Phylogenetic relationships among Synallaxini spinetails (Aves: Furnariidae) reveal a new biogeographic pattern across the Amazon and Paraná river basins

Claramunt, Santiago

doi:10.1016/j.ympev.2014.05.011

Cited by 11 publications

(9 citation statements)

References 48 publications

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“…albigularis and M . propinqua diverged from their sister groups before the Pleistocene (Claramunt, 2014; Derryberry et al, 2011; Harvey et al, 2020) and co‐occur along western Amazonian floodplains, but have distinct habitat associations. Although these two species have a relatively long history within Amazonian floodplains, our results recover distinct crown ages (260 and 38 ka), distinct patterns of population structure as inferred from mitochondrial genomes, distinct patterns of effective migration, and, although their populations have shown a predominant signal of demographic expansion in the last 15 ka, their demographic histories show distinct patterns in the Late Pleistocene.…”

Section: Discussionmentioning

confidence: 99%

“…Mazaria propinqua split from its non-Amazonian sister group, Schoeniophylax phryganophilus, from the Paraná River basin, at about 4.6 Ma according to genomic (UCE) markers in an analysis of the whole Suboscine radiation (Harvey et al, 2020). A previous study using two mtDNA protein coding genes (cytb and ND2) found a date of ~6.0 Ma for this split (Claramunt, 2014). During the Late Miocene and Pliocene, western South America probably had more extensive patches of open vegetation habitats and wetlands (Latrubesse et al, 2010, Wilkinson et al, 2006, favouring the occurrence of species adapted to these habitats.…”

Section: Origin Of Species and Population Historiesmentioning

confidence: 95%

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Habitat association constrains population history in two sympatric ovenbirds along Amazonian floodplains

Barbosa

Ferreira

Schultz

et al. 2021

Journal of Biogeography

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Aim Amazonian floodplains include distinct types of seasonally flooded habitats, determined by the flooding regime and sedimentation dynamics. Some bird species prefer specific habitat types within the floodplains. To investigate whether distinct habitats are differentially affected by geologic and climatic history, we compare population history in a sympatric and closely related pair of ovenbird species with different habitat associations. Location Amazonian floodplains. Taxa Synallaxis albigularis and Mazaria propinqua (Aves; Furnariidae). Methods Occurrence records were obtained from museums and public databases. Genomic data included nuclear loci (UCE) and the mitogenome for 49 samples. SNPs from UCE data were used to infer population genetic structure and effective migration. Mitogenomes were used to build phylogenetic trees and chronograms. Both datasets were used to infer historical demographic changes and test demographic scenarios. Results S. albigularis includes geographically structured mtDNA clades with a crown age of 250 ka, whereas M. propinqua includes a single clade with a crown age of 38 ka. Effective migration is lower at the base of the Andes for S. albigularis and at the lower Negro River for M. propinqua. Population expansion is detected for both species during the Quaternary, but was steeper and more recent in M. propinqua. Main conclusions The differences in population histories relate to distinct habitat associations along Amazonian floodplains. Preference of M. propinqua for more ephemeral island habitats may favour local extinctions, leading to demographic change, low genetic variability, no population structure and smaller effective population size. In contrast, more resilient habitats along the floodplains inhabited by S. albigularis may sustain local populations, generating and maintaining local diversity. Our results suggest that climatic variations of the late Pleistocene and Holocene caused changes in distribution and connectivity of the different types of habitats along the Amazonian floodplains, affecting gene flow and population sizes of associated bird populations.

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Section: Discussionmentioning

confidence: 99%

Section: Origin Of Species and Population Historiesmentioning

confidence: 95%

Habitat association constrains population history in two sympatric ovenbirds along Amazonian floodplains

Barbosa

Ferreira

Schultz

et al. 2021

Journal of Biogeography

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“…Consequently, the Hypostomus species of these rivers, which have a tropical origin, contrast with the xerophilous forests and temperate steppes (grassland and savannas) through which most of the rivers run. The effect of the Paraná River as biogeographical corridor of tropical freshwater-related biota towards temperate latitudes is a pattern described by numerous authors in relation to a number of diverse plant and animal groups [77][78][79] . However, this suggestion is less supported nowadays, as many of the cases mentioned by Carvalho & Albert 26 and others 80 have recently been recognized as distinct species by their genetics and/or morphology.…”

Section: Discussionmentioning

confidence: 99%

Multilocus phylogeny and historical biogeography ofHypostomusshed light on the processes of fish diversification in La Plata Basin

Cardoso

Queiroz

Bahechar

et al. 2020

Preprint

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Distribution history of the widespread Neotropical genus Hypostomus to shed light on the processes that shaped species diversity. We inferred a calibrated phylogeny; ancestral habitat preference, ancestral areas distribution, and the history of dispersal and vicariance events of this genus. The phylogenetic and distributional analyses indicate that Hypostomus species inhabiting La Plata Basin do not form a monophyletic clade, suggesting that several unrelated ancestral species colonized this basin in the Miocene (~17 Mya). Dispersal to other rivers of La Plata Basin started about 8 Mya, followed by habitat shifts and an increased rate of cladogenesis. Amazonian Hypostomus species colonized La Plata Basin several times in the Middle Miocene, probably via the Upper Paraná and the Paraguay rivers that acted as biogeographic corridors. During the Miocene, La Plata Basin experienced marine incursions; and geomorphological and climatic changes that reconfigured its drainage pattern, driving the dispersal and diversification of Hypostomus. The Miocene marine incursion was a strong barrier and its retraction triggered Hypostomus dispersal, increased speciation rate and ecological diversification. The timing of hydrogeological changes in La Plata Basin coincides well with Hypostomus cladogenetic events, indicating that the history of this basin has acted on the diversification of its biota.

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“…This topology of the tree suggests weak phylogenetic distinctiveness of Synallaxis, which explains the difficulties encountered in providing this genus a robust DNA-based diagnosis. In the treatment of Derryberry et al (2011), the genera Schoeniophylax and Certhiaxis are considered separate from Synallaxis (shown by red arrows of fig 5B); however, their status relative to Synallaxis is disputable (Claramunt 2014). If Synallaxis is considered in the expanded boundaries (i.e.…”

Section: Robustness Of the Pdnc-based Diagnosis Of Supraspecific Taxamentioning

confidence: 99%

“…CAOS ) identifies private as well as pure characters of a focus taxon, and also allows compilation of composite DNA characters. This functionality makes CAOS a powerful and versatile program to identify DNA barcodes that can be directly used in DNA based descriptions (Goldstein and DeSalle 2011;Jörger and Schrödl 2013;2014). However, CAOS implements a tree based approach, which, on one hand, has an obvious merit -the identified characters, (termed Characteristic Attributes or CAs) are meaningful in evolutionary context, but, on the other hand, also has a drawback -only clades in the input tree can be diagnosed.…”

Section: Mold and Other Tools For Diagnostic Dna Characters Recoverymentioning

confidence: 99%

Revisiting use of DNA characters in taxonomy with MolD - a tree independent algorithm to retrieve diagnostic nucleotide characters from monolocus datasets

Fedosov

Puillandre

Achaz

2019

Preprint

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While DNA characters are increasingly used for phylogenetic inference, taxa delimitation and identification, their use for formal description of taxa (i.e. providing either a formal description or a diagnosis) remains scarce and inconsistent. The impediments are neither nomenclatural, nor conceptual, but rather methodological issues: lack of agreement of what DNA character should be provided, and lack of a suitable operational algorithm to identify such characters. Furthermore, the reluctance of using DNA data in taxonomy may also be due to the concerns of insufficient reliability of DNA characters as robustness of the DNA based diagnoses has never been thoroughly assessed. Removing these impediments will enhance integrity of systematics, and will enable efficient treatment of traditionally problematic cases, such as for example, cryptic species. We have developed a novel versatile and scalable algorithm MolD to recover diagnostic combinations of nucleotides (DNCs) for pre-defined groups of DNA sequences, corresponding to taxa. We applied MolD to four published monolocus datasets to examine 1) which type of DNA characters compilation allows for more robust diagnosis, and 2) how the robustness of DNA based diagnosis changes depending on the sampled fraction of taxons diversity. We demonstrate that the redundant DNCs, termed herein sDNCs, allow for higher robustness. Furthermore, we show that a reliable DNA-based diagnosis may be obtained when a rather small fraction of the entire data set is available. Based on our results we propose improvements to the existing practices of handling DNA data in taxonomic descriptions, and discuss a workflow of contemporary systematic study, where the integrative taxonomy part precedes the proposition of a DNA based diagnosis and the diagnosis itself can be efficiently used as a DNA barcode. Our analysis fills existing methodological gaps, thus setting stage for a wider use of the DNA data in taxa description.

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Phylogenetic relationships among Synallaxini spinetails (Aves: Furnariidae) reveal a new biogeographic pattern across the Amazon and Paraná river basins

Cited by 11 publications

References 48 publications

Habitat association constrains population history in two sympatric ovenbirds along Amazonian floodplains

Habitat association constrains population history in two sympatric ovenbirds along Amazonian floodplains

Multilocus phylogeny and historical biogeography ofHypostomusshed light on the processes of fish diversification in La Plata Basin

Revisiting use of DNA characters in taxonomy with MolD - a tree independent algorithm to retrieve diagnostic nucleotide characters from monolocus datasets

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