l_raty
laurent raty
Which .nex file and what do you want to do with it ?
(Merely view the tree in the .nex file in the first .zip ?)
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Galliformes (1 Viewer)
- Thread starter Peter Kovalik
- Start date
Which .nex file and what do you want to do with it ?
(Merely view the tree in the .nex file in the first .zip ?)
Jim LeNomenclatoriste
Je suis un mignon petit Traquet rubicole
Yep. Each zip files contains one .nex files. It would have been easier if they contained a .tree file
mb1848
Well-known member
about .nex files use Opera?
There is an open access paper co-authored by Kimball:
Protein Structure, Models of Sequence Evolution, and Data Type Effects in Phylogenetic Analyses of Mitochondrial Data: A Case Study in Birds .
A paper that cites When Good Mitichondria go bad:
https://onlinelibrary.wiley.com/doi/10.1002/ece3.8199 .
There is an open access paper co-authored by Kimball:
Protein Structure, Models of Sequence Evolution, and Data Type Effects in Phylogenetic Analyses of Mitochondrial Data: A Case Study in Birds .
A paper that cites When Good Mitichondria go bad:
https://onlinelibrary.wiley.com/doi/10.1002/ece3.8199 .
l_raty
laurent raty
Had a slightly closer look at it -- there are actually 21 different trees in the .nex in the first zip file.
("ML_unpartitioned" and "ML_partitioned".
"Unpartitioned_GAMMA_Boot" and "Partitioned_GAMMA_Boot"
"Unpartitioned_PSR_Boot" and "Partitioned_PSR_Boot".
"BL_adjusted_CYBND2_GAMMA_unpart_Figure6".
"Ultrametric_MLunpartitioned" and "Ultrametric_BLadjusted".
"KimballTopology_BrownTaxaEquivalents", "Brown2017Topology_MatchesKimballNames" and "BrownConsensus". "
"KimballTopology_BurleighTaxaEquivalents", "BurleighTopology_MatchesKimballNames" and "BurleighConsensus".
"KimballTopology_JetzTaxaEquivalent", "JetzMajRule_Matched" and "JetzConsensus".
"KimballTopology_SteinTaxaEquivalent", "Stein_Matched" and "SteinConsensus".)
The .nex in the second zip file contains a data matrix, not trees.
("ML_unpartitioned" and "ML_partitioned".
"Unpartitioned_GAMMA_Boot" and "Partitioned_GAMMA_Boot"
"Unpartitioned_PSR_Boot" and "Partitioned_PSR_Boot".
"BL_adjusted_CYBND2_GAMMA_unpart_Figure6".
"Ultrametric_MLunpartitioned" and "Ultrametric_BLadjusted".
"KimballTopology_BrownTaxaEquivalents", "Brown2017Topology_MatchesKimballNames" and "BrownConsensus". "
"KimballTopology_BurleighTaxaEquivalents", "BurleighTopology_MatchesKimballNames" and "BurleighConsensus".
"KimballTopology_JetzTaxaEquivalent", "JetzMajRule_Matched" and "JetzConsensus".
"KimballTopology_SteinTaxaEquivalent", "Stein_Matched" and "SteinConsensus".)
The .nex in the second zip file contains a data matrix, not trees.
Jim LeNomenclatoriste
Je suis un mignon petit Traquet rubicole
Opera is a search engine? I have to install it then. How does it work afterwards?
Is there a figure with divergence times?
l_raty
laurent raty
Don't think so.
Peter Kovalik
Well-known member
Wang, P., Liu, S., Hu, J., Zhang, J., Wang, Z., Xu, J., Yao, H., Wang, B., Chen, D., Zhang, Z. and Liu, Y. (2022) Disentangling the relative roles of geographical and ecological factors in driving genomic variations of a widely distributed bird [Phasianus colchicus] across a longitudinal gradient. Journal of Avian Biology e02979.
https://doi.org/10.1111/jav.02979
Abstract
Unraveling geographical modes of speciation processes has been a longstanding topic in biogeography. Divergence can be driven by factors operating on multiple spatial scales, such as geographical distance (isolation by distance, IBD), landscape resistance (isolation by resistance, IBR) and environmental heterogeneity (isolation by environment, IBE). However, it is challenging to assess the relative contributions of such factors, which are usually autocorrelated with each other. On the basis of ~294 K nuclear single-nucleotide polymorphisms from 53 samples, we integrated population genomics, geographical information and environmental variables to delineate genetic differentiation in the common pheasant Phasianus colchicus across a longitudinal gradient in northern China. Generalized dissimilarity modeling (GDM) was used to analyze the relative importance of IBD, IBR and IBE. We found that the common pheasant in northern China was grouped into six genetic clusters, which was consistent with the taxonomic affinities. Genetic diversity changed along the longitudinal gradient, reaching its lowest level at the eastern edge of the Qinghai–Tibetan Plateau (QTP). The spatial pattern of gene flow suggested that the mountains surrounding the QTP and the mountains in central China have acted as geographical barriers impeding common pheasant dispersal. GDM analysis indicated that environmental heterogeneity is the most important driver explaining the lineage divergence, which supports the IBE model. These results suggest that multiple isolation mechanisms shaped genetic diversity and genomic divergence in this wide-ranging bird species. Together, our results underscore the importance of leveraging genome-wide variations and ecological modeling to facilitate a deeper understanding of population divergence processes.
https://doi.org/10.1111/jav.02979
Abstract
Unraveling geographical modes of speciation processes has been a longstanding topic in biogeography. Divergence can be driven by factors operating on multiple spatial scales, such as geographical distance (isolation by distance, IBD), landscape resistance (isolation by resistance, IBR) and environmental heterogeneity (isolation by environment, IBE). However, it is challenging to assess the relative contributions of such factors, which are usually autocorrelated with each other. On the basis of ~294 K nuclear single-nucleotide polymorphisms from 53 samples, we integrated population genomics, geographical information and environmental variables to delineate genetic differentiation in the common pheasant Phasianus colchicus across a longitudinal gradient in northern China. Generalized dissimilarity modeling (GDM) was used to analyze the relative importance of IBD, IBR and IBE. We found that the common pheasant in northern China was grouped into six genetic clusters, which was consistent with the taxonomic affinities. Genetic diversity changed along the longitudinal gradient, reaching its lowest level at the eastern edge of the Qinghai–Tibetan Plateau (QTP). The spatial pattern of gene flow suggested that the mountains surrounding the QTP and the mountains in central China have acted as geographical barriers impeding common pheasant dispersal. GDM analysis indicated that environmental heterogeneity is the most important driver explaining the lineage divergence, which supports the IBE model. These results suggest that multiple isolation mechanisms shaped genetic diversity and genomic divergence in this wide-ranging bird species. Together, our results underscore the importance of leveraging genome-wide variations and ecological modeling to facilitate a deeper understanding of population divergence processes.
Jim LeNomenclatoriste
Je suis un mignon petit Traquet rubicole
Historical specimens and the limits of subspecies phylogenomics in the New World quails (Odontophoridae)
As phylogenomics focuses on comprehensive taxon sampling at the species and population/subspecies levels, incorporating genomic data from historical s…
Peter Kovalik
Well-known member
Salter, J.F., Hosner, P.A., Tsai, W.L.E., McCormack, J.E., Braun, E.L., Kimball, R.T., Brumfield, R.T., and Faircloth, B.C. (2022) Historical specimens and the limits of subspecies phylogenomics in the New World quails (Odontophoridae). Molecular Phylogenetics and Evolution, published online 5 July 2022.Historical specimens and the limits of subspecies phylogenomics in the New World quails (Odontophoridae)
As phylogenomics focuses on comprehensive taxon sampling at the species and population/subspecies levels, incorporating genomic data from historical s…www.sciencedirect.com
Redirecting
Abstract
As phylogenomics focuses on comprehensive taxon sampling at the species and population/subspecies levels, incorporating genomic data from historical specimens has become increasingly common. While historical samples can fill critical gaps in our understanding of the evolutionary history of diverse groups, they also introduce additional sources of phylogenomic uncertainty, making it difficult to discern novel evolutionary relationships from artifacts caused by sample quality issues. These problems highlight the need for improved strategies to disentangle artifactual patterns from true biological signal as historical specimens become more prevalent in phylogenomic datasets. Here, we tested the limits of historical specimen-driven phylogenomics to resolve subspecies-level relationships within a highly polytypic family, the New World quails (Odontophoridae), using thousands of ultraconserved elements (UCEs). We found that relationships at and above the species-level were well-resolved and highly supported across all analyses, with the exception of discordant relationships within the two most polytypic genera which included many historical specimens. We examined the causes of discordance and found that inferring phylogenies from subsets of taxa resolved the disagreements, suggesting that analyzing subclades can help remove artifactual causes of discordance in datasets that include historical samples. At the subspecies-level, we found well-resolved geographic structure within the two most polytypic genera, including the most polytypic species in this family, Northern Bobwhites (Colinus virginianus), demonstrating that variable sites within UCEs are capable of resolving phylogenetic structure below the species level. Our results highlight the importance of complete taxonomic sampling for resolving relationships among polytypic species, often through the inclusion of historical specimens, and we propose an integrative strategy for understanding and addressing the uncertainty that historical samples sometimes introduce to phylogenetic analyses.
Jim LeNomenclatoriste
Je suis un mignon petit Traquet rubicole
Available on Biorxiv
albertonykus
Well-known member
Albayrak, T., J.A. Dávila García, Ö. Özmen, F. Karadas, D. Ateş, and M. Wink (2022)
Evidence for genetic hybridization between released and wild game birds: phylogeography and genetic structure of Chukar Partridge, Alectoris chukar, in Turkey
Diversity 14: 571
doi: 10.3390/d14070571
The Chukar Partridge (Alectoris chukar, Galliformes) is one of the most important game birds in its native range, spanning from the Balkans to eastern Asia, and the regions of Europe, North America and New Zealand where it was introduced. Previous studies found two main genetic lineages of the species forming an eastern and a western clade. Chukar Partridges are raised in game farms and released to supplement natural populations for shooting in the USA, Canada, Greece, and Turkey. To explore intraspecific genetic structure, phylogeography, and possible genetic admixture events of A. chukar in Turkey, we genotyped individuals from fourteen wild and five captive populations at two mitochondrial and ten microsatellite DNA loci in. Wild and farmed Chukar Partridge samples were analyzed together to investigate possible influences of intraspecific hybridizations. We found that the farmed chukars, which mainly (85%) cluster into the eastern clade, and wild ones were genetically distinct. The latter could be separated into six management units (MUs), with partridges from Gökçeada Island in the Aegean Sea forming the most divergent population. Intraspecific hybridization was detected between wild and captive populations. This phenomenon causes rampant introgression and homogenization. The phylogeographic analysis revealed admixture among wild populations; nevertheless, this did not impair pointing to Anatolia as likely having a “refugia-within-refugia” structure. We recommend that the genetic structure of Chukar Partridge and its MUs be taken into account when developing the policy of hunting, production, and release to preserve the genetic integrity of this species.
Evidence for genetic hybridization between released and wild game birds: phylogeography and genetic structure of Chukar Partridge, Alectoris chukar, in Turkey
Diversity 14: 571
doi: 10.3390/d14070571
The Chukar Partridge (Alectoris chukar, Galliformes) is one of the most important game birds in its native range, spanning from the Balkans to eastern Asia, and the regions of Europe, North America and New Zealand where it was introduced. Previous studies found two main genetic lineages of the species forming an eastern and a western clade. Chukar Partridges are raised in game farms and released to supplement natural populations for shooting in the USA, Canada, Greece, and Turkey. To explore intraspecific genetic structure, phylogeography, and possible genetic admixture events of A. chukar in Turkey, we genotyped individuals from fourteen wild and five captive populations at two mitochondrial and ten microsatellite DNA loci in. Wild and farmed Chukar Partridge samples were analyzed together to investigate possible influences of intraspecific hybridizations. We found that the farmed chukars, which mainly (85%) cluster into the eastern clade, and wild ones were genetically distinct. The latter could be separated into six management units (MUs), with partridges from Gökçeada Island in the Aegean Sea forming the most divergent population. Intraspecific hybridization was detected between wild and captive populations. This phenomenon causes rampant introgression and homogenization. The phylogeographic analysis revealed admixture among wild populations; nevertheless, this did not impair pointing to Anatolia as likely having a “refugia-within-refugia” structure. We recommend that the genetic structure of Chukar Partridge and its MUs be taken into account when developing the policy of hunting, production, and release to preserve the genetic integrity of this species.
albertonykus
Well-known member
Alfieri, J.M., T. Johnson, A. Linderholm, H. Blackmon, and G.N. Athrey (2023)
Genomic investigation refutes record of most diverged avian hybrid
Ecology and Evolution 13: e9689
doi: 10.1002/ece3.9689
The most diverged avian hybrid that has been documented (Numida meleagris × Penelope superciliaris) was reported in 1957. This identification has yet to be confirmed, and like most contemporary studies of hybridization, the identification was based on phenotype, which can be misleading. In this study, we sequenced the specimen in question and performed analyses to validate the specimen's parentage. We extracted DNA from the specimen in a dedicated ancient DNA facility and performed whole-genome short-read sequencing. We used BLAST to find Galliformes sequences similar to the hybrid specimen reads. We found that the proportion of BLAST hits mapped overwhelmingly to two species, N. meleagris and Gallus gallus. Additionally, we constructed phylogenies using avian orthologs and parsed the species placed as sister to the hybrid. Again, the hybrid specimen was placed as a sister to N. meleagris and G. gallus. Despite not being a hybrid between N. meleagris and P. superciliaris, the hybrid still represents the most diverged avian hybrid confirmed with genetic data. In addition to correcting the “record” of the most diverged avian hybrid, these findings support recent assertions that morphological and behavioral-based identifications of avian hybrids can be error-prone. Consequently, this study serves as a cautionary tale to researchers of hybridization.
Genomic investigation refutes record of most diverged avian hybrid
Ecology and Evolution 13: e9689
doi: 10.1002/ece3.9689
The most diverged avian hybrid that has been documented (Numida meleagris × Penelope superciliaris) was reported in 1957. This identification has yet to be confirmed, and like most contemporary studies of hybridization, the identification was based on phenotype, which can be misleading. In this study, we sequenced the specimen in question and performed analyses to validate the specimen's parentage. We extracted DNA from the specimen in a dedicated ancient DNA facility and performed whole-genome short-read sequencing. We used BLAST to find Galliformes sequences similar to the hybrid specimen reads. We found that the proportion of BLAST hits mapped overwhelmingly to two species, N. meleagris and Gallus gallus. Additionally, we constructed phylogenies using avian orthologs and parsed the species placed as sister to the hybrid. Again, the hybrid specimen was placed as a sister to N. meleagris and G. gallus. Despite not being a hybrid between N. meleagris and P. superciliaris, the hybrid still represents the most diverged avian hybrid confirmed with genetic data. In addition to correcting the “record” of the most diverged avian hybrid, these findings support recent assertions that morphological and behavioral-based identifications of avian hybrids can be error-prone. Consequently, this study serves as a cautionary tale to researchers of hybridization.
thyoloalethe
Well-known member
Funny, I read Penelope superciliaris and for some reason visualized Mareca penelope!
albertonykus
Well-known member
van Grouw, H. and W. Dekkers (2023)
The taxonomic history of Black-shouldered Peafowl; with Darwin's help downgraded from species to variation
Bulletin of the British Ornithologists' Club 143: 111–121
doi: 10.25226/bboc.v143i1.2023.a7
In the 19th century the black-shouldered variety of Indian Peafowl Pavo cristatus was erroneously viewed by many as a separate species, named P. nigripennis. Others had doubts about its taxonomic status, but Darwin presented firm evidence for it being a variety under domestication, which treatment is now well established and accepted. It being a colour variation rather than a wild species was important for Darwin to prove, as otherwise it could undermine his theory of slow modification by natural selection in the wild.
The taxonomic history of Black-shouldered Peafowl; with Darwin's help downgraded from species to variation
Bulletin of the British Ornithologists' Club 143: 111–121
doi: 10.25226/bboc.v143i1.2023.a7
In the 19th century the black-shouldered variety of Indian Peafowl Pavo cristatus was erroneously viewed by many as a separate species, named P. nigripennis. Others had doubts about its taxonomic status, but Darwin presented firm evidence for it being a variety under domestication, which treatment is now well established and accepted. It being a colour variation rather than a wild species was important for Darwin to prove, as otherwise it could undermine his theory of slow modification by natural selection in the wild.
Jim LeNomenclatoriste
Je suis un mignon petit Traquet rubicole
Overlooked
Taxonomic status of Great Argus (Argusianus argus) Sumatra and Borneo based on cytochrome B gene. CYNTHIA ERICCA, DJONG HON TJONG, DEWI IMELDA ROESMA, WILSON NOVARINO, SYAIFULLAH, MUHAMMAD NAZRI JANRA, AADREAN
Taxonomic status of Great Argus (Argusianus argus) Sumatra and Borneo based on cytochrome B gene. CYNTHIA ERICCA, DJONG HON TJONG, DEWI IMELDA ROESMA, WILSON NOVARINO, SYAIFULLAH, MUHAMMAD NAZRI JANRA, AADREAN
albertonykus
Well-known member
Luna, L.W., L.M. Williams, K. Duren, R. Tyl, D.P.L. Toews, and J.D. Avery (2023)
Whole genome assessment of a declining game bird reveals cryptic genetic structure and insights for population management
Molecular Ecology (advance online publication)
doi: 10.1111/mec.17129
Population genomics applied to game species conservation can help delineate management units, ensure appropriate harvest levels and identify populations needing genetic rescue to safeguard their adaptive potential. The ruffed grouse (Bonasa umbellus) is rapidly declining in much of the eastern USA due to a combination of forest maturation and habitat fragmentation. More recently, mortality from West Nile Virus may have affected connectivity of local populations; however, genetic approaches have never explicitly investigated this issue. In this study, we sequenced 54 individual low-coverage (~5X) grouse genomes to characterize population structure, assess migration rates across the landscape to detect potential barriers to gene flow and identify genomic regions with high differentiation. We identified two genomic clusters with no clear geographic correlation, with large blocks of genomic differentiation associated with chromosomes 4 and 20, likely due to chromosomal inversions. After excluding these putative inversions from the data set, we found weak but nonsignificant signals of population subdivision. Estimated gene flow revealed reduced rates of migration in areas with extensive habitat fragmentation and increased genetic connectivity in areas with less habitat fragmentation. Our findings provide a benchmark for wildlife managers to compare and scale the genetic diversity and structure of ruffed grouse populations in Pennsylvania and across the eastern USA, and we also reveal structural variation in the grouse genome that requires further study to understand its possible effects on individual fitness and population distribution.
Whole genome assessment of a declining game bird reveals cryptic genetic structure and insights for population management
Molecular Ecology (advance online publication)
doi: 10.1111/mec.17129
Population genomics applied to game species conservation can help delineate management units, ensure appropriate harvest levels and identify populations needing genetic rescue to safeguard their adaptive potential. The ruffed grouse (Bonasa umbellus) is rapidly declining in much of the eastern USA due to a combination of forest maturation and habitat fragmentation. More recently, mortality from West Nile Virus may have affected connectivity of local populations; however, genetic approaches have never explicitly investigated this issue. In this study, we sequenced 54 individual low-coverage (~5X) grouse genomes to characterize population structure, assess migration rates across the landscape to detect potential barriers to gene flow and identify genomic regions with high differentiation. We identified two genomic clusters with no clear geographic correlation, with large blocks of genomic differentiation associated with chromosomes 4 and 20, likely due to chromosomal inversions. After excluding these putative inversions from the data set, we found weak but nonsignificant signals of population subdivision. Estimated gene flow revealed reduced rates of migration in areas with extensive habitat fragmentation and increased genetic connectivity in areas with less habitat fragmentation. Our findings provide a benchmark for wildlife managers to compare and scale the genetic diversity and structure of ruffed grouse populations in Pennsylvania and across the eastern USA, and we also reveal structural variation in the grouse genome that requires further study to understand its possible effects on individual fitness and population distribution.
albertonykus
Well-known member
Johnson, J.A., B. Novak, G. Athrey, A.G. Sharo, T. Chase, and J. Toepfer (2023)
Phylogenomics of the extinct Heath Hen provides support for sex-biased introgression among extant prairie grouse
Molecular Phylogenetics and Evolution (advance online publication)
doi: 10.1016/j.ympev.2023.107927
Rapid divergence and subsequent reoccurring patterns of gene flow can complicate our ability to discern phylogenetic relationships among closely related species. To what degree such patterns may differ across the genome can provide an opportunity to extrapolate better how life history constraints may influence species boundaries. By exploring differences between autosomal and Z (or X) chromosomal-derived phylogenetic patterns, we can better identify factors that may limit introgression despite patterns of incomplete lineage sorting among closely related taxa. Here, using a whole-genome resequencing approach coupled with an exhaustive sampling of subspecies within the recently divergent prairie grouse complex (genus: Tympanuchus), including the extinct Heath Hen (T. cupido cupido), we show that their phylogenomic history differs depending on autosomal or Z-chromosome partitioned SNPs. Because the Heath Hen was allopatric relative to the other prairie grouse taxa, its phylogenetic signature should not be influenced by gene flow. In contrast, all the other extant prairie grouse taxa, except Attwater’s Prairie-chicken (T. c. attwateri), possess overlapping contemporary geographic distributions and have been known to hybridize. After excluding samples that were likely translocated prairie grouse from the Midwest to the eastern coastal states or their resulting hybrids with mainland Heath Hens, species tree analyses based on autosomal SNPs consistently identified a paraphyletic relationship with regard to the Heath Hen with Lesser Prairie-chicken (T. pallidicinctus) sister to Greater Prairie-chicken (T. c. pinnatus) regardless of genic or intergenic partitions. In contrast, species trees based on the Z-chromosome were consistent with Heath Hen sister to a clade that included its conspecifics, Greater and Attwater’s Prairie-chickens (T. c. attwateri). These results were further explained by historic gene flow, as shown with an excess of autosomal SNPs shared between Lesser and Greater Prairie-chickens but not with the Z-chromosome. Phylogenetic placement of Sharp-tailed Grouse (T. phasianellus), however, did not differ among analyses and was sister to a clade that included all other prairie grouse despite low levels of autosomal gene flow with Greater Prairie-chicken. These results, along with strong sexual selection (i.e., male hybrid behavioral isolation) and a lek breeding system (i.e., high variance in male mating success), are consistent with a pattern of female-biased introgression between prairie grouse taxa with overlapping geographic distributions. Additional study is warranted to explore how genotype associated with the Z-chromosome influences the phenotype and thereby impacts species limits among prairie grouse taxa despite ongoing contemporary gene flow.
Phylogenomics of the extinct Heath Hen provides support for sex-biased introgression among extant prairie grouse
Molecular Phylogenetics and Evolution (advance online publication)
doi: 10.1016/j.ympev.2023.107927
Rapid divergence and subsequent reoccurring patterns of gene flow can complicate our ability to discern phylogenetic relationships among closely related species. To what degree such patterns may differ across the genome can provide an opportunity to extrapolate better how life history constraints may influence species boundaries. By exploring differences between autosomal and Z (or X) chromosomal-derived phylogenetic patterns, we can better identify factors that may limit introgression despite patterns of incomplete lineage sorting among closely related taxa. Here, using a whole-genome resequencing approach coupled with an exhaustive sampling of subspecies within the recently divergent prairie grouse complex (genus: Tympanuchus), including the extinct Heath Hen (T. cupido cupido), we show that their phylogenomic history differs depending on autosomal or Z-chromosome partitioned SNPs. Because the Heath Hen was allopatric relative to the other prairie grouse taxa, its phylogenetic signature should not be influenced by gene flow. In contrast, all the other extant prairie grouse taxa, except Attwater’s Prairie-chicken (T. c. attwateri), possess overlapping contemporary geographic distributions and have been known to hybridize. After excluding samples that were likely translocated prairie grouse from the Midwest to the eastern coastal states or their resulting hybrids with mainland Heath Hens, species tree analyses based on autosomal SNPs consistently identified a paraphyletic relationship with regard to the Heath Hen with Lesser Prairie-chicken (T. pallidicinctus) sister to Greater Prairie-chicken (T. c. pinnatus) regardless of genic or intergenic partitions. In contrast, species trees based on the Z-chromosome were consistent with Heath Hen sister to a clade that included its conspecifics, Greater and Attwater’s Prairie-chickens (T. c. attwateri). These results were further explained by historic gene flow, as shown with an excess of autosomal SNPs shared between Lesser and Greater Prairie-chickens but not with the Z-chromosome. Phylogenetic placement of Sharp-tailed Grouse (T. phasianellus), however, did not differ among analyses and was sister to a clade that included all other prairie grouse despite low levels of autosomal gene flow with Greater Prairie-chicken. These results, along with strong sexual selection (i.e., male hybrid behavioral isolation) and a lek breeding system (i.e., high variance in male mating success), are consistent with a pattern of female-biased introgression between prairie grouse taxa with overlapping geographic distributions. Additional study is warranted to explore how genotype associated with the Z-chromosome influences the phenotype and thereby impacts species limits among prairie grouse taxa despite ongoing contemporary gene flow.
albertonykus
Well-known member
Black, A.N., A.J. Mularo, J.Y. Jeon, D. Haukos, K.J. Bondo, K.A. Fricke, A. Gregory, B. Grisham, Z.E. Lowe, and J.A. DeWoody (2024)
Discordance between taxonomy and population genomic data: an avian example relevant to the United States Endangered Species Act
PNAS Nexus (advance online publication)
doi: 10.1093/pnasnexus/pgae298
Population genomics can reveal cryptic biological diversity that may impact fitness while simultaneously serving to delineate relevant conservation units. Here, we leverage the power of whole genome resequencing for conservation by studying 433 individual Lesser Prairie-Chicken (Tympanuchus pallidicinctus; LEPC, a federally endangered species of conservation concern in the United States) and Greater Prairie-Chicken (T. cupido; GRPC, a legally huntable species throughout much of its range). The genomic diversity of two formally recognized Distinct Population Segments (DPSs) of LEPCs is similar but they are genetically distinct. Neither DPS is depleted of its genomic diversity, neither is especially inbred, and temporal diversity is relatively stable in both conservation units. Interspecific differentiation between the two species was only slightly higher than that observed between LEPC DPSs, due largely to bidirectional introgression. The high resolution provided by our dataset identified a genomic continuum between the two species such that individuals sampled from the hybrid zone were imperfectly assigned to their presumptive species when considering only their physical characteristics. The admixture between the two species is reflected in the spectrum of individual ancestry coefficients, which has legal implications for the “take” of individuals under the Endangered Species Act (ESA). Overall, our data highlight the recurring dissonance between static policies and dynamic species boundaries that are increasingly obvious in the population genomic era.
Discordance between taxonomy and population genomic data: an avian example relevant to the United States Endangered Species Act
PNAS Nexus (advance online publication)
doi: 10.1093/pnasnexus/pgae298
Population genomics can reveal cryptic biological diversity that may impact fitness while simultaneously serving to delineate relevant conservation units. Here, we leverage the power of whole genome resequencing for conservation by studying 433 individual Lesser Prairie-Chicken (Tympanuchus pallidicinctus; LEPC, a federally endangered species of conservation concern in the United States) and Greater Prairie-Chicken (T. cupido; GRPC, a legally huntable species throughout much of its range). The genomic diversity of two formally recognized Distinct Population Segments (DPSs) of LEPCs is similar but they are genetically distinct. Neither DPS is depleted of its genomic diversity, neither is especially inbred, and temporal diversity is relatively stable in both conservation units. Interspecific differentiation between the two species was only slightly higher than that observed between LEPC DPSs, due largely to bidirectional introgression. The high resolution provided by our dataset identified a genomic continuum between the two species such that individuals sampled from the hybrid zone were imperfectly assigned to their presumptive species when considering only their physical characteristics. The admixture between the two species is reflected in the spectrum of individual ancestry coefficients, which has legal implications for the “take” of individuals under the Endangered Species Act (ESA). Overall, our data highlight the recurring dissonance between static policies and dynamic species boundaries that are increasingly obvious in the population genomic era.
albertonykus
Well-known member
Eleiwa, A., J. Nadal, E. Vilaprinyo, A. Marin-Sanguino, A. Sorribas, O. Basallo, A. Lucido, C. Richart, R.N. Pena, R. Ros-Freixedes, A. Usie, and R. Alves (2024)
Hybrid assembly and comparative genomics unveil insights into the evolution and biology of the red-legged partridge
Scientific Reports 14: 19531
doi: 10.1038/s41598-024-70018-0
The red-legged partridge Alectoris rufa plays a crucial role in the ecosystem of southwestern Europe, and understanding its genetics is vital for conservation and management. Here we sequence, assemble, and annotate a highly contiguous and nearly complete version of its genome. This assembly encompasses 96.9% of the avian genes flagged as essential in the BUSCO aves_odb10 dataset. Moreover, we pinpointed RNA and protein-coding genes, 95% of which had functional annotations. Notably, we observed significant chromosome rearrangements in comparison to quail (Coturnix japonica) and chicken (Gallus gallus). In addition, a comparative phylogenetic analysis of these genomes suggests that A. rufa and C. japonica diverged roughly 20 million years ago and that their common ancestor diverged from G. gallus 35 million years ago. Our assembly represents a significant advancement towards a complete reference genome for A. rufa, facilitating comparative avian genomics, and providing a valuable resource for future research and conservation efforts for the red-legged partridge.
Hybrid assembly and comparative genomics unveil insights into the evolution and biology of the red-legged partridge
Scientific Reports 14: 19531
doi: 10.1038/s41598-024-70018-0
The red-legged partridge Alectoris rufa plays a crucial role in the ecosystem of southwestern Europe, and understanding its genetics is vital for conservation and management. Here we sequence, assemble, and annotate a highly contiguous and nearly complete version of its genome. This assembly encompasses 96.9% of the avian genes flagged as essential in the BUSCO aves_odb10 dataset. Moreover, we pinpointed RNA and protein-coding genes, 95% of which had functional annotations. Notably, we observed significant chromosome rearrangements in comparison to quail (Coturnix japonica) and chicken (Gallus gallus). In addition, a comparative phylogenetic analysis of these genomes suggests that A. rufa and C. japonica diverged roughly 20 million years ago and that their common ancestor diverged from G. gallus 35 million years ago. Our assembly represents a significant advancement towards a complete reference genome for A. rufa, facilitating comparative avian genomics, and providing a valuable resource for future research and conservation efforts for the red-legged partridge.
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