scholarly journals River network rearrangements promote speciation in lowland Amazonian birds

2021 ◽  
Author(s):  
Lukas J Musher ◽  
Melina Giakoumis ◽  
James Albert ◽  
Glaucia Del Rio ◽  
Marco Rego ◽  
...  
Keyword(s):  
Small Rivers ◽  
River Networks ◽  
Secondary Contact ◽  
Small Populations ◽  
Hybrid Speciation ◽  
River Dynamics ◽  
Species Complexes ◽  
Genome Wide ◽  
Potential Case ◽  
Displacement Processes

Large Amazonian rivers impede dispersal for many species, but lowland river networks frequently rearrange, thereby altering the location and effectiveness of river-barriers through time. These rearrangements may promote biotic diversification by facilitating episodic allopatry and secondary contact among populations. We sequenced genome-wide markers to evaluate histories of divergence and introgression in six Amazonian avian species-complexes. We first tested the assumption that rivers are barriers for these taxa and found that even relatively small rivers facilitate divergence. We then tested whether species diverged with gene flow and recovered reticulate histories for all species, including one potential case of hybrid speciation. Our results support the hypothesis that river dynamics promote speciation and reveal that many rainforest taxa are micro-endemic, unrecognized and thus threatened with imminent extinction. We propose that Amazonian hyper-diversity originates in part from fine-scale barrier displacement processes, including river dynamics, which allow small populations to differentiate and disperse into secondary contact.

scholarly journals Blockwise Site Frequency Spectra for Inferring Complex Population Histories and Recombination

2016 ◽  
Author(s):  
Champak R. Beeravolu ◽  
Michael J. Hickerson ◽  
Laurent A.F. Frantz ◽  
Konrad Lohse
Keyword(s):  
Demographic History ◽  
Composite Likelihood ◽  
Model Organisms ◽  
Secondary Contact ◽  
Parameter Estimates ◽  
Genome Sequences ◽  
Frequency Spectra ◽  
Genome Wide ◽  
Complex Population ◽  
History Of

AbstractWe introduce ABLE (Approximate Blockwise Likelihood Estimation), a novel composite likelihood framework based on a recently introduced summary of sequence variation: the blockwise site frequency spectrum (bSFS). This simulation-based framework uses the the frequencies of bSFS configurations to jointly model demographic history and recombination and is explicitly designed to make inference using multiple whole genomes or genome-wide multi-locus data (e.g. RADSeq) catering to the needs of researchers studying model or non-model organisms respectively. The flexible nature of our method further allows for arbitrarily complex population histories using unphased and unpolarized whole genome sequences. In silico experiments demonstrate accurate parameter estimates across a range of divergence models with increasing complexity, and as a proof of principle, we infer the demographic history of the two species of orangutan from multiple genome sequences (over 160 Mbp in length) from each species. Our results indicate that the two orangutan species split approximately 650-950 thousand years ago but experienced a pulse of secondary contact much more recently, most likely during a period of low sea-level South East Asia (∼300,000 years ago). Unlike previous analyses we can reject a history of continuous gene flow and co-estimate genome-wide recombination. ABLE is available for download at https://github.com/champost/ABLE.

scholarly journals Parallel adaptations to an altitudinal gradient persist in tetraploid snowtrout (Cyprinidae: Schizothorax), despite extensive genomic exchange within adjacent Himalayan rivers

2021 ◽  
Author(s):  
Tyler K Chafin ◽  
Binod Regmi ◽  
Marlis R. Douglas ◽  
David R. Edds ◽  
Karma Wangchuk ◽  
...  
Keyword(s):  
De Novo ◽  
Genomic Islands ◽  
Secondary Contact ◽  
Evolutionary Patterns ◽  
Ploidy Levels ◽  
Reduced Representation ◽  
Genome Wide ◽  
Genealogical Concordance ◽  
Genomic Approach ◽  
The Ganges

Replicated evolutionary patterns are often attributed to recurrent emergence following parallel selective pressures. However, similar genetic patterns (e.g., 'genomic islands') can also emerge following extensive homogenization in secondary contact, as a by-product of heterogeneous introgression. For example, within Himalayan tributaries of the Ganges/Brahmaputra rivers, drainage-specific mtDNA clades of polyploid snowtrout (Cyprinidae: Schizothorax) are partitioned as co-occurring morphological 'ecotypes,' hypothesized to represent parallel divergence among adjacent streams. To evaluate this scenario, we utilized a reduced-representation genomic approach (N=35,319 de-novo and N=10,884 transcriptome-aligned SNPs) applied to high-altitude Nepali/Bhutanese snowtrout (N=48 each). We unambiguously quantified ploidy levels by first deriving genome-wide allelic depths followed by ploidy-aware Bayesian models that produced genotypes statistically consistent with diploid/tetraploid expectations. When genotyped SNPs were clustering within drainages, the convergence of eco-phenotypes was sustained. However, subsequent partitioned analyses of phylogeny and population admixture instead identified subsets of loci under selection which retained genealogical concordance with morphology, with apparent patterns of parallel ecotype emergence instead driven by widespread genomic homogenization. Here, prior isolation is effectively masked by admixture occurring in secondary contact. We note two salient factors:1) Polyploidy has promoted homogenization in tetraploid Himalayan snowtrout; and 2) Homogenization varies across Himalayan tributaries, presumably in lockstep with extent of anthropogenic modification.

scholarly journals Quasi-neutral molecular evolution — When positive and negative selection cancel out

2018 ◽  
Author(s):  
Bingjie Chen ◽  
Zongkun Shi ◽  
Qingjian Chen ◽  
Darryl Shibata ◽  
Haijun Wen ◽  
...  
Keyword(s):  
Dna Sequences ◽  
Negative Selection ◽  
Evolutionary Rate ◽  
Neutral Evolution ◽  
Stem Cell Population ◽  
Small Populations ◽  
Phenotypic Evolution ◽  
Normal Tissues ◽  
Genome Wide ◽  
Population Sizes

AbstractIn the absence of both positive and negative selection, DNA sequences evolve at the neutral rate, R = 1. Due to the prevalence of negative selection, R∼1 is rarely achieved in organismal evolution. However, when R ∼ 1 is observed, it does not necessarily indicate neutral evolution because positive and negative selection could be equally strong but in opposite directions - hereby referred to as quasi-neutrality. We now show that somatic-cell evolution could be the paradigm of quasi-neutral evolution for these reasons: 1) Quasi-neutrality is much more likely in small populations (size N < 50) than in large ones; 2) Stem cell population sizes in single niches of normal tissues, from which tumors likely emerges, have small N’s (usually < 50); 3) the genome-wide evolutionary rate across tissue types is close to R = 1; 4) Relative to the average of R ∼ 1, many genes evolve at a much higher or lower rate, thus hinting both positive and negative selection; 5) When N < 50, selection efficacy decreases rapidly as N decreases even when the selection intensity stays constant; 6) Notably, N is smaller in the small intestine (SmI) than in the colon (CO); hence, the ∼ 70 fold higher rate of phenotypic evolution (observed as cancer risk) in the latter can be explained by the greater efficacy of selection, which then leads to the fixation of more advantageous mutations and fewer deleterious ones in the CO. Under quasineutrality, positive and negative selection can be measured in the same system as the two forces are simultaneously present or absent.

scholarly journals Quaternary climate changes as speciation drivers in the Amazon floodplains

2020 ◽  
Vol 6 (11) ◽  
pp. eaax4718 ◽  
Author(s):  
Gregory Thom ◽  
Alexander T. Xue ◽  
André O. Sawakuchi ◽  
Camila C. Ribas ◽  
Michael J. Hickerson ◽  
...  
Keyword(s):  
Environmental Changes ◽  
Demographic History ◽  
Secondary Contact ◽  
Phylogenomic Analysis ◽  
Population Isolation ◽  
Quaternary Climate ◽  
Species Complexes ◽  
Historical Processes ◽  
Quaternary Climate Changes

The role of climate as a speciation driver in the Amazon has long been discussed. Phylogeographic studies have failed to recover synchronous demographic responses across taxa, although recent evidence supports the interaction between rivers and climate in promoting speciation. Most studies, however, are biased toward upland forest organisms, while other habitats are poorly explored and could hold valuable information about major historical processes. We conducted a comparative phylogenomic analysis of floodplain forest birds to explore the effects of historical environmental changes and current connectivity on population differentiation. Our findings support a similar demographic history among species complexes, indicating that the central portion of the Amazon River basin is a suture zone for taxa isolated across the main Amazonian sub-basins. Our results also suggest that changes in the fluvial landscape induced by climate variation during the Mid- and Late Pleistocene drove population isolation, leading to diversification with subsequent secondary contact.

scholarly journals The origin and remolding of genomic islands of differentiation in the European sea bass

2017 ◽  
Author(s):  
Maud Duranton ◽  
François Allal ◽  
Christelle Fraïsse ◽  
Nicolas Bierne ◽  
François Bonhomme ◽  
...  
Keyword(s):  
Reproductive Isolation ◽  
Sea Bass ◽  
Genomic Islands ◽  
Secondary Contact ◽  
European Sea Bass ◽  
Closely Related Species ◽  
Fitness Effects ◽  
Genome Wide ◽  
Complex Process ◽  
Linked Selection

AbstractSpeciation is a complex process that leads to the progressive establishment of reproductive isolation barriers between diverging populations. Genome-wide comparisons between closely related species have revealed the existence of heterogeneous divergence patterns, dominated by genomic islands of increased divergence supposed to contain reproductive isolation loci. However, this divergence landscape only provides a static picture of the dynamic process of speciation, during which confounding mechanisms unlinked to speciation can interfere. Here, we used haplotype-resolved whole-genome sequences to identify the mechanisms responsible for the formation of genomic islands between Atlantic and Mediterranean sea bass lineages. We show that genomic islands first emerged in allopatry through the effect of linked selection acting on a heterogeneous recombination landscape. Upon secondary contact, preexisting islands were strongly remolded by differential introgression, revealing variable fitness effects among regions involved in reproductive isolation. Interestingly, we found that divergent regions containing ancient polymorphisms conferred the strongest resistance to introgression.

scholarly journals Speciation driven by hybridization and chromosomal plasticity in a wild yeast

2015 ◽  
Author(s):  
Jean-Baptiste Leducq ◽  
Lou Nielly-Thibault ◽  
Guillaume Charron ◽  
Chris Eberlein ◽  
Jukka-Pekka Verta ◽  
...  
Keyword(s):  
Rapid Evolution ◽  
Natural Populations ◽  
Secondary Contact ◽  
Hybrid Speciation ◽  
Hybrid Species ◽  
Chromosome Architecture ◽  
The North ◽  
Wild Yeast ◽  
Homoploid Hybrid ◽  
Powerful Mechanism

Hybridization is recognized as a powerful mechanism of speciation and a driving force in generating biodiversity. However, only few multicellular species, limited to a handful of plants and animals, have been shown to fulfill all the criteria of homoploid hybrid speciation. This lack of evidence could lead to the misconception that speciation by hybridization has a limited role in eukaryotes, particularly in single-celled organisms. Laboratory experiments have revealed that fungi such as budding yeasts can rapidly develop reproductive isolation and novel phenotypes through hybridization, showing that in principle homoploid speciation could occur in nature. Here we report a case of homoploid hybrid speciation in natural populations of the budding yeast Saccharomyces paradoxus inhabiting the North American forests. We show that the rapid evolution of chromosome architecture and an ecological context that led to secondary contact between nascent species drove the formation of an incipient hybrid species with a potentially unique ecological niche.

scholarly journals Locus-specific introgression in young hybrid swarms: drift dominates selection

2020 ◽  
Author(s):  
S. Eryn McFarlane ◽  
Helen V. Senn ◽  
Stephanie L. Smith ◽  
Josephine M. Pemberton
Keyword(s):  
Reproductive Isolation ◽  
Policy Implications ◽  
Secondary Contact ◽  
Hybrid Zones ◽  
Policy Makers ◽  
Adaptive Introgression ◽  
Allelic Replacement ◽  
Hybrid Swarms ◽  
Genome Wide ◽  
Future Work

AbstractClosely related species that have previously inhabited geographically separated ranges are hybridizing at an increasing rate due to human disruptions. These anthropogenic hybrid zones can be used to study reproductive isolation between species at secondary contact, including examining locus-specific rates of introgression. Introgression is expected to be heterogenous across the genome, reflecting variation in selection. Those loci that introgress especially slowly are good candidates for being involved in reproductive isolation, while those loci that introgress quickly may be involved in adaptive introgression. In the context of conservation, policy makers are especially concerned about introduced alleles moving quickly into the background of a native or endemic species, as these alleles could replace the native alleles in the population, leading to extinction via hybridization. We applied genomic cline analyses to 44997 SNPs to identify loci introgressing at excessive rates when compared to the genome wide expectation in an anthropogenic hybridizing population of red deer and sika in Kintyre Scotland. We found 11.4% of SNPs had cline centers that were significantly different from the genome wide expectation, and 17.6% had excessive rates of introgression. Based on simulations, we believe that many of these markers have diverged from average due to drift, rather than because of selection. Future work could determine the policy implications of allelic-replacement due to drift rather than selection, and could use replicate, geographically distinct hybrid zones to narrow down those loci that are indeed responding to selection in anthropogenic hybrid zones.

scholarly journals Genomic islands of divergence or opportunities for introgression?

2017 ◽  
Vol 284 (1850) ◽  
pp. 20162414 ◽  
Author(s):  
Rachael A. Bay ◽  
Kristen Ruegg
Keyword(s):  
Gene Flow ◽  
Reproductive Isolation ◽  
Genomic Islands ◽  
Secondary Contact ◽  
Catharus Ustulatus ◽  
Adaptive Introgression ◽  
Evolutionary Forces ◽  
Genome Wide ◽  
Isolating Mechanisms ◽  
Migratory Songbird

In animals, introgression between species is often perceived as the breakdown of reproductive isolating mechanisms, but gene flow between incipient species can also represent a source for potentially beneficial alleles. Recently, genome-wide datasets have revealed clusters of differentiated loci (‘genomic islands of divergence’) that are thought to play a role in reproductive isolation and therefore have reduced gene flow. We use simulations to further examine the evolutionary forces that shape and maintain genomic islands of divergence between two subspecies of the migratory songbird, Swainson's thrush ( Catharus ustulatus ), which have come into secondary contact since the last glacial maximum. We find that, contrary to expectation, gene flow is high within islands and is highly asymmetric. In addition, patterns of nucleotide diversity at highly differentiated loci suggest selection was more frequent in a single ecotype. We propose a mechanism whereby beneficial alleles spread via selective sweeps following a post-glacial demographic expansion in one subspecies and move preferentially across the hybrid zone. We find no evidence that genomic islands are the result of divergent selection or reproductive isolation, rather our results suggest that differentiated loci both within and outside islands could provide opportunities for adaptive introgression across porous species boundaries.

scholarly journals Evolutionary dynamics driving continental radiations of Fagaceae forests across the Northern Hemisphere

2021 ◽  
Author(s):  
Biao-Feng Zhou ◽  
Shuai Yuan ◽  
Andrew Crowl ◽  
Yi-Ye Liang ◽  
Yong Shi ◽  
...  
Keyword(s):  
Northern Hemisphere ◽  
Evolutionary Dynamics ◽  
Pollen Dispersal ◽  
Multiple Time Scales ◽  
Secondary Contact ◽  
Multiple Time ◽  
Competitive Edge ◽  
Adaptive Introgression ◽  
Genome Wide ◽  
Rapid Diversification

Abstract Northern Hemisphere forests changed drastically in the early Eocene with the diversification of the oak family (Fagaceae). Cooling climates over the next 20 million years fostered the spread of temperate biomes that became increasingly dominated by oaks and their chestnut relatives. Here we investigate the timing and pattern of major macroevolutionary events and ancient genome-wide signatures of hybridization across Fagaceae. An unparalleled transformation of forest dynamics began with the rapid diversification of major lineages within 15 million years following the K-Pg extinction. Innovations related to seed and pollen dispersal are implicated in triggering waves of continental radiations, while fungal symbioses fortified a competitive edge underground. We detected introgression at multiple time scales, including ancient events predating the origination of genus-level diversity. As oak lineages moved into newly available temperate habitats in the early Miocene, secondary contact between previously isolated species occurred. This resulted in adaptive introgression, further amplifying global proliferation.

scholarly journals Selection and gene flow define polygenic barriers between incipient butterfly species

2020 ◽  
Author(s):  
Steven M. Van Belleghem ◽  
Jared M. Cole ◽  
Gabriela Montejo-Kovacevich ◽  
Caroline N. Bacquet ◽  
W. Owen McMillan ◽  
...  
Keyword(s):  
Gene Flow ◽  
Recombination Rate ◽  
Genomic Variation ◽  
Species Boundaries ◽  
Secondary Contact ◽  
Butterfly Species ◽  
Demographic Modeling ◽  
Incipient Species ◽  
Genome Wide ◽  
Genomic Divergence

AbstractCharacterizing the genetic architecture of species boundaries remains a difficult task. Hybridizing species provide a powerful system to identify the factors that shape genomic variation and, ultimately, identify the regions of the genome that maintain species boundaries. Unfortunately, complex histories of isolation, admixture and selection can generate heterogenous genomic landscapes of divergence which make inferences about the regions that are responsible for species boundaries problematic. However, as the signal of admixture and selection on genomic loci varies with recombination rate, their relationship can be used to infer their relative importance during speciation. Here, we explore patterns of genomic divergence, admixture and recombination rate among hybridizing lineages across the Heliconius erato radiation. We focus on the incipient species, H. erato and H. himera, and distinguish the processes that drive genomic divergence across three contact zones where they frequently hybridize. Using demographic modeling and simulations, we infer that periods of isolation and selection have been major causes of genome-wide correlation patterns between recombination rate and divergence between these incipient species. Upon secondary contact, we found surprisingly highly asymmetrical introgression between the species pair, with a paucity of H. erato alleles introgressing into the H. himera genomes. We suggest that this signal may result from a current polygenic species boundary between the hybridizing lineages. These results contribute to a growing appreciation for the importance of polygenic architectures of species boundaries and pervasive genome-wide selection during the early stages of speciation with gene flow.

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