Peter Kovalik
Well-known member
DID NOT PASS
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Furnariidae (2 Viewers)
- Thread starter Peter Kovalik
- Start date
Jim LeNomenclatoriste
Je suis un mignon petit Traquet rubicole
Duchene A., Montoya P., Claramunt S., Cadena D.A. (2020). Flight demand and environmental niche are associated with molecular evolutionary rates in a large avian radiation. https://www.biorxiv.org/content/10.1101/2020.01.16.908368v4
Peter Kovalik
Well-known member
Antonita Santana, Sofia Marques Silva, Nayron Francês Do Nascimento, Iracilda Sampaio, Alexandre Aleixo. Phylogeography of the Dendrocolaptes picumnus (Aves: Dendrocolaptidae) species complex: new insights on the diversification of a trans‐American lineage. Journal of Avian Biology, First Published: 21 June 2021. https://doi.org/10.1111/jav.02723
Abstract:
Molecular studies have shown that many polytypic species of birds are paraphyletic and may actually consist of multiple independent species, some of them phenotypically cryptic. One of such cases is Dendrocolaptes picumnus, which was found to be a paraphyletic species, with Dendrocolaptes hoffmannsi nested in it. Recent evidence also showed that multiple independent evolutionary lineages exist in the polytypic D. picumnus that may be characterized as distinct species, however, conclusions were weakened due to small sample sizes. To further evaluate phylogenetic relationships, species limits, and the diversification history of the D. picumnus species complex, herein we performed the densest sampling ever registered for the complex, and analyzed sequences of mitochondrial and nuclear genes from 106 specimens, belonging to all but four taxa grouped in the complex. Our phylogenetic analyses confirmed the monophyly of D. hoffmannsi and D. platyrostris, as well as the paraphyly of the polytypic D. picumnus. A combination of coalescent and population genetic structure analyses further supported an evolutionary independent status for D. picumnus transfasciatus, but were ambiguous with respect to the statuses of nominate D. picumnus, D. picumnus pallescens, D. picumnus validus, and D. picumnus costaricensis. In contrast, D. picumnus olivaceus and D. platyrostris intermedius were polyphyletic and not genetically structured with respect to D. picumnus pallescens and D. platyrostris platyrostris, respectively. Our results did not support the monophyly of the previously defined ‘Amazonian' and ‘montane' subspecies groups of D. picumnus, further indicating that at least one ‘montane' taxon may actually belong to the ‘Chaco' group, a relationship that highlights a close historical connection between the Andean and Chacoan biotas. When interpreted together with previous morphological studies, our results support the split of the polytypic D. picumnus into at least two species, while keeping the status of D. hoffmannsi and D. platyrostris as distinct species.
Abstract:
Molecular studies have shown that many polytypic species of birds are paraphyletic and may actually consist of multiple independent species, some of them phenotypically cryptic. One of such cases is Dendrocolaptes picumnus, which was found to be a paraphyletic species, with Dendrocolaptes hoffmannsi nested in it. Recent evidence also showed that multiple independent evolutionary lineages exist in the polytypic D. picumnus that may be characterized as distinct species, however, conclusions were weakened due to small sample sizes. To further evaluate phylogenetic relationships, species limits, and the diversification history of the D. picumnus species complex, herein we performed the densest sampling ever registered for the complex, and analyzed sequences of mitochondrial and nuclear genes from 106 specimens, belonging to all but four taxa grouped in the complex. Our phylogenetic analyses confirmed the monophyly of D. hoffmannsi and D. platyrostris, as well as the paraphyly of the polytypic D. picumnus. A combination of coalescent and population genetic structure analyses further supported an evolutionary independent status for D. picumnus transfasciatus, but were ambiguous with respect to the statuses of nominate D. picumnus, D. picumnus pallescens, D. picumnus validus, and D. picumnus costaricensis. In contrast, D. picumnus olivaceus and D. platyrostris intermedius were polyphyletic and not genetically structured with respect to D. picumnus pallescens and D. platyrostris platyrostris, respectively. Our results did not support the monophyly of the previously defined ‘Amazonian' and ‘montane' subspecies groups of D. picumnus, further indicating that at least one ‘montane' taxon may actually belong to the ‘Chaco' group, a relationship that highlights a close historical connection between the Andean and Chacoan biotas. When interpreted together with previous morphological studies, our results support the split of the polytypic D. picumnus into at least two species, while keeping the status of D. hoffmannsi and D. platyrostris as distinct species.
Jim LeNomenclatoriste
Je suis un mignon petit Traquet rubicole
This interest me
Peter Kovalik
Well-known member
Pseudocolaptes spp
Giovanni Forcina, Peter Boesman, and Michael J. Jowers. 2021. Cryptic diversity in a neotropical avian species complex untangled by neglected genetic evidence. Studies on Neotropical Fauna and Environment, published online 12 July 2021.
https://doi.org/10.1080/01650521.2021.1915674
ABSTRACT
Over the last two decades, vocal and genetic data have been extensively used in avian studies addressing taxonomic and systematic issues. However, even when multiple lines of evidence lean toward lumping or splitting of species, some taxonomic committees refuse to acknowledge their validity until convincing genetic evidence is produced and integrated with other sources of data. As a case in point, the genus Pseudocolaptes (Furnariidae) consists of three mostly allopatric and overtly distinct neotropical taxa differing in plumage and vocal features: the Streaked Tuftedcheek (P. boissonneautii), the Buffy Tuftedcheek (P. lawrencii), and the contentious Pacific Tuftedcheek (P. johnsoni). In this study, we assemble already available mitochondrial and nuclear DNA sequences to assess their taxonomy and to provide appointed committees with specific proof to ascertain the number of Pseudocolaptes species. Phylogenetic inference and species delimitation analysis indicate three species equally divergent from each other. We hope that this work will contribute to resolve the long-lasting taxonomical confusion regarding this genus, and that proper future conservation plans will be adopted to preserve each species within the inhabited biodiversity hotspot.
Giovanni Forcina, Peter Boesman, and Michael J. Jowers. 2021. Cryptic diversity in a neotropical avian species complex untangled by neglected genetic evidence. Studies on Neotropical Fauna and Environment, published online 12 July 2021.
https://doi.org/10.1080/01650521.2021.1915674
ABSTRACT
Over the last two decades, vocal and genetic data have been extensively used in avian studies addressing taxonomic and systematic issues. However, even when multiple lines of evidence lean toward lumping or splitting of species, some taxonomic committees refuse to acknowledge their validity until convincing genetic evidence is produced and integrated with other sources of data. As a case in point, the genus Pseudocolaptes (Furnariidae) consists of three mostly allopatric and overtly distinct neotropical taxa differing in plumage and vocal features: the Streaked Tuftedcheek (P. boissonneautii), the Buffy Tuftedcheek (P. lawrencii), and the contentious Pacific Tuftedcheek (P. johnsoni). In this study, we assemble already available mitochondrial and nuclear DNA sequences to assess their taxonomy and to provide appointed committees with specific proof to ascertain the number of Pseudocolaptes species. Phylogenetic inference and species delimitation analysis indicate three species equally divergent from each other. We hope that this work will contribute to resolve the long-lasting taxonomical confusion regarding this genus, and that proper future conservation plans will be adopted to preserve each species within the inhabited biodiversity hotspot.
Jim LeNomenclatoriste
Je suis un mignon petit Traquet rubicole
Aaaaaah oui, ouiii
albertonykus
Well-known member
Luna, L.W., C.C. Ribas, and A. Aleixo (2021)
Genomic differentiation with gene flow in a widespread Amazonian floodplain-specialist bird species
Journal of Biogeography (advance online publication)
doi: 10.1111/jbi.14257
Aim
Ecological, climatic and palaeogeographical processes drive biological diversification. However, the evolutionary outcomes of those mechanisms are complex and difficult to discriminate. Here, we test how alternative drivers affected connectivity along the Amazonian floodplains generating current patterns of population structure and diversity within the Striped Woodcreeper, a widespread bird species tied to forests seasonally flooded by Amazonian rivers.
Location
Amazonian floodplains.
Taxon
Xiphorhynchus obsoletus (Aves, Furnariidae).
Methods
We sequenced 2213 loci of ultraconserved elements (UCEs) and 20 exons to investigate patterns of genetic structure and connectivity across the Striped Woodcreeper distribution, using a set of spatially explicit methods. Population genetics statistics were calculated for each sampled drainage and within each identified cluster. We tested alternative evolutionary scenarios and estimated past and current demographic parameters implementing a simulation-based framework.
Results
Three genetic clusters with high admixture proportions were identified. These clusters are distributed in the western, central and eastern parts of the Amazon Basin and are not correlated with different river water types representing ecological gradients along the floodplains. Instead, migration rates indicate two putative historical barriers along the main channel of the Amazonas-Solimões River. Demographic model tests suggest a process of sequential differentiation, partitioned across the Amazon Basin, with stable population sizes and continuous gene flow.
Main conclusion
Our results support the hypothesis that late Quaternary changes in connectivity between the eastern and western Amazonian drainages were responsible for driving genetic differentiation in the Striped Woodcreeper. Genomic differentiation occurred in the presence of long-term gene flow throughout the X. obsoletus distribution, suggesting some degree of continuous historical connectivity across Amazonian floodplains. Compared to previous studies, our results suggest that although connectivity among populations of Amazonian bird species specialized in floodplain habitats varies in response to the same abiotic mechanisms, species-specific differences in habitat use may be a strong predictor of population divergence.
Genomic differentiation with gene flow in a widespread Amazonian floodplain-specialist bird species
Journal of Biogeography (advance online publication)
doi: 10.1111/jbi.14257
Aim
Ecological, climatic and palaeogeographical processes drive biological diversification. However, the evolutionary outcomes of those mechanisms are complex and difficult to discriminate. Here, we test how alternative drivers affected connectivity along the Amazonian floodplains generating current patterns of population structure and diversity within the Striped Woodcreeper, a widespread bird species tied to forests seasonally flooded by Amazonian rivers.
Location
Amazonian floodplains.
Taxon
Xiphorhynchus obsoletus (Aves, Furnariidae).
Methods
We sequenced 2213 loci of ultraconserved elements (UCEs) and 20 exons to investigate patterns of genetic structure and connectivity across the Striped Woodcreeper distribution, using a set of spatially explicit methods. Population genetics statistics were calculated for each sampled drainage and within each identified cluster. We tested alternative evolutionary scenarios and estimated past and current demographic parameters implementing a simulation-based framework.
Results
Three genetic clusters with high admixture proportions were identified. These clusters are distributed in the western, central and eastern parts of the Amazon Basin and are not correlated with different river water types representing ecological gradients along the floodplains. Instead, migration rates indicate two putative historical barriers along the main channel of the Amazonas-Solimões River. Demographic model tests suggest a process of sequential differentiation, partitioned across the Amazon Basin, with stable population sizes and continuous gene flow.
Main conclusion
Our results support the hypothesis that late Quaternary changes in connectivity between the eastern and western Amazonian drainages were responsible for driving genetic differentiation in the Striped Woodcreeper. Genomic differentiation occurred in the presence of long-term gene flow throughout the X. obsoletus distribution, suggesting some degree of continuous historical connectivity across Amazonian floodplains. Compared to previous studies, our results suggest that although connectivity among populations of Amazonian bird species specialized in floodplain habitats varies in response to the same abiotic mechanisms, species-specific differences in habitat use may be a strong predictor of population divergence.
albertonykus
Well-known member
Barbosa, W.E.S., M. Ferreira, E.D. Schultz, L.W. Luna, T.O. Laranjeiras, A. Aleixo, and C.C. Ribas (2021)
Habitat association constrains population history in two sympatric ovenbirds along Amazonian floodplains
Journal of Biogeography (advance online publication)
doi: 10.1111/jbi.14266
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.
Habitat association constrains population history in two sympatric ovenbirds along Amazonian floodplains
Journal of Biogeography (advance online publication)
doi: 10.1111/jbi.14266
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.
Jim LeNomenclatoriste
Je suis un mignon petit Traquet rubicole
Taxonomic challenges posed by discordant evolutionary scenarios supported by molecular and morphological data in the Amazonian Synallaxis rutilans group (Aves: Furnariidae)
Abstract. Alpha taxonomy endeavours to propose a coherent vision of existing species and, simultaneously, to individualize the natural entities useful to u
academic.oup.com
Looks interesting !
Last edited:
Peter Kovalik
Well-known member
PASSED (24 July 2022)
Jim LeNomenclatoriste
Je suis un mignon petit Traquet rubicole
[Ornithology • 2022] <i>Aphrastura subantarctica</i> • A New Bird Species <small>(Passeriformes: Furnariidae)</small> on the Southernmost Islands of the Americas
Aphrastura subantarctica Rozzi, Quilodrán, Botero-Delgadillo, Crego, Napolitano, Barroso, Torres-Mura & Vásquez, in Rozzi, Quilodrán, Bo...
novataxa.blogspot.com
pbjosh
missing the neotropics
Subantarctic Rayadito here as well, perhaps a bit easier to read (formatting):
www.nature.com
The Subantarctic Rayadito (Aphrastura subantarctica), a new bird species on the southernmost islands of the Americas - Scientific Reports
We describe a new taxon of terrestrial bird of the genus Aphrastura (rayaditos) inhabiting the Diego Ramírez Archipelago, the southernmost point of the American continent. This archipelago is geographically isolated and lacks terrestrial mammalian predators as well as woody plants, providing a...
www.nature.com
l_raty
laurent raty
Subantarctic Rayadito here as well, perhaps a bit easier to read (formatting):
The Subantarctic Rayadito (Aphrastura subantarctica), a new bird species on the southernmost islands of the Americas - Scientific Reports
We describe a new taxon of terrestrial bird of the genus Aphrastura (rayaditos) inhabiting the Diego Ramírez Archipelago, the southernmost point of the American continent. This archipelago is geographically isolated and lacks terrestrial mammalian predators as well as woody plants, providing a...
Not validly published ?
(Online-only journal, no ZooBank registration.)
Mysticete
Well-known member
oops
Surprised an editor wouldn't catch this...it's not like Scientific Reports is some obscure publication that only intermittently publishes.
Paul Clapham
Well-known member
Definitely not obscure -- I first heard about this paper on CBC Radio this morning.
Jacana
Will Jones
Scientific Reports is a bit of a dodgy publication in many ways. Certainly hasn't gone completely down the predatory route, but it is very close. They are happy to take their massive publishing fee without as much oversight as one would usually expect from a reputable journal.
Norbert R. B.
Active member
Editors, reviewers and authors apparently have not yet heard about the rules of the Code concerning online-only publication after 10 years they are in force! How often will that happen again? There are no excuses.
l_raty
laurent raty
(I disagree with the last message in Vitor's thread, though. The work not being registered in ZooBank makes it unpublished, and no requirements of the Code can be fulfilled by referring to unpublished material. To scoop the authors, you'd need to publish a diagnosis.)
Beware that this journal has recently issued attempted "corrections" to such problems that, so far as I can tell, failed to achieve their purpose. E.g. :
In these cases, the authors of an unregistered (= unpublished) work registered it retrospectively in ZooBank, and provided the registration data in an "Author correction". This "Author correction" itself, however, was not registered in Zoobank, hence remains unpublished; and the original work was left untouched (a new .pdf citing the registation data was not issued), hence it, too, remains unpublished.
Peter Kovalik
Well-known member
Subantarctic Rayadito here as well, perhaps a bit easier to read (formatting):
The Subantarctic Rayadito (Aphrastura subantarctica), a new bird species on the southernmost islands of the Americas - Scientific Reports
We describe a new taxon of terrestrial bird of the genus Aphrastura (rayaditos) inhabiting the Diego Ramírez Archipelago, the southernmost point of the American continent. This archipelago is geographically isolated and lacks terrestrial mammalian predators as well as woody plants, providing a...
Rozzi, R., Quilodrán, C.S., Botero-Delgadillo, E., Crego, R.D., Napolitano, C., Barroso, O., Torres-Mura, J.C., and Vásquez, R.A. (2022) El Rayadito subantártico: disponibilidad del binomio Aphrastura subantarctica (Passeriformes, Furnariidae). Boletín Museo Nacional De Historia Natural 71: 9–15.
El Rayadito subantártico: disponibilidad del binomio Aphrastura subantarctica (Passeriformes, Furnariidae) | Boletín Museo Nacional de Historia Natural
Abstract
The name of the passerine species Aphrastura subantarctica, proposed by Rozzi et al.(2022), is not available, since the publication where it was proposed did not meet all the requirements of the International Code of Zoological Nomenclature. In this note we establish the availability of the name of the species Aphrastura subantarctica, fulfilling these requirements.
