Ecological niche differentiation in Chiroxiphia and Antilophia manakins (Aves: Pipridae)

Ecological Niche Differentiation and Response to Climate Change of the African Endemic Family Myrothamnaceae

Studying the ecological niches of species and their responses to climate change can provide better conservation strategies for these species. Myrothamnaceae is endemic to Africa, comprising only two species that belong to Myrothamnus (M. flabellifolius and M. moschatus). These closely related species exhibit allopatric distributions, positioning them as ideal materials for studying the species ecological adaptation. This study explores the ecological niche differentiation between M. flabellifolius and M. moschatus and their response capabilities to future climate change. The results indicate that M. flabellifolius and M. moschatus have undergone niche differentiation. The main drivers of niche differences are the minimum temperature of the coldest month (Bio6) for M. flabellifolius, precipitation of the driest month (Bio14), and precipitation of the coldest quarter (Bio19) for M. moschatus. M. flabellifolius demonstrated a stronger adaptation to environments characterized by lower precipitation, relatively lower temperatures, and greater annual temperature variations compared to M. moschatus. Under future climate scenarios (SSP5-8.5, 2081-2100 years), the results show that approximately 85% of the total suitable habitat for M. flabellifolius will be lost, with an 85% reduction in high-suitability areas and almost complete loss of the original mid-low suitability areas. Concurrently, about 29% of the total suitable habitat for M. moschatus will be lost, with a 34% reduction in high suitability areas and roughly 60% of the original mid-low suitability areas becoming unsuitable. This suggests that M. flabellifolius will face greater threats under future climate change. This study contributes novel insight into niche differentiation in Myrothamnaceae and provides useful information for the conservation of this distinctive African lineage.

Exploring Conflicts in Whole Genome Phylogenetics: A Case Study Within Manakins (Aves: Pipridae)

Some phylogenetic problems remain unresolved even when large amounts of sequence data are analyzed and methods that accommodate processes such as incomplete lineage sorting are employed. In addition to investigating biological sources of phylogenetic incongruence, it is also important to reduce noise in the phylogenomic dataset by using appropriate filtering approach that addresses gene tree estimation errors. We present the results of a case study in manakins, focusing on the very difficult clade comprising the genera Antilophia and Chiroxiphia. Previous studies suggest that Antilophia is nested within Chiroxiphia, though relationships among Antilophia+Chiroxiphia species have been highly unstable. We extracted more than 11,000 loci (ultra-conserved elements and introns) from whole genomes and conducted analyses using concatenation and multispecies coalescent methods. Topologies resulting from analyses using all loci differed depending on the data type and analytical method, with 2 clades (Antilophia+Chiroxiphia and Manacus+Pipra+Machaeopterus) in the manakin tree showing incongruent results. We hypothesized that gene trees that conflicted with a long coalescent branch (e.g., the branch uniting Antilophia+Chiroxiphia) might be enriched for cases of gene tree estimation error, so we conducted analyses that either constrained those gene trees to include monophyly of Antilophia+Chiroxiphia or excluded these loci. While constraining trees reduced some incongruence, excluding the trees led to completely congruent species trees, regardless of the data type or model of sequence evolution used. We found that a suite of gene metrics (most importantly the number of informative sites and likelihood of intralocus recombination) collectively explained the loci that resulted in non-monophyly of Antilophia+Chiroxiphia. We also found evidence for introgression that may have contributed to the discordant topologies we observe in Antilophia+Chiroxiphia and led to deviations from expectations given the multispecies coalescent model. Our study highlights the importance of identifying factors that can obscure phylogenetic signal when dealing with recalcitrant phylogenetic problems, such as gene tree estimation error, incomplete lineage sorting, and reticulation events. [Birds; c-gene; data type; gene estimation error; model fit; multispecies coalescent; phylogenomics; reticulation].

Genomics and ecological modelling clarify species integrity in a confusing group of butterflies

Recent advances in both genomics and ecological modelling present new, multidisciplinary opportunities for resolving species boundaries and understanding the mechanisms that maintain their integrity in regions of contact. Here, we use a combination of high-throughput DNA sequencing and ecological niche modelling to resolve species boundaries and niche divergence within the Speyeria atlantis-hesperis (Lepidoptera: Nymphalidae) complex, a confusing group of North American butterflies. This complex is notorious for its muddled species delimitations, morphological ambiguity, and extensive mito-nuclear discordance. Our admixture and multispecies coalescent-based analyses of single nucleotide polymorphisms identified substantial divergences between S. atlantis and S. hesperis in areas of contact, as well as between distinct northern and southern lineages within S. hesperis. Our results also provide evidence of past introgression relating to another species, S. zerene, which previous work has shown to be more distantly related to the S. atlantis-hesperis complex. We then used ecological models to predict habitat suitability for each of the three recovered genomic lineages in the S. atlantis-hesperis complex and assess their pairwise niche divergence. These analyses resolved that these three lineages are significantly diverged in their respective niches and are not separated by discontinuities in suitable habitat that might present barriers to gene flow. We therefore infer that ecologically-mediated selection resulting in disparate habitat associations is a principal mechanism reinforcing their genomic integrity. Overall, our results unambiguously support significant evolutionary and ecological divergence between the northern and southern lineages of S. hesperis, sufficient to recognize the southern evolutionary lineage as a distinct species, called S. nausicaa based on taxonomic priority.