Genetic and morphological differentiation among populations of the Rivoli’s Hummingbird (Eugenes fulgens) species complex (Aves: Trochilidae)

The Auk ◽  
2020 ◽  
Vol 137 (4) ◽  
Author(s):  
Luz E Zamudio-Beltrán ◽  
Juan Francisco Ornelas ◽  
Andreia Malpica ◽  
Blanca E Hernández-Baños
Keyword(s):  
Genetic Variation ◽  
Gene Flow ◽  
Genetic Differentiation ◽  
Species Complex ◽  
Ecological Niche Modeling ◽  
Demographic History ◽  
Morphological Differentiation ◽  
Last Interglacial ◽  
Haplotype Networks ◽  
Isthmus Of Tehuantepec

Abstract Genetic variation and phylogeographic studies have been crucial for understanding mechanisms of speciation. We analyzed genetic variation and phylogeography to reconstruct the demographic history of the Rivoli’s Hummingbird (Eugenes fulgens) species complex and also evaluated their morphological differentiation. This widely distributed species inhabits the highlands of Mexico and northern Central America, with 2 subspecies separated by the Isthmus of Tehuantepec (west: E. f. fulgens, east: E. f. viridiceps). We surveyed genetic variation in 2 mitochondrial DNA markers (mtDNA, with 129 individuals) and nuclear DNA (6 microsatellites, with 85 individuals). We also inferred the demographic history, estimated divergence times, and analyzed morphological variation using 470 vouchered specimens. We modeled the current potential distribution of the species using ecological niche modeling and projected it into the past to model the effects of the Pleistocene climatic cycles. Haplotype networks, pairwise FST comparisons, AMOVA, and morphological analysis revealed differences between geographically isolated populations separated by the Isthmus of Tehuantepec (IT; corresponding to the 2 recognized subspecies: fulgens and viridiceps), and by the Motagua-Polochic-Jocotán (MPJ) system fault. Demographic scenarios revealed a contraction in distribution during the last interglacial, and expansion during the Last Glacial Maximum (LGM) with little change since the LGM. Divergence between groups separated by the Isthmus of Tehuantepec ~59,600 yr ago occurred in the presence of gene flow, suggesting that the Isthmus of Tehuantepec is a semipermeable barrier to gene flow. STRUCTURE analyses of microsatellite data detected 3 genetically differentiated groups. Several results fit a model of recent lineage divergence, including a significant signal of genetic differentiation, demographic expansion, decreased gene flow from past to present, and northward expansion during the LGM and contraction during the interglacial periods. We conclude that the genetic differentiation of E. fulgens in the Madrean Pine-Oak Woodlands resulted from recent geographical isolation of populations separated by natural barriers (IT and MPJ).

scholarly journals Elucidating the drivers of genetic differentiation in Malaysian torrent frogs (Anura: Ranidae: Amolops): a landscape genomics approach

2019 ◽  
Vol 190 (1) ◽  
pp. 65-78 ◽  
Author(s):  
Kin Onn Chan ◽  
Rafe M Brown
Keyword(s):  
Genetic Variation ◽  
Gene Flow ◽  
Genetic Differentiation ◽  
Isolation By Distance ◽  
Variance Partitioning ◽  
Nucleotide Polymorphisms ◽  
Landscape Genomics ◽  
Mountain Ranges ◽  
Historical Factors ◽  
Environmental Attributes

Abstract The interplay between environmental attributes and evolutionary processes can provide valuable insights into how biodiversity is generated, partitioned and distributed. This study investigates the role of spatial, environmental and historical factors that could potentially drive diversification and shape genetic variation in Malaysian torrent frogs. Torrent frogs are ecologically conserved, and we hypothesize that this could impose tight constraints on dispersal routes, gene flow and consequently genetic structure. Moreover, levels of gene flow were shown to vary among populations from separate mountain ranges, indicating that genetic differentiation could be influenced by landscape features. Using genome-wide single nucleotide polymorphisms, in conjunction with landscape variables derived from Geographic Information Systems, we performed distance-based redundancy analyses and variance partitioning to disentangle the effects of isolation-by-distance (IBD), isolation-by-resistance (IBR) and isolation-by-colonization (IBC). Our results demonstrated that IBR contributed minimally to genetic variation. Intraspecific population structure can be largely attributed to IBD, whereas interspecific diversification was primarily driven by IBC. We also detected two distinct population bottlenecks, indicating that speciation events were likely driven by vicariance or founder events.

Contrasting evolutionary processes drive morphological and genetic differentiation in a subtropical fir (Abies, Pinaceae) species complex

2019 ◽  
Author(s):  
Jorge Cruz-Nicolás ◽  
Gustavo Giles-Pérez ◽  
Eréndira González-Linares ◽  
Julia Múgica-Gallart ◽  
Andrés Lira-Noriega ◽  
...  
Keyword(s):  
Genetic Differentiation ◽  
Population Size ◽  
Species Complex ◽  
Isolation By Distance ◽  
Morphological Differentiation ◽  
Resin Duct ◽  
Evolutionary Force ◽  
Ssr Loci ◽  
Selective Forces ◽  
Species Descriptions

Abstract Interacting stochastic and selective forces drive population and species divergence. Such interaction may generate contrasting clines between genetic and phenotypic factors, which can be related to either geographical or environmental variation depending on the predominant evolutionary force (which in its turn is partly determined by population size). Here, we investigated whether the morphological and genetic differentiation across a species complex in Abies in central Mexico fits isolation by distance (IBD) or isolation-by-adaptation (IBA) frameworks. This complex includes two species (A. religiosa and A. flinckii) with discernible morphological and environmental differences and dissimilar range sizes. After comparing variation at nuclear SSR loci and diagnostic morphological traits of needles with the climate variables contributing to ecological differentiation, we found that the widely distributed A. religiosa has more genetic diversity and is morphologically more heterogeneous than the geographically restricted A. flinckii. Morphological differentiation at three physiologically important traits (needle thickness, number of stomata rows and location of the resin duct) is significantly correlated with geography in A. flinckii (indicative of IBD), but is significantly associated with climate variation in A. religiosa (suggesting IBA). In agreement with quantitative genetics theory, PST (phenotypic differentiation)-G’ST (genetic differentiation) comparisons indicate contrasting contributions of putatively adaptive (A. religiosa) and stochastic (A. flinckii) factors to the morphological differentiation of species related to their population size. The integration of such quantitative genetic/evolutionary aspects may reinforce species descriptions and help in disentangling resilient taxonomic discordance.

scholarly journals Large-scale geographic survey provides insights into the colonization history of a major aphid pest on its cultivated apple host in Europe, North America and North Africa

2020 ◽  
Author(s):  
S.G. Olvera-Vazquez ◽  
C. Remoue ◽  
A. Venon ◽  
A. Rousselet ◽  
O. Grandcolas ◽  
...  
Keyword(s):  
Gene Flow ◽  
North America ◽  
Genetic Differentiation ◽  
North Africa ◽  
Large Scale ◽  
Demographic History ◽  
High Genetic Diversity ◽  
The North ◽  
The Us ◽  
History Of

With frequent host shifts involving the colonization of new hosts across large geographical ranges, crop pests are good models for examining the mechanisms of rapid colonization. The microbial partners of pest insects may be involved or affected by colonization, which has been little studied so far. We investigated the demographic history of the rosy apple aphid, Dysaphis plantaginea, a major pest of the cultivated apple (Malus domestica) in Europe, North Africa and North America, as well as the diversity of its endosymbiotic bacterial community. We genotyped a comprehensive sample of 714 colonies from Europe, Morocco and the US using mitochondrial (CytB and CO1), bacterial (16s rRNA and TrnpB), and 30 microsatellite markers. We detected five populations spread across the US, Morocco, Western and Eastern Europe, and Spain. Populations showed weak genetic differentiation and high genetic diversity, except the Moroccan and the North American that are likely the result of recent colonization events. Coalescent-based inferences releaved high levels of gene flow among populations during the colonization, but did not allow determining the sequence of colonization of Europe, America and Morroco by D. plantaginea, likely because of the weak genetic differentiation and the occurrence of gene flow among populations. Finally, we found that D. plantaginea rarely hosts any other endosymbiotic bacteria than its obligate nutritional symbiont Buchnera aphidicola. This suggests that secondary endosymbionts did not play any role in the rapid spread of the rosy apple aphid. These findings have fundamental importance for understanding pest colonization processes and implications for sustainable pest control programs.

scholarly journals Microsatellite Characterization of Malaysian Mahseer (Tor spp.) for Improvement of Broodstock Management and Utilization

Animals ◽  
2021 ◽  
Vol 11 (9) ◽  
pp. 2633
Author(s):  
Poh Chiang Chew ◽  
Annie Christianus ◽  
Jaapar M. Zudaidy ◽  
Md Yasin Ina-Salwany ◽  
Chou Min Chong ◽  
...  
Keyword(s):  
Genetic Variation ◽  
Gene Flow ◽  
Genetic Differentiation ◽  
Genetic Relatedness ◽  
Genetic Distances ◽  
Group Method ◽  
Genetic Management ◽  
Principal Coordinates Analysis ◽  
Principal Coordinates ◽  
Geographical Regions

In this study, a mixture of Tor tambra and T. tambroides with unknown genetic background were collected from 11 localities in Malaysia for broodstock development and sperm cryo-banking. This study aims to assess the microsatellite (simple sequence repeat, SSR) variation, genetic diversity, genetic differentiation, level of gene flow, population structure, genetic relatedness and their demographic aspects among these Tor populations, in addition to establishing their SSR profile by employing 22 SSR markers via fragment analysis. Total genomic DNA was extracted from 181 samples (91 cryopreserved milt samples and 90 scale samples of live broodfish). Results showed the Tor spp. collection retained their genetic variation but exhibited excessive homozygosity among individuals within population. Moderate genetic differentiation was shown among the populations, with highly significant (p < 0.001) fixation indices (FST, FIS and FIT). A low gene flow over all loci (Nm 1.548) indicates little genetic variation transfer between populations. The genetic structures of all the populations were successfully resolved into four main clusters by an unweighted pair group method with arithmetic mean (UPGMA) dendrogram generated based on Nei’s genetic distances. The population structures based on principal coordinates analysis (PCoA) and the Bayesian model also suggested four distinct clusters following geographical regions and eight closely related populations. This study provided a useful baseline reference for better genetic management and utilization of the Tor spp. stocks in their breeding and conservation programmes.

scholarly journals Phylogeographical Structure of Liquidambar formosana Hance Revealed by Chloroplast Phylogeography and Species Distribution Models

Forests ◽  
2019 ◽  
Vol 10 (10) ◽  
pp. 858 ◽  
Author(s):  
Sun ◽  
Lin ◽  
Huang ◽  
Ye ◽  
Lai ◽  
...  
Keyword(s):  
Genetic Variation ◽  
Genetic Differentiation ◽  
Species Distribution ◽  
Species Distribution Models ◽  
Central China ◽  
Recent Common Ancestor ◽  
Interglacial Period ◽  
Last Interglacial ◽  
Distribution Models ◽  
Last Interglacial Period

To understand the origin and evolutionary history, and the geographical and historical causes for the formation of the current distribution pattern of Lquidambar formosana Hance, we investigated the phylogeography by using chloroplasts DNA (cpDNA) non-coding sequences and species distribution models (SDM). Four cpDNA intergenic spacer regions were amplified and sequenced for 251 individuals from 25 populations covering most of its geographical range in China. A total of 20 haplotypes were recovered. The species had a high level of chloroplast genetic variation (Ht = 0.909 ± 0.0192) and a significant phylogeographical structure (genetic differentiation takes into account distances among haplotypes (Nst) = 0.730 > population differentiation that does not consider distances among haplotypes (Gst) = 0.645; p < 0.05), whereas the genetic variation within populations (Hs = 0.323 ± 0.0553) was low. The variation of haplotype mainly occurred among populations (genetic differentiation coefficient (Fst) = 0.73012). The low genetic diversity within populations may be attributed to the restricted gene flow (Nm = 0.18). The time of the most recent common ancestor for clade V mostly distributed in Southwestern China, Central China, Qinling and Dabieshan mountains was 10.30 Ma (95% Highest posterior density (HPD): 9.74–15.28) dating back to the middle Miocene, which revealed the genetic structure of L. formosana was of ancient origin. These results indicated that dramatic changes since the Miocene may have driven the ancestors of L. formosana to retreat from the high latitudes of the Northern Hemisphere to subtropical China in which the establishment and initial intensification of the Asian monsoon provided conditions for their ecological requirements. This scenario was confirmed by the fossil record. SDM results indicated there were no contraction–expansion dynamics, and there was a stable range since the last interglacial period (LIG, 130 kya). Compared with the population expansion detected by Fu’s Fs value and the mismatch distribution, we speculated the expansion time may happen before the interglacial period. Evidence supporting L. formosana was the ancient origin and table range since the last interglacial period.

scholarly journals Local differentiation in the presence of gene flow in the citril finch Serinus citrinella

2005 ◽  
Vol 2 (1) ◽  
pp. 85-87 ◽  
Author(s):  
Juan Carlos Senar ◽  
Antoni Borras ◽  
Josep Cabrera ◽  
Toni Cabrera ◽  
Mats Björklund
Keyword(s):  
Gene Flow ◽  
Genetic Differentiation ◽  
High Probability ◽  
Bird Species ◽  
Morphological Differentiation ◽  
Citril Finch ◽  
Geographical Scale ◽  
Local Differentiation ◽  
The Relationship ◽  
Very High

It is well known theoretically that gene flow can impede genetic differentiation between populations. In this study, we show that in a highly mobile bird species, where dispersal is well documented, there is a strong genetic and morphological differentiation over a very short geographical scale (less than 5 km). Allocation tests revealed that birds caught in one area were assigned genetically to the same area with a very high probability, in spite of current gene flow. Populations were also morphologically differentiated. The results suggest that the relationship between gene flow and differentiation can be rather complicated and non-intuitive.

scholarly journals Low genetic divergence and variation in coastal dune populations of the widespread terrestrial orchid Epipactis helleborine

2020 ◽  
Vol 193 (3) ◽  
pp. 419-430 ◽  
Author(s):  
Hans Jacquemyn ◽  
Hanne De Kort ◽  
An Vanden Broeck ◽  
Rein Brys
Keyword(s):  
Genetic Variation ◽  
Gene Flow ◽  
Genetic Differentiation ◽  
Genetic Divergence ◽  
Coastal Dune ◽  
Terrestrial Orchid ◽  
Colonization Event ◽  
History Of ◽  
Epipactis Helleborine ◽  
Seed Introduction

Abstract Reconstructing the early history of species divergence and quantifying the level of standing genetic variation in diverging populations are central to our understanding of ecotype formation and ultimately speciation. In this study, we used single nucleotide polymorphisms to reconstruct the evolutionary history of species divergence in coastal dune populations of the widespread terrestrial orchid Epipactis helleborine and to investigate the level of standing genetic variation in 29 coastal dune populations in a fragmented dune landscape along the Belgian and French coast. Additionally, we used seed introduction experiments to assess the potential for gene flow into existing populations after long-distance seed dispersal and the ability to colonize vacant sites. Our results showed that coastal dune populations diverged only recently from inland populations, went through a significant bottleneck and were most probably the result of a single colonization event. Current levels of population genetic diversity are low and not related to population size or spatial isolation. The sampled dune populations also showed little genetic differentiation, and no apparent spatial genetic structure was observed. Seed introduction experiments showed that seeds of coastal dune populations germinated easily in both occupied and unoccupied sites in dune habitat, indicating that the availability of suitable mycorrhizal fungi is not limiting the distribution of coastal dune populations and that gene flow through seeds has probably contributed to the observed low levels of genetic differentiation. Overall, these results are consistent with a process of genetic divergence after a single, recent colonization event, followed by extensive gene flow among populations.

The Quaternary range dynamics of Noccaea iberidea (Brassicaceae), a typical representative of subalpine/alpine steppe communities of Anatolian mountains

2020 ◽  
Vol 131 (4) ◽  
pp. 986-1001
Author(s):  
Bariş Özüdoğru ◽  
Kurtuluş Özgi̇şi ◽  
Utku Perktaş ◽  
Hakan Gür
Keyword(s):  
Ecological Niche ◽  
Global Climate ◽  
Demographic History ◽  
Population Expansion ◽  
Ecological Niche Modelling ◽  
Last Interglacial ◽  
Niche Modelling ◽  
Typical Representative ◽  
Haplotype Networks ◽  
Steppe Communities

Abstract The responses of Anatolian plants to global climate change have been poorly investigated. In this study, we aimed to understand how climatic oscillation during the Quaternary period helped to shape the current distribution patterns of the Anatolian endemic Noccaea iberidea, a typical representative of tragacanthic (thorny cushion) steppe communities of Anatolia. We used ecological niche modelling combined with statistical phylogeography, based on nuclear ribosomal ITS and plastidic trnL-F and trnS-ycf9 regions. Both the structure of the haplotype networks and the results of the extended Bayesian skyline plot analysis clearly indicated that N. iberidea has been through a recent population expansion. This interpretation was also supported by ecological niche modelling analysis, which showed that the availability of areas of high suitability expanded from the Last Interglacial to the Last Glacial Maximum, suggesting that N. iberidea might have expanded its range during the glacial periods. In conclusion, the study improves our understanding of the demographic history and responses of steppe plant communities of Anatolia to global climate changes through the Late Quaternary glacial–interglacial cycles, which in turn might aid in the development of future conservation strategies.

scholarly journals Genetic differentiation and diversity of Callosobruchus chinensis collections from China

2015 ◽  
Vol 106 (1) ◽  
pp. 124-134 ◽  
Author(s):  
C.X. Duan ◽  
W.C. Li ◽  
Z.D. Zhu ◽  
D.D. Li ◽  
S.L. Sun ◽  
...  
Keyword(s):  
Genetic Variation ◽  
Gene Flow ◽  
Genetic Differentiation ◽  
Genetic Distances ◽  
Fixation Index ◽  
Group Method ◽  
Callosobruchus Chinensis ◽  
Chain Reactions ◽  
Information Index ◽  
Geographic Populations

AbstractCallosobruchus chinensis (Linnaeus) is one of the most destructive pests of leguminous seeds. Genetic differentiation and diversity analysis of 345 C. chinensis individuals from 23 geographic populations using 20 polymorphic simple sequence repeats revealed a total of 149 alleles with an average of 7.45 alleles per locus. The average Shannon's information index was 1.015. The gene flow and genetic differentiation rate values at the 20 loci ranged from 0.201 to 1.841 and 11.0–47.2%, with averages of 0.849 and 24.4%, respectively. In the 23 geographic populations, the effective number of alleles and observed heterozygosity ranged from 1.441 to 2.218 and 0.191–0.410, respectively. Shannon's information index ranged from 0.357 to 0.949, with the highest value in Hohhot and the lowest in Rudong. In all comparisons, the fixation index (FST) values ranged from 0.049 to 0.441 with a total FST value of 0.254 among the 23 C. chinensis populations, indicating a moderate level of genetic differentiation and gene flow among these populations. Analysis of molecular variance revealed that the genetic variation within populations accounted for 76.7% of the total genetic variation. The genetic similarity values between populations varied from 0.617 to 0.969, whereas genetic distances varied from 0.032 to 0.483. Using unweighted pair-group method using arithmetical averages cluster analysis, the 23 geographic collections were classified into four distinct genetic groups but most of them were clustered into a single group. The pattern of the three concentrated groups from polymerase chain reactions analysis showed a somewhat different result with cluster.

scholarly journals Global drivers of diversification in a marine species complex

2019 ◽  
Author(s):  
Catarina N.S. Silva ◽  
Nicholas P. Murphy ◽  
James J. Bell ◽  
Bridget S. Green ◽  
Guy Duhamel ◽  
...  
Keyword(s):  
Gene Flow ◽  
Genetic Differentiation ◽  
Continental Shelf ◽  
Demographic History ◽  
Significant Proportion ◽  
Secondary Contact ◽  
Larval Duration ◽  
Genome Wide ◽  
Extant Species ◽  
Species Pairs

AbstractInvestigating historical gene flow in species complexes can indicate how environmental and reproductive barriers shape genome divergence before speciation. The processes influencing species diversification under environmental change remain one of the central focal points of evolutionary biology, particularly for marine organisms with high dispersal potential. We investigated genome-wide divergence, introgression patterns and inferred demographic history between species pairs of all extant rock lobster species (Jasus spp.), a complex with long larval duration, that has populated continental shelf and seamount habitats around the globe at approximately 40°S. Genetic differentiation patterns revealed the effects of the environment and geographic isolation. Species associated with the same habitat structure (either continental shelf or seamount/island) shared a common ancestry, even though the habitats were not adjacent. Differences in benthic temperature explained a significant proportion (41.3%) of the genetic differentiation. The Eastern Pacific species pair of J. caveorum and J. frontalis retained a signal of strict isolation following ancient migration, whereas species pairs from Australia and Africa and seamounts in the Indian and Atlantic oceans included events of introgression after secondary contact. Parameters estimated for time in isolation and gene flow were congruent with genetic differentiation metrics suggesting that the observed differentiation patterns are the product of migration and genetic drift. Our results reveal important effects of habitat and demographic processes on the divergence of species within the genus Jasus providing the first empirical study of genome-wide drivers of diversification that incorporates all extant species in a marine genus with long pelagic larval duration.

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