Two hundred and five newly assembled mitogenomes provide mixed evidence for rivers as drivers of speciation for Amazonian primates

Janiak, Mareike C.; Silva, Felipe Ennes; Beck, Robin M. D.; Vries, Dorien de; Kuderna, Lukas F. K.; Torosin, Nicole S.; Melin, Amanda D.; Marquès‐Bonet, Tomàs; Goodhead, Ian; Messias, Mariluce Rezende; Silva, Maria N. F. da; Sampaio, Iracilda; Farias, Izeni Pires; Rossi, Rogério Vieira; Melo, Fabiano Rodrigues de; Valsecchi, João; Hrbek, Tomas; Boubli, Jean P.

doi:10.1111/mec.16554

Cited by 17 publications

(15 citation statements)

References 163 publications

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“…Mitochondrial (mt) genes have a long history of use for phylogenetic reconstruction in animals 1 , and the relative ease with which complete mt genomes can now be obtained has fueled an increase in their use to resolve phylogenetic relationships within many groups 2 – 4 . Animal mt genomes typically include a highly conserved set of protein-coding genes with few non-coding intergenic regions; are inherited uniparentally without undergoing recombination; and in many cases have rates of substitution that may be an order of magnitude higher than those of the nuclear genome 5 .…”

Section: Introductionmentioning

confidence: 99%

Mito-nuclear discordance within Anthozoa, with notes on unique properties of their mitochondrial genomes

Quattrini

Snyder

Purow-Ruderman

et al. 2023

Sci Rep

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Whole mitochondrial genomes are often used in phylogenetic reconstruction. However, discordant patterns in species relationships between mitochondrial and nuclear phylogenies are commonly observed. Within Anthozoa (Phylum Cnidaria), mitochondrial (mt)-nuclear discordance has not yet been examined using a large and comparable dataset. Here, we used data obtained from target-capture enrichment sequencing to assemble and annotate mt genomes and reconstruct phylogenies for comparisons to phylogenies inferred from hundreds of nuclear loci obtained from the same samples. The datasets comprised 108 hexacorals and 94 octocorals representing all orders and > 50% of extant families. Results indicated rampant discordance between datasets at every taxonomic level. This discordance is not attributable to substitution saturation, but rather likely caused by introgressive hybridization and unique properties of mt genomes, including slow rates of evolution driven by strong purifying selection and substitution rate variation. Strong purifying selection across the mt genomes caution their use in analyses that rely on assumptions of neutrality. Furthermore, unique properties of the mt genomes were noted, including genome rearrangements and the presence of nad5 introns. Specifically, we note the presence of the homing endonuclease in ceriantharians. This large dataset of mitochondrial genomes further demonstrates the utility of off-target reads generated from target-capture data for mt genome assembly and adds to the growing knowledge of anthozoan evolution.

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Section: Introductionmentioning

confidence: 99%

Mito-nuclear discordance within Anthozoa, with notes on unique properties of their mitochondrial genomes

Quattrini

Snyder

Purow-Ruderman

et al. 2023

Sci Rep

View full text Add to dashboard Cite

show abstract

“…This large dataset of mitochondrial genomes further demonstrates the utility of off-target reads generated from target-capture data for mitochondrial genome assembly and adds to the growing knowledge of anthozoan evolution. d r a f t Introduction Mitochondrial (mt) genes have a long history of use for phylogenetic reconstruction in animals [1], and the relative ease with which complete mt genomes can now be obtained has fueled an increase in their use to resolve phylogenetic relationships within many groups [2][3][4].…”

Section: Introductionmentioning

confidence: 99%

“…Mitochondrial (mt) genes have a long history of use for phylogenetic reconstruction in animals [1], and the relative ease with which complete mt genomes can now be obtained has fueled an increase in their use to resolve phylogenetic relationships within many groups [2][3][4].…”

Section: Introductionmentioning

confidence: 99%

Extreme mito-nuclear discordance within Anthozoa, with notes on unique properties of their mitochondrial genomes

Quattrini

Snyder

Purow-Ruderman

et al. 2022

Preprint

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Whole mitochondrial genomes are often used in phylogenetic reconstruction. However, discordant patterns in species relationships between mitochondrial and nuclear phylogenies are commonly observed. Within Anthozoa (Phylum Cnidaria), mitochondrial-nuclear discordance has not yet been examined using a large and comparable dataset. Here, we used data obtained from target-capture enrichment sequencing to assemble and annotate mitochondrial genomes and reconstruct phylogenies for comparisons to phylogenies inferred from 100s of nuclear loci obtained from the same samples. The datasets comprised 108 hexacorals and 94 octocorals representing all orders and >50% of extant families. Results indicated rampant discordance between datasets at every taxonomic level. This discordance is not attributable to substitution saturation, but rather likely caused by recent and ancient introgressive hybridization and selection. We also found strong purifying selection across the mitochondrial genomes, cautioning their use in analyses that rely on assumptions of neutrality. Furthermore, unique properties of the mitochondrial genomes were noted, including genome rearrangements and the presence of nad5 introns. Specifically, we note the presence of the homing endonuclease in ceriantharians. This large dataset of mitochondrial genomes further demonstrates the utility of off-target reads generated from target-capture data for mitochondrial genome assembly and adds to the growing knowledge of anthozoan evolution.

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“…For example, Fluck et al (2020) found that temperature and precipitation were more important than rivers in terms of explaining species composition across Amazonia. This conclusion is surprising because Amazonian rivers are known to delineate the distributions of hundreds of avian taxa and are widely recognised as dispersal barriers for birds and other terrestrial taxa (Byrne et al, 2021;Capparella, 1988Capparella, , 1991Cracraft, 1985;Haffer, 1985;Janiak et al, 2022;Mourthé et al, 2022;Ribas et al, 2012;Sick, 1967;Silva et al, 2019). Whether the results obtained by Fluck et al (2020) would have changed if these authors used avian subspecies is worth exploring.…”

Section: How Does Taxonomic Scale Influence Downstream Analyses?mentioning

confidence: 99%

Subspecies‐level distribution maps for birds of the Amazon basin and adjacent areas

Rego,

Del‐Rio,

Brumfield

2023

Journal of Biogeography

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AimDistribution maps for Amazonian birds are often limited to species‐level taxonomy even though many subspecies represent biological species. We provide digital maps depicting subspecies‐level distributions of Neotropical birds in the Amazonas River basin and adjoining areas.LocationAmazon region, which includes the entire Amazon basin, the east slope of the tropical Andes, French Guiana, Suriname, Guyana, south Venezuela (Bolivar and Amazonas departments), parts of the Brazilian Cerrado and the Araguaia‐Tocantins basin.TaxonBirds (Class Aves).MethodsTo build the distribution maps, we compiled a point‐locality database of 620,000 records, 90% of which represent specimens vouchered in research collections. After manually cleaning and optimising the quality of the point localities, we generated extent‐of‐occurrence polygons at the subspecies level using a concave hull function. We corrected each polygon based on the literature and expert knowledge. We used this data set to define zoogeographical regions based on multidimensional scaling and clustering analyses, and then compared subspecies‐defined regions to zoogeographic regions inferred from species‐level data.ResultsWe inferred range polygons for 3990 subspecies, representing 2043 species from 65 families. The average distribution size was 955,739 km2, with half of the taxa having range sizes smaller than 230,484 km2 (median value) and nearly one‐quarter of all subspecies having ranges smaller than 50,000 km2. We identified 10 zoogeographical regions from the subspecies data set in comparison with four areas based on a species‐level analysis of the same data. The 10 zoogeographical regions are largely congruent with previously identified areas of endemism.Main ConclusionsThe new maps of Amazonian bird subspecies distributions allow biodiversity studies (e.g. macroecology, evolution, and conservation) to be conducted at the subspecies level, and facilitate biogeographic, ecological, evolutionary and conservation research on birds in the most biologically diverse region in the world.

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Two hundred and five newly assembled mitogenomes provide mixed evidence for rivers as drivers of speciation for Amazonian primates

Cited by 17 publications

References 163 publications

Mito-nuclear discordance within Anthozoa, with notes on unique properties of their mitochondrial genomes

Mito-nuclear discordance within Anthozoa, with notes on unique properties of their mitochondrial genomes

Extreme mito-nuclear discordance within Anthozoa, with notes on unique properties of their mitochondrial genomes

Subspecies‐level distribution maps for birds of the Amazon basin and adjacent areas

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