Biology subjects

Haryoko, T.

Publications and source records attributed to Haryoko, T..

3 recordsLinked to original sources

bioRxiv2022

The formation of the Indo-Pacific montane avifauna

Mountain biotas have considerable conservation and research importance, but the formation of montane communities remains incompletely understood. Study of Indo-Pacific island faunas has inspired two main hypotheses for the generation of montane diversity. The first posits that montane populations arise via direct colonization from other mountain areas, while the second invokes recruitment from adjacent lowland populations. We sought to reconcile these apparently conflicting hypotheses by asking whether a species ancestral geographic origin determines its mode of mountain colonization. To this end, island-dwelling passerine birds at the faunal crossroads between Eurasia and Australo-Papua provide an ideal study system. We recovered the phylogenetic relationships of the regions montane species, and used this information to reconstruct their ancestral geographic ranges, elevational ranges, and migratory behavior. We also performed genomic population studies of three super-dispersive montane species/clades with broad island distributions. Eurasian-origin species populated archipelagos via direct colonization between mountains. This mode of colonization appears related to ancestral adaptations to cold and seasonal Palearctic climates, specifically short-distance migration. Australo-Papuan-origin mountain populations, by contrast, evolved from lowland ancestors, and highland distribution mostly precludes their further colonization of island mountains. The patterns and processes revealed for this group are compatible with taxon cycles, a hypothesized process of lowland lineage expansion followed by montane relictualization. Collectively, our analyses explain much of the distributional variation within a complex biological system, and provide a synthesis of two seemingly discordant hypotheses for montane community formation.

evolutionary biology↗

bioRxiv2022

Population genomics of the island thrush elucidates one of earth's great archipelagic radiations

Tropical islands are renowned as natural laboratories for evolutionary study. Lineage radiations across tropical archipelagos are ideal systems for investigating how colonization, speciation, and extinction processes shape biodiversity patterns. The expansion of the island thrush across the Indo-Pacific represents one of the largest yet most perplexing island radiations of any songbird species. The island thrush exhibits a complex mosaic of pronounced plumage variation across its range, and is arguably the worlds most polytypic bird. It is a sedentary species largely restricted to mountain forests, yet it has colonized a vast island region spanning a quarter of the globe. We conducted comprehensive sampling of island thrush populations and obtained genome-wide SNP data, which we used to reconstruct its phylogeny, population structure, gene flow, and demographic history. The island thrush evolved from migratory Palearctic ancestors and radiated explosively across the Indo-Pacific during the Pleistocene, with numerous instances of gene flow between populations. Its bewildering plumage variation masks a biogeographically intuitive stepping stone colonization path from the Philippines through the Greater Sundas, Wallacea and New Guinea to Polynesia. The island thrushs success in colonizing Indo-Pacific mountains can be understood in light of its ancestral mobility and adaptation to cool climates; however, shifts in elevational range, degree of plumage variation and apparent dispersal rates in the eastern part of its range raise further intriguing questions about its biology.

evolutionary biology↗

bioRxiv2020

The avian W chromosome is a refugium for endogenous retroviruses with likely effects on female-biased mutational load and genetic incompatibilities

It is a broadly observed pattern that the non-recombining regions of sex-limited chromosomes (Y and W) accumulate more repeats than the rest of the genome, even in species like birds with a low genome-wide repeat content. Here we show that in birds with highly heteromorphic sex chromosomes, the W chromosome has a transposable element (TE) density of >55% compared to the genome-wide density of <10%, and contains over half of all full-length (thus potentially active) endogenous retroviruses (ERVs) of the entire genome. Using RNA-seq and protein mass spectrometry data, we were able to detect signatures of female-specific ERV expression. We hypothesise that the avian W chromosome acts as a refugium for active ERVs, likely leading to female-biased mutational load that may influence female physiology similar to the "toxic-Y" effect in Drosophila. Furthermore, Haldanes rule predicts that the heterogametic sex has reduced fertility in hybrids. We propose that the excess of W-linked active ERVs over the rest of the genome may be an additional explanatory variable for Haldanes rule, with consequences for genetic incompatibilities between species through TE/repressor mismatches in hybrids. Together, our results suggest that the sequence content of female-specific W chromosomes can have effects far beyond sex determination and gene dosage.

evolutionary biology↗