thyoloalethe
Well-known member
John Boyd (TiF):
http://www.jboyd.net/Taxo/changes.html (28 May 2016)
http://www.jboyd.net/Taxo/List30.html#passerellidae
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Passerellidae (1 Viewer)
- Thread starter Richard Klim
- Start date
John Boyd (TiF):
http://www.jboyd.net/Taxo/changes.html (28 May 2016)
http://www.jboyd.net/Taxo/List30.html#passerellidae
l_raty
laurent raty
Peter Kovalik
Well-known member
Peter Kovalik
Well-known member
Junco
Guillermo Friis, Angeles de Cara, Borja Mila. Testing the role of selection and demography in driving a rapid postglacial radiation in the songbird genus Junco. Society for Molecular Biology and Evolution Conference 2016.
Abstract:
Rapid evolutionary radiations likely result from the combined effects of selective pressures and demographic processes. The songbird genus Junco of North America includes several phenotypically divergent northern forms which have arisen within the last 10,000 years as a result of a rapid postglacial expansion across North America. These northern forms contrast with more genetically divergent ancestral southern forms that are geographically isolated, yet show moderate phenotypic divergence. In addition to the role of geographic and historical factors, the wide range of habitat types and the highly diversified patterns of plumage coloration suggest the role of multiple selective factors in driving lineage divergence. Here we combine whole-genome and genotyping-by-sequencing (GBS) data to reconstruct the evolutionary history of the genus and explore how genomic patterns of variation relate to demographic events and selective factors. We use MSMC (multiple sequentially Markovian coalescent) and G-Phocs (generalized phylogenetic coalescent sampler) to test the population-expansion and recent-divergence hypotheses in northern junco forms. MSMC revealed recent demographic expansions for all the northern junco forms, reinforcing the hypothesis of multiple lineage differentiation driven by a postglacial northward recolonization of North America. We also used Bayescan to calculate FSTand posterior probabilities per SNP to infer selection-mediated divergence, and found no specific regions of high differentiation but rather a number of highly divergent variants scattered across the genome. This suggests the role of selection acting on numerous loci across the genome from the early stages of the speciation process. Our analyses show that juncos represent one of the fastest radiations documented in birds, with major roles for historical, demographic and selective factors.
Guillermo Friis, Angeles de Cara, Borja Mila. Testing the role of selection and demography in driving a rapid postglacial radiation in the songbird genus Junco. Society for Molecular Biology and Evolution Conference 2016.
Abstract:
Rapid evolutionary radiations likely result from the combined effects of selective pressures and demographic processes. The songbird genus Junco of North America includes several phenotypically divergent northern forms which have arisen within the last 10,000 years as a result of a rapid postglacial expansion across North America. These northern forms contrast with more genetically divergent ancestral southern forms that are geographically isolated, yet show moderate phenotypic divergence. In addition to the role of geographic and historical factors, the wide range of habitat types and the highly diversified patterns of plumage coloration suggest the role of multiple selective factors in driving lineage divergence. Here we combine whole-genome and genotyping-by-sequencing (GBS) data to reconstruct the evolutionary history of the genus and explore how genomic patterns of variation relate to demographic events and selective factors. We use MSMC (multiple sequentially Markovian coalescent) and G-Phocs (generalized phylogenetic coalescent sampler) to test the population-expansion and recent-divergence hypotheses in northern junco forms. MSMC revealed recent demographic expansions for all the northern junco forms, reinforcing the hypothesis of multiple lineage differentiation driven by a postglacial northward recolonization of North America. We also used Bayescan to calculate FSTand posterior probabilities per SNP to infer selection-mediated divergence, and found no specific regions of high differentiation but rather a number of highly divergent variants scattered across the genome. This suggests the role of selection acting on numerous loci across the genome from the early stages of the speciation process. Our analyses show that juncos represent one of the fastest radiations documented in birds, with major roles for historical, demographic and selective factors.
Peter Kovalik
Well-known member
Melozone and Aimophila
Luis Sandoval, Kevin L. Epperly, John Klicka, Daniel J. Mennill. The biogeographic and evolutionary history of an endemic clade of Middle American sparrows: Melozone and Aimophila (Aves: Passerellidae). Molecular Phylogenetics and Evolution, In Press, Accepted Manuscript, Available online 7 March 2017
Abstract:
The large number of endemic species in Middle America is frequently attributed to the interplay of geographical barriers and historical climatic changes in the region. This process promotes genetic divergence between populations, and given enough time, may yield new species. Animals that inhabit mid-elevation or highland habitats may be disproportionately affected in this way. Genetic analyses of animals in this region allow us to better understand how historical patterns of isolation have influenced the generation of new species in this biodiversity hotspot. We studied the biogeography and systematics of two closely related genera of sparrows (Passerellidae): Melozone and Aimophila. Collectively, this group is distributed from the southwestern United States and southward as far as central Costa Rica. We sampled 81 individuals of 8 Melozone and 2 Aimophila species, from 19 localities distributed throughout their ranges. We reconstructed phylogenetic relationships and time-calibrated species trees using multilocus sequence data comprised of one mitochondrial gene and five nuclear genes. We conducted an ancestral area reconstruction analysis to determine the probability of ancestral range at each divergent event. Despite analyzing six loci, we were unable to obtain a fully resolved phylogenetic tree. We recovered four main lineages: lineage 1 includes four Melozone species distributed north of Isthmus of Tehuantepec (M. albicollis, M. crissalis, M. aberti, M. fusca); lineage 2 includes three Melozone species distributed south of the Isthmus of Tehuantepec (M. biarcuata, M. cabanisi, M. leucotis); lineage 3 lineage consists of a single species endemic to the Pacific coast of Mexico (M. kieneri); and lineage 4 includes the more widely distributed sparrows in the genus Aimophila. Our analyses suggest that these genera probably originated during the late Miocene in the Madrean Highlands of southern Mexico. We identified dispersal as the prevalent cause of speciation in this clade with most lineages dispersing to their current distributions from southern Mexico either to the north following a developing and expanding Madro-Tertiary flora, or to the south across the Isthmus of Tehuantepec. A similar pattern of dispersal from this biogeographic region has been reported in other taxa including fishes, reptiles, and birds. Our results reveal that the four lineages identified represent geographically coherent and ecologically similar assemblages of taxa. Finally, when our genetic results are considered, along with apparent differences in morphology and song, the allopatric forms M. b. cabanisi and M. l. occipitalis warrant recognition as biological species.
Luis Sandoval, Kevin L. Epperly, John Klicka, Daniel J. Mennill. The biogeographic and evolutionary history of an endemic clade of Middle American sparrows: Melozone and Aimophila (Aves: Passerellidae). Molecular Phylogenetics and Evolution, In Press, Accepted Manuscript, Available online 7 March 2017
Abstract:
The large number of endemic species in Middle America is frequently attributed to the interplay of geographical barriers and historical climatic changes in the region. This process promotes genetic divergence between populations, and given enough time, may yield new species. Animals that inhabit mid-elevation or highland habitats may be disproportionately affected in this way. Genetic analyses of animals in this region allow us to better understand how historical patterns of isolation have influenced the generation of new species in this biodiversity hotspot. We studied the biogeography and systematics of two closely related genera of sparrows (Passerellidae): Melozone and Aimophila. Collectively, this group is distributed from the southwestern United States and southward as far as central Costa Rica. We sampled 81 individuals of 8 Melozone and 2 Aimophila species, from 19 localities distributed throughout their ranges. We reconstructed phylogenetic relationships and time-calibrated species trees using multilocus sequence data comprised of one mitochondrial gene and five nuclear genes. We conducted an ancestral area reconstruction analysis to determine the probability of ancestral range at each divergent event. Despite analyzing six loci, we were unable to obtain a fully resolved phylogenetic tree. We recovered four main lineages: lineage 1 includes four Melozone species distributed north of Isthmus of Tehuantepec (M. albicollis, M. crissalis, M. aberti, M. fusca); lineage 2 includes three Melozone species distributed south of the Isthmus of Tehuantepec (M. biarcuata, M. cabanisi, M. leucotis); lineage 3 lineage consists of a single species endemic to the Pacific coast of Mexico (M. kieneri); and lineage 4 includes the more widely distributed sparrows in the genus Aimophila. Our analyses suggest that these genera probably originated during the late Miocene in the Madrean Highlands of southern Mexico. We identified dispersal as the prevalent cause of speciation in this clade with most lineages dispersing to their current distributions from southern Mexico either to the north following a developing and expanding Madro-Tertiary flora, or to the south across the Isthmus of Tehuantepec. A similar pattern of dispersal from this biogeographic region has been reported in other taxa including fishes, reptiles, and birds. Our results reveal that the four lineages identified represent geographically coherent and ecologically similar assemblages of taxa. Finally, when our genetic results are considered, along with apparent differences in morphology and song, the allopatric forms M. b. cabanisi and M. l. occipitalis warrant recognition as biological species.
lewis20126
Well-known member
Good to get back up from genetics, but a result that surprises nobody that has seen the taxa in the field...or even looked at pictures of them! Two species under Tobias et al., BLI checklist vol 2.
cheers, alan
Jim LeNomenclatoriste
Je suis un mignon petit Traquet rubicole
Tif Update March 8, 2017
American Sparrows:
I've changed the family name from Passerellidae (Cabanis and Heine 1850-51) to Arremonidae (Lafresnaye 1842) for priority reasons.
Based on Sandoval et al. (2017) and the HBW BirdLife Checklist (del Hoyo and Collar, 2016) I have split Gray-crowned Ground-Sparrow, Melozone occipitalis, from White-eared Ground-Sparrow, Melozone leucotis (inc. nigrior) and with the assistance of Sandoval (2014) split Cabanis's Ground-Sparrow, Melozone cabanisi, from Prevost's Ground-Sparrow, Melozone biarcuata (inc. hartwegi). I have also rearranged Aimophila, Kieneria, and Melozone using information from Sandoval et al. (2017).
[Arremonidae, Core Passeroidea III, 3.04]
American Sparrows:
I've changed the family name from Passerellidae (Cabanis and Heine 1850-51) to Arremonidae (Lafresnaye 1842) for priority reasons.
Based on Sandoval et al. (2017) and the HBW BirdLife Checklist (del Hoyo and Collar, 2016) I have split Gray-crowned Ground-Sparrow, Melozone occipitalis, from White-eared Ground-Sparrow, Melozone leucotis (inc. nigrior) and with the assistance of Sandoval (2014) split Cabanis's Ground-Sparrow, Melozone cabanisi, from Prevost's Ground-Sparrow, Melozone biarcuata (inc. hartwegi). I have also rearranged Aimophila, Kieneria, and Melozone using information from Sandoval et al. (2017).
[Arremonidae, Core Passeroidea III, 3.04]
Jim LeNomenclatoriste
Je suis un mignon petit Traquet rubicole
http://www.mapress.com/j/zt/article/view/zootaxa.4291.1.9
Phenotypic variation and vocal divergence reveals a species complex in White-eared Ground-sparrows (Cabanis) (Aves: Passerellidae)
LUIS SANDOVAL, PIERRE-PAUL BITTON, ALANA D. DEMKO, STÉPHANIE M. DOUCET, DANIEL J. MENNILL
Abstract
The taxonomy of the genus Melozone has recently been analyzed from genus to subspecies level, leading to a significant revision of our understanding of this group of birds. Previous studies quantified differences in phenotypic traits, behavior, and genotypes, to provide a better understanding of the underappreciated diversity within Melozone and the relationship between species within this genus. Yet the relationship between the subspecies of White-eared Ground-sparrows, Melozone leucotis, has not received thorough taxonomic scrutiny. In this study, we evaluate the taxonomic status of the three recognized subspecies of M. leucotis using multiple morphometric characteristics, plumage color features, and vocalizations. We measured plumage patterns and reflectance from museum specimens, morphometric features from museum specimens and live birds, and vocal characteristics from sound recordings. We observed substantial variation between subspecies in plumage, morphometry, and voice, especially between northern and southern birds. The phenotypic and vocal differences exhibited by M. l. occipitalis (from Chiapas, Mexico; Guatemala; and El Salvador) suggest that its taxonomic relationship with the M. l. leucotis and M. l. nigrior complex (from Costa Rica and Nicaragua, respectively) needs to be reevaluated, because these two groups are highly diagnosable from one another. Additionally, M. l. occipitalis is geographically isolated from the other two subspecies, reducing the probability of contact by natural causes in the near future. Based on the clear differences in voice, plumage, and morphometric features reported here, we propose that M. l. occipitalis be recognized as a distinct species, M. occipitalis (Salvin's Ground-sparrow), diagnosed on the basis of its longer tail, longer bill, duller plumage, and songs with a lower frequency of maximum amplitude.
Phenotypic variation and vocal divergence reveals a species complex in White-eared Ground-sparrows (Cabanis) (Aves: Passerellidae)
LUIS SANDOVAL, PIERRE-PAUL BITTON, ALANA D. DEMKO, STÉPHANIE M. DOUCET, DANIEL J. MENNILL
Abstract
The taxonomy of the genus Melozone has recently been analyzed from genus to subspecies level, leading to a significant revision of our understanding of this group of birds. Previous studies quantified differences in phenotypic traits, behavior, and genotypes, to provide a better understanding of the underappreciated diversity within Melozone and the relationship between species within this genus. Yet the relationship between the subspecies of White-eared Ground-sparrows, Melozone leucotis, has not received thorough taxonomic scrutiny. In this study, we evaluate the taxonomic status of the three recognized subspecies of M. leucotis using multiple morphometric characteristics, plumage color features, and vocalizations. We measured plumage patterns and reflectance from museum specimens, morphometric features from museum specimens and live birds, and vocal characteristics from sound recordings. We observed substantial variation between subspecies in plumage, morphometry, and voice, especially between northern and southern birds. The phenotypic and vocal differences exhibited by M. l. occipitalis (from Chiapas, Mexico; Guatemala; and El Salvador) suggest that its taxonomic relationship with the M. l. leucotis and M. l. nigrior complex (from Costa Rica and Nicaragua, respectively) needs to be reevaluated, because these two groups are highly diagnosable from one another. Additionally, M. l. occipitalis is geographically isolated from the other two subspecies, reducing the probability of contact by natural causes in the near future. Based on the clear differences in voice, plumage, and morphometric features reported here, we propose that M. l. occipitalis be recognized as a distinct species, M. occipitalis (Salvin's Ground-sparrow), diagnosed on the basis of its longer tail, longer bill, duller plumage, and songs with a lower frequency of maximum amplitude.
Peter Kovalik
Well-known member
Baird's Junco
TiF Update August 2:
Baird's Junco, Junco bairdi has been split from the Yellow-eyed Junco, Junco phaeonotus as per the AOS 58th Supplement. The phylogeny follows Friis et al., 2016), where Baird's Junco is not even sister to the Yellow-eyed Junco.
TiF Update August 2:
Baird's Junco, Junco bairdi has been split from the Yellow-eyed Junco, Junco phaeonotus as per the AOS 58th Supplement. The phylogeny follows Friis et al., 2016), where Baird's Junco is not even sister to the Yellow-eyed Junco.
Peter Kovalik
Well-known member
Arremon taciturnus
Carina Carneiro De Melo Moura, Alexandre M. Fernandes, Alexandre Aleixo, Helder Farias Pereira De Araújo, Erich De Freitas Mariano & Michael Wink. Evolutionary history of the Pectoral Sparrow Arremon taciturnus: Evidence for diversification during the Late Pleistocene. Ibis, First published: 08 January 2020 https://doi.org/10.1111/ibi.12813
Abstract:
We focus on reconstructing a spatiotemporal scenario of diversification of the widespread South American species, the Pectoral Sparrow (Aves: Passerellidae). This species is widely distributed in both the humid and dry forests of South America and therefore provides an interesting model for understanding the connection between different biomes of South America. We examined nucleotide sequences of the mitochondrial genes Cytochrome b (cyt‐b) and NADH subunit 2 (ND2) from 107 specimens, and one nuclear marker (intron 7 of the β‐fibrinogen gene) from a subset of samples collected across the distribution ranges of A. t. taciturnus and A. t. nigrirostris. Six major lineages were recovered in the phylogenies that displayed high levels of variance of allele frequencies and corresponded to distinct geographic locations. The estimation of divergence times provided evidence that diversification of the six lineages of the pectoral sparrow occurred throughout the Late Pleistocene across major Cis‐Andean biomes and Amazonian interfluves. Our dataset for A. taciturnus provides further evidence that rivers in Amazonia constitute barriers promoting allopatric speciation, with occasional sharing of alleles among lineages, particularly those with adjacent distributions.
Carina Carneiro De Melo Moura, Alexandre M. Fernandes, Alexandre Aleixo, Helder Farias Pereira De Araújo, Erich De Freitas Mariano & Michael Wink. Evolutionary history of the Pectoral Sparrow Arremon taciturnus: Evidence for diversification during the Late Pleistocene. Ibis, First published: 08 January 2020 https://doi.org/10.1111/ibi.12813
Abstract:
We focus on reconstructing a spatiotemporal scenario of diversification of the widespread South American species, the Pectoral Sparrow (Aves: Passerellidae). This species is widely distributed in both the humid and dry forests of South America and therefore provides an interesting model for understanding the connection between different biomes of South America. We examined nucleotide sequences of the mitochondrial genes Cytochrome b (cyt‐b) and NADH subunit 2 (ND2) from 107 specimens, and one nuclear marker (intron 7 of the β‐fibrinogen gene) from a subset of samples collected across the distribution ranges of A. t. taciturnus and A. t. nigrirostris. Six major lineages were recovered in the phylogenies that displayed high levels of variance of allele frequencies and corresponded to distinct geographic locations. The estimation of divergence times provided evidence that diversification of the six lineages of the pectoral sparrow occurred throughout the Late Pleistocene across major Cis‐Andean biomes and Amazonian interfluves. Our dataset for A. taciturnus provides further evidence that rivers in Amazonia constitute barriers promoting allopatric speciation, with occasional sharing of alleles among lineages, particularly those with adjacent distributions.
Peter Kovalik
Well-known member
IOC Updates Diary May 29
Revise sequence and genera of Passerellidae based primarily on Klicka et al. (2014); SACC 633; NACC 2019-B-9.
Revise sequence and genera of Passerellidae based primarily on Klicka et al. (2014); SACC 633; NACC 2019-B-9.
Paul Clapham
Well-known member
So Ammospiza is back!
albertonykus
Well-known member
Maxwell, L.M., J. Walsh, B.J. Olsen, and A.I. Kovach (2021)
Patterns of introgression vary within an avian hybrid zone
BMC Ecology and Evolution 21: 14
doi: 10.1186/s12862-021-01749-1
https://bmcecolevol.biomedcentral.com/articles/10.1186/s12862-021-01749-1
Background
Exploring hybrid zone dynamics at different spatial scales allows for better understanding of local factors that influence hybrid zone structure. In this study, we tested hypotheses about drivers of introgression at two spatial scales within the Saltmarsh Sparrow (Ammospiza caudacuta) and Nelson’s Sparrow (A. nelsoni) hybrid zone. Specifically, we evaluated the influence of neutral demographic processes (relative species abundance), natural selection (exogenous environmental factors and genetic incompatibilities), and sexual selection (assortative mating) in this mosaic hybrid zone. By intensively sampling adults (n = 218) and chicks (n = 326) at two geographically proximate locations in the center of the hybrid zone, we determined patterns of introgression on a fine scale across sites of differing habitat. We made broadscale comparisons of patterns from the center with those of prior studies in the southern edge of the hybrid zone.
Results
A panel of fixed SNPs (135) identified from ddRAD sequencing was used to calculate a hybrid index and determine genotypic composition/admixture level of the populations. Another panel of polymorphic SNPs (589) was used to assign paternity and reconstruct mating pairs to test for sexual selection. On a broad-scale, patterns of introgression were not explained by random mating within marshes. We found high rates of back-crossing and similarly low rates of recent-generation (F1/F2) hybrids in the center and south of the zone. Offspring genotypic proportions did not meet those expected from random mating within the parental genotypic distribution. Additionally, we observed half as many F1/F2 hybrid female adults than nestlings, while respective male groups showed no difference, in support of Haldane’s Rule. The observed proportion of interspecific mating was lower than expected when accounting for mate availability, indicating assortative mating was limiting widespread hybridization. On a fine spatial scale, we found variation in the relative influence of neutral and selective forces between inland and coastal habitats, with the smaller, inland marsh influenced primarily by neutral demographic processes, and the expansive, coastal marsh experiencing higher selective pressures in the form of natural (exogenous and endogenous) and sexual selection.
Conclusions
Multiple drivers of introgression, including neutral and selective pressures (exogenous, endogenous, and sexual selection), are structuring this hybrid zone, and their relative influence is site and context-dependent.
Patterns of introgression vary within an avian hybrid zone
BMC Ecology and Evolution 21: 14
doi: 10.1186/s12862-021-01749-1
https://bmcecolevol.biomedcentral.com/articles/10.1186/s12862-021-01749-1
Background
Exploring hybrid zone dynamics at different spatial scales allows for better understanding of local factors that influence hybrid zone structure. In this study, we tested hypotheses about drivers of introgression at two spatial scales within the Saltmarsh Sparrow (Ammospiza caudacuta) and Nelson’s Sparrow (A. nelsoni) hybrid zone. Specifically, we evaluated the influence of neutral demographic processes (relative species abundance), natural selection (exogenous environmental factors and genetic incompatibilities), and sexual selection (assortative mating) in this mosaic hybrid zone. By intensively sampling adults (n = 218) and chicks (n = 326) at two geographically proximate locations in the center of the hybrid zone, we determined patterns of introgression on a fine scale across sites of differing habitat. We made broadscale comparisons of patterns from the center with those of prior studies in the southern edge of the hybrid zone.
Results
A panel of fixed SNPs (135) identified from ddRAD sequencing was used to calculate a hybrid index and determine genotypic composition/admixture level of the populations. Another panel of polymorphic SNPs (589) was used to assign paternity and reconstruct mating pairs to test for sexual selection. On a broad-scale, patterns of introgression were not explained by random mating within marshes. We found high rates of back-crossing and similarly low rates of recent-generation (F1/F2) hybrids in the center and south of the zone. Offspring genotypic proportions did not meet those expected from random mating within the parental genotypic distribution. Additionally, we observed half as many F1/F2 hybrid female adults than nestlings, while respective male groups showed no difference, in support of Haldane’s Rule. The observed proportion of interspecific mating was lower than expected when accounting for mate availability, indicating assortative mating was limiting widespread hybridization. On a fine spatial scale, we found variation in the relative influence of neutral and selective forces between inland and coastal habitats, with the smaller, inland marsh influenced primarily by neutral demographic processes, and the expansive, coastal marsh experiencing higher selective pressures in the form of natural (exogenous and endogenous) and sexual selection.
Conclusions
Multiple drivers of introgression, including neutral and selective pressures (exogenous, endogenous, and sexual selection), are structuring this hybrid zone, and their relative influence is site and context-dependent.
Peter Kovalik
Well-known member
Jennifer Walsh, Adrienne I. Kovach, Phred M. Benham, Gemma V. Clucas, Virginia L. Winder, and Irby J. Lovette. Genomic data reveal the biogeographical and demographic history of Ammospiza sparrows in northeast tidal marshes. Journal of Biogeography, first published 13 July 2021.
https://doi.org/10.1111/jbi.14208
Abstract
Aim
Shaped by climate change and sea-level rise, tidal salt marshes represent ephemeral systems that are home to only a few species. The dynamic ecological histories of these habitats, however, render it challenging to reconstruct the complete biogeographical histories of their endemic taxa. To better understand the evolutionary history of tidal marsh endemic sparrows, we employ genomic data to evaluate the timing and direction of tidal marsh colonization events and leverage these data to test a series of models describing the biogeographical history of our study taxa.
Location
North America.
Taxon
Ammospiza Sparrows.
Methods
We sampled 54 individuals from the Ammospiza clade from freshwater and saltwater habitats. We sequenced whole genomes and generated a dataset containing 21 million SNPs. Detailed phylogenomic analyses were conducted to identify relationships between tidal marsh and freshwater species. These phylogenies were then used to date divergence times and reconstruct the biogeographical history of the clade as well as identify historic signals of introgression.
Results
Phylogenies based on several million SNPs supported well-resolved clades that correspond to all previous species designations. Demographic modelling within A. nelsoni provided further resolution into the subspecies topology. Phylogenetic and biogeographical reconstructions support a series of saltwater to freshwater colonization events, with some endemic taxa exhibiting associations with tidal marsh habitat over longer evolutionary time-scales and some habitat transitions occurring as recently as 5,000 years ago.
Main Conclusions
Biogeographical and phylogenomic reconstructions support an original freshwater origin of the Ammospiza sparrows currently inhabiting tidal marshes in North America. We also found strong evidence for a saltwater to freshwater transition in A. n. subvirgatus as opposed to the long hypothesized freshwater origin of this group. We conclude that the increased resolution from genomic data paired with an integrative framework of phylogenomic, demographic and biogeographical reconstructions is important for resolving evolutionary histories in complex and ephemeral environments.
https://doi.org/10.1111/jbi.14208
Abstract
Aim
Shaped by climate change and sea-level rise, tidal salt marshes represent ephemeral systems that are home to only a few species. The dynamic ecological histories of these habitats, however, render it challenging to reconstruct the complete biogeographical histories of their endemic taxa. To better understand the evolutionary history of tidal marsh endemic sparrows, we employ genomic data to evaluate the timing and direction of tidal marsh colonization events and leverage these data to test a series of models describing the biogeographical history of our study taxa.
Location
North America.
Taxon
Ammospiza Sparrows.
Methods
We sampled 54 individuals from the Ammospiza clade from freshwater and saltwater habitats. We sequenced whole genomes and generated a dataset containing 21 million SNPs. Detailed phylogenomic analyses were conducted to identify relationships between tidal marsh and freshwater species. These phylogenies were then used to date divergence times and reconstruct the biogeographical history of the clade as well as identify historic signals of introgression.
Results
Phylogenies based on several million SNPs supported well-resolved clades that correspond to all previous species designations. Demographic modelling within A. nelsoni provided further resolution into the subspecies topology. Phylogenetic and biogeographical reconstructions support a series of saltwater to freshwater colonization events, with some endemic taxa exhibiting associations with tidal marsh habitat over longer evolutionary time-scales and some habitat transitions occurring as recently as 5,000 years ago.
Main Conclusions
Biogeographical and phylogenomic reconstructions support an original freshwater origin of the Ammospiza sparrows currently inhabiting tidal marshes in North America. We also found strong evidence for a saltwater to freshwater transition in A. n. subvirgatus as opposed to the long hypothesized freshwater origin of this group. We conclude that the increased resolution from genomic data paired with an integrative framework of phylogenomic, demographic and biogeographical reconstructions is important for resolving evolutionary histories in complex and ephemeral environments.
albertonykus
Well-known member
Enloe, C., W.A. Cox, A. Pandey, S.S. Taylor, S. Woltmann, and R.T. Kimball (2021)
Genome-wide assessment of population structure in Florida’s coastal seaside sparrows
Conservation Genetics (advance online publication)
doi: 10.1007/s10592-021-01411-9
The distribution and genetic relatedness of subspecies among the populations of seaside sparrow (Ammospiza maritima [Wilson 1810]) along the coast of Florida are poorly understood. We evaluated genetic support for three defined Florida Gulf coast subspecies, as well as a fourth subspecies on the Atlantic coast, and assessed whether genetic clusters corresponded geographically with the defined ranges of subspecific designations. Data generated using double digest restriction site-associated DNA sequencing (ddRADseq) suggest that the Florida endemics, A. m. peninsulae and A. m. juncicola, are genetically indistinguishable, but that the third Gulf coast subspecies, A. m. fisheri, and the Atlantic coast subspecies, A. m. macgillivraii, are genetically distinct units. These three distinct genetic groups were identified in three main geographic areas within the state of Florida, USA: (1) Florida’s panhandle (2) Florida’s Gulf coast peninsula, and (3) the Atlantic coast. Admixture was detected between genetic clusters in sites near the transition zone between the Florida panhandle and peninsula. Geographic distributions of genetic clusters on the Gulf coast do not match currently defined subspecific ranges for A. m. fisheri and A. m. peninsulae.
Genome-wide assessment of population structure in Florida’s coastal seaside sparrows
Conservation Genetics (advance online publication)
doi: 10.1007/s10592-021-01411-9
The distribution and genetic relatedness of subspecies among the populations of seaside sparrow (Ammospiza maritima [Wilson 1810]) along the coast of Florida are poorly understood. We evaluated genetic support for three defined Florida Gulf coast subspecies, as well as a fourth subspecies on the Atlantic coast, and assessed whether genetic clusters corresponded geographically with the defined ranges of subspecific designations. Data generated using double digest restriction site-associated DNA sequencing (ddRADseq) suggest that the Florida endemics, A. m. peninsulae and A. m. juncicola, are genetically indistinguishable, but that the third Gulf coast subspecies, A. m. fisheri, and the Atlantic coast subspecies, A. m. macgillivraii, are genetically distinct units. These three distinct genetic groups were identified in three main geographic areas within the state of Florida, USA: (1) Florida’s panhandle (2) Florida’s Gulf coast peninsula, and (3) the Atlantic coast. Admixture was detected between genetic clusters in sites near the transition zone between the Florida panhandle and peninsula. Geographic distributions of genetic clusters on the Gulf coast do not match currently defined subspecific ranges for A. m. fisheri and A. m. peninsulae.
Peter Kovalik
Well-known member
Buainain, N., Ferreira, M., Avendaño, J. E., Cadena, C. D., Faircloth, B. C., Brumfield, R. T., Cracraft, J., and Ribas, C. C. (2022) Biogeography of a neotropical songbird radiation [Arremon, Passerellidae] reveals similar diversification dynamics between montane and lowland clades. Journal of Biogeography. First published: 05 May 2022
https://doi.org/10.1111/jbi.14379
Abstract:
Aim
Continental evolutionary radiations provide opportunities to understand how landscape evolution and biotic factors interact to generate species diversity. Additionally, understanding whether diversification dynamics differ between montane and lowland environments is a long-standing question with few comparative analyses in the Neotropics. To address these questions, we investigated the biogeographical patterns and the evolutionary processes underlying the diversification of a songbird genus, and compared diversification dynamics of clades occurring in lowland and montane Neotropical habitats.
Location
Neotropical montane and lowland forests.
Taxon
Arremon (Aves: Passerellidae).
Methods
We sequenced genomic data (ultra-conserved elements, UCEs) of 92 individuals (including historical skin specimens) comprising 47 of 50 currently recognized subspecies in the genus and collected habitat association data to (1) build the most complete phylogenetic hypothesis for the genus to date using maximum likelihood and Bayesian methods with a concatenated matrix, and a multi-species coalescent method based on quartets; and (2) reconstruct the evolution of their ancestral ranges, habitat association and diversification rates.
Results
All phylogenetic methods recovered essentially the same topology with strong support values for most interspecific nodes revealing relationships among species. We found evidence for a montane and humid ancestral range in Central America in the late Miocene and a later expansion into the lowlands of Central America, as well as into the lowlands and mountains of South America. Despite some temporal variation in diversification rate, we found overall similar diversification dynamics between montane and lowland clades.
Main conclusion
Species diversity within the genus is likely underestimated by the current taxonomic arrangement. The colonization of lowlands and dry forests, and expansion across South America, may have provided new geographical and ecological opportunities for speciation resulting in high species diversification. Overall diversification dynamics were comparable between montane and lowland clades, contrasting with previous studies focused on such comparisons for Neotropical birds.
https://doi.org/10.1111/jbi.14379
Abstract:
Aim
Continental evolutionary radiations provide opportunities to understand how landscape evolution and biotic factors interact to generate species diversity. Additionally, understanding whether diversification dynamics differ between montane and lowland environments is a long-standing question with few comparative analyses in the Neotropics. To address these questions, we investigated the biogeographical patterns and the evolutionary processes underlying the diversification of a songbird genus, and compared diversification dynamics of clades occurring in lowland and montane Neotropical habitats.
Location
Neotropical montane and lowland forests.
Taxon
Arremon (Aves: Passerellidae).
Methods
We sequenced genomic data (ultra-conserved elements, UCEs) of 92 individuals (including historical skin specimens) comprising 47 of 50 currently recognized subspecies in the genus and collected habitat association data to (1) build the most complete phylogenetic hypothesis for the genus to date using maximum likelihood and Bayesian methods with a concatenated matrix, and a multi-species coalescent method based on quartets; and (2) reconstruct the evolution of their ancestral ranges, habitat association and diversification rates.
Results
All phylogenetic methods recovered essentially the same topology with strong support values for most interspecific nodes revealing relationships among species. We found evidence for a montane and humid ancestral range in Central America in the late Miocene and a later expansion into the lowlands of Central America, as well as into the lowlands and mountains of South America. Despite some temporal variation in diversification rate, we found overall similar diversification dynamics between montane and lowland clades.
Main conclusion
Species diversity within the genus is likely underestimated by the current taxonomic arrangement. The colonization of lowlands and dry forests, and expansion across South America, may have provided new geographical and ecological opportunities for speciation resulting in high species diversification. Overall diversification dynamics were comparable between montane and lowland clades, contrasting with previous studies focused on such comparisons for Neotropical birds.
Jim LeNomenclatoriste
Je suis un mignon petit Traquet rubicole
I'm interested, in particular to know if they propose a taxonomic revision
pbjosh
missing the neotropics
I found an image of the tree by googling but didn’t find the text. A couple clear non-monophyletic things. Particularly Amazonian Orange-billed Sparrow stood out, at least if their tree is to be believed.
Snapdragyn
Well-known member
My 'google-fu' is weak; I cannot even find a tree image.
