Peter Kovalik
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AOS 2018 Annual Conference (1 Viewer)
- Thread starter Peter Kovalik
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Peter Kovalik
Well-known member
Sumudu W Fernando, Shou-Hsien Li, Andrew Townsend Peterson
Reconstructing the geographic origin of the New World jays
The New World jays (NWJs) are a monophyletic lineage of corvids, presently considered to comprise 7 genera and 36 species, and represent the product of a radiation across much of the Americas. The group has long been a focus of research in behavioral ecology, in light of complex behavioral repertoires, particularly as regards social behavior. Several previous studies have examined NWJ evolutionary history, and biogeography, but invariably have been based on sparse representation of NWJ genera and limited outgroup sampling. This sampling has indeed been too thin to permit a thorough understanding of the geographic origin of NWJs, particularly in terms of representation of the deepest branches of the corvid phylogeny. Hence, we derived a denser phylogenetic hypothesis by deriving DNA sequences for the key early lineages, to permit development of more robust biogeographic analyses regarding the geographic origin of the NWJ clade. We produced a multilocus phylogeny from sequences of three nuclear introns and three mitochondrial genes, and included at least one species from each NWJ genus and 29 species representing the rest of the five corvid subfamilies in the analysis. We used S-DIVA, S-DEC, and BBM analyses implemented in RASP to create biogeographic reconstructions, and BEAST to estimate timing of NWJ diversification. Biogeographic reconstructions indicated that NWJs originated from an ancestor in the Eastern Palearctic or Eastern + Western Palearctic, diversified in Mesoamerica and spread to North and South America subsequently; our analysis indicates that the group has been diversifying in the New World since the late Miocene.
Antonio Arnaiz-Villena, Cristina Campos, Ester Muniz, Jose Palacio-Gruber, Valentin Ruiz-del.Valle
Definition of arid-Zone Carduelini Finches by DNA Phylogeography:American and Asian G. Carpodacus is Taxonomically Split
A group of bird species included within the Carduelini tribe (genera Rhodopechys, Carpodacus and Leucosticte) belongs to the same radiation according to molecular phylogenetic analyses. Our phylogenetic analyses based on nucleotide sequences of the cytochrome b gene (cyt-b) indicate that some of these species (Rhodopechys mongolica, R. githaginea and Carpodacus nipalensis) do not cluster together with their respective phenetically defined allies. Thus, a new group of birds thrives in both hot and cold arid zones and are phenetically distinct, probably because of their adaptation to different extreme environments but may be considered as a new Genus group.. Both maximum likelihood and Bayesian inference methods support the existence of this new evolutionary basal group among finches which might have originated about 14 MYA. A redefinition of genus Carpodacus is needed: one American, and one different Eurasian evolutionary group at least. Also, a new definition of genus Rhodopechys is found: Rhodopechys obsoleta is a greenfinch ancestor, while R. githaginea and mongolica, along with Carpodacus nipalensis, Leucosticte arctoa, and L. tephrocotis, at least, are the “Arid Zone” group of finches defined in this work. The possibility of existence of more phylogenetic splits within genus Carpodacus is put forward.
Lukas J Musher, Anya Auerbach, Joel Cracraft, Jessica Shearer McKay
Testing the ancient Amazonian origins of a group of open-habitat suboscine birds (Pachyramphus)
The open and semi-open habitats of the Neotropics harbor a large portion of South America's endemic biodiversity, yet the biogeographic history of these regions is poorly-studied when compared with other high biodiversity regions. As the South American continent dried during the Miocene, large swaths of open habitat developed across the continent, perhaps facilitating the diversification of many open-habitat groups of organisms. Around the same time, the ancient Amazonian landscape was dominated by a wetland system that likely consisted of open-canopy environments similar to the Pantanal today. How these changing habitats affected diversification in organisms that specialize on open habitats across the Neotropics is uncertain. One clade of birds that is common in open habitats is the becards (Pachyramphus). Using this genus as a case study, we evaluated the clocklike tendency of over 4,000 genomic markers, and used the most clocklike loci to (1) estimate the timing of divergence events across the tree, (2) model the biogeographic and ecological history through time, and (3) test the hypothesis that either the ancient Amazon or arid corridor were diversification sources for open-biome diversity in the Neotropics. We found that Pachyramphus originated in Amazonian open habitats during the late Miocene, and showed higher rates of in situ diversification within the Amazon than other regions. These results suggest that ancient Amazonia served as a source for Pachyramphus diversity.
Jenna M McCullough, Michael J Andersen, Robert G Moyle, Brian T Smith
Biogeography and trait evolution of the pantropical avian order Coraciiformes
Factors ranging from large-scale environmental change to local resource competition can drive diversification within groups of organisms. Determining the drivers of diversification requires the reconciliation of biogeography with niche and trait evolution in a phylogenomic framework. Though the avian order Coraciiformes (kingfishers, motmots, bee-eaters, and allies) has radiated into assemblages with diverse ecologies and morphological characteristics, the group lacks a coherent species tree in which to study the evolutionary dynamics and disparate species richness of the order. This study investigates species-level diversification dynamics using the first species-level, time-calibrated phylogeny of Coraciiformes. We used ultraconserved elements (UCEs) and high-throughput sequencing to produce a 75\% complete matrix of over 3,061 loci totaling 1.6 Mb. Our dataset comprised all 177 extant species currently recognized by the IOC checklist (v 7.1). We recovered a time-calibrated species tree based on stem- and crown-group fossils of rollers, todies, motmots, and kingfishers. We used BioGeoBears to investigate the biogeographic origins of the group since its divergence from Piciformes during the Eocene, as well as to explore patterns of global colonization. To better understand trait evolution of bills (a trait intimately tied to a species' niche) within the order, we discuss morphometric analyses of linear bill measurements. Finally, we review novel species limits revealed by our analysis and discuss the extent of selective forces that have shaped diversification dynamics within Coraciiformes.
David P Mindell, Jérôme Fuchs, Jeff A. Johnson
Phylogeny, taxonomy and geographic diversity of diurnal raptors
We present analyses of phylogeny and classification for diurnal raptors (Accipitriformes, Cathartiformes, Falconiformes). This includes equilibration of orders and families by age, and new supermatrix analyses of published DNA sequences from 10 loci for Accipitriformes. We estimate that divergences within the family Accipitridae began around the Eocene/Oligocene boundary 34 million years ago (mya), with the split of the Elanus/Gampsonyx clade from the other Accipitridae genera. Point estimates for ages of current Accipitridae genera range from 2 to 20 mya. This fits a broad pattern of age inconsistency for avian genera. In our phylogenetic analyses of 33 of 51 (65\%) currently recognized Accipiter species, the genus was found to be non-monophyletic stemming from placement among Accipiter species of eight other Accipitriformes genera (Circus, Megatriorchis, Erythrotriorchis, Melierax, Urotriorchis, Micronisus, Kaupifalco, Harpagus). Taxonomic revisions for Accipitridae genera are warranted, but sampling of taxa remains incomplete. Within Falconiformes, we suggest recognition of Herpetotheridae based on similarity of age to Falconidae. Comprehensive assessment of within species genetic variation has not been done for most diurnal raptor species, and has potential to reveal currently unrecognized species, especially for morphologically distinctive subspecies, geographically isolated populations and polytypic species. We also assess geographic distribution of species richness (SR) and phylogenetic diversity (PD). Accipitriformes has its highest SR and PD measures in African East Sudanian savanna and Victoria Basin forest-savanna. Falconiformes has its highest SR and PD measures in South American Eastern Cordillera real montane forest and Northern Andean páramo eco-regions.
Sarah A. Cowles, J. Albert C. Uy
Genomic Consequences of Secondary Contact in the Kolombangara White-eyes
Examining what happens when two closely-related species come into secondary contact provides unique insights into the final stages of the speciation process. The Zosterops genus of birds is one of the most rapidly speciating vertebrate lineages. Members of this speciose genus, however, are highly vagile and are geographically widespread, begging the question of how divergence can occur if populations can easily come into contact. On the small, mountainous island of Kolombangara within the New Georgia Province of the Solomon Islands, two closely-related non-sister species of White-eyes, Z. kulambangrae and Z. murphyi, are distributed along an elevational gradient, with one species endemic to high altitude while the other is found in lower elevations. At mid-elevation, the two species come into secondary contact. Over the summers of 2016-2017, we captured 134 individuals of both species along two elevational transects on different slopes of Kolombangara Island. Using genotype-by-sequencing SNP data, we find evidence of past hybridization events and the persistence of present-day species boundaries. This evidence for limited hybridization at the contact zone from nuclear markers is consistent with patterns from mitochondrial markers. We explore potential reproductive barriers that allow the two species to coexist in sympatry, including premating isolation based on divergence in plumage color and body size.
Daniel Kenneth Pierce, Alan Brelsford, Darren E. Irwin, David P. L. Toews
Barriers to gene flow and speciation in the yellow-rumped warbler
Identifying regions of the genome involved in speciation remains an important area of research in biology. Early work has focused on regions of the genome that are highly differentiated between species. These regions of high differentiation may be misleading, however, since heterogeneity in allele frequency can be produced by factors not related to divergence with gene flow such as drift and local adaptation in allopatry. We obtained sequence data on single-nucleotide polymorphisms (SNPs) via genotyping-by-sequencing from a natural hybrid zone between myrtle and Audubon's warblers (Setophaga coronata coronata \& S. c. auduboni). We fit clines to SNPs with a difference in allele frequency greater than 20\% between allopatric populations with hzar (hybrid zone analysis using R) and used these data to analyze the movement of alleles across the hybrid zone. In this study, we find evidence of a general barrier to gene flow for the majority of the genome and a small number of loci that experience higher and asymmetric introgression from myrtle to Audubon's warblers. Clusters of these higher introgression loci are found on every chromosome. We also find that clines do not differ between SNPs that lie on the Z chromosome and autosomal SNPs, suggesting that sex-linkage is not an important factor affecting gene flow between these species. By characterizing patterns of introgression across natural hybrid zones, we can gain insight into the process of speciation and the nature of genetic barriers to gene flow.
Thilina Nethmin De Silva, Andrew Townsend Peterson
Phylogenetic relationships of weaverbirds: A first species-level molecular phylogeny of the family Ploceidae
Weaverbirds are small-to-medium-sized, mostly seed-eating songbirds distributed mostly in Sub-Saharan Africa; a few species are found in tropical Asia and on islands in the Indian Ocean. The group comprises 116 species in 17 genera. The family shows intriguing variation in behavior, nest structure, and plumage coloration, yet their relationships have seen no comprehensive phylogenetic study. We developed a first near-species-level phylogeny for the family Ploceidae, including 95\% of species, based on a multilocus dataset of four mitochondrial loci and five nuclear markers. Our analyses found strong support for monophyly of the family, revealing eight distinct clades within the Ploceidae. Results indicated broad polyphyly of Ploceus sensu lato: Asian Ploceus species retain the generic name, whereas African Ploceus, together with Anaplectes, would be placed in Malimbus. In light of deep divergence, we assign the Ploceus species of Madagascar to their own genus, Nelicurvius. We place Amblyospiza albifrons in a reestablished monotypic subfamily Amblyospizinae based on our DNA data, and also considering behavior and morphology. The study further revealed that Histurgops ruficauda is a weaver species originating early in the family's history, and all ploceid genera were placed on the family tree. Divergence time analysis based on DNA substitution rates suggests a mid-Miocene origin of the family. Our study also estimates that brood parasitic behavior originated 8–11 million years ago in African finches, considerably later than previously thought. This study lays a comprehensive foundation to an array of future studies of character evolution, biogeography, and evolutionary history in the family.
Peter Houde, Siavash Mir Arabbaygi (Mirarab), Edward L Braun
Phylogeny of avian orders based on genome-wide coalescent analysis of insertion/deletion mutations (indels)
Jarvis et al 2014 presented an interordinal phylogeny of birds estimated using the MP-EST* multispecies coalescent (MSC) from 2022 binned gene trees built from 14,446 exonic, intronic, and UCE loci. MSC analyses are a class of methods designed to overcome gene tree conflict accruing from the vagaries of segregation and incomplete lineage sorting (ILS). While gene tree conflict may represent truly distinct evolutionary histories of different genes, it may also result from incorrectly reconstructed gene phylogenies. Gene phylogenies maybe particularly susceptible because there are often insufficient phylogenetically informative characters in short, selectively constrained gene sequences to resolve all nodes in large phylogenies. Structural variants (SV), like indels, could complement nucleotide data. Indeed, Jarvis et al 2014 presented a maximum likelihood analysis of concatenated indel data. We reanalyzed 2,515 binned indel gene trees using the MSC ASTRAL program modified for binary indel data. We recover a well-resolved and strongly-supported phylogeny that is highly congruent with that produced using nucleotide sequence data. Interestingly, we detected high levels of gene tree conflict, especially on short internodes. While this is consistent with ILS, we caution that the input data for ASTRAL consist of indel trees, which, like gene trees, may be poorly resolved. We envision methods by which indels may be filtered for reliability and treated as discrete character data rather than tree data, circumventing a potential source of error in the MSC approach. We conclude that indels and other SVs will provide valuable phylogenetic data that will improve future phylogenomic analyses.
Libby C. Megna, Matthew D. Carling
Genome-wide patterns of divergence in Passerina and Cyanocompsa buntings
Recently, genomic datasets have been harnessed to elucidate the underlying genetic architecture of speciation and thus can illuminate important evolutionary processes. Here, we take a novel approach to correlate patterns of genome-wide divergence with degree of reproductive isolation among three closely related species pairs within Cardinalidae (Aves: Passeriformes). These species pairs represent varying degrees of reproductive isolation (hybridizing vs. non-hybridizing) and different geographic relationships (allopatric vs. sympatric). Our study provides empirical data to inform theory of genome-wide divergence by making comparisons of 1) different geographic outcomes of speciation, and 2) different levels of reproductive isolation upon secondary contact. We first generated a reference genome for Passerina amoena. Our sequencing generated 760 million reads; the resultant assembly is 0.92 Gb with a contig N50 of 62.7 kb. We will align whole-genome resequencing data (1.5 billion reads) from 56 individuals of P. amoena, P. cyanea, P. ciris, P. versicolor, Cyanocompsa parellina, and C. brissonii to this reference. P. amoena and P. cyanea hybridize extensively in the Great Plains, while P. ciris and P. versicolor do not hybridize despite sympatry in Texas and Mexico. The Cyanocompsa species are completely allopatric. We will quantify patterns of genome-wide divergence for these species pairs and identify specific genomic divergence patterns associated with degree of reproductive isolation by comparing among species pairs. For example, comparing the location of divergence peaks between the hybridizing, sympatric species pair to those between the non-hybridizing, sympatric species pair will allow us to investigate how gene flow impacts patterns of genome-wide divergence.
etc.
Reconstructing the geographic origin of the New World jays
The New World jays (NWJs) are a monophyletic lineage of corvids, presently considered to comprise 7 genera and 36 species, and represent the product of a radiation across much of the Americas. The group has long been a focus of research in behavioral ecology, in light of complex behavioral repertoires, particularly as regards social behavior. Several previous studies have examined NWJ evolutionary history, and biogeography, but invariably have been based on sparse representation of NWJ genera and limited outgroup sampling. This sampling has indeed been too thin to permit a thorough understanding of the geographic origin of NWJs, particularly in terms of representation of the deepest branches of the corvid phylogeny. Hence, we derived a denser phylogenetic hypothesis by deriving DNA sequences for the key early lineages, to permit development of more robust biogeographic analyses regarding the geographic origin of the NWJ clade. We produced a multilocus phylogeny from sequences of three nuclear introns and three mitochondrial genes, and included at least one species from each NWJ genus and 29 species representing the rest of the five corvid subfamilies in the analysis. We used S-DIVA, S-DEC, and BBM analyses implemented in RASP to create biogeographic reconstructions, and BEAST to estimate timing of NWJ diversification. Biogeographic reconstructions indicated that NWJs originated from an ancestor in the Eastern Palearctic or Eastern + Western Palearctic, diversified in Mesoamerica and spread to North and South America subsequently; our analysis indicates that the group has been diversifying in the New World since the late Miocene.
Antonio Arnaiz-Villena, Cristina Campos, Ester Muniz, Jose Palacio-Gruber, Valentin Ruiz-del.Valle
Definition of arid-Zone Carduelini Finches by DNA Phylogeography:American and Asian G. Carpodacus is Taxonomically Split
A group of bird species included within the Carduelini tribe (genera Rhodopechys, Carpodacus and Leucosticte) belongs to the same radiation according to molecular phylogenetic analyses. Our phylogenetic analyses based on nucleotide sequences of the cytochrome b gene (cyt-b) indicate that some of these species (Rhodopechys mongolica, R. githaginea and Carpodacus nipalensis) do not cluster together with their respective phenetically defined allies. Thus, a new group of birds thrives in both hot and cold arid zones and are phenetically distinct, probably because of their adaptation to different extreme environments but may be considered as a new Genus group.. Both maximum likelihood and Bayesian inference methods support the existence of this new evolutionary basal group among finches which might have originated about 14 MYA. A redefinition of genus Carpodacus is needed: one American, and one different Eurasian evolutionary group at least. Also, a new definition of genus Rhodopechys is found: Rhodopechys obsoleta is a greenfinch ancestor, while R. githaginea and mongolica, along with Carpodacus nipalensis, Leucosticte arctoa, and L. tephrocotis, at least, are the “Arid Zone” group of finches defined in this work. The possibility of existence of more phylogenetic splits within genus Carpodacus is put forward.
Lukas J Musher, Anya Auerbach, Joel Cracraft, Jessica Shearer McKay
Testing the ancient Amazonian origins of a group of open-habitat suboscine birds (Pachyramphus)
The open and semi-open habitats of the Neotropics harbor a large portion of South America's endemic biodiversity, yet the biogeographic history of these regions is poorly-studied when compared with other high biodiversity regions. As the South American continent dried during the Miocene, large swaths of open habitat developed across the continent, perhaps facilitating the diversification of many open-habitat groups of organisms. Around the same time, the ancient Amazonian landscape was dominated by a wetland system that likely consisted of open-canopy environments similar to the Pantanal today. How these changing habitats affected diversification in organisms that specialize on open habitats across the Neotropics is uncertain. One clade of birds that is common in open habitats is the becards (Pachyramphus). Using this genus as a case study, we evaluated the clocklike tendency of over 4,000 genomic markers, and used the most clocklike loci to (1) estimate the timing of divergence events across the tree, (2) model the biogeographic and ecological history through time, and (3) test the hypothesis that either the ancient Amazon or arid corridor were diversification sources for open-biome diversity in the Neotropics. We found that Pachyramphus originated in Amazonian open habitats during the late Miocene, and showed higher rates of in situ diversification within the Amazon than other regions. These results suggest that ancient Amazonia served as a source for Pachyramphus diversity.
Jenna M McCullough, Michael J Andersen, Robert G Moyle, Brian T Smith
Biogeography and trait evolution of the pantropical avian order Coraciiformes
Factors ranging from large-scale environmental change to local resource competition can drive diversification within groups of organisms. Determining the drivers of diversification requires the reconciliation of biogeography with niche and trait evolution in a phylogenomic framework. Though the avian order Coraciiformes (kingfishers, motmots, bee-eaters, and allies) has radiated into assemblages with diverse ecologies and morphological characteristics, the group lacks a coherent species tree in which to study the evolutionary dynamics and disparate species richness of the order. This study investigates species-level diversification dynamics using the first species-level, time-calibrated phylogeny of Coraciiformes. We used ultraconserved elements (UCEs) and high-throughput sequencing to produce a 75\% complete matrix of over 3,061 loci totaling 1.6 Mb. Our dataset comprised all 177 extant species currently recognized by the IOC checklist (v 7.1). We recovered a time-calibrated species tree based on stem- and crown-group fossils of rollers, todies, motmots, and kingfishers. We used BioGeoBears to investigate the biogeographic origins of the group since its divergence from Piciformes during the Eocene, as well as to explore patterns of global colonization. To better understand trait evolution of bills (a trait intimately tied to a species' niche) within the order, we discuss morphometric analyses of linear bill measurements. Finally, we review novel species limits revealed by our analysis and discuss the extent of selective forces that have shaped diversification dynamics within Coraciiformes.
David P Mindell, Jérôme Fuchs, Jeff A. Johnson
Phylogeny, taxonomy and geographic diversity of diurnal raptors
We present analyses of phylogeny and classification for diurnal raptors (Accipitriformes, Cathartiformes, Falconiformes). This includes equilibration of orders and families by age, and new supermatrix analyses of published DNA sequences from 10 loci for Accipitriformes. We estimate that divergences within the family Accipitridae began around the Eocene/Oligocene boundary 34 million years ago (mya), with the split of the Elanus/Gampsonyx clade from the other Accipitridae genera. Point estimates for ages of current Accipitridae genera range from 2 to 20 mya. This fits a broad pattern of age inconsistency for avian genera. In our phylogenetic analyses of 33 of 51 (65\%) currently recognized Accipiter species, the genus was found to be non-monophyletic stemming from placement among Accipiter species of eight other Accipitriformes genera (Circus, Megatriorchis, Erythrotriorchis, Melierax, Urotriorchis, Micronisus, Kaupifalco, Harpagus). Taxonomic revisions for Accipitridae genera are warranted, but sampling of taxa remains incomplete. Within Falconiformes, we suggest recognition of Herpetotheridae based on similarity of age to Falconidae. Comprehensive assessment of within species genetic variation has not been done for most diurnal raptor species, and has potential to reveal currently unrecognized species, especially for morphologically distinctive subspecies, geographically isolated populations and polytypic species. We also assess geographic distribution of species richness (SR) and phylogenetic diversity (PD). Accipitriformes has its highest SR and PD measures in African East Sudanian savanna and Victoria Basin forest-savanna. Falconiformes has its highest SR and PD measures in South American Eastern Cordillera real montane forest and Northern Andean páramo eco-regions.
Sarah A. Cowles, J. Albert C. Uy
Genomic Consequences of Secondary Contact in the Kolombangara White-eyes
Examining what happens when two closely-related species come into secondary contact provides unique insights into the final stages of the speciation process. The Zosterops genus of birds is one of the most rapidly speciating vertebrate lineages. Members of this speciose genus, however, are highly vagile and are geographically widespread, begging the question of how divergence can occur if populations can easily come into contact. On the small, mountainous island of Kolombangara within the New Georgia Province of the Solomon Islands, two closely-related non-sister species of White-eyes, Z. kulambangrae and Z. murphyi, are distributed along an elevational gradient, with one species endemic to high altitude while the other is found in lower elevations. At mid-elevation, the two species come into secondary contact. Over the summers of 2016-2017, we captured 134 individuals of both species along two elevational transects on different slopes of Kolombangara Island. Using genotype-by-sequencing SNP data, we find evidence of past hybridization events and the persistence of present-day species boundaries. This evidence for limited hybridization at the contact zone from nuclear markers is consistent with patterns from mitochondrial markers. We explore potential reproductive barriers that allow the two species to coexist in sympatry, including premating isolation based on divergence in plumage color and body size.
Daniel Kenneth Pierce, Alan Brelsford, Darren E. Irwin, David P. L. Toews
Barriers to gene flow and speciation in the yellow-rumped warbler
Identifying regions of the genome involved in speciation remains an important area of research in biology. Early work has focused on regions of the genome that are highly differentiated between species. These regions of high differentiation may be misleading, however, since heterogeneity in allele frequency can be produced by factors not related to divergence with gene flow such as drift and local adaptation in allopatry. We obtained sequence data on single-nucleotide polymorphisms (SNPs) via genotyping-by-sequencing from a natural hybrid zone between myrtle and Audubon's warblers (Setophaga coronata coronata \& S. c. auduboni). We fit clines to SNPs with a difference in allele frequency greater than 20\% between allopatric populations with hzar (hybrid zone analysis using R) and used these data to analyze the movement of alleles across the hybrid zone. In this study, we find evidence of a general barrier to gene flow for the majority of the genome and a small number of loci that experience higher and asymmetric introgression from myrtle to Audubon's warblers. Clusters of these higher introgression loci are found on every chromosome. We also find that clines do not differ between SNPs that lie on the Z chromosome and autosomal SNPs, suggesting that sex-linkage is not an important factor affecting gene flow between these species. By characterizing patterns of introgression across natural hybrid zones, we can gain insight into the process of speciation and the nature of genetic barriers to gene flow.
Thilina Nethmin De Silva, Andrew Townsend Peterson
Phylogenetic relationships of weaverbirds: A first species-level molecular phylogeny of the family Ploceidae
Weaverbirds are small-to-medium-sized, mostly seed-eating songbirds distributed mostly in Sub-Saharan Africa; a few species are found in tropical Asia and on islands in the Indian Ocean. The group comprises 116 species in 17 genera. The family shows intriguing variation in behavior, nest structure, and plumage coloration, yet their relationships have seen no comprehensive phylogenetic study. We developed a first near-species-level phylogeny for the family Ploceidae, including 95\% of species, based on a multilocus dataset of four mitochondrial loci and five nuclear markers. Our analyses found strong support for monophyly of the family, revealing eight distinct clades within the Ploceidae. Results indicated broad polyphyly of Ploceus sensu lato: Asian Ploceus species retain the generic name, whereas African Ploceus, together with Anaplectes, would be placed in Malimbus. In light of deep divergence, we assign the Ploceus species of Madagascar to their own genus, Nelicurvius. We place Amblyospiza albifrons in a reestablished monotypic subfamily Amblyospizinae based on our DNA data, and also considering behavior and morphology. The study further revealed that Histurgops ruficauda is a weaver species originating early in the family's history, and all ploceid genera were placed on the family tree. Divergence time analysis based on DNA substitution rates suggests a mid-Miocene origin of the family. Our study also estimates that brood parasitic behavior originated 8–11 million years ago in African finches, considerably later than previously thought. This study lays a comprehensive foundation to an array of future studies of character evolution, biogeography, and evolutionary history in the family.
Peter Houde, Siavash Mir Arabbaygi (Mirarab), Edward L Braun
Phylogeny of avian orders based on genome-wide coalescent analysis of insertion/deletion mutations (indels)
Jarvis et al 2014 presented an interordinal phylogeny of birds estimated using the MP-EST* multispecies coalescent (MSC) from 2022 binned gene trees built from 14,446 exonic, intronic, and UCE loci. MSC analyses are a class of methods designed to overcome gene tree conflict accruing from the vagaries of segregation and incomplete lineage sorting (ILS). While gene tree conflict may represent truly distinct evolutionary histories of different genes, it may also result from incorrectly reconstructed gene phylogenies. Gene phylogenies maybe particularly susceptible because there are often insufficient phylogenetically informative characters in short, selectively constrained gene sequences to resolve all nodes in large phylogenies. Structural variants (SV), like indels, could complement nucleotide data. Indeed, Jarvis et al 2014 presented a maximum likelihood analysis of concatenated indel data. We reanalyzed 2,515 binned indel gene trees using the MSC ASTRAL program modified for binary indel data. We recover a well-resolved and strongly-supported phylogeny that is highly congruent with that produced using nucleotide sequence data. Interestingly, we detected high levels of gene tree conflict, especially on short internodes. While this is consistent with ILS, we caution that the input data for ASTRAL consist of indel trees, which, like gene trees, may be poorly resolved. We envision methods by which indels may be filtered for reliability and treated as discrete character data rather than tree data, circumventing a potential source of error in the MSC approach. We conclude that indels and other SVs will provide valuable phylogenetic data that will improve future phylogenomic analyses.
Libby C. Megna, Matthew D. Carling
Genome-wide patterns of divergence in Passerina and Cyanocompsa buntings
Recently, genomic datasets have been harnessed to elucidate the underlying genetic architecture of speciation and thus can illuminate important evolutionary processes. Here, we take a novel approach to correlate patterns of genome-wide divergence with degree of reproductive isolation among three closely related species pairs within Cardinalidae (Aves: Passeriformes). These species pairs represent varying degrees of reproductive isolation (hybridizing vs. non-hybridizing) and different geographic relationships (allopatric vs. sympatric). Our study provides empirical data to inform theory of genome-wide divergence by making comparisons of 1) different geographic outcomes of speciation, and 2) different levels of reproductive isolation upon secondary contact. We first generated a reference genome for Passerina amoena. Our sequencing generated 760 million reads; the resultant assembly is 0.92 Gb with a contig N50 of 62.7 kb. We will align whole-genome resequencing data (1.5 billion reads) from 56 individuals of P. amoena, P. cyanea, P. ciris, P. versicolor, Cyanocompsa parellina, and C. brissonii to this reference. P. amoena and P. cyanea hybridize extensively in the Great Plains, while P. ciris and P. versicolor do not hybridize despite sympatry in Texas and Mexico. The Cyanocompsa species are completely allopatric. We will quantify patterns of genome-wide divergence for these species pairs and identify specific genomic divergence patterns associated with degree of reproductive isolation by comparing among species pairs. For example, comparing the location of divergence peaks between the hybridizing, sympatric species pair to those between the non-hybridizing, sympatric species pair will allow us to investigate how gene flow impacts patterns of genome-wide divergence.
etc.
Jim LeNomenclatoriste
Je suis un mignon petit Traquet rubicole
omg, omg, omg, I suppose it is impossible to read these works?
These were talks at a conference. Patience, as getting them to print can take a while.
mb1848
Well-known member
Looking at the AOS website about the April meeting I was saddened to read about the death of James D. Rising.
http://www.legacy.com/obituaries/thestar/obituary.aspx?n=james-david-rising&pid=188478571 .
https://amornithnews.org/2018/05/03...newly-inaugurated-aos-president-kathy-martin/ .
http://www.legacy.com/obituaries/thestar/obituary.aspx?n=james-david-rising&pid=188478571 .
https://amornithnews.org/2018/05/03...newly-inaugurated-aos-president-kathy-martin/ .
Jim LeNomenclatoriste
Je suis un mignon petit Traquet rubicole
Are these conferences filmed?
Daniel Philippe
Well-known member
Sumudu W.F., Peterson A.T. & Li S.-H., 2017. Reconstructing the geographic origin of the New World jays. Neotrop. Biodivers. 3 (1): 80-92.
Toews, D.P.L., Brelsford A., Grossen C., Milá B. & Irwin D., 2016. Genomic variation across the Yellow-rumped Warbler species complex. Auk 133 (4): 698-717.
de Silva T.N., Peterson A.T., Fernando S.W., Bates J.M., Marks B.D. & Girard M., 2017. Phylogenetic relationships of weaverbirds (Aves: Ploceidae): A first robust phylogeny based on mitochondrial and nuclear markers. Mol. Phylogen. Evol. 109: 21-32.
etc.
Mysticete
Well-known member
People generally don't like to mass disseminate the unpublished results presented in talks for various reasons:
A: It's a talk: the results are often varying degrees of incomplete, and further analysis may reveal completely different results. Even if the data is incomplete, a 15 minute talk can't really go into the details that a full manuscript can.
B: the results presented are often the result of granted funded research, that folks would often like to keep on the downlow. Mass dissemination of this research at early stages can undermine attempts to publish in higher impact journal, or result in less ethical researchers taking the data presented and publishing first.
But on the other hand: in some contexts, a result that has been talked about at a conference is already considered published. For example, you cannot patent something if a part of it has been talked about at a conference. I have also seen conferences where you cannot get on the agenda unless you provide what essentially becomes a short paper in the conference proceedings.
Niels
Mysticete
Well-known member
True...I am only giving my perspective as someone who attends Vert Paleo meetings. At any rate, I would view any result in an abstract with great caution. Some of those abstracts are based off of months of hard work with a paper in the pipeline. Some of those other abstracts might literally have had their results thrown together hours before the abstract deadline. At least that is true of many of my colleagues in paleontology
True...I am only giving my perspective as someone who attends Vert Paleo meetings. At any rate, I would view any result in an abstract with great caution. Some of those abstracts are based off of months of hard work with a paper in the pipeline. Some of those other abstracts might literally have had their results thrown together hours before the abstract deadline. At least that is true of many of my colleagues in paleontology
True also for most ornithology meetings. In anthropology, presented papers are often written out before presenting and published at such. The presentations, however, are often terrible in person, when the paper is drolly read.
Andy
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