Assessing phylogenetic information to reveal uncertainty in historical data: An example using Goodeinae (Teleostei: Cyprinodontiformes: Goodeidae)

Evidence for gene flow and trait reversal during radiation of Mexican Goodeid fish

Understanding the phylogeographic history of a group and identifying the factors contributing to speciation is an important challenge in evolutionary biology. The Goodeinae are a group of live-bearing fishes endemic to Mexico. Here, we develop genomic resources for species within the Goodeinae and use phylogenomic approaches to characterise their evolutionary history. We sequenced, assembled and annotated the genomes of four Goodeinae species, including Ataeniobius toweri, the only matrotrophic live-bearing fish without a trophotaenia in the group. We estimated timings of species divergence and examined the extent and timing of introgression between the species to assess if this may have occurred during an early radiation, or in more recent episodes of secondary contact. We used branch-site models to detect genome-wide positive selection across Goodeinae, and we specifically asked whether this differs in A. toweri, where loss of placental viviparity has recently occurred. We found evidence of gene flow between geographically isolated species, suggesting vicariant speciation was supplemented by limited post-speciation gene flow, and gene flow may explain previous uncertainties about Goodeid phylogeny. Genes under positive selection in the group are likely to be associated with the switch to live-bearing. Overall, our studies suggest that both volcanism-driven vicariance and changes in reproductive mode influenced radiation in the Goodeinae.

Placing human gene families into their evolutionary context

Following the draft sequence of the first human genome over 20 years ago, we have achieved unprecedented insights into the rules governing its evolution, often with direct translational relevance to specific diseases. However, staggering sequence complexity has also challenged the development of a more comprehensive understanding of human genome biology. In this context, interspecific genomic studies between humans and other animals have played a critical role in our efforts to decode human gene families. In this review, we focus on how the rapid surge of genome sequencing of both model and non-model organisms now provides a broader comparative framework poised to empower novel discoveries. We begin with a general overview of how comparative approaches are essential for understanding gene family evolution in the human genome, followed by a discussion of analyses of gene expression. We show how homology can provide insights into the genes and gene families associated with immune response, cancer biology, vision, chemosensation, and metabolism, by revealing similarity in processes among distant species. We then explain methodological tools that provide critical advances and show the limitations of common approaches. We conclude with a discussion of how these investigations position us to gain fundamental insights into the evolution of gene families among living organisms in general. We hope that our review catalyzes additional excitement and research on the emerging field of comparative genomics, while aiding the placement of the human genome into its existentially evolutionary context.

Morphological basis for maternal nutrient provision to embryos in the viviparous fish Ataeniobius toweri (Teleostei: Goodeidae)

In viviparous Mexican fishes of the family Goodeidae, embryos develop in the maternal ovarian lumen. They typically absorb maternal nutrients during gestation by means of "trophotaeniae," that is, specialized, elongated extensions of the hindgut that are exposed to the fluids, which occupy the ovarian lumen. The sole exception is Ataeniobius toweri, whose embryos lack trophotaeniae but are nevertheless matrotrophic. Thus, how its embryos obtain maternal nutrients is unclear. We studied a series of non-pregnant and pregnant ovaries of A. toweri using histology to identify the mechanism of maternal-embryo nutrient transfer. By early-gestation, embryos have depleted their yolk supplies. Yolks are released into the ovarian lumen and are ingested by the developing embryos, as shown by yolk material in their digestive tracts. The embryonic gut is lined by an epithelium consisting of columnar cells with apical microvilli, providing a means for nutrient absorption. Contrary to statements in the literature, embryos develop minuscule trophotaenial rudiments that extend slightly into the ovarian lumen. These structures are formed of an absorptive epithelium that overlies a vascular stroma, similar to the trophotaeniae of other goodeids. Through late gestation, vitellogenic follicles form and oocytes are discharged into the ovarian lumen, contributing to embryonic nutrition. Thus, histological evidence suggests that embryos chiefly obtain nutrients from ingestion of yolk and maternal secretions released into the ovarian lumen. This function possibly is supplemented by uptake via the small hindgut protrusions and other absorptive surfaces (e.g., the skin and the gill epithelium). Our observations are consistent with two evolutionary interpretations of the hindgut protrusions: (a) that they are rudimentary, evolutionary precursors of trophotaeniae formed by exteriorized hindgut; and (b) that they are vestigial remnants of trophotaeniae that were lost during a switch to a form of matrotrophy involving nutrient ingestion.

Genetic differentiation among populations of the blackfin goodea Goodea atripinnis (Cyprinodontiformes: Goodeidae): implications for its evolutionary history

Central Mexico is characterized by a complex topography that is the result of historic and contemporary tectonic and climatic factors. These events have influenced the evolutionary history of numerous freshwater fishes in the region. Nonetheless, recent studies have shown that life-history traits and ecological characteristics of species may influence dispersal capabilities and the degree of genetic connectivity. Goodea (Cyprinodontiformes: Goodeidae) is one of the most widely distributed and environmentally tolerant genera of goodeids. In this study, the authors analysed variation in the mitochondrial cytochrome b gene to evaluate the phylogeographic relationships, genetic structure, genetic diversity and demographic history of Goodea from across its distribution range. They found low genetic differentiation and identified shared haplotypes among several regions. Geographic segregation was found in samples southwest and northeast of the Lower Lerma region, with some internal isolated groups showing phylogeographic differentiation and unique haplotypes. The AMOVA best explained genetic structure when grouped by haplogroups rather than when grouped by recognized biogeographic regions. Several regions showed null genetic diversity, raising the possibility of dispersal mediated by humans. Finally, Bayesian Skyline Plot analysis showed a population expansion for the Southwest haplogroup, except for the Armería population and sub-group II of the Northeast haplogroup. All this suggests a recent colonization of Goodea atripinnis throughout some of the biogeographic regions currently inhabited by this species.

Phylogenomic Analysis of a Putative Missing Link Sparks Reinterpretation of Leech Evolution

Leeches (Hirudinida) comprise a charismatic, yet often maligned group of worms. Despite their ecological, economic, and medical importance, a general consensus on the phylogenetic relationships of major hirudinidan lineages is lacking. This absence of a consistent, robust phylogeny of early-diverging lineages has hindered our understanding of the underlying processes that enabled evolutionary diversification of this clade. Here, we used an anchored hybrid enrichment-based phylogenomic approach, capturing hundreds of loci to investigate phylogenetic relationships among major hirudinidan lineages and their closest living relatives. We recovered Branchiobdellida as sister to a clade that includes all major lineages of hirudinidans and Acanthobdella, casting doubt on the utility of Acanthobdella as a “missing link” between hirudinidans and the clitellate group formerly known as Oligochaeta. Further, our results corroborate the reciprocal monophyly of jawed and proboscis-bearing leeches. Our phylogenomic resolution of early-diverging leeches provides a useful framework for illuminating the evolution of key adaptations and host–symbiont associations that have allowed leeches to colonize a wide diversity of habitats worldwide.