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Passerellidae (6 Viewers)
- Thread starter Richard Klim
- Start date
pbjosh
missing the neotropics
Also, just re-engaged and am looking at these images in case anyone else cares to:
l_raty
laurent raty
There is a draft version of the text in the PhD thesis of the third author: https://repositorio.uniandes.edu.co/bitstream/handle/1992/53493/24468.pdf
Appendix 3, starting on p. 232.
Appendix 3, starting on p. 232.
Jim LeNomenclatoriste
Je suis un mignon petit Traquet rubicole
Potential split
Arremon rufidorsalis
Arremon erythrorhynchus
Arremon occidentalis
Arremon canidorsum
Arremon spectabilis
Arremon suttoni
Arremon macrourus
Arremon alleni
Arremon frontalis
Arremon poliophrys
Arremon larensis
Arremon eurous
A bunch of interesting stuff!
- the form ”eurous” from eastern Panama, known only from the type, is closer to castaneiceps
- A. assimilis larensis is sister to A. perijanus
- A. aurantiirostris spectabilis is not at all close to other auratiirostris, rather sister to dorbignii+(flavirostris+polionotus)
mb1848
Well-known member
In the original description of A. eurous Wetmore says that eurous and casteneiceps "these are indications of relationship...but the two have been seperated long.
http://www.gorgas.gob.pa/BiblioGorg...the avifauna of panama. Alexander Wetmore.pdf .
Jim LeNomenclatoriste
Je suis un mignon petit Traquet rubicole
Potential split
Arremon rufidorsalis
Arremon erythrorhynchus
Arremon occidentalis
Arremon canidorsum
Arremon spectabilis
Arremon suttoni
Arremon macrourus
Arremon alleni
Arremon frontalis
Arremon poliophrys
Arremon larensis
Arremon eurous
albertonykus
Well-known member
Clark, J.D., P.M. Benham, J.E. Maldonado, D.A. Luther, and H.C. Lim (2022)
Maintenance of local adaptation despite gene flow in a coastal songbird
Evolution (advance online publication)
doi: 10.1111/evo.14538
Adaptation to local environments is common in widespread species and the basis of ecological speciation. The song sparrow (Melospiza melodia) is a widespread, polytypic passerine that occurs in shrubland habitats throughout North America. We examined the population structure of two parapatric subspecies that inhabit different environments: the Atlantic song sparrow (M. m. atlantica), a coastal specialist; and the eastern song sparrow (M. m. melodia), a shrubland generalist. These populations lacked clear mitochondrial population structure, yet coastal birds formed a distinct nuclear genetic cluster. We found weak overall genomic differentiation between these subspecies, suggesting either recent divergence, extensive gene flow, or a combination thereof. There was a steep genetic cline at the transition to coastal habitats, consistent with isolation by environment (IBE), not isolation by distance (IBD). A phenotype under divergent selection, bill size, varied with the amount of coastal ancestry in transitional areas, but larger bill size was maintained in coastal habitats regardless of ancestry, further supporting a role for selection in the maintenance of these subspecies. Demographic modeling suggested a divergence history of limited gene flow followed by secondary contact, which has emerged as a common theme in adaptive divergence across taxa.
Maintenance of local adaptation despite gene flow in a coastal songbird
Evolution (advance online publication)
doi: 10.1111/evo.14538
Adaptation to local environments is common in widespread species and the basis of ecological speciation. The song sparrow (Melospiza melodia) is a widespread, polytypic passerine that occurs in shrubland habitats throughout North America. We examined the population structure of two parapatric subspecies that inhabit different environments: the Atlantic song sparrow (M. m. atlantica), a coastal specialist; and the eastern song sparrow (M. m. melodia), a shrubland generalist. These populations lacked clear mitochondrial population structure, yet coastal birds formed a distinct nuclear genetic cluster. We found weak overall genomic differentiation between these subspecies, suggesting either recent divergence, extensive gene flow, or a combination thereof. There was a steep genetic cline at the transition to coastal habitats, consistent with isolation by environment (IBE), not isolation by distance (IBD). A phenotype under divergent selection, bill size, varied with the amount of coastal ancestry in transitional areas, but larger bill size was maintained in coastal habitats regardless of ancestry, further supporting a role for selection in the maintenance of these subspecies. Demographic modeling suggested a divergence history of limited gene flow followed by secondary contact, which has emerged as a common theme in adaptive divergence across taxa.
Peter Kovalik
Well-known member
William E Brooks and Peter H Wimberger. 2022. Asymmetric song recognition does not influence gene flow in an emergent songbird hybrid zone [White-crowned Sparrow Zonotrichia leucophrys]. Ornithology, published online 4 November 2022.
Asymmetric song recognition does not influence gene flow in an emergent songbird hybrid zone
Abstract
Hybrid zones can be used to examine the mechanisms, like song recognition, that affect reproductive isolation and speciation. Song has mixed support as a driver of speciation; we did not find song to be associated with reproductive isolation in White-crowned Sparrow subspecies (Zonotrichia leucophrys pugetensis and Z. l. gambelii). We examined an emerging secondary contact zone in these subspecies by measuring song variation, song recognition, plumage, morphology, and mitochondrial DNA (mtDNA). Plumage and morphological characters provided evidence of hybridization in the contact zone, with some birds possessing intermediate phenotype and song characteristics, and some possessing discordant phenotype and mitochondrial haplotype. Playback experiments revealed asymmetric song recognition: male pugetensis displayed greater response to their own song than gambelii song, whereas gambelii did not discriminate significantly. If female choice operates similarly to male song discrimination, we predicted asymmetric gene flow, resulting in a greater number of hybrids with gambelii mtDNA. Contrary to our prediction, more gambelii and putative hybrids in the contact zone possessed pugetensis mtDNA haplotypes, possibly due to greater pugetensis abundance and female-biased dispersal.
Asymmetric song recognition does not influence gene flow in an emergent songbird hybrid zone
Abstract
Hybrid zones can be used to examine the mechanisms, like song recognition, that affect reproductive isolation and speciation. Song has mixed support as a driver of speciation; we did not find song to be associated with reproductive isolation in White-crowned Sparrow subspecies (Zonotrichia leucophrys pugetensis and Z. l. gambelii). We examined an emerging secondary contact zone in these subspecies by measuring song variation, song recognition, plumage, morphology, and mitochondrial DNA (mtDNA). Plumage and morphological characters provided evidence of hybridization in the contact zone, with some birds possessing intermediate phenotype and song characteristics, and some possessing discordant phenotype and mitochondrial haplotype. Playback experiments revealed asymmetric song recognition: male pugetensis displayed greater response to their own song than gambelii song, whereas gambelii did not discriminate significantly. If female choice operates similarly to male song discrimination, we predicted asymmetric gene flow, resulting in a greater number of hybrids with gambelii mtDNA. Contrary to our prediction, more gambelii and putative hybrids in the contact zone possessed pugetensis mtDNA haplotypes, possibly due to greater pugetensis abundance and female-biased dispersal.
albertonykus
Well-known member
DeRaad, D.A., E.E. Applewhite, W.L.E. Tsai, R.S. Terrill, S.E. Kingston, M.J. Braun, and J.E. McCormack (2022)
Hybrid zone or hybrid lineage: a genomic reevaluation of Sibley’s classic species conundrum in Pipilo towhees
Evolution (advance online publication)
doi: 10.1093/evolut/qpac068
Hybrid zones can be studied by modeling clines of trait variation (e.g., morphology, genetics) over a linear transect. Yet, hybrid zones can also be spatially complex, can shift over time, and can even lead to the formation of hybrid lineages with the right combination of dispersal and vicariance. We reassessed Sibley’s (1950) gradient between Collared Towhee (Pipilo ocai) and Spotted Towhee (P. maculatus) in Central Mexico to test whether it conformed to a typical tension-zone cline model. By comparing historical and modern data, we found that cline centers for genetic and phenotypic traits have not shifted over the course of 70 years. This equilibrium suggests that secondary contact between these species, which originally diverged over 2 million years ago, likely dates to the Pleistocene. Given the amount of mtDNA divergence, parental ends of the cline have very low autosomal nuclear differentiation (FST = 0.12). Dramatic and coincident cline shifts in mtDNA and throat color suggest the possibility of sexual selection as a factor in differential introgression, while a contrasting cline shift in green back color hints at a role for natural selection. Supporting the idea of a continuum between clinal variation and hybrid lineage formation, the towhee gradient can be analyzed as one population under isolation-by-distance, as a two-population cline, and as three lineages experiencing divergence with gene flow. In the middle of the gradient, a hybrid lineage has become partly isolated, likely due both to forested habitat shrinking and fragmenting as it moved upslope after the last glacial maximum and a stark environmental transition. The towhee system offers a window into the potential outcomes of hybridization across a dynamic landscape including the creation of novel genomic and phenotypic combinations and incipient hybrid lineages.
Hybrid zone or hybrid lineage: a genomic reevaluation of Sibley’s classic species conundrum in Pipilo towhees
Evolution (advance online publication)
doi: 10.1093/evolut/qpac068
Hybrid zones can be studied by modeling clines of trait variation (e.g., morphology, genetics) over a linear transect. Yet, hybrid zones can also be spatially complex, can shift over time, and can even lead to the formation of hybrid lineages with the right combination of dispersal and vicariance. We reassessed Sibley’s (1950) gradient between Collared Towhee (Pipilo ocai) and Spotted Towhee (P. maculatus) in Central Mexico to test whether it conformed to a typical tension-zone cline model. By comparing historical and modern data, we found that cline centers for genetic and phenotypic traits have not shifted over the course of 70 years. This equilibrium suggests that secondary contact between these species, which originally diverged over 2 million years ago, likely dates to the Pleistocene. Given the amount of mtDNA divergence, parental ends of the cline have very low autosomal nuclear differentiation (FST = 0.12). Dramatic and coincident cline shifts in mtDNA and throat color suggest the possibility of sexual selection as a factor in differential introgression, while a contrasting cline shift in green back color hints at a role for natural selection. Supporting the idea of a continuum between clinal variation and hybrid lineage formation, the towhee gradient can be analyzed as one population under isolation-by-distance, as a two-population cline, and as three lineages experiencing divergence with gene flow. In the middle of the gradient, a hybrid lineage has become partly isolated, likely due both to forested habitat shrinking and fragmenting as it moved upslope after the last glacial maximum and a stark environmental transition. The towhee system offers a window into the potential outcomes of hybridization across a dynamic landscape including the creation of novel genomic and phenotypic combinations and incipient hybrid lineages.
Peter Kovalik
Well-known member
Jennifer Walsh, Lindsey E. Fenderson, Chris S. Elphick, Jonathan B. Cohen, Christopher R. Field, Laura K. Garey, Thomas P. Hodgman, Alison R. Kocek, Rebecca Longenecker, Kathleen M. O'Brien, Brian J. Olsen, Katharine J. Ruskin, W. Gregory Shriver, and Adrienne I. Kovach (2023) Surrounding landscape, habitat and hybridization dynamics drive population structure and genetic diversity in the Saltmarsh Sparrow [Ammospiza caudacuta]. Ornithological Applications, 06 July 2023.
Surrounding landscape, habitat and hybridization dynamics drive population structure and genetic diversity in the Saltmarsh Sparrow
Abstract:
Determining factors that shape a species’ population genetic structure is beneficial for identifying effective conservation practices. We assessed population structure and genetic diversity for Saltmarsh Sparrow (Ammospiza caudacuta), an imperiled tidal marsh specialist, using 13 microsatellite markers and 964 individuals sampled from 24 marshes across the breeding range. We show that Saltmarsh Sparrow populations are structured regionally by isolation-by-distance, with gene flow occurring among marshes within ~110–135 km of one another. Isolation-by-resistance and isolation-by-environment also shape genetic variation; several habitat and landscape features are associated with genetic diversity and genetic divergence among populations. Human development in the surrounding landscape isolates breeding marshes, reducing genetic diversity and increasing population genetic divergence, while surrounding marshland and patch habitat quality (proportion high marsh and sea-level-rise trend) have the opposite effect. The distance of the breeding marsh to the Atlantic Ocean also influences genetic variation, with marshes farther inland being more divergent than coastal marshes. In northern marshes, hybridization with Nelson’s Sparrow (A. nelsoni) strongly influences Saltmarsh Sparrow genetic variation, by increasing genetic diversity in the population; this has a concomitant effect of increasing genetic differentiation of marshes with high levels of introgression. From a conservation perspective, we found that the majority of population clusters have low effective population sizes, suggesting a lack of resiliency. To conserve the representative breadth of genetic and ecological diversity and to ensure redundancy of populations, it will be important to protect a diversity of marsh types across the latitudinal gradient of the species range, including multiple inland, coastal and urban populations, which we have shown to exhibit signals of genetic differentiation. It will also require maintaining connectivity at a regional level, by promoting high marsh habitat at the scale of gene flow (~130 km), while also ensuring "stepping stone" populations across the range.
Surrounding landscape, habitat and hybridization dynamics drive population structure and genetic diversity in the Saltmarsh Sparrow
Abstract:
Determining factors that shape a species’ population genetic structure is beneficial for identifying effective conservation practices. We assessed population structure and genetic diversity for Saltmarsh Sparrow (Ammospiza caudacuta), an imperiled tidal marsh specialist, using 13 microsatellite markers and 964 individuals sampled from 24 marshes across the breeding range. We show that Saltmarsh Sparrow populations are structured regionally by isolation-by-distance, with gene flow occurring among marshes within ~110–135 km of one another. Isolation-by-resistance and isolation-by-environment also shape genetic variation; several habitat and landscape features are associated with genetic diversity and genetic divergence among populations. Human development in the surrounding landscape isolates breeding marshes, reducing genetic diversity and increasing population genetic divergence, while surrounding marshland and patch habitat quality (proportion high marsh and sea-level-rise trend) have the opposite effect. The distance of the breeding marsh to the Atlantic Ocean also influences genetic variation, with marshes farther inland being more divergent than coastal marshes. In northern marshes, hybridization with Nelson’s Sparrow (A. nelsoni) strongly influences Saltmarsh Sparrow genetic variation, by increasing genetic diversity in the population; this has a concomitant effect of increasing genetic differentiation of marshes with high levels of introgression. From a conservation perspective, we found that the majority of population clusters have low effective population sizes, suggesting a lack of resiliency. To conserve the representative breadth of genetic and ecological diversity and to ensure redundancy of populations, it will be important to protect a diversity of marsh types across the latitudinal gradient of the species range, including multiple inland, coastal and urban populations, which we have shown to exhibit signals of genetic differentiation. It will also require maintaining connectivity at a regional level, by promoting high marsh habitat at the scale of gene flow (~130 km), while also ensuring "stepping stone" populations across the range.
albertonykus
Well-known member
Mikles, C.S., P. Arcese, I.J. Lovette, S.M. Aguillon, Y.L. Chan, P.M. Benham, K. Carbeck, and J. Walsh (2023)
Evolutionary divergence and adaptive capacity in morphologically distinct song sparrow subspecies
Conservation Genetics (advance online publication)
doi: 10.1007/s10592-023-01547-w
Spatial variation in the environment can affect population fitness and individual phenotype by facilitating natural selection and local adaptation, and thereby enhance the diversity and adaptive capacity and persistence of species at regional to continental scales. The song sparrow subspecies complex endemic to the San Francisco Bay region, which has received over a century of close study, presents an opportunity to evaluate the adaptive potential of distinct subspecies faced with habitat loss, population decline, and threats of future environmental change. We used whole-genome sequences from 39 individuals representing five morphologically distinct song sparrow subspecies to evaluate the role of neutral and adaptive evolutionary processes in driving divergence within physiologically challenging habitats across multiple environmental clines. We found that natural selection for traits explained by ecological variables, including temperature and salinity, are drivers of adaptive genetic variation in these song sparrows. Differentiation was highest for candidate loci under selection (compared to neutral markers), as predicted if local ecological processes are at least partially responsible for the rapid radiation of these subspecies. Our findings inform management aimed at conserving and prioritizing population-level diversity in species displaying local adaptation and inhabiting a diverse range of environments.
Evolutionary divergence and adaptive capacity in morphologically distinct song sparrow subspecies
Conservation Genetics (advance online publication)
doi: 10.1007/s10592-023-01547-w
Spatial variation in the environment can affect population fitness and individual phenotype by facilitating natural selection and local adaptation, and thereby enhance the diversity and adaptive capacity and persistence of species at regional to continental scales. The song sparrow subspecies complex endemic to the San Francisco Bay region, which has received over a century of close study, presents an opportunity to evaluate the adaptive potential of distinct subspecies faced with habitat loss, population decline, and threats of future environmental change. We used whole-genome sequences from 39 individuals representing five morphologically distinct song sparrow subspecies to evaluate the role of neutral and adaptive evolutionary processes in driving divergence within physiologically challenging habitats across multiple environmental clines. We found that natural selection for traits explained by ecological variables, including temperature and salinity, are drivers of adaptive genetic variation in these song sparrows. Differentiation was highest for candidate loci under selection (compared to neutral markers), as predicted if local ecological processes are at least partially responsible for the rapid radiation of these subspecies. Our findings inform management aimed at conserving and prioritizing population-level diversity in species displaying local adaptation and inhabiting a diverse range of environments.
albertonykus
Well-known member
Carbeck, K., P. Arcese, I. Lovette, C. Pruett, K. Winker, and J. Walsh (2023)
Candidate genes under selection in song sparrows co-vary with climate and body mass in support of Bergmann’s Rule
Nature Communications 14: 6974
doi: 10.1038/s41467-023-42786-2
Ecogeographic rules denote spatial patterns in phenotype and environment that may reflect local adaptation as well as a species’ capacity to adapt to change. To identify genes underlying Bergmann’s Rule, which posits that spatial correlations of body mass and temperature reflect natural selection and local adaptation in endotherms, we compare 79 genomes from nine song sparrow (Melospiza melodia) subspecies that vary ~300% in body mass (17 − 50 g). Comparing large- and smaller-bodied subspecies revealed 9 candidate genes in three genomic regions associated with body mass. Further comparisons to the five smallest subspecies endemic to California revealed eight SNPs within four of the candidate genes (GARNL3, RALGPS1, ANGPTL2, and COL15A1) associated with body mass and varying as predicted by Bergmann’s Rule. Our results support the hypothesis that co-variation in environment, body mass and genotype reflect the influence of natural selection on local adaptation and a capacity for contemporary evolution in this diverse species.
Candidate genes under selection in song sparrows co-vary with climate and body mass in support of Bergmann’s Rule
Nature Communications 14: 6974
doi: 10.1038/s41467-023-42786-2
Ecogeographic rules denote spatial patterns in phenotype and environment that may reflect local adaptation as well as a species’ capacity to adapt to change. To identify genes underlying Bergmann’s Rule, which posits that spatial correlations of body mass and temperature reflect natural selection and local adaptation in endotherms, we compare 79 genomes from nine song sparrow (Melospiza melodia) subspecies that vary ~300% in body mass (17 − 50 g). Comparing large- and smaller-bodied subspecies revealed 9 candidate genes in three genomic regions associated with body mass. Further comparisons to the five smallest subspecies endemic to California revealed eight SNPs within four of the candidate genes (GARNL3, RALGPS1, ANGPTL2, and COL15A1) associated with body mass and varying as predicted by Bergmann’s Rule. Our results support the hypothesis that co-variation in environment, body mass and genotype reflect the influence of natural selection on local adaptation and a capacity for contemporary evolution in this diverse species.
Peter Kovalik
Well-known member
Brett L. Walker (2024) Applying citizen science data to quantify differences in song between controversial avian taxa, the Sagebrush and Timberline subspecies of the Brewer's Sparrow (Spizella breweri). Western North American Naturalist 83: 550-568.
Applying Citizen Science Data to Quantify Differences in Song between Controversial Avian Taxa, the Sagebrush and Timberline Subspecies of the Brewer's Sparrow (Spizella breweri)
Abstract
Divergence in the acoustic structure of mate-attraction signals between closely related taxa can contribute to reproductive isolation and speciation, and acoustic differences are often useful for identifying otherwise similar taxa from recordings. The Brewer's Sparrow (Spizella breweri) is a migratory oscine songbird with 2 recently diverged subspecies. The nominate subspecies (S. b. breweri) primarily breeds in sagebrush (Artemisia spp.) shrublands in the western United States and southwestern Canada, whereas the Timberline Sparrow (S. b. taverneri) breeds in alpine shrubs and conifer krummholz near treeline in mountain ranges from east-central Alaska to northwestern Montana. Quantitative comparison of the acoustic structure of Brewer's Sparrow mate-attraction songs is needed to help resolve the outstanding debate regarding the taxonomic status of S. b. taverneri and improve subspecific identification from song recordings. I compared the acoustic structure of 181 short song types from 180 male S. b. breweri and 22 short song types from 20 male S. b. taverneri recorded from across each subspecies' breeding range. Despite extreme variation in acoustic structure of short songs among individuals, 19 acoustic variables differed between subspecies. Short song types of S. b. taverneri averaged 19.3%–22.1% lower maximum frequency, 4.9%–15.9% higher minimum frequency, 36.7%–42.6% narrower frequency bandwidth, and 12.9%–26.0% lower aggregate entropy (a measure of sound complexity) than those of S. b. breweri across acoustic elements (song, section, syllable, and note). Random forest classification analysis identified 10 acoustic variables important for distinguishing between short songs of the 2 subspecies and correctly classified 89.2% (95% CI 84.1% to 93.1%) of songs overall. Principal component scores representing overall acoustic structure showed an abrupt change near the breeding boundary between S. b. breweri and S. b. taverneri but overlapped sufficiently that they did not meet an established “75%–99% rule” for reciprocal diagnosability of subspecies. An easy-to-measure logistic regression threshold based on song bandwidth and mean note bandwidth accurately classified >90% of short songs to subspecies. Additional recordings of S. b. taverneri are needed to improve our understanding of geographic variation in the song of that subspecies. Data on responses of males and females to songs of the other subspecies would inform whether acoustic differences are sufficient to impede mate recognition and attraction in areas of potential breeding overlap.
Applying Citizen Science Data to Quantify Differences in Song between Controversial Avian Taxa, the Sagebrush and Timberline Subspecies of the Brewer's Sparrow (Spizella breweri)
Abstract
Divergence in the acoustic structure of mate-attraction signals between closely related taxa can contribute to reproductive isolation and speciation, and acoustic differences are often useful for identifying otherwise similar taxa from recordings. The Brewer's Sparrow (Spizella breweri) is a migratory oscine songbird with 2 recently diverged subspecies. The nominate subspecies (S. b. breweri) primarily breeds in sagebrush (Artemisia spp.) shrublands in the western United States and southwestern Canada, whereas the Timberline Sparrow (S. b. taverneri) breeds in alpine shrubs and conifer krummholz near treeline in mountain ranges from east-central Alaska to northwestern Montana. Quantitative comparison of the acoustic structure of Brewer's Sparrow mate-attraction songs is needed to help resolve the outstanding debate regarding the taxonomic status of S. b. taverneri and improve subspecific identification from song recordings. I compared the acoustic structure of 181 short song types from 180 male S. b. breweri and 22 short song types from 20 male S. b. taverneri recorded from across each subspecies' breeding range. Despite extreme variation in acoustic structure of short songs among individuals, 19 acoustic variables differed between subspecies. Short song types of S. b. taverneri averaged 19.3%–22.1% lower maximum frequency, 4.9%–15.9% higher minimum frequency, 36.7%–42.6% narrower frequency bandwidth, and 12.9%–26.0% lower aggregate entropy (a measure of sound complexity) than those of S. b. breweri across acoustic elements (song, section, syllable, and note). Random forest classification analysis identified 10 acoustic variables important for distinguishing between short songs of the 2 subspecies and correctly classified 89.2% (95% CI 84.1% to 93.1%) of songs overall. Principal component scores representing overall acoustic structure showed an abrupt change near the breeding boundary between S. b. breweri and S. b. taverneri but overlapped sufficiently that they did not meet an established “75%–99% rule” for reciprocal diagnosability of subspecies. An easy-to-measure logistic regression threshold based on song bandwidth and mean note bandwidth accurately classified >90% of short songs to subspecies. Additional recordings of S. b. taverneri are needed to improve our understanding of geographic variation in the song of that subspecies. Data on responses of males and females to songs of the other subspecies would inform whether acoustic differences are sufficient to impede mate recognition and attraction in areas of potential breeding overlap.
