scholarly journals The Legacy of Recurrent Introgression during the Radiation of Hares

2020 ◽  
Author(s):  
Mafalda S Ferreira ◽  
Matthew R Jones ◽  
Colin M Callahan ◽  
Liliana Farelo ◽  
Zelalem Tolesa ◽  
...  
Keyword(s):  
Incomplete Lineage Sorting ◽  
Introgressive Hybridization ◽  
Lineage Sorting ◽  
Whole Exome ◽  
Extant Species ◽  
The Last Glacial Maximum ◽  
Shared Genetic ◽  
The Last Glacial ◽  
Shared Variation

Abstract Hybridization may often be an important source of adaptive variation, but the extent and long-term impacts of introgression have seldom been evaluated in the phylogenetic context of a radiation. Hares (Lepus) represent a widespread mammalian radiation of 32 extant species characterized by striking ecological adaptations and recurrent admixture. To understand the relevance of introgressive hybridization during the diversification of Lepus, we analyzed whole exome sequences (61.7 Mb) from 15 species of hares (1- 4 individuals per species), spanning the global distribution of the genus, and two outgroups. We used a coalescent framework to infer species relationships and divergence times, despite extensive genealogical discordance. We found high levels of allele sharing among species and show that this reflects extensive incomplete lineage sorting and temporally layered hybridization. Our results revealed recurrent introgression at all stages along the Lepus radiation, including recent gene flow between extant species since the last glacial maximum, but also pervasive ancient introgression occurring since near the origin of the hare lineages. We show that ancient hybridization between northern hemisphere species has resulted in shared variation of potential adaptive relevance to highly seasonal environments, including genes involved in circadian rhythm regulation, pigmentation, and thermoregulation. Our results illustrate how the genetic legacy of ancestral hybridization may persist across a radiation, leaving a long-lasting signature of shared genetic variation that may contribute to adaptation.

scholarly journals The legacy of recurrent introgression during the radiation of hares

2020 ◽  
Author(s):  
Mafalda S. Ferreira ◽  
Matthew R. Jones ◽  
Colin M. Callahan ◽  
Liliana Farelo ◽  
Zelalem Tolesa ◽  
...  
Keyword(s):  
Incomplete Lineage Sorting ◽  
Introgressive Hybridization ◽  
Lineage Sorting ◽  
Whole Exome ◽  
Extant Species ◽  
The Last Glacial Maximum ◽  
Shared Genetic ◽  
The Last Glacial ◽  
Shared Variation

AbstractHybridization may often be an important source of adaptive variation, but the extent and long-term impacts of introgression have seldom been evaluated in the phylogenetic context of a radiation. Hares (Lepus) represent a widespread mammalian radiation of 32 extant species characterized by striking ecological adaptations and recurrent admixture. To understand the relevance of introgressive hybridization during the diversification of Lepus, we analyzed whole exome sequences (61.7 Mb) from 15 species of hares (1- 4 individuals per species), spanning the global distribution of the genus, and two outgroups. We used a coalescent framework to infer species relationships and divergence times, despite extensive genealogical discordance. We found high levels of allele sharing among species and show that this reflects extensive incomplete lineage sorting and temporally layered hybridization. Our results revealed recurrent introgression at all stages along the Lepus radiation, including recent gene flow between extant species since the last glacial maximum, but also pervasive ancient introgression occurring since near the origin of the hare lineages. We show that ancient hybridization between northern hemisphere species has resulted in shared variation of potential adaptive relevance to highly seasonal environments, including genes involved in circadian rhythm regulation, pigmentation, and thermoregulation. Our results illustrate how the genetic legacy of ancestral hybridization may persist across a radiation, leaving a long-lasting signature of shared genetic variation that may contribute to adaptation within and among species.

Bidirectional introgression between Betula tianshanica and Betula microphylla and its implications for conservation

2020 ◽  
Author(s):  
Junyi Ding ◽  
Donglai Hua ◽  
James S. Borrell ◽  
Richard J.A. Buggs ◽  
Luwei Wang ◽  
...  
Keyword(s):  
Incomplete Lineage Sorting ◽  
List Type ◽  
Allele Sharing ◽  
Ecological Niche Models ◽  
Lineage Sorting ◽  
Adaptive Introgression ◽  
Altay Mountains ◽  
Selection For ◽  
The Last Glacial Maximum ◽  
The Last Glacial

SummaryMolecular markers can allow us to differentiate species that occupy a morphological continuum, and detect patterns of allele sharing that can help us understand the dynamics of geographic zones where they meet. Betula microphylla is a declining wetland species in NW China that forms a continuum of leaf morphology with its relative Betula tianshanica.We use ecological niche models (ENM) to predict the distribution of B. microphylla, B. tianshanica and the more commonly occurring B. platyphylla. We use restriction-site associated DNA sequencing and SSRs to resolve their genetic structure and patterns of allele sharing.ENM predicted an expansion of suitable range of B. tianshanica into B. microphylla since the Last Glacial Maximum and the contraction of B. microphylla’s range in the future. We resolved the species identification of some intermediate morphotypes. We found signatures of bidirectional introgression between B. microphylla and B. tianshanica with SNPs showing more admixture than SSRs. Introgression from B. microphylla into B. tianshanica was greater in the Tianshan Mountains where the two species have occurred in proximity. Unexpectedly, introgression from B. tianshanica into B. microphylla was widespread in the Altay Mountains where there are no records of B. tianshanica occurrence.This presence of B. tianshanica-derived alleles far beyond the species’ current range could be due to unexpectedly high pollen flow, undiscovered populations of B. tianshanica in the region, incomplete lineage sorting, or selection for adaptive introgression in B. microphylla. These different interpretations have contrasting implications for the conservation of B. microphylla.

Spatial variation of East Asian winter monsoon evolution between northern and southern China since the last glacial maximum

2021 ◽  
pp. 1-14
Author(s):  
Qin Li ◽  
Haibin Wu ◽  
Jun Cheng ◽  
Shuya Zhu ◽  
Chunxia Zhang ◽  
...  
Keyword(s):  
East Asian Winter Monsoon ◽  
Southern China ◽  
Ice Sheets ◽  
Northern China ◽  
Winter Monsoon ◽  
Asian Winter Monsoon ◽  
Spatial Differences ◽  
The Last Glacial Maximum ◽  
The Last Glacial

Abstract The East Asian winter monsoon (EAWM) is one of the most dynamic components of the global climate system. Although poorly understood, knowledge of long-term spatial differences in EAWM variability during the glacial–interglacial cycles is important for understanding the dynamic processes of the EAWM. We reconstructed the spatiotemporal characteristics of the EAWM since the last glacial maximum (LGM) using a comparison of proxy records and long-term transient simulations. A loess grain-size record from northern China (a sensitive EAWM proxy) and the sea surface temperature gradient of an EAWM index in sediments of the southern South China Sea were compared. The data–model comparison indicates pronounced spatial differences in EAWM evolution, with a weakened EAWM since the LGM in northern China but a strengthened EAWM from the LGM to the early Holocene, followed by a weakening trend, in southern China. The model results suggest that variations in the EAWM in northern China were driven mainly by changes in atmospheric carbon dioxide (CO2) concentration and Northern Hemisphere ice sheets, whereas orbital insolation and ice sheets were important drivers in southern China. We propose that the relative importance of insolation, ice sheets, and atmospheric CO2 for EAWM evolution varied spatially within East Asia.

scholarly journals Comparative Performance of Popular Methods for Hybrid Detection using Genomic Data

2020 ◽  
Author(s):  
Sungsik Kong ◽  
Laura S. Kubatko
Keyword(s):  
Statistical Power ◽  
Evolutionary Dynamics ◽  
Mean Squared Error ◽  
Incomplete Lineage Sorting ◽  
Introgressive Hybridization ◽  
Genomic Data ◽  
Lineage Sorting ◽  
Comparative Performance ◽  
Pattern Frequency ◽  
Hybrid Detection

AbstractInterspecific hybridization is an important evolutionary phenomenon that generates genetic variability in a population and fosters species diversity in nature. The availability of large genome scale datasets has revolutionized hybridization studies to shift from the examination of the presence or absence of hybrids in nature to the investigation of the genomic constitution of hybrids and their genome-specific evolutionary dynamics. Although a handful of methods have been proposed in an attempt to identify hybrids, accurate detection of hybridization from genomic data remains a challenging task. The available methods can be classified broadly as site pattern frequency based and population genetic clustering approaches, though the performance of the two classes of methods under different hybridization scenarios has not been extensively examined. Here, we use simulated data to comparatively evaluate the performance of four tools that are commonly used to infer hybridization events: the site pattern frequency based methods HyDe and the D-statistic (i.e., the ABBA-BABA test), and the population clustering approaches structure and ADMIXTURE. We consider single hybridization scenarios that vary in the time of hybridization and the amount of incomplete lineage sorting (ILS) for different proportions of parental contributions (γ); introgressive hybridization; multiple hybridization scenarios; and a mixture of ancestral and recent hybridization scenarios. We focus on the statistical power to detect hybridization, the false discovery rate (FDR) for the D-statistic and HyDe, and the accuracy of the estimates of γ as measured by the mean squared error for HyDe, structure, and ADMIXTURE. Both HyDe and the D-statistic demonstrate a high level of detection power in all scenarios except those with high ILS, although the D-statistic often has an unacceptably high FDR. The estimates of γ in HyDe are impressively robust and accurate whereas structure and ADMIXTURE sometimes fail to identify hybrids, particularly when the proportional parental contributions are asymmetric (i.e., when γ is close to 0). Moreover, the posterior distribution estimated using structure exhibits multimodality in many scenarios, making interpretation difficult. Our results provide guidance in selecting appropriate methods for identifying hybrid populations from genomic data.

scholarly journals Disentangling Population History and Character Evolution among Hybridizing Lineages

2020 ◽  
Vol 37 (5) ◽  
pp. 1295-1305 ◽  
Author(s):  
Sean P Mullen ◽  
Nicholas W VanKuren ◽  
Wei Zhang ◽  
Sumitha Nallu ◽  
Evan B Kristiansen ◽  
...  
Keyword(s):  
Evolutionary Biology ◽  
De Novo ◽  
Balancing Selection ◽  
Incomplete Lineage Sorting ◽  
Introgressive Hybridization ◽  
Character Evolution ◽  
Population History ◽  
Lineage Sorting ◽  
Evolutionary Origins ◽  
Whole Genome Resequencing

Abstract Understanding the origin and maintenance of adaptive phenotypic novelty is a central goal of evolutionary biology. However, both hybridization and incomplete lineage sorting can lead to genealogical discordance between the regions of the genome underlying adaptive traits and the remainder of the genome, decoupling inferences about character evolution from population history. Here, to disentangle these effects, we investigated the evolutionary origins and maintenance of Batesian mimicry between North American admiral butterflies (Limenitis arthemis) and their chemically defended model (Battus philenor) using a combination of de novo genome sequencing, whole-genome resequencing, and statistical introgression mapping. Our results suggest that balancing selection, arising from geographic variation in the presence or absence of the unpalatable model, has maintained two deeply divergent color patterning haplotypes that have been repeatedly sieved among distinct mimetic and nonmimetic lineages of Limenitis via introgressive hybridization.

scholarly journals High-Throughput Sequencing of 5S-IGS rDNA in Fagus L. (Fagaceae) reveals complex evolutionary patterns and hybrid origin of modern species

2021 ◽  
Author(s):  
Simone Cardoni ◽  
Roberta Piredda ◽  
Thomas Denk ◽  
Guido W. Grimm ◽  
Aristotelis C. Papageorgiou ◽  
...  
Keyword(s):  
High Throughput ◽  
High Throughput Sequencing ◽  
Incomplete Lineage Sorting ◽  
Intergenic Spacer ◽  
5S Rdna ◽  
Fagus Crenata ◽  
Hybrid Origin ◽  
Lineage Sorting ◽  
Temperate Trees ◽  
Extant Species

Standard models of speciation assume strictly dichotomous genealogies in which a species, the ancestor, is replaced by two offspring species. The reality is more complex: plant species can evolve from other species via isolation when genetic drift exceeds gene flow; lineage mixing can give rise to new species (hybrid taxa such as nothospecies and allopolyploids). The multi–copy, potentially multi–locus 5S rDNA is one of few gene regions conserving signal from dichotomous and reticulate evolutionary processes down to the level of intra-genomic recombination. Here, we provide the first high-throughput sequencing (HTS) 5S intergenic spacer (5S – IGS) data for a lineage of wind-pollinated subtropical to temperate trees, the Fagus crenata – F. sylvatica s.l. lineage, and its distant relative F. japonica. The observed 4,963 unique 5S – IGS variants reflect a long history of repeated incomplete lineage sorting and lineage mixing since the early Cenozoic of two or more paralogous-homoeologous 5S rDNA lineages. Extant species of Fagus are genetic mosaics and, at least to some part, of hybrid origin.

scholarly journals Climate impacts on deglaciation and vegetation dynamics since the Last Glacial Maximum at Moossee (Switzerland)

2019 ◽  
Author(s):  
Fabian Rey ◽  
Erika Gobet ◽  
Christoph Schwörer ◽  
Albert Hafner ◽  
Willy Tinner
Keyword(s):  
Climate Change ◽  
Last Glacial Maximum ◽  
Fagus Sylvatica ◽  
Glacial Maximum ◽  
Future Climate ◽  
Central European ◽  
Last Glacial ◽  
The Last Glacial Maximum ◽  
The Last Glacial

Abstract. Since the Last Glacial Maximum (LGM, end ca. 19 000 cal BP) Central European plant communities were shaped by changing climatic and anthropogenic disturbances. Understanding long-term ecosystem reorganizations in response to past environmental changes is crucial to draw conclusions about the impact of future climate change. So far, it has been difficult to address the post-deglaciation timing and ecosystem dynamics due to a lack of well-dated and continuous sediment sequences covering the entire period after the LGM. Here, we present a new palaeoecological study with exceptional chronological time control using pollen, spores and microscopic charcoal from Moossee (Swiss Plateau, 521 m a.s.l.) to reconstruct the vegetation and fire history over the last ca. 19 000 years. After lake formation in response to deglaciation, five major pollen-inferred ecosystem rearrangements occurred at ca. 18 800 cal BP (establishment of steppe tundra), 16 000 cal BP (spread of shrub tundra), 14 600 cal BP (expansion of boreal forests), 11 600 cal BP (establishment of first temperate deciduous tree stands composed of e.g. Quercus, Ulmus, Alnus) and 8200 cal BP (first occurence of mesophilous Fagus sylvatica trees). These vegetation shifts were released by climate changes at 19 000, 16 000, 14 700, 11 700 and 8200 cal BP. Vegetation responses occurred with no apparent time lag to climate change, if the mutual chronological uncertainties are considered. This finding is in agreement with further evidence from Southern and Central Europe and might be explained with proximity to the refugia of boreal and temperate trees (< 400 km) and rapid species spreads. Our palynological record sets the beginning of millennial-scale land use with periodically increased fire and agricultural activities of the Neolithic period at ca. 7000 cal BP (5050 cal BC). Subsequently, humans rather than climate triggered changes in vegetation composition and structure. We conclude that Fagus sylvatica forests were resilient to long-term anthropogenic and climatic impacts of the mid and the late Holocene. However, future climate warming and in particular declining moisture availability may cause unprecedented reorganizations of Central European beech-dominated forest ecosystems.

scholarly journals Rapid phenotypic evolution during incipient speciation in a continental avian radiation

2011 ◽  
Vol 279 (1734) ◽  
pp. 1847-1856 ◽  
Author(s):  
Leonardo Campagna ◽  
Pilar Benites ◽  
Stephen C. Lougheed ◽  
Darío A. Lijtmaer ◽  
Adrián S. Di Giacomo ◽  
...  
Keyword(s):  
Phenotypic Diversity ◽  
Incomplete Lineage Sorting ◽  
Introgressive Hybridization ◽  
Molecular Data ◽  
Species Group ◽  
Adult Males ◽  
Lineage Sorting ◽  
Male Plumage ◽  
Recent Group ◽  
Genetic Signatures

Adaptive radiations have helped shape how we view animal speciation, particularly classic examples such as Darwin's finches, Hawaiian fruitflies and African Great Lakes cichlids. These ‘island’ radiations are comparatively recent, making them particularly interesting because the mechanisms that caused diversification are still in motion. Here, we identify a new case of a recent bird radiation within a continentally distributed species group; the capuchino seedeaters comprise 11 Sporophila species originally described on the basis of differences in plumage colour and pattern in adult males. We use molecular data together with analyses of male plumage and vocalizations to understand species limits of the group. We find marked phenotypic variation despite lack of mitochondrial DNA monophyly and few differences in other putatively neutral nuclear markers. This finding is consistent with the group having undergone a recent radiation beginning in the Pleistocene, leaving genetic signatures of incomplete lineage sorting, introgressive hybridization and demographic expansions. We argue that this apparent uncoupling between neutral DNA homogeneity and phenotypic diversity is expected for a recent group within the framework of coalescent theory. Finally, we discuss how the ecology of open habitats in South America during the Pleistocene could have helped promote this unique and ongoing radiation.

scholarly journals Interrogating Phylogenetic Discordance Resolves Deep Splits in the Rapid Radiation of Old World Fruit Bats (Chiroptera: Pteropodidae)

2021 ◽  
Author(s):  
Nicolas Nesi ◽  
Georgia Tsagkogeorga ◽  
Susan M Tsang ◽  
Violaine Nicolas ◽  
Aude Lalis ◽  
...  
Keyword(s):  
Information Content ◽  
Incomplete Lineage Sorting ◽  
Gene Tree ◽  
Fruit Bats ◽  
Lineage Sorting ◽  
Protein Coding ◽  
Old World ◽  
Nectar Feeding ◽  
Extant Species ◽  
Evolutionary Distinctiveness

Abstract The family Pteropodidae (Old World fruit bats) comprises $&gt;$200 species distributed across the Old World tropics and subtropics. Most pteropodids feed on fruit, suggesting an early origin of frugivory, although several lineages have shifted to nectar-based diets. Pteropodids are of exceptional conservation concern with $&gt;$50% of species considered threatened, yet the systematics of this group has long been debated, with uncertainty surrounding early splits attributed to an ancient rapid diversification. Resolving the relationships among the main pteropodid lineages is essential if we are to fully understand their evolutionary distinctiveness, and the extent to which these bats have transitioned to nectar-feeding. Here we generated orthologous sequences for $&gt;$1400 nuclear protein-coding genes (2.8 million base pairs) across 114 species from 43 genera of Old World fruit bats (57% and 96% of extant species- and genus-level diversity, respectively), and combined phylogenomic inference with filtering by information content to resolve systematic relationships among the major lineages. Concatenation and coalescent-based methods recovered three distinct backbone topologies that were not able to be reconciled by filtering via phylogenetic information content. Concordance analysis and gene genealogy interrogation show that one topology is consistently the best supported, and that observed phylogenetic conflicts arise from both gene tree error and deep incomplete lineage sorting. In addition to resolving long-standing inconsistencies in the reported relationships among major lineages, we show that Old World fruit bats have likely undergone at least seven independent dietary transitions from frugivory to nectarivory. Finally, we use this phylogeny to identify and describe one new genus. [Chiroptera; coalescence; concordance; incomplete lineage sorting; nectar feeder; species tree; target enrichment.]

scholarly journals Committed and projected future changes in global peatlands – continued transient model simulations since the Last Glacial Maximum

2021 ◽  
Vol 18 (12) ◽  
pp. 3657-3687
Author(s):  
Jurek Müller ◽  
Fortunat Joos
Keyword(s):  
Last Glacial Maximum ◽  
Glacial Maximum ◽  
Future Scenarios ◽  
Dynamic Global Vegetation Model ◽  
Last Glacial ◽  
Climate Anomalies ◽  
The Future ◽  
The Last Glacial Maximum ◽  
The Last Glacial

Abstract. Peatlands are diverse wetland ecosystems distributed mostly over the northern latitudes and tropics. Globally they store a large portion of the global soil organic carbon and provide important ecosystem services. The future of these systems under continued anthropogenic warming and direct human disturbance has potentially large impacts on atmospheric CO2 and climate. We performed global long-term projections of peatland area and carbon over the next 5000 years using a dynamic global vegetation model forced with climate anomalies from 10 models of the Coupled Model Intercomparison Project (CMIP6) and three standard future scenarios. These projections are seamlessly continued from a transient simulation from the Last Glacial Maximum to the present to account for the full transient history and are continued beyond 2100 with constant boundary conditions. Our results suggest short to long-term net losses of global peatland area and carbon, with higher losses under higher-emission scenarios. Large parts of today's active northern peatlands are at risk, whereas peatlands in the tropics and, in case of mitigation, eastern Asia and western North America can increase their area and carbon stocks. Factorial simulations reveal committed historical changes and future rising temperature as the main driver of future peatland loss and increasing precipitations as the driver for regional peatland expansion. Additional simulations forced with climate anomalies from a subset of climate models which follow the extended CMIP6 scenarios, transient until 2300, show qualitatively similar results to the standard scenarios but highlight the importance of extended transient future scenarios for long-term carbon cycle projections. The spread between simulations forced with different climate model anomalies suggests a large uncertainty in projected peatland changes due to uncertain climate forcing. Our study highlights the importance of quantifying the future peatland feedback to the climate system and its inclusion into future earth system model projections.

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