We sampled 105 wallabies from seven colonies 1.2 km to 250 km apart. Mitochondrial DNA (mtDNA) control region sequence analysis was conducted on samples from all colonies and microsatellite analysis (10 loci) on samples from the three largest colonies. The microsatellite data revealed no evidence of inbreeding within colonies, but higher levels of genetic diversity were found in the Kakadu National Park population compared with the smaller, more isolated colonies at Litchfield National Park. Both the mtDNA and microsatellite results showed that populations of P. brachyotis are naturally highly structured even within this relatively intact landscape, with only limited contemporary and long-term gene flow between colonies more than 1.2 km apart. Nine mtDNA control region haplotypes were identified within the seven colonies. There were unusually high levels of sequence divergence (up to 6.9%) within colonies at Litchfield NP. This divergence suggests that multiple taxa may exist within what is currently recognised as P. brachyotis. Alternatively, if current taxonomy is correct, the high levels of divergence raise the possibility of ancestral isolation and divergence of populations in allopatry with subsequent admixture at a secondary contact zone. The possibility that these unusually divergent haplotypes result from introgressive interspecific hybridisation with the sympatric P. concinna appears unlikely.

scholarly journals Whole-genome analysis of multiple wood ant population pairs supports similar speciation histories, but different degrees of gene flow, across their European range

2021 ◽  
Author(s):  
Beatriz Portinha ◽  
Amaury Avril ◽  
Christian Bernasconi ◽  
Heikki Helanterä ◽  
Josie Monaghan ◽  
...  
Keyword(s):  
Gene Flow ◽  
Demographic History ◽  
Geographic Region ◽  
Secondary Contact ◽  
Whole Genome ◽  
Whole Genome Analysis ◽  
Formica Polyctena ◽  
Population Pair ◽  
Contemporary Gene Flow ◽  
Whole Genome Resequencing

AbstractThe application of demographic history modeling and inference to the study of divergence between species is becoming a cornerstone of speciation genomics. The demographic history is usually reconstructed by analysing a single population from each species, assuming that the divergence history inferred between these populations represents the actual speciation history. However, this assumption is rarely explicitly tested, and it may not be met when species diverge with gene flow. For instance, secondary contact between two species after a range expansion may be confined into a specific geographic region. In this study, we tested to what extent the divergence history inferred from two heterospecific populations would vary depending on their geographic locations, using mound-building red wood ants. The wood ant species Formica polyctena and F. aquilonia have contrasting distributions in Europe and naturally hybridize in Finland. We first performed whole-genome resequencing of 20 individuals sampled in multiple populations across both species ranges. We then reconstructed the divergence histories of distinct heterospecific population pairs using a coalescent-based approach. We found that the analysis of these different population pairs always supported a scenario of divergence with gene flow, suggesting that species divergence started in the Pleistocene (ca. 500 kya) and occurred with continuous asymmetrical gene flow from F. aquilonia to F. polyctena until a recent time, when migration stopped (2-19 kya, depending on the population pair considered). However, we found support for contemporary gene flow in the sympatric population pair from Finland, where hybrids have been described. Overall, our results suggest that divergence histories reconstructed from a few individuals may be reliable and applicable at the species level. Nonetheless, the geographical context of populations chosen to represent their species should be taken into account, as it may affect estimates of migration rates between species when gene flow is heterogeneous across their geographical ranges.

Differentiation and Interrelations of Two Representatives of Laudakia stellio Complex (Reptilia: Agamidae) in Israel

2011 ◽  
Vol 4 (2) ◽  
pp. 102-114 ◽  
Author(s):  
Evgenyi N. Panov ◽  
Larissa Yu. Zykova
Keyword(s):  
Population Structure ◽  
Gene Flow ◽  
Habitat Preference ◽  
Additional Data ◽  
Near East ◽  
Field Studies ◽  
Subspecies Level ◽  
Limited Gene Flow ◽  
Study Sites ◽  
And Behavior

Field studies were conducted in Central Negev within the breeding range of Laudakia stellio brachydactyla and in NE Israel (Qyriat Shemona) in the range of an unnamed form (tentatively “Near-East Rock Agama”), during March – May 1996. Additional data have been collected in Jerusalem at a distance of ca. 110 km from the first and about 170 km from the second study sites. A total of 63 individuals were caught and examined. The animals were marked and their subsequent movements were followed. Social and signal behavior of both forms were described and compared. Lizards from Negev and Qyriat Shemona differ from each other sharply in external morphology, habitat preference, population structure, and behavior. The differences obviously exceed the subspecies level. At the same time, the lizards from Jerusalem tend to be intermediate morphologically between those from both above-named localities, which permits admitting the existence of a limited gene flow between lizard populations of Negev and northern Israel. The lizards from NE Israel apparently do not belong to the nominate subspecies of L. stellio and should be regarded as one more subspecies within the species.

Population fragmentation causes inadequate gene flow and increases extinction risk

2017 ◽  
Author(s):  
Richard Frankham ◽  
Jonathan D. Ballou ◽  
Katherine Ralls ◽  
Mark D. B. Eldridge ◽  
Michele R. Dudash ◽  
...  
Keyword(s):  
Gene Flow ◽  
Extinction Risk ◽  
Random Mating ◽  
Large Population ◽  
Isolated Population ◽  
Population Fragmentation ◽  
Single Population ◽  
Total Size ◽  
Limited Gene Flow

Most species now have fragmented distributions, often with adverse genetic consequences. The genetic impacts of population fragmentation depend critically upon gene flow among fragments and their effective sizes. Fragmentation with cessation of gene flow is highly harmful in the long term, leading to greater inbreeding, increased loss of genetic diversity, decreased likelihood of evolutionary adaptation and elevated extinction risk, when compared to a single population of the same total size. The consequences of fragmentation with limited gene flow typically lie between those for a large population with random mating and isolated population fragments with no gene flow.

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