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

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.

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

10.1101/2020.08.20.259549 ◽

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.

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Reticulate Evolutionary History in a Recent Radiation of Montane Grasshoppers Revealed by Genomic Data

10.1101/2021.01.12.426362 ◽

2021 ◽

Author(s):

Vanina Tonzo ◽

AdriÀ Bellvert ◽

Joaquín Ortego

Keyword(s):

Gene Flow ◽

Biological Diversity ◽

Sequence Data ◽

Incomplete Lineage Sorting ◽

Phylogenetic Analyses ◽

Secondary Contact ◽

Lineage Sorting ◽

Glacial Cycles ◽

Reciprocal Monophyly ◽

Geometric Morphometric

AbstractInferring the ecological and evolutionary processes underlying lineage and phenotypic diversification is of paramount importance to shed light on the origin of contemporary patterns of biological diversity. However, reconstructing phylogenetic relationships in recent evolutionary radiations represents a major challenge due to the frequent co-occurrence of incomplete lineage sorting and introgression. In this study, we combined high throughput sequence data (ddRADseq), geometric morphometric information, and novel phylogenetic inference methods that explicitly account for gene flow to infer the evolutionary relationships and the timing and mode of diversification in a complex of Ibero-Maghrebian montane grasshoppers of the subgenus Dreuxius (genus Omocestus). Our analyses supported the phenotypic distinctiveness of most sister taxa, two events of historical introgression involving lineages at different stages of the diversification continuum, and the recent Pleistocene origin (< 1 Ma) of the complex. Phylogenetic analyses did not recover the reciprocal monophyly of taxa from Iberia and northwestern Africa, supporting overseas migration between the two continents during the Pleistocene. Collectively, these results indicate that periods of isolation and secondary contact linked to Pleistocene glacial cycles likely contributed to both allopatric speciation and post divergence gene flow in the complex. This study exemplifies how the integration of multiple lines of evidence can help to reconstruct complex histories of reticulated evolution and highlights the important role of Quaternary climatic oscillations as a diversification engine in the Ibero-Maghrebian biodiversity hotspot.

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A test statistic to quantify treelikeness in phylogenetics

10.1101/2021.02.16.431544 ◽

2021 ◽

Author(s):

Caitlin Cherryh ◽

Bui Quang Minh ◽

Rob Lanfear

Keyword(s):

Evolutionary History ◽

Incomplete Lineage Sorting ◽

Phylogenetic Analyses ◽

Phylogenetic Network ◽

Parametric Bootstrap ◽

Lineage Sorting ◽

Test Statistic ◽

Sequence Alignments ◽

Wide Range ◽

History Of

AbstractMost phylogenetic analyses assume that the evolutionary history of an alignment (either that of a single locus, or of multiple concatenated loci) can be described by a single bifurcating tree, the so-called the treelikeness assumption. Treelikeness can be violated by biological events such as recombination, introgression, or incomplete lineage sorting, and by systematic errors in phylogenetic analyses. The incorrect assumption of treelikeness may then mislead phylogenetic inferences. To quantify and test for treelikeness in alignments, we develop a test statistic which we call the tree proportion. This statistic quantifies the proportion of the edge weights in a phylogenetic network that are represented in a bifurcating phylogenetic tree of the same alignment. We extend this statistic to a statistical test of treelikeness using a parametric bootstrap. We use extensive simulations to compare tree proportion to a range of related approaches. We show that tree proportion successfully identifies non-treelikeness in a wide range of simulation scenarios, and discuss its strengths and weaknesses compared to other approaches. The power of the tree-proportion test to reject non-treelike alignments can be lower than some other approaches, but these approaches tend to be limited in their scope and/or the ease with which they can be interpreted. Our recommendation is to test treelikeness of sequence alignments with both tree proportion and mosaic methods such as 3Seq. The scripts necessary to replicate this study are available at https://github.com/caitlinch/treelikeness

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Dissecting the basis of novel trait evolution in a radiation with widespread phylogenetic discordance

10.1101/201376 ◽

2017 ◽

Cited By ~ 3

Author(s):

Meng Wu ◽

Jamie L. Kostyun ◽

Matthew W. Hahn ◽

Leonie Moyle

Keyword(s):

De Novo ◽

Incomplete Lineage Sorting ◽

Phylogenetic Analyses ◽

Gene Tree ◽

Fruit Color ◽

Species Tree ◽

Color Variation ◽

Lineage Sorting ◽

Floral Character ◽

Trait Evolution

ABSTRACTPhylogenetic analyses of trait evolution can provide insight into the evolutionary processes that initiate and drive phenotypic diversification. However, recent phylogenomic studies have revealed extensive gene tree-species tree discordance, which can lead to incorrect inferences of trait evolution if only a single species tree is used for analysis. This phenomenon—dubbed “hemiplasy”—is particularly important to consider during analyses of character evolution in rapidly radiating groups, where discordance is widespread. Here we generate whole-transcriptome data for a phylogenetic analysis of 14 species in the plant genus Jaltomata (the sister clade to Solanum), which has experienced rapid, recent trait evolution, including in fruit and nectar color, and flower size and shape. Consistent with other radiations, we find evidence for rampant gene tree discordance due to incomplete lineage sorting (ILS) and several introgression events among the well-supported subclades. Since both ILS and introgression increase the probability of hemiplasy, we perform several analyses that take discordance into account while identifying genes that might contribute to phenotypic evolution. Despite discordance, the history of fruit color evolution in Jaltomata can be inferred with high confidence, and we find evidence of de novo adaptive evolution at individual genes associated with fruit color variation. In contrast, hemiplasy appears to strongly affect inferences about floral character transitions in Jaltomata, and we identify candidate loci that could arise either from multiple lineage-specific substitutions or standing ancestral polymorphisms. Our analysis provides a generalizable example of how to manage discordance when identifying loci associated with trait evolution in a radiating lineage.

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Two new species of Lagenandra (Araceae) from the Wet Zone of Sri Lanka

Phytotaxa ◽

10.11646/phytotaxa.522.3.2 ◽

2021 ◽

Vol 522 (3) ◽

pp. 187-199

Author(s):

INDRAKHEELA MADOLA ◽

DEEPTHI YAKANDAWALA ◽

KAPILA YAKANDAWALA ◽

SENANI KARUNARATNE

Keyword(s):

New Species ◽

Sri Lanka ◽

The Other ◽

Critically Endangered ◽

Sri Lankan ◽

Taxonomic Key ◽

The World ◽

Two New Species ◽

Conservation Assessments ◽

Wet Zone

Taxonomic revisions are the most reliable pathway in unfolding new species to the world. During such a revision of the genus Lagenandra in Sri Lankan, we came across two new species: Lagenandra kalugalensis and Lagenandra srilankensis from the Wet Zone of Sri Lanka. The two new species were studied in detail and compared with the morphology of the other species described in the genus, and based on field collected data conservation assessments were performed. A detailed description for the two new species and an updated taxonomic key to the Sri Lankan Lagenandra is presented here for easy identification. Recognizing two new endemic members enhances the number of Sri Lankan species of Lagenandra to eleven and global to nineteen. According to the IUCN red data category guidelines, L. kalugalensis qualifies for Critically Endangered category under Criterion B1ab (ii,iii,v) + B2ab (ii,iii,v) while L. srilankensis qualifies for Critically Endangered category under B1ab (iii, iv) + C2 (a) (i, ii). Hence, immediate conservation measures are imperative.

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Morphometric analysis of the genus Monochoria (Pontederiaceae) in Sri Lanka

Bangladesh Journal of Plant Taxonomy ◽

10.3329/bjpt.v24i1.33001 ◽

2017 ◽

Vol 24 (1) ◽

pp. 13-22

Author(s):

Savithri Sarojani Udage ◽

Deepthi Yakandawala

Keyword(s):

Sri Lanka ◽

Morphometric Analysis ◽

Species Complex ◽

Morphological Diversity ◽

Morphological Data ◽

Sri Lankan ◽

The Family ◽

Plant Taxon ◽

Reproductive Characters ◽

Informative Character

The genus Monochoria is represented in Sri Lanka by only two species, M. hastata and M. vaginalis. Of the two species M. vaginalis exhibits a high morphological diversity. A morphometric analysis was performed on the Sri Lankan members of the genus Monochoria to evaluate the morphological diversity exhibited by comparing 34 vegetative, anatomical and reproductive characters. Both cluster and principal coordinate analyses resulted in four clusters of which one corresponded to M. hastata, while M. vaginalis was divided into three phenetic groups indicating that the Sri Lankan M. vaginalis is a species complex involving more than one taxon. The length ratio of the lower spathe petiole to inflorescence stalk was identified as an informative character in delimiting the phenetic groups, a character that has not been considered before. Further, the occurrence of sub-palisade cavities that are filled with a red colored liquid in the leaves of two phenetic groups was a novel character for the genus as well as the family Pontederiaceae.Keywords: Monochoria vaginalis; Morphological data; Sub-palisade cavities; Principal coordinate anaysis.Bangladesh J. Plant Taxon. 24(1): 1322, 2017 (June)

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A new genus and a major temperate bamboo lineage of the Arundinarieae (Poaceae: Bambusoideae) from Sri Lanka based on a multi-locus plastid phylogeny

Phytotaxa ◽

10.11646/phytotaxa.174.4.1 ◽

2014 ◽

Vol 174 (4) ◽

pp. 187 ◽

Cited By ~ 18

Author(s):

Lakshmi Attigala ◽

Jimmy K. Triplett ◽

Hashendra-Suvini Kathriarachchi ◽

Lynn G Clark

Keyword(s):

Sri Lanka ◽

Sequence Data ◽

Alternative Hypothesis ◽

Phylogenetic Analyses ◽

Morphological Characters ◽

Sri Lankan ◽

Data Set ◽

Woody Bamboos ◽

Cpdna Markers ◽

Combined Data

Kuruna, a new temperate woody bamboo (Poaceae, Bambusoideae, Arundinarieae) genus from Sri Lanka, is recognized based on chloroplast sequence data from five markers (coding: ndhF 3’ end; non-coding: rps16-trnQ, trnC-rpoB, trnD-trnT, trnT-trnL). This genus represents the twelfth major lineage of temperate woody bamboos and is characterized by pachymorph culm bases with short necks, unicaespitose clumps, culm leaf girdles ca. 1 mm wide, usually abaxially hispid culm leaves with non-irritating hairs, persistent foliage leaf sheaths, complete branch sheathing and acute to biapiculate palea apices. Maximum Parsimony, Bayesian Inference and Maximum Likelihood analyses of a combined data set consistently strongly supported the monophyly of this Sri Lankan temperate woody bamboo clade. Although the Kishino-Hasegawa test is unable to reject the alternative hypothesis of monophyly of the Sri Lankan clade plus Bergbambos tessellata from South Africa, Kuruna and Bergbambos are distinguishable by a combination of morphological characters. A few additional cpDNA markers not previously used in phylogenetic analyses of Arundinarieae were tested to evaluate their utility in this taxonomically difficult tribe.

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Phylogeny and Species Delimitation of Chinese Medicago (Leguminosae) and Its Relatives Based on Molecular and Morphological Evidence

Frontiers in Plant Science ◽

10.3389/fpls.2020.619799 ◽

2021 ◽

Vol 11 ◽

Author(s):

Jinyuan Chen ◽

Guili Wu ◽

Nawal Shrestha ◽

Shuang Wu ◽

Wei Guo ◽

...

Keyword(s):

Phylogenetic Relationship ◽

Species Delimitation ◽

Large Scale ◽

Incomplete Lineage Sorting ◽

Phylogenetic Analyses ◽

Population Based ◽

Integrative Approach ◽

Morphological Evidence ◽

Sampling Errors ◽

Lineage Sorting

Medicago and its relatives, Trigonella and Melilotus comprise the most important forage resources globally. The alfalfa selected from the wild relatives has been cultivated worldwide as the forage queen. In the Flora of China, 15 Medicago, eight Trigonella, and four Melilotus species are recorded, of which six Medicago and two Trigonella species are introduced. Although several studies have been conducted to investigate the phylogenetic relationship within the three genera, many Chinese naturally distributed or endemic species are not included in those studies. Therefore, the taxonomic identity and phylogenetic relationship of these species remains unclear. In this study, we collected samples representing 18 out of 19 Chinese naturally distributed species of these three genera and three introduced Medicago species, and applied an integrative approach by combining evidences from population-based morphological clusters and molecular data to investigate species boundaries. A total of 186 individuals selected from 156 populations and 454 individuals from 124 populations were collected for genetic and morphological analyses, respectively. We sequenced three commonly used DNA barcodes (trnH-psbA, trnK-matK, and ITS) and one nuclear marker (GA3ox1) for phylogenetic analyses. We found that 16 out of 21 species could be well delimited based on phylogenetic analyses and morphological clusters. Two Trigonella species may be merged as one species or treated as two subspecies, and Medicago falcata should be treated as a subspecies of the M. sativa complex. We further found that major incongruences between the chloroplast and nuclear trees mainly occurred among the deep diverging lineages, which may be resulted from hybridization, incomplete lineage sorting and/or sampling errors. Further studies involving a finer sampling of species associated with large scale genomic data should be employed to better understand the species delimitation of these three genera.

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Identification of Novel Rodent-Borne Orthohantaviruses in an Endemic Area of Chronic Kidney Disease of Unknown Etiology (CKDu) in Sri Lanka

Viruses ◽

10.3390/v13101984 ◽

2021 ◽

Vol 13 (10) ◽

pp. 1984

Author(s):

Devinda S. Muthusinghe ◽

Kenta Shimizu ◽

Sithumini M. W. Lokupathirage ◽

Zhouoxing Wei ◽

Yomani D. Sarathkumara ◽

...

Keyword(s):

Chronic Kidney Disease ◽

Sri Lanka ◽

Kidney Disease ◽

Small Mammals ◽

Endemic Area ◽

Phylogenetic Analyses ◽

Rattus Rattus ◽

Genetic Evidence ◽

Unknown Etiology ◽

Sri Lankan

We reported the genetic evidence of circulating hantaviruses from small mammals captured in a chronic kidney disease of unknown etiology (CKDu) hotspot area of Sri Lanka. The high seroprevalence of anti-hantavirus antibodies against Thailand orthohantavirus (THAIV) has been reported among CKDu patients and rodents in Sri Lankan CKDu hotspots. We captured 116 small mammals from CKDu endemic regions in the Polonnaruwa District of Sri Lanka. Seven animals (five out of 11 Mus booduga and two out of 99 Rattus rattus) were PCR-positive for the hantavirus. A rat-borne sequence was grouped with a THAIV-like Anjozorobe virus. In contrast, Mus-borne sequences belonged to the THAIV lineage, suggesting a novel orthohantavirus species according to the phylogenetic analyses and whole-genome comparisons. Our genetic evidence indicates the presence of two THAIV-related viruses circulating in this CKDu endemic area, suggesting a basis for further investigations to identify the infectious virus in patients with CKDu and the CKDu induction mechanism of these viruses.

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Pollinators drive floral evolution in an Atlantic Forest genus

AoB Plants ◽

10.1093/aobpla/plaa046 ◽

2020 ◽

Vol 12 (5) ◽

Cited By ~ 1

Author(s):

Beatriz Neves ◽

Igor M Kessous ◽

Ricardo L Moura ◽

Dayvid R Couto ◽

Camila M Zanella ◽

...

Keyword(s):

Functional Groups ◽

Atlantic Forest ◽

Incomplete Lineage Sorting ◽

Phylogenetic Analyses ◽

Floral Traits ◽

Lineage Sorting ◽

Pollination Syndromes ◽

Angiosperm Diversification ◽

Species Complexes ◽

As Species

Abstract Pollinators are important drivers of angiosperm diversification at both micro- and macroevolutionary scales. Both hummingbirds and bats pollinate the species-rich and morphologically diverse genus Vriesea across its distribution in the Brazilian Atlantic Forest. Here, we (i) determine if floral traits predict functional groups of pollinators as documented, confirming the pollination syndromes in Vriesea and (ii) test if genetic structure in Vriesea is driven by geography (latitudinal and altitudinal heterogeneity) or ecology (pollination syndromes). We analysed 11 floral traits of 58 Vriesea species and performed a literature survey of Vriesea pollination biology. The genealogy of haplotypes was inferred and phylogenetic analyses were performed using chloroplast (rps16-trnk and matK) and nuclear (PHYC) molecular markers. Floral traits accurately predict functional groups of pollinators in Vriesea. Genetic groupings match the different pollination syndromes. Species with intermediate position were found between the groups, which share haplotypes and differ morphologically from the typical hummingbird- and bat-pollinated flowers of Vriesea. The phylogeny revealed moderately to well-supported clades which may be interpreted as species complexes. Our results suggest a role of pollinators driving ecological isolation in Vriesea clades. Incipient speciation and incomplete lineage sorting may explain the overall low genetic divergence within and among morphologically defined species, precluding the identification of clear species boundaries. The intermediate species with mixed floral types likely represent a window into shifts between pollinator syndromes. This study reports the morphological-genetic continuum that may be typical of ongoing pollinator-driven speciation in biodiversity hotspots.

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