Species tree estimation from multi-locus datasets is extremely challenging, especially in the presence of gene tree heterogeneity across the genome due to incomplete lineage sorting (ILS). Summary methods have been developed which estimate gene trees and then combine the gene trees to estimate a species tree by optimizing various optimization scores. In this study, we have extended and adapted the concept of phylogenetic terraces to species tree estimation by “summarizing” a set of gene trees, where multiple species trees with distinct topologies may have exactly the same optimality score (i.e., quartet score, extra lineage score, etc.). We particularly investigated the presence and impacts of equally optimal trees in species tree estimation from multi-locus data using summary methods by taking ILS into account. We analyzed two of the most popular ILS-aware optimization criteria: maximize quartet consistency (MQC) and minimize deep coalescence (MDC). Methods based on MQC are provably statistically consistent, whereas MDC is not a consistent criterion for species tree estimation. We present a comprehensive comparative study of these two optimality criteria. Our experiments, on a collection of datasets simulated under ILS, indicate that MDC may result in competitive or identical quartet consistency score as MQC, but could be significantly worse than MQC in terms of tree accuracy – demonstrating the presence and impacts of equally optimal species trees. This is the first known study that provides the conditions for the datasets to have equally optimal trees in the context of phylogenomic inference using summary methods.

Background:The indiscriminate uses of antimicrobials in either human or animal husbandry generate selection pressure to develop resistance in diverse microbial populations. Colistin is a polymyxin group antibiotic used for the treatment of critical human infections by multidrug-resistant (MDR) Gram-negative bacteria (GNB) and veterinary healthcare. In recent years, colistin usage has been expanded considerably in Argo, fishery, and food animal farming in Bangladesh. This study investigated phenotypic colistin-resistance and the prevalence of colistin-resistance mcr-1 gene in bacterial isolates from droppings of poultry chickens and household native chickens.Methods and materials: A cross-sectional study was conducted and colistin usage history to chickens was collected by a structured questionnaire. Bacteria were isolated from chicken droppings by inoculating on different selective culture media. The purified bacterial colonies were identified by conventional biochemical procedures followed by a rapid biochemical-test kit (API 20E, BioMérieux, Durham, NC). A part of bacterial identification was validated further by genotyping using 16S rDNA analyses. The colistin susceptibility of the isolates were determined by disk-diffusion and minimal inhibitory concentration (MIC) measurement. mcr-1 gene was detected by polymerase chain reactions (PCR) and confirmed by sequence blasting.Results: Overall 39.6% (59/159) isolates showed colistinresistant by disk-diffusion assessment. The resistance prevalence was significantly higher in poultry-chicken isolates (48.5%, 48/99) than in native-chicken isolates (22%, 11/50; p = 002). All the resistant isolates showed MIC level, between >8 g/mL to >256 g/mL. Likely, the mcr-1 gene was detected more in poultry gut bacteria (34%) than in native-chicken isolates (14%, p = 0.02). mcr-1 appeared significantly associated with phenotypic colistinresistance phenomena (p < 0.001). Previous colistin usage yielded a substantially higher proportion of mcr-1 in bacteria (p = 0.06).Conclusion: mcr-1 gene circulates in bacteria isolated from both poultry chicken and native chicken. Higher acquisition of mcr-1 in bacteria was associated with colistin-usage for chickens. The increased mcr-1 prevalence may increase the risk of critical human disease transmission. Specifically, mcr-1 can enter humans via zoonotic infections from poultry-human interface, which poses a big threat to public health.

15Species tree estimation from multi-locus dataset is extremely challenging, espe-16 cially in the presence of gene tree heterogeneity across the genome due to incomplete 17 lineage sorting (ILS). Summary methods have been developed which estimate gene 18 trees and then combine the gene trees to estimate a species tree by optimizing 19 various optimization scores. In this study, we have formalized the concept of "phy-20 logenomic terraces" in the species tree space, where multiple species trees with 21 distinct topologies may have exactly the same optimization score (quartet score, 22 extra lineage score, etc.) with respect to a collection of gene trees. We investigated 23 the presence and implication of terraces in species tree estimation from multi-locus 24 data by taking ILS into account. We analyzed two of the most popular ILS-aware 25 optimization criteria: maximize quartet consistency (MQC) and minimize deep co-26 alescence (MDC). Methods based on MQC are provably statistically consistent, 27 1 whereas MDC is not a consistent criterion for species tree estimation. Our exper-28 iments, on a collection of dataset simulated under ILS, indicate that MDC-based 29 methods may achieve competitive or identical quartet consistency score as MQC 30 but could be significantly worse than MQC in terms of tree accuracy -demon- 31 strating the presence and affect of phylogenomic terraces. This is the first known 32 study that formalizes the concept of phylogenomic terraces in the context of species 33 tree estimation from multi-locus data, and reports the presence and implications of 34 terraces in species tree estimation under ILS. 35 Introduction 38 A species tree can be defined as the pattern of branching of species lineages via the 39 process of speciation, while a gene tree represents the evolution of a particular "gene" 40 within a group of species. Biological processes can result in different loci having different 41 evolutionary histories, and therefore species tree estimation involves the estimation of 42 trees and alignments on many different genes, so that the species tree can be based 43 upon many different parts of the genome. While many processes can result in discord 44 between gene trees and species trees, incomplete lineage sorting (ILS) is considered to 45 be a dominant cause for gene tree heterogeneity, which is best understood under the 46 coalescent model [1][2][3][4][5][6][7][8]. ILS or deep coalescence refers to the case in which two lineages 47 fail to coalesce at their speciation point. Under the coalescent model, deep coalescence 48 can be a source of discordance, because the common ancestry of gene copies at a single 49 locus can extend deeper than speciation events. 50In the presence of gene tree heterogeneity, standard methods for estimating species 51 trees, such as concatenation (which combines sequence alignments from different loci into 52 a single "supermatrix", and then computes a tree on the supermatrix) can be statistically 53 2 inconsistent [9, 10], and produce incorrect trees wi...

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