Species limits and cryptic biogeographic structure in a widespread complex of Australian monsoon tropics trees (broad-leaf paperbarks: Melaleuca, Myrtaceae)

2018 ◽  
Author(s):  
Robert D. Edwards ◽  
Michael D. Crisp ◽  
Lyn G. Cook
Keyword(s):  
Incomplete Lineage Sorting ◽  
Phylogeographic Structure ◽  
Lineage Sorting ◽  
Species Limits ◽  
Widespread Species ◽  
Australian Monsoon ◽  
Network Analyses ◽  
The North ◽  
Broad Leaf ◽  
Drying Trend

The Australian monsoon tropics are currently dominated by savanna and tropical woodland biomes that have arisen in response to a cooling and drying trend within the past ~3 million years. It is expected that organisms well adapted to these conditions have expanded into available habitats, leading to the differentiation of populations and species across this landscape, a process that could be magnified by the presence of several biogeographic barriers. The broad-leaved paperbark (Melaleuca leucadendra (L.) L.) complex is one such group of plants, with 14 poorly morphologically differentiated species occupying large overlapping distributions across the region, and across several recognised biogeographic barriers. Using phylogenetic and network analyses of nuclear and plastid sequences, we tested species limits among currently described species within the complex and for phylogeographic structure within species across seven of these barriers. Overall, our data suggested patterns of differentiation among species consistent with the early to middle stages of incomplete lineage sorting, and evidence for an idiosyncratic cryptic response of species to biogeographic barriers. Unexpectedly, we found a deep molecular split across all species, broadly coinciding with the northern part of the Great Dividing Range, a feature not typically considered to be a barrier to dispersal. Our study has offered one of the first insights into the dynamics within and among widespread species across the north of Australia, suggesting considerably more geographic structure than was previously recognised.

scholarly journals Cytonuclear discordance in the crowned-sparrows, Zonotrichia atricapilla and Zonotrichia leucophrys: a mitochondrial selective sweep?

2020 ◽  
Author(s):  
Rebecca S. Taylor ◽  
Ashley C. Bramwell ◽  
Rute Clemente-Carvalho ◽  
Nicholas A. Cairns ◽  
Frances Bonier ◽  
...  
Keyword(s):  
Mitochondrial Dna ◽  
Environmental Changes ◽  
Incomplete Lineage Sorting ◽  
Mitochondrial Gene ◽  
Nuclear Gene ◽  
Phylogeographic Structure ◽  
Gene Trees ◽  
Lineage Sorting ◽  
Reciprocal Monophyly ◽  
Mitochondrial Introgression

ABSTRACTThe golden-crowned (Zonotrichia atricapilla) and white-crowned (Z. leucophrys) sparrows have been presented as a compelling case for rapid speciation. They display divergence in song and plumage with overlap in their breeding ranges implying reproductive isolation, but have almost identical mitochondrial genomes. Previous research proposed hybridization and subsequent mitochondrial introgression as an alternate explanation, but lacked robust nuclear gene trees to distinguish between introgression and incomplete lineage sorting. We test for signatures of these processes between Z. atricapilla and Z. leucophrys, and investigate the relationships among Z. leucophrys subspecies, using mitochondrial sequencing and a reduced representation nuclear genomic dataset. Contrary to the paraphyly evident in mitochondrial gene trees, we confirmed the reciprocal monophyly of Z. atricapilla and Z. leucophrys using large panels of single nucleotide polymorphism (SNPs). The pattern of cytonuclear discordance is consistent with limited, historical hybridization and mitochondrial introgression, rather than a recent origin and incomplete lineage sorting between recent sister species. We found evidence of nuclear phylogeographic structure within Z. leucophrys with two distinct clades. Altogether, our results support the true species status of Z. atricapilla and Z. leucophrys, and indicate deeper divergences between the two species than inferred using mitochondrial markers. Our results demonstrate the limitations of relying solely on mitochondrial DNA for taxonomy, and raise questions about the possibility of selection on the mitochondrial genome during temperature oscillations (e.g. during the Pleistocene). Historical mitochondrial introgression facilitated by past environmental changes could cause erroneous dating of lineage splitting in other taxa when based on mitochondrial DNA alone.

Molecular systematics and phylogeography of a widespread Neotropical avian lineage: evidence for cryptic speciation with protracted gene flow throughout the Late Quaternary

2020 ◽  
Author(s):  
Leonardo S Miranda ◽  
Bernardo O Prestes ◽  
Alexandre Aleixo
Keyword(s):  
Gene Flow ◽  
Incomplete Lineage Sorting ◽  
Late Quaternary ◽  
Integrative Approach ◽  
Lineage Sorting ◽  
Distribution Models ◽  
The North ◽  
History Of ◽  
Andean South America ◽  
Spatio Temporal

Abstract Here we use an integrative approach, including coalescent-based methods, isolation–migration and species distribution models, to infer population structure, divergence times and diversification in the two species of the genus Cymbilaimus (Aves, Thamnophilidae). Our results support a recent and rapid diversification with both incomplete lineage sorting and gene flow shaping the evolutionary history of Cymbilaimus. The spatio-temporal pattern of cladogenesis suggests that Cymbilaimus originated in the north/western portion of cis-Andean South America and then diversified into the Brazilian Shield and Central America after consolidation of the modern Amazonian drainage and the Andean range. This evolutionary scenario is explained by cycles of range expansion and dispersal, followed by isolation, and recurrent gene flow, during the last 1.2 Myr. Our results agree with those recently reported for other closely related suboscine lineages, whereby the window of introgression between closely related taxa remains open for up to a few million years after their original split. In Cymbilaimus, introgression was recurrent between C. lineatus and C. sanctaemariae, even after they acquired vocal and ecological differentiation, supporting the claim that at least in Neotropical suboscines, full reproductive compatibility may take millions of years to evolve and cannot be interpreted as synonymous with a lack of speciation.

scholarly journals Phylogenomic Analyses Clarify True Species within the Butterfly Genus Speyeria despite Evidence of a Recent Adaptive Radiation

Insects ◽  
2019 ◽  
Vol 10 (7) ◽  
pp. 209
Author(s):  
Erin Thompson ◽  
Jason Baumsteiger ◽  
Ryan I. Hill
Keyword(s):  
Adaptive Radiation ◽  
North American ◽  
Incomplete Lineage Sorting ◽  
Legal Protection ◽  
Evolutionary Model ◽  
Morphological Characters ◽  
Anthropogenic Factors ◽  
Lineage Sorting ◽  
The North ◽  
Phylogenetic Resolution

When confronted with an adaptive radiation, considerable evidence is needed to resolve the evolutionary relationships of these closely related lineages. The North American genus Speyeria is one especially challenging radiation of butterflies due to potential signs of incomplete lineage sorting, ongoing hybridization, and similar morphological characters between species. Previous studies have found species to be paraphyletic and have been unable to disentangle taxa, often due to a lack of data and/or incomplete sampling. As a result, Speyeria remains unresolved. To achieve phylogenetic resolution of the genus, we conducted phylogenomic and population genomic analyses of all currently recognized North American Speyeria species, as well as several subspecies, using restriction-site-associated DNA sequencing (RADseq). Together, these analyses confirm the 16 canonical species, and clarify many internal relationships. However, a few relationships within Speyeria were poorly supported depending on the evolutionary model applied. This lack of resolution among certain taxa corroborates Speyeria is experiencing an ongoing adaptive radiation, with incomplete lineage sorting and lack of postzygotic reproductive barriers contributing to hybridization and further ambiguity. Given that many Speyeria taxa are under duress from anthropogenic factors, their legal protection must be viewed cautiously and on a case by case basis in order to properly conserve the diversity being generated.

Phylogeographical analysis of cpDNA variation in Eucalyptus loxophleba (Myrtaceae)

2004 ◽  
Vol 52 (4) ◽  
pp. 459 ◽  
Author(s):  
M. Byrne ◽  
B. Hines
Keyword(s):  
Western Australia ◽  
Incomplete Lineage Sorting ◽  
Rflp Analysis ◽  
Major Influence ◽  
Arid Zones ◽  
Lineage Sorting ◽  
Ancestral Polymorphism ◽  
Widespread Species ◽  
Dominant Component ◽  
Cp Genome

Comparative phylogeography can reveal significant historical events that have had common influences on species with similar distributions. Phylogeographic analyses of eucalypts should provide insight into the influence of historical processes, since eucalypts are a dominant component of the Australian flora. However, use of chloroplast DNA in eucalypts is complicated by sharing of haplotypes among species, which has been attributed to hybridisation and introgression, although these patterns could also be accounted for by incomplete lineage sorting of ancestral polymorphism. Phylogeographic patterns in the cp genome of E. loxophleba Benth., a widespread species throughout southern Western Australia, were investigated by using RFLP analysis. The chloroplast diversity was structured into two geographically distinct lineages and nested clade analysis inferred historical fragmentation as the major influence on the phylogeographic pattern. The divergence between the lineages and their geographic distributions were similar to geographically discrete divergent lineages that have been identified in two other unrelated species from different families in southern Western Australia. Congruence of phylogeographic patterns in the three species provides evidence to support the hypothesis of significant influence of climatic instability during the Pleistocene caused by cyclic contraction and expansion of the mesic and arid zones.

scholarly journals Robustness of RADseq for evolutionary network reconstruction from gene trees

2018 ◽  
Author(s):  
José Luis Blanco-Pastor ◽  
Yann J.K. Bertrand ◽  
Isabel María Liberal ◽  
Yanling Wei ◽  
E.Charles Brummer ◽  
...  
Keyword(s):  
High Throughput Sequencing ◽  
Incomplete Lineage Sorting ◽  
Molecular Data ◽  
Hybrid Origin ◽  
Gene Trees ◽  
Lineage Sorting ◽  
Network Analyses ◽  
Evolutionary Network ◽  
Complex Patterns ◽  
Evolutionary Networks

AbstractAlthough hybridization has played an important role in the evolution of many species, phylogenetic reconstructions that include hybridizing lineages have been historically constrained by the available models and data. Recently, the combined development of high-throughput sequencing and evolutionary network models offer new opportunities for phylogenetic inference under complex patterns of hybridization in the context of incomplete lineage sorting. Restriction site associated DNA sequencing (RADseq) has been a popular sequencing technique for evolutionary reconstructions of close relatives in the Next Generation Sequencing (NGS) era. However, the utility of RADseq data for the reconstruction of complex evolutionary networks has not been thoroughly discussed. Here, we used new molecular data collected from diploid perennial Medicago species using single-digest RADseq to reconstruct evolutionary networks from gene trees, an approach that is computationally tractable with datasets that include several species and complex patterns of hybridization. Our analyses revealed that complex network reconstructions from RADseq-derived gene trees were not robust under variations of the assembly parameters and filters. Filters to exclusively select loci with high phylogenetic information created datasets that retrieved the most anomalous topologies. Conversely, alternative clustering thresholds or filters on the number of samples per locus affected the level of missing data but had a lower impact on networks. When most anomalous networks were discarded, all remaining network analyses consistently supported a hybrid origin for M. carstiensis and M. cretacea.

scholarly journals Molecular phylogeny and phylogeography of the freshwater-fish genus Pethia (Teleostei: Cyprinidae) in Sri Lanka

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Hiranya Sudasinghe ◽  
Tharindu Ranasinghe ◽  
Jayampathi Herath ◽  
Kumudu Wijesooriya ◽  
Rohan Pethiyagoda ◽  
...  
Keyword(s):  
Sri Lanka ◽  
Incomplete Lineage Sorting ◽  
Phylogenetic Analyses ◽  
Morphological Diversity ◽  
Phylogeographic Structure ◽  
Sri Lankan ◽  
Lineage Sorting ◽  
Multiple Sources ◽  
Reciprocal Monophyly ◽  
Wet Zone

Abstract Background Sri Lanka is a continental island separated from India by the Palk Strait, a shallow-shelf sea, which was emergent during periods of lowered sea level. Its biodiversity is concentrated in its perhumid south-western ‘wet zone’. The island’s freshwater fishes are dominated by the Cyprinidae, characterized by small diversifications of species derived from dispersals from India. These include five diminutive, endemic species of Pethia (P. bandula, P. cumingii, P. melanomaculata, P. nigrofasciata, P. reval), whose evolutionary history remains poorly understood. Here, based on comprehensive geographic sampling, we explore the phylogeny, phylogeography and morphological diversity of the genus in Sri Lanka. Results The phylogenetic analyses, based on mitochondrial and nuclear loci, recover Sri Lankan Pethia as polyphyletic. The reciprocal monophyly of P. bandula and P. nigrofasciata, and P. cumingii and P. reval, is not supported. Pethia nigrofasciata, P. cumingii, and P. reval show strong phylogeographic structure in the wet zone, compared with P. melanomaculata, which ranges across the dry and intermediate zones. Translocated populations of P. nigrofasciata and P. reval in the Central Hills likely originate from multiple sources. Morphological analyses reveal populations of P. nigrofasciata proximal to P. bandula, a narrow-range endemic, to have a mix of characters between the two species. Similarly, populations of P. cumingii in the Kalu basin possess orange fins, a state between the red-finned P. reval from Kelani to Deduru and yellow-finned P. cumingii from Bentara to Gin basins. Conclusions Polyphyly in Sri Lankan Pethia suggests two or three colonizations from mainland India. Strong phylogeographic structure in P. nigrofasciata, P. cumingii and P. reval, compared with P. melanomaculata, supports a model wherein the topographically complex wet zone harbors greater genetic diversity than the topographically uniform dry-zone. Mixed morphological characters between P. bandula and P. nigrofasciata, and P. cumingii and P. reval, and their unresolved phylogenies, may suggest recent speciation scenarios with incomplete lineage sorting, or hybridization.

Genetic divergence and phylogeography of the alpine plant taxon Onobrychis transsilvanica (Fabaceae)

Botany ◽  
2015 ◽  
Vol 93 (5) ◽  
pp. 257-266 ◽  
Author(s):  
Ioan Bãcilã ◽  
Dana Şuteu ◽  
Gheorghe Coldea
Keyword(s):  
Genetic Divergence ◽  
Incomplete Lineage Sorting ◽  
Distinct Species ◽  
Phylogeographic Structure ◽  
Alpine Plant ◽  
Lineage Sorting ◽  
The Carpathians ◽  
The Status ◽  
Plant Taxon ◽  
Divergent Haplotype

Although the Carpathians represent one of the main elements of the European Alpine System and an important area of endemism, only a few phylogeographic studies concerning this region have focused on the detailed intraspecific variation in alpine plant species. Using two molecular marker systems, we (1) aimed to elucidate the controversy concerning the status of the endemic Carpathian taxon Onobrychis transsilvanica Simonk. in relation to the more widespread Onobrychis montana DC. and (2) determined the phylogeographic structure of O. transsilvanica within the Carpathians. For O. transsilvanica, our data suggest either a recent postglacial speciation with incomplete lineage sorting or genetic divergence followed by subsequent continuous gene flow during the glacial period. The genetic structure of the complex does not support O. transsilvanica as a distinct species from O. montana. Within the Carpathians, the extant populations of O. transsilvanica comprise two major allopatric lineages, which have been isolated from each other for a long period of time. Unexpectedly, the major genetic break was not in line with a classical biogeographical boundary in the Carpathians but rather separated a group from the southwestern edge of the mountains. We also discovered an additional divergent haplotype lineage, with weaker genetic support, within the O. transsilvanica populations.

scholarly journals Complete mitochondrial genomes do not distinguish phenotypically distinct lineages of Andean Coeligena hummingbirds

2020 ◽  
Author(s):  
Catalina Palacios ◽  
Leonardo Campagna ◽  
Juan Luis Parra ◽  
Carlos Daniel Cadena
Keyword(s):  
Genetic Differentiation ◽  
Incomplete Lineage Sorting ◽  
Haplotype Network ◽  
Mitochondrial Genomes ◽  
Lineage Sorting ◽  
Evolutionary Mechanisms ◽  
Phenotypic Differences ◽  
Network Analyses ◽  
Alternative Hypotheses ◽  
Complete Mitochondrial Genomes

AbstractLack of divergence in mitochondrial DNA between species with clear phenotypic differences may be the result of low resolution of markers, incomplete lineage sorting, introgression, or the interplay of various evolutionary mechanisms acting on different traits and genomic regions through time. Previous work revealed that the Andean hummingbirds Coeligena bonapartei and C. helianthea lack genetic divergence in the mitochondrial ND2 gene, which shows variation discordant with coloration phenotype but consistent with geography. We sequenced and analyzed complete mitochondrial genomes for C. b. bonapartei, C. b. consita, C. h. helianthea and C. h. tamai to assess whether patterns revealed by ND2 analyses hold when considering the entire mitogenome, and to shed light into the evolutionary history of these hummingbirds. We found very low genetic differentiation in mitogenomes among the four lineages of Coeligena, confirming patterns based on ND2 data. Estimates of genetic differentiation, phylogenies and haplotype network analyses of complete mitogenomes did not separate phenotypically distinct taxa, but were consistent with a previously described pattern of northern vs. southern divergence along the Cordillera Oriental of Colombia. Mitogenomes of C. b. bonapartei and C. h. helianthea are indistinguishable, suggesting incomplete lineage sorting or strong introgression. Mitogenomes of C. b. consita and C. h. tamai are slightly differentiated, but they are more similar to each other than either is to that of its respective nominate subspecies, a result also suggestive of mtDNA introgression despite distinct phenotypic differences. Our results indicate that various evolutionary mechanisms playing out over a complex biogeographic scenario in the Colombian Andes drove divergence in phenotypes and mitochondrial genomes of Coeligena hummingbirds, and lead to alternative hypotheses to be tested with whole-genome analyses.

scholarly journals A phylogenomic perspective on gene tree conflict and character evolution in Caprifoliaceae using target enrichment data, with Zabelioideae recognized as a new subfamily

2020 ◽  
Author(s):  
Hong-Xin Wang ◽  
Diego F. Morales-Briones ◽  
Michael J. Moore ◽  
Jun Wen ◽  
Hua-Feng Wang
Keyword(s):  
Incomplete Lineage Sorting ◽  
Gene Tree ◽  
Nuclear Gene ◽  
Morphological Characters ◽  
Ancestral State ◽  
Target Enrichment ◽  
Lineage Sorting ◽  
Protein Coding ◽  
Network Analyses ◽  
Chloroplast Genomes

AbstractThe use of diverse datasets in phylogenetic studies aiming for understanding evolutionary histories of species can yield conflicting inference. Phylogenetic conflicts observed in animal and plant systems have often been explained by hybridization, incomplete lineage sorting (ILS), or horizontal gene transfer. Here, we employed target enrichment data and species tree and species network approaches to infer the backbone phylogeny of the family Caprifoliaceae, while distinguishing among sources of incongruence. We used 713 nuclear loci and 46 protein-coding sequences of plastome data from 43 samples representing 38 species from all major clades to reconstruct the phylogeny of the group using concatenation and coalescence approaches. We found significant nuclear gene tree conflict as well as cytonuclear discordance. Additionally, coalescent simulations and phylogenetic species network analyses suggest putative ancient hybridization among subfamilies of Caprifoliaceae, which seems to be the main source of phylogenetic discordance. Ancestral state reconstruction of six morphological characters revealed some homoplasy for each character examined. By dating the branching events, we inferred the origin of Caprifoliaceae at approximately 69.38 Ma in the late Cretaceous. By integrating evidence from molecular phylogeny, divergence times, and morphology, we herein recognize Zabelioideae as a new subfamily in Caprifoliaceae. This work shows the necessity to use a combination of multiple approaches to identify the sources of gene tree discordance. Our study also highlights the importance of using data from both nuclear and chloroplast genomes to reconstruct deep and shallow phylogenies of plants.

A chloroplast phylogeny of Zieria (Rutaceae) in Australia and New Caledonia shows widespread incongruence with species-level taxonomy

2014 ◽  
Vol 27 (6) ◽  
pp. 427 ◽  
Author(s):  
Rosemary A. Barrett ◽  
Michael J. Bayly ◽  
Marco F. Duretto ◽  
Paul I. Forster ◽  
Pauline Y. Ladiges ◽  
...  
Keyword(s):  
Nuclear Dna ◽  
New Caledonia ◽  
Incomplete Lineage Sorting ◽  
Species Level ◽  
Lineage Sorting ◽  
Widespread Species ◽  
Geographic Ranges ◽  
Cpdna Markers ◽  
Insight Into ◽  
Chloroplast Phylogeny

This study presents a molecular phylogeny of Zieria Sm., a genus of shrubs and small trees, with 59 species in Australia and one endemic to New Caledonia. The phylogeny is based on four cpDNA markers and 116 samples representing all species of Zieria except one, and the monotypic outgroup Neobyrnesia suberosa. The New Caledonian species, Z. chevalieri, was resolved as sister to a well supported clade of all Australian taxa. There was widespread incongruence between the cpDNA tree and species-level taxonomy, with 14 species shown as polyphyletic or paraphyletic. These included widespread species (e.g. Z. smithii and Z. arborescens, each falling in at least four well supported clades) and some with narrow geographic ranges (e.g. Z. alata and Z. oreocena). No species represented by three or more samples was resolved as monophyletic. We suggest that a combination of factors explains this incongruence, including regional cpDNA introgression (chloroplast capture), incomplete lineage sorting and inappropriate taxonomic boundaries. The cpDNA phylogeny provides useful insight into the evolution of Zieria but, because of its complexity, does not provide a clear basis for assessing phylogenetic relationships and monophyly of taxa. Better understanding of relationships, taxon limits and evolutionary processes in Zieria will require comparisons with nuclear DNA markers and critical assessment of morphological and genetic variation in widespread species.

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