scholarly journals Pliocene Origin, Ice Ages and Postglacial Population Expansion Have Influenced a Panmictic Phylogeography of the European Bee-Eater Merops apiaster

Diversity ◽  
2019 ◽  
Vol 11 (1) ◽  
pp. 12 ◽  
Author(s):  
Carina Carneiro de Melo Moura ◽  
Hans-Valentin Bastian ◽  
Anita Bastian ◽  
Erjia Wang ◽  
Xiaojuan Wang ◽  
...  
Keyword(s):  
Genetic Differentiation ◽  
Nuclear Dna ◽  
Bird Species ◽  
Population Expansion ◽  
Genetic Connectivity ◽  
Middle Pleistocene ◽  
Ice Ages ◽  
Breeding Sites ◽  
Late Tertiary ◽  
Merops Apiaster

Oscillations of periods with low and high temperatures during the Quaternary in the northern hemisphere have influenced the genetic composition of birds of the Palearctic. During the last glaciation, ending about 12,000 years ago, a wide area of the northern Palearctic was under lasting ice and, consequently, breeding sites for most bird species were not available. At the same time, a high diversity of habitats was accessible in the subtropical and tropical zones providing breeding grounds and refugia for birds. As a result of long-term climatic oscillations, the migration systems of birds developed. When populations of birds concentrated in refugia during ice ages, genetic differentiation and gene flow between populations from distinct areas was favored. In the present study, we explored the current genetic status of populations of the migratory European bee-eater. We included samples from the entire Palearctic-African distribution range and analyzed them via mitochondrial and nuclear DNA markers. DNA data indicated high genetic connectivity and panmixia between populations from Europe, Asia and Africa. Negative outcomes of Fu’s Fs and Tajima’s D tests point to recent expansion events of the European bee-eater. Speciation of Merops apiaster started during the Pliocene around three million years ago (Mya), with the establishment of haplotype lineages dated to the Middle Pleistocene period circa 0.7 Mya. M. apiaster, which breed in Southern Africa are not distinguished from their European counterparts, indicating a recent separation event. The diversification process of the European bee-eater was influenced by climatic variation during the late Tertiary and Quaternary. Bee-eaters must have repeatedly retracted to refugia in the Mediterranean and subtropical Africa and Asia during ice ages and expanded northwards during warm periods. These processes favored genetic differentiation and repeated lineage mixings, leading to a genetic panmixia, which we still observe today.

Genetic variation and phylogeography of Psammosilene tunicoides (Caryophyllaceae), a narrowly distributed and endemic species in south-western China

2011 ◽  
Vol 59 (5) ◽  
pp. 450 ◽  
Author(s):  
Qing-Ying Zhang ◽  
Yu-Juan Zhao ◽  
Xun Gong
Keyword(s):  
Genetic Differentiation ◽  
Endemic Species ◽  
Nuclear Dna ◽  
Isolation By Distance ◽  
Population Expansion ◽  
Population History ◽  
Western China ◽  
Phylogeographic Structure ◽  
Population Subdivision ◽  
Chloroplast Haplotypes

Psammosilene tunicoides is a narrowly distributed and endemic species in south-western China. An investigation of sequence variation at two chloroplast DNA (cpDNA) regions (rpL16, trnQ-5′rps16) and one nuclear DNA (nDNA) locus (GPA1) were carried out to survey the population structure and population history of the species. Among the 22 populations across its geographical range, nine chloroplast haplotypes and 17 nuclear alleles were identified. Both cpDNA and nDNA consistently revealed high levels of population differentiation (GST = 0.604 and 0.540, respectively), suggesting a distinct phylogeographic structure (NST > GST, P < 0.01). This high genetic differentiation might be a combined effect of breeding system, limited pollen and seed dispersal and geographic isolation of populations. The level of haplotype diversities (cpDNA, hT = 0.575; nDNA, hT = 0.724) were high, but the nucleotide diversities (cpDNA, π = 0.00099; nDNA, π = 0.00105) were low. These results together with the star-like phylogenetic pattern and neutrality tests indicate that P. tunicoides has experienced a population expansion event in its evolution. Limited genetic exchange after population expansion was supported by the pronounced genetic differentiation among populations as well as evidence for ‘isolation-by-distance’ revealed by cpDNA. Due to high population subdivision and complex landscape, as many populations as possible should be considered for genetic conservation.

Neanderthals and modern humans

2017 ◽  
Author(s):  
Francisco J. Ayala ◽  
Camilo J. Cela-Conde
Keyword(s):  
Genetic Differentiation ◽  
Nuclear Dna ◽  
Homo Sapiens ◽  
Whole Genome ◽  
Upper Palaeolithic ◽  
Modern Humans ◽  
Homo Neanderthalensis ◽  
Modern Mind ◽  
Similarities And Differences ◽  
Mode 3

This chapter deals with the similarities and differences between Homo neanderthalensis and Homo sapiens, by considering genetic, brain, and cognitive evidence. The genetic differentiation emerges from fossil genetic evidence obtained first from mtDNA and later from nuclear DNA. With high throughput whole genome sequencing, sequences have been obtained from the Denisova Cave (Siberia) fossils. Nuclear DNA of a third species (“Denisovans”) has been obtained from the same cave and used to define the phylogenetic relationships among the three species during the Upper Palaeolithic. Archaeological comparisons make it possible to advance a four-mode model of the evolution of symbolism. Neanderthals and modern humans would share a “modern mind” as defined up to Symbolic Mode 3. Whether the Neanderthals reached symbolic Mode 4 remains unsettled.

scholarly journals Evolutionary history and genetic connectivity across highly fragmented populations of an endangered daisy

Heredity ◽  
2021 ◽  
Author(s):  
Yael S. Rodger ◽  
Alexandra Pavlova ◽  
Steve Sinclair ◽  
Melinda Pickup ◽  
Paul Sunnucks
Keyword(s):  
Genetic Diversity ◽  
Gene Flow ◽  
Genetic Differentiation ◽  
Evolutionary History ◽  
Livestock Grazing ◽  
Genetic Connectivity ◽  
Evolutionary Divergence ◽  
Common Component ◽  
A Genome ◽  
Eastern Australia

AbstractConservation management can be aided by knowledge of genetic diversity and evolutionary history, so that ecological and evolutionary processes can be preserved. The Button Wrinklewort daisy (Rutidosis leptorrhynchoides) was a common component of grassy ecosystems in south-eastern Australia. It is now endangered due to extensive habitat loss and the impacts of livestock grazing, and is currently restricted to a few small populations in two regions >500 km apart, one in Victoria, the other in the Australian Capital Territory and nearby New South Wales (ACT/NSW). Using a genome-wide SNP dataset, we assessed patterns of genetic structure and genetic differentiation of 12 natural diploid populations. We estimated intrapopulation genetic diversity to scope sources for genetic management. Bayesian clustering and principal coordinate analyses showed strong population genetic differentiation between the two regions, and substantial substructure within ACT/NSW. A coalescent tree-building approach implemented in SNAPP indicated evolutionary divergence between the two distant regions. Among the populations screened, the last two known remaining Victorian populations had the highest genetic diversity, despite having among the lowest recent census sizes. A maximum likelihood population tree method implemented in TreeMix suggested little or no recent gene flow except potentially between very close neighbours. Populations that were more genetically distinctive had lower genetic diversity, suggesting that drift in isolation is likely driving population differentiation though loss of diversity, hence re-establishing gene flow among them is desirable. These results provide background knowledge for evidence-based conservation and support genetic rescue within and between regions to elevate genetic diversity and alleviate inbreeding.

scholarly journals Awifauna wodno-błotna środkowej Wisły w okresie lęgowym: wpływ działalności człowieka na rozmieszczenie, liczebność i bogactwo gatunkowe

2011 ◽  
Vol 9 (2) ◽  
pp. 67-86 ◽  
Author(s):  
Dariusz Bukaciński ◽  
Monika Bukacińska ◽  
Arkadiusz Buczyński
Keyword(s):  
Bird Species ◽  
Natura 2000 ◽  
River Channel ◽  
River Valley ◽  
Breeding Bird ◽  
Breeding Sites ◽  
Vistula River ◽  
Breeding Habitats ◽  
Natura 2000 Site ◽  
River Bottom

The inventory of birds was conducted in the years 2005-2010 on the Vistula River section between Dęblin (388 km of the river) and Podwierzbie (435 km of the river). The study area includes a southern section of the European Ecological Natura 2000 Site in Poland PLB140004 „Middle Vistula River Valley” (IBA, PL083). In most areas the Vistula flows here within unregulated or relatively little modified riverbed, having features of natural, lowland, braided river. Sandy islands and braid bars within the main channel, steep banks, and old riparian afforestation create the unique breeding habitats of the Vistula River Valley. Especially the river channel habitats provide suitable breeding sites for many rare bird species, constituting some of them the key-breeding sites. There are, however, fragments of several kilometers, where people transformed the Vistula River in a more visible way (Table 1). These are, among others: an urban section within Dęblin boundaries (km 388-393 of the river), a fragment adjacent to Kozienice Power Plant (km 421-426), and the area, where since 2007 gravel for the industry has been mining from the river bottom (km 426-431). The aim of this inventory was the comparison of richness and abundance of breeding bird species associated directly with the river channel on fragments mentioned above. It will allow us to estimate soberly how very the intensity of human utilization of the river affects the distribution of avifauna of the Vistula, determining the richness and abundance of valuable and/or endangered species breeding in a given area.

scholarly journals Morphological and genetic differentiation of Bufo toads: two cryptic species in Western Europe (Anura, Bufonidae)

2013 ◽  
Vol 82 (4) ◽  
pp. 147-169 ◽  
Author(s):  
Jan W. Arntzen ◽  
Jacob McAtear ◽  
Ernesto Recuero ◽  
Janine M. Ziermann ◽  
Annemarie Ohler ◽  
...  
Keyword(s):  
Mitochondrial Dna ◽  
Genetic Differentiation ◽  
Western Europe ◽  
Nuclear Dna ◽  
Sequence Data ◽  
Bufo Bufo ◽  
Sensu Stricto ◽  
Additional Species ◽  
Morphometric Characters ◽  
Evolutionary Context

The Common toad Bufo bufo sensu lato is a widespread, morphologically conserved taxon. Recent studies have uncovered deep genetic differentiation between population groups, highlighting the need to revise the current taxonomy of the group and recognize additional species. Here we investigate patterns of variation in molecular (a mitochondrial DNA restriction enzyme assay and sequence data for two nuclear DNA fragments totalling 979 bp) and 17 morphological variables in Northern France where two of these groups meet (B. bufo sensu stricto and B. spinosus), in order to delineate their contact zone and uncover characters that would allow discrimination of the two taxa. Mitochondrial DNA data show an abrupt transition from areas where B. bufo is present to those inhabited by B. spinosus, with a narrow area of overlap east of the city of Caen. Morphometric characters, particularly those related to the positioning of the parotoid glands and metatarsal tubercle shape and size, proved useful in discriminating between species (AUC ≥ 0.97, kappa ≥ 0.79). We then used the differentiating character states to allocate over 300 museum specimens from Western Europe to either species with consistent results, including comparable values of AUC and kappa of the identification models, indicating that models could successfully be applied across datasets. We summarize available evidence relevant to the delineation of the distribution of B. bufo and B. spinosus in France and discuss the characters differentiating both species in an evolutionary context. In view of the observed morphological and genetic differentiation and the absence of unequivocal evidence for widespread hybridization we support the view that B. bufo and B. spinosus are best considered different species. Finally, we propose that ‘parotoids in parallel position’ and a thin and smooth skin are derived character states for B. bufo over the northern part of its range.

Genetic homogeneity of weathervane scallops (Patinopecten caurinus) in the northeastern Pacific

2010 ◽  
Vol 67 (11) ◽  
pp. 1827-1839 ◽  
Author(s):  
Patrick M. Gaffney ◽  
Carita M. Pascal ◽  
Jeffery Barnhart ◽  
W. Stewart Grant ◽  
James E. Seeb
Keyword(s):  
Genetic Differentiation ◽  
Gene Diversity ◽  
Isolation By Distance ◽  
Population Expansion ◽  
Gulf Of Alaska ◽  
Nucleotide Sequencing ◽  
Mt Dna ◽  
Northeastern Pacific ◽  
Nuclear Loci ◽  
Allozyme Loci

We assessed genetic differentiation among populations of weathervane scallop ( Patinopecten caurinus ) in the northeastern Pacific, extending over 2500 km in the Gulf of Alaska and southeastern Bering Sea. Variability was surveyed at nuclear loci with allozyme, microsatellite, and single nucleotide polymorphism (SNP) methods, and at mitochondrial (mt)DNA loci with SNPs and nucleotide sequencing. High levels of gene diversity were detected for allozymes (H = 0.080), microsatellites (H = 0.734), and mtDNA (h = 0.781). Genotypes at nuclear loci generally fit Hardy–Weinberg proportions, except for some microsatellite loci, for which null-allele frequencies of 0.02 to 0.34 were estimated. No allele-frequency differences were detected among samples, except for the allozyme loci Gpi and Pep-4. Overall levels of differentiation ranged from FST = 0.0004 for allozymes, FST = 0.0008 for mtDNA to FST = 0.0004 for microsatellites. No isolation by distance was found for any of the markers. A unimodal mtDNA mismatch distribution and significant excesses of low-frequency variants for allozymes, microsatellites, and mtDNA may reflect a post-glacial population expansion. The lack of genetic differentiation measured by neutral markers does not preclude the existence of locally adapted, self-sustaining populations that are important in the harvest management of this species.

The Northern Bald Ibis Geronticus eremita in Morocco since 1900: Analysis of ecological requirements

2019 ◽  
Vol 30 (1) ◽  
pp. 117-138 ◽  
Author(s):  
ANDRE SCHENKER ◽  
FABIAN CAHENZLI ◽  
KARL G. GUTBROD ◽  
MICHEL THEVENOT ◽  
ANDREAS ERHARDT
Keyword(s):  
National Park ◽  
Satellite Images ◽  
Atlantic Coast ◽  
Bird Species ◽  
Earth Satellite ◽  
Google Earth ◽  
Mean Annual Precipitation ◽  
Breeding Sites ◽  
Ecological Requirements ◽  
Geronticus Eremita

SummaryThe Northern Bald Ibis (NBI) Geronticus eremita, is an ‘Endangered’ bird species of which only very few wild breeding colonies have survived along the Atlantic coast of south-west Morocco. This paper analyses ecological conditions of the 72 breeding sites of the NBI that have been known since 1900 in Morocco. Characterisation of breeding sites is based on physical criteria (elevation above sea level, geomorphology, mean annual precipitation and types of landscape) as well as land use, vegetation cover, infrastructure and types of settlement within three perimeters (0–1 km, > 1–5 km and > 5–10(20) km) using Google Earth satellite images. Statistical analyses of the number of breeding pairs, fledglings and rainfall during different quarters of the year from 1994 to 2016 in the two remaining breeding sites in Souss-Massa National Park and Tamri showed expected patterns as well as unexpected differences between the two localities. Based on our findings and indications in the literature, we suggest general and specific recommendations for potential future translocation projects of the NBI. Based on the analysis of the 28 breeding colonies existing after 1977, two elements emerge as the most important prerequisites: a low level of disturbances at the breeding sites and adequate feeding areas at a reasonable distance of 5–15 km.

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 Divergent mitochondrial and nuclear OXPHOS genes are candidates for genetic incompatibilities inFicedulaFlycatchers

2019 ◽  
Author(s):  
Eva van der heijden ◽  
S. Eryn McFarlane ◽  
Tom van der Valk ◽  
Anna Qvarnström
Keyword(s):  
Energy Metabolism ◽  
Nuclear Dna ◽  
Resting Metabolic Rate ◽  
Population Expansion ◽  
Nuclear Genes ◽  
F1 Hybrids ◽  
Relative Role ◽  
Synonymous Mutations ◽  
Genes Encoding ◽  
Hybrid Dysfunction

AbstractHybrid dysfunction is an important source of reproductive isolation between emerging species. Bateson-Dobzhansky-Muller incompatibilities are theoretically well-recognized as the underlying cause of low hybrid dysfunction. However, especially in wild populations, little empirical evidence exists for which genes are involved in such incompatibilities. The relative role of ecological divergence in causing the build-up of genetic incompatibilities in relation to other processes such as genomic conflict therefore remains largely unknown. Genes involved in energy metabolism are potential candidates for genetic incompatibilities, since energy metabolism depends on co-expression of mitochondrial DNA (mtDNA) and nuclear DNA (nDNA) leading to mitonuclear coadaptation. When mitochondrial and nuclear genes lacking a co-evolutionary history appear together in hybrids, incompatibilities could arise.Ficedulaflycatcher F1 hybrids have a higher resting metabolic rate (RMR) compared to the parental species, which could be a sign of genetic incompatibilities between energy metabolism genes that diverged in response to environmental differences while the species were in allopatry. Based on sequences of 15 mitochondrial genes of 264 individuals, we show that the two species have divergent mtDNA caused by the build-up of mainly synonymous mutations and a few non-synonymous mutations. Pied flycatcher mitogenomes show evidence of non-neutrality, indicating a selective sweep or population expansion. There is little variation in the nuclear OXPHOS-related proteins and no significant deviation from neutrality, however, specific codon identified sites might be under positive selection in both mitochondrial and nuclear genes encoding OXPHOS proteins for complex I and III. Taken together, these diverged mitonuclear genes therefore constitute possible candidates underlying, at least part of the genetic incompatibilities that cause hybrid dysfunction in crosses between collared and pied flycatchers.

Sign in / Sign up

Export Citation Format

Share Document