Unraveling patterns and processes of diversification in the South Andean-Patagonian Nassauvia subgenus Strongyloma (Asteraceae, Nassauvieae)

Nicola, Marcela Viviana; Johnson, Leigh A.; Pozner, Raúl

doi:10.1016/j.ympev.2019.03.004

Cited by 14 publications

(6 citation statements)

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“…Cases of topological dissimilarity are often reported in phylogenetic studies ( Wendel and Doyle, 1998 ; reviewed by Degnan and Rosenberg, 2009 ). This phenomenon can be best explained by a number of factors including differences in taxon sampling, incomplete lineage sorting, hybridization/introgression, paralogy, gene duplication and/or loss, and horizontal gene transfer ( Degnan and Rosenberg, 2006 ; Naciri and Linder, 2015 ; Lin et al, 2019 ; Nicola et al, 2019 ). Hence, as more samples become available, future studies should investigate the factors responsible for the observed conflicting relationships within the Urticeae.…”

Section: Discussionmentioning

confidence: 99%

Deep Insights Into the Plastome Evolution and Phylogenetic Relationships of the Tribe Urticeae (Family Urticaceae)

et al. 2022

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Urticeae s.l., a tribe of Urticaceae well-known for their stinging trichomes, consists of more than 10 genera and approximately 220 species. Relationships within this tribe remain poorly known due to the limited molecular and taxonomic sampling in previous studies, and chloroplast genome (CP genome/plastome) evolution is still largely unaddressed. To address these concerns, we used genome skimming data—CP genome and nuclear ribosomal DNA (18S-ITS1-5.8S-ITS2-26S); 106 accessions—for the very first time to attempt resolving the recalcitrant relationships and to explore chloroplast structural evolution across the group. Furthermore, we assembled a taxon rich two-locus dataset of trnL-F spacer and ITS sequences across 291 accessions to complement our genome skimming dataset. We found that Urticeae plastomes exhibit the tetrad structure typical of angiosperms, with sizes ranging from 145 to 161 kb and encoding a set of 110–112 unique genes. The studied plastomes have also undergone several structural variations, including inverted repeat (IR) expansions and contractions, inversion of the trnN-GUU gene, losses of the rps19 gene, and the rpl2 intron, and the proliferation of multiple repeat types; 11 hypervariable regions were also identified. Our phylogenomic analyses largely resolved major relationships across tribe Urticeae, supporting the monophyly of the tribe and most of its genera except for Laportea, Urera, and Urtica, which were recovered as polyphyletic with strong support. Our analyses also resolved with strong support several previously contentious branches: (1) Girardinia as a sister to the Dendrocnide-Discocnide-Laportea-Nanocnide-Zhengyia-Urtica-Hesperocnide clade and (2) Poikilospermum as sister to the recently transcribed Urera sensu stricto. Analyses of the taxon-rich, two-locus dataset showed lower support but was largely congruent with results from the CP genome and nuclear ribosomal DNA dataset. Collectively, our study highlights the power of genome skimming data to ameliorate phylogenetic resolution and provides new insights into phylogenetic relationships and chloroplast structural evolution in Urticeae.

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Section: Discussionmentioning

confidence: 99%

Deep Insights Into the Plastome Evolution and Phylogenetic Relationships of the Tribe Urticeae (Family Urticaceae)

et al. 2022

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“…3c). Gene tree heterogeneity may be due to high levels of ILS, which is common in Andean radiations (Gómez-Gutiérrez et al 2017; Pouchon et al 2018; Nicola et al 2019). However, a mixture of long and short internal branches, measured both in millions of years and coalescent units (Fig.…”

Section: Discussionmentioning

confidence: 99%

Strong phylogenetic signal despite high phylogenomic complexity in an Andean plant radiation (Freziera,Pentaphylacaceae)

Lagomarsino

2021

Preprint

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The Andes mountains in South America are a biodiversity hotspot within a hotspot, the New World Tropics, for seed plants. Much of this diversity is concentrated at middle-elevations in cloud forests, yet the evolutionary patterns underlying this extraordinary diversity remain poorly understood. This is partially due to a paucity of resolved phylogenies for cloud forest plant lineages: the young age of the Andes and generally high diversification rates among Andean systems precludes robust phylogenetic inference, and remote populations, few genomic resources, and generally understudied organisms make acquiring high-quality data difficult. We present the first phylogeny of Freziera (Pentaphylacaceae), an Andean-centered, cloud forest radiation with potential to provide insight into some of the abiotic and extrinsic factors that promote the highest diversity observed on the globe. Our dataset, representing data for 50 of the ca. 75 spp. obtained almost entirely from herbarium specimens via hybrid-enriched target sequence capture with the universal bait set Angiosperms353, included a proportion of poorly assembled loci likely representing multi-copy genes, but with insufficient data to be flagged by paralog filters: cryptic paralogs. These cryptic paralogs likely result from limitations in data collection that are common in herbariomics combined with a history of genome duplication and are likely common in other plant phylogenomic datasets. Standard empirical metrics for identifying poor-quality genes, which typically focus on filtering for genes with high phylogenetic informativeness, failed to identify problematic loci in our dataset where strong but inaccurate signal was a greater problem. Filtering by bipartition support was the most successful method for selecting genes and resulted in a species tree with lower discordance, higher support, and a more accurate topology relative to a consensus tree. Using known paralogs, we investigate the utility of multi-copy genes in phylogenetic inference and find a role for paralogs in resolving deep nodes and major clades, though at the expense of gene tree concordance and support. With the first phylogeny, we infer the biogeographic history of Freziera and identify the northern Andes as a source region. We also identify distinct modes of diversification in the northern and central Andes, highlighting the importance of fine-scale biogeographic study in Andean cloud forest systems.

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“…Since the footprints get erased with time and with the occurrence of subsequent events, such inferences have limitations (Avise, 2009). The body of literature accumulated on the phylogeography of the biota from southern South America, including plants (e.g., Premoli et al, 2010;Achimón et al, 2018;Biersma et al, 2018;Nicola et al, 2019), reptiles (e.g., Victoriano et al, 2008;Femenias et al, 2020), amphibians (e.g., Nuñez et al, 2011), fishes (e.g., Ruzzante et al, 2006;Zemlak et al, 2008;Ruzzante et al, 2020), birds (Norambuena et al, 2018), and mammals (e.g., Lessa et al, 2010;Palma et al, 2012), reveals that the responses to Quaternary dynamics were varied and mostly species-specific (e.g., Lessa et al, 2010;Sersic et al, 2011). Two general patterns were described by Lessa et al (2010) for Patagonian sigmodontine rodents.…”

Section: Introductionmentioning

confidence: 99%

Genetic Diversity and Demographic History of the Shaggy Soft-Haired Mouse Abrothrix hirta (Cricetidae; Abrotrichini)

Valdez

D’Elı́a

2021

Front. Genet.

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Genetic information on species can inform decision making regarding conservation of biodiversity since the response of organisms to changing environments depend, in part, on their genetic makeup. Territories of central-southern Chile and Argentina have undergone a varying degree of impact during the Quaternary, where the response of local fauna and flora was rather species-specific. Here, we focus on the sigmodontine rodent Abrothrix hirta, distributed from 35° S in Chile and Argentina to northern Tierra del Fuego. Based on 119,226 transcriptome-derived SNP loci from 46 individuals of A. hirta, we described the geographic distribution of the genetic diversity of this species using a maximum likelihood tree, principal component and admixture analyses. We also addressed the demographic history of the main intraspecific lineages of A. hirta using GADMA. We found that A. hirta exhibited four allopatric intraspecific lineages. Three main genetic groups were identified by a Principal Component Analysis and by Ancestry analysis. The demographic history of A. hirta was characterized by recent population stability for populations at the northernmost part of the range, while southern populations experienced a recent population expansion.

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Unraveling patterns and processes of diversification in the South Andean-Patagonian Nassauvia subgenus Strongyloma (Asteraceae, Nassauvieae)

Cited by 14 publications

References 91 publications

Deep Insights Into the Plastome Evolution and Phylogenetic Relationships of the Tribe Urticeae (Family Urticaceae)

Deep Insights Into the Plastome Evolution and Phylogenetic Relationships of the Tribe Urticeae (Family Urticaceae)

Strong phylogenetic signal despite high phylogenomic complexity in an Andean plant radiation (Freziera,Pentaphylacaceae)

Genetic Diversity and Demographic History of the Shaggy Soft-Haired Mouse Abrothrix hirta (Cricetidae; Abrotrichini)

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