Biology subjects

Moyle, R. G.

Publications and source records attributed to Moyle, R. G..

4 recordsLinked to original sources

bioRxiv2025

Efficient Inference of Macrophylogenies: Insights from the Avian Tree of Life

The exponential growth of molecular sequence data over the past decade has enabled the construction of numerous clade-specific phylogenies encompassing hundreds or thousands of taxa. These independent studies often include overlapping data, presenting a unique opportunity to build macrophylogenies (phylogenies sampling > 1,000 taxa) for entire classes across the Tree of Life. However, the inference of large trees remains constrained by logistical, computational, and methodological challenges. The Avian Tree of Life provides an ideal model for evaluating strategies to robustly infer macrophylogenies from intersecting datasets derived from smaller studies. In this study, we leveraged a comprehensive resource of sequence capture datasets to evaluate the phylogenetic accuracy and computational costs of four methodological approaches: (1) supermatrix approaches using concatenation, including the "fast" maximum likelihood (ML) methods, (2) filtering datasets to reduce heterogeneity, (3) supertree estimation based on published phylogenomic trees, and (4) a "divide-and-conquer" strategy, wherein smaller ML trees were estimated and subsequently combined using a supertree approach. Additionally, we examined the impact of these methods on divergence time estimation using a dataset that includes newly vetted fossil calibrations for the Avian Tree of Life. Our findings highlight that recently developed fast tree search approaches offer a reasonable compromise between computational efficiency and phylogenetic accuracy, facilitating inference of macrophylogenies.

evolutionary biology↗

bioRxiv2024

Waves of Colonization and Gene Flow in a Great Speciator

Secondary contact between previously allopatric lineages offers a test of reproductive isolating mechanisms that may have accrued in isolation. Such instances of contact can produce stable hybrid zones--where reproductive isolation can further develop via reinforcement or phenotypic displacement--or result in the lineages merging. Ongoing secondary contact is most visible in continental systems, where steady input from parental taxa can occur readily. In oceanic island systems, however, secondary contact between closely related species of birds is relatively rare. When observed on sufficiently small islands, relative to population size, secondary contact likely represents a recent phenomenon. Here, we examine the dynamics of a group of birds whose apparent widespread hybridization influenced Ernst Mayrs foundational work on allopatric speciation: the whistlers of Fiji (Aves: Pachycephala). We demonstrate two clear instances of secondary contact within the Fijian archipelago, one resulting in a hybrid zone on a larger island, and the other resulting in a wholly admixed population on a smaller, adjacent island. We leveraged low genome-wide divergence in the hybrid zone to pinpoint a single genomic region associated with observed phenotypic differences. We use genomic data to present a new hypothesis that emphasizes rapid plumage evolution and post-divergence gene flow.

evolutionary biology↗

bioRxiv2023

Recent secondary contact, genome-wide admixture, and limited introgression of neo-sex chromosomes between two Pacific island bird species

Secondary contact between closely related taxa represents a "moment of truth" for speciation. Removal of geographic barriers allows us to test the strength of reproductive isolation that evolved in allopatry and identify the genetic, behavioral, and/or ecological barriers that separate species in sympatry. Sex chromosomes are known to rapidly accumulate differences between species, an effect that may be exacerbated for neo-sex chromosomes because they are regions of the genome that have recently become linked to sex chromosomes and are transitioning from autosomal to sex-specific inheritance. Two closely related bird species in the honeyeater family -- Myzomela cardinalis and Myzomela tristrami -- carry neo-sex chromosomes and have come into recent secondary contact in the Solomon Islands after being isolated for [~]3 my. Hybrids of these two species have been observed in sympatry for at least 100 years. To determine the genetic consequences of hybridization, we use population genomic analyses of individuals sampled in allopatry and sympatry to characterize gene flow in the contact zone. Using genome-wide estimates of diversity, differentiation, and divergence, we find that the degree and direction of introgression varies dramatically across the genome. Autosomal introgression is bidirectional, with phenotypic hybrids and phenotypic parentals of both species showing admixed ancestry. On the sex and neo-sex chromosomes, the story is different. Introgression of Z is limited and neo-Z sequence shows no evidence of introgression, whereas introgression of W and neo-W is strong but highly asymmetric, moving only from the invasive M. cardinalis to the resident M. tristrami. Thus, reproductive isolation is incomplete, but sex and neo-sex chromosome regions have prevented gene flow in one (W/neo-W) or both (Z/neo-Z) directions. The recent contact between previously isolated species indicates that hybridization may permit gene flow between taxa in some genomic regions, but species divergence can be maintained by barriers to gene flow associated with rapidly evolving sex-linked regions of the genome. Author SummaryWhen a new species colonizes an island and interacts with a closely related native species, we are provided with a rare opportunity to identify the factors that keep species distinct and the consequences of interbreeding. Regions of the genome that evolve rapidly or influence mate choice may be especially likely to act as barriers to gene flow. The red Myzomela cardinalis, birds in the honeyeater family, have recently arrived to Makira in the Solomon Islands, joining the endemic, all black Myzomela tristrami. We used population genomic analyses of individuals in geographic isolation, as well as those in geographic contact with the other species, to understand the history of these two species and the consequences of their recent range overlap on Makira. We found that regions of the genome that are sex-specific (i.e., sex chromosomes) were either limited in their ability to move between species, or only moved in one direction, from the invading M. cardinalis to the native M. tristrami. This work highlights how certain regions of the genome may be especially important in defining species boundaries and the generation and maintenance of biodiversity.

evolutionary biology↗

bioRxiv2019

Parachute geckos free fall into synonymy: Gekko phylogeny, and a new subgeneric classification, inferred from thousands of ultraconserved elements

Recent phylogenetic studies of gekkonid lizards have revealed unexpected, widespread paraphyly and polyphyly among genera, unclear generic boundaries, and a tendency towards the nesting of taxa exhibiting specialized, apomorphic morphologies within geographically widespread \"generalist\" clades. This is especially true in the Australasia, where the monophyly of Gekko proper has been questioned with respect to phenotypically ornate flap-legged geckos of the genus Luperosaurus, the Philippine false geckos of the genus Pseudogekko, and even the elaborately \"derived\" parachute geckos of the genus Ptychozoon. Here we employ sequence capture targeting 5060 ultraconserved elements to infer phylogenomic relationships among 42 representative ingroup gekkonine lizard taxa. We analyzed multiple datasets of varying degrees of completeness (10, 50, 75, 95, and 100 percent complete with 4715, 4051, 3376, 2366, and 772 UCEs, respectively) using concatenated maximum likelihood and multispecies coalescent methods. Our sampling scheme was designed to address four persistent systematic questions in this group: (1) Are Luperosaurus and Ptychozoon monophyletic and are any of these named species truly nested within Gekko? (2) Are prior phylogenetic estimates of Sulawesis L. iskandari as sister to Melanesian G. vittatus supported by our genome-scale dataset? (3) Is the high elevation L. gulat of Palawan Island correctly placed within Gekko? (4) And, finally, where do the enigmatic taxa P. rhacophorus and L. browni fall in a higher-level gekkonid phylogeny? We resolve these issues; confirm with strong support some previously inferred findings (placement of Ptychozoon taxa within Gekko; the sister relationship between L. iskandari and G. vittatus); resolve the systematic position of unplaced taxa (L. gulat, and L. browni); and transfer L. iskandari, L. gulat, L. browni, and all members of the genus Ptychozoon to the genus Gekko. Our unexpected and novel systematic inference of the placement of Ptychozoon rhacophorus suggests that this species is not related to Ptychozoon or even Luperosaurus (as previously expected) but may, in fact, be most closely related to several Indochinese species of Gekko. With our final, well-supported topologies, we recognize seven newly defined subgenera to accommodate [~]60 species within the more broadly defined and maximally-inclusive Australasian genus Gekko. The newly defined subgenera will aide taxonomists and systematists in species descriptions by allowing them to only diagnose putatively new species from the most relevant members of the same subgenus, not necessarily the phenotypically variable genus Gekko as a whole, and we argue that it appropriately recognizes geographically circumscribed units (e.g., a new subgenus for a novel clade, entirely endemic to the Philippines) while simultaneously recognizing several of the most systematically controversial, phenotypically distinct, and phylogenetically unique lineages. An added benefit of recognizing the most inclusive definition of Gekko, containing multiple phylogenetically-defined subgenera, is that this practice has the potential to alleviate taxonomic vandalism, if widely adopted, by creating formally available, supraspecific taxa, accompanied by character-based diagnoses and properly assigned type species, such that future, more atomized classifications would necessarily be required to adopt todays subgenera as tomorrows genera under the guidelines of The Code of Zoological Nomenclature. Not only does this simple practice effectively eliminate the nefarious motivation behind taxonomic vandalism, but it also ensures that supraspecific names are created only when accompanied by data, that they are coined with reference to a phylogenetic estimate, and that they explicitly involve appropriate specifiers in the form of type species and, ultimately, type specimens.

zoology↗