A genome-wide assessment of stages of elevational parapatry in Bornean passerine birds reveals no introgression: implications for processes and patterns of speciation

Moyle, Robert G.; Manthey, Joseph D.; Hosner, Peter A.; Rahman, Mustafa Abdul; Lakim, Maklarin; Sheldon, Frederick H.

doi:10.7717/peerj.3335

Cited by 23 publications

(20 citation statements)

References 52 publications

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“…Occupancy by putative competitors appears to play a secondary role in limiting the boundaries of both groups, and acts to limit lowland species more strongly. These findings also contrast with the phylogeographical inference that several montane species in Borneo (a forktail, swiftlet, spiderhunter, and leafbird) once occupied wider elevational ranges (including lowlands) but have been pushed or restricted to higher elevation by invasion of the lowlands by congeners from other islands (Moyle et al, ; Sheldon, Lim, & Moyle, ). Interestingly, though, our results mesh well with inferences from studies of phylogenetic community structure.…”

Section: Discussionmentioning

confidence: 61%

Biotic interactions help explain variation in elevational range limits of birds among Bornean mountains

Burner

Boyce

Bernasconi

et al. 2020

Journal of Biogeography

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Aim Physiological tolerances and biotic interactions along habitat gradients are thought to influence species occurrence. Distributional differences caused by such forces are particularly noticeable on tropical mountains, where high species turnover along elevational gradients occurs over relatively short distances and elevational distributions of particular species can shift among mountains. Such shifts are interpreted as evidence of the importance of spatial variation in interspecific competition and habitat or climatic gradients. To assess the relative importance of competition and compression of habitat and climatic zones in setting range limits, we examined differences in elevational ranges of forest bird species among four Bornean mountains with distinct features. Location Bornean mountains Kinabalu, Mulu, Pueh and Topap Oso. Taxon Rain forest bird communities along elevational gradients. Methods We surveyed the elevational ranges of rain forest birds on four mountains in Borneo to test which environmental variables—habitat zone compression or presence of likely competitors—best predicted differences in elevational ranges of species among mountains. For this purpose, we used two complementary tests: a comparison of elevational range limits between pairs of mountains, and linear mixed models with naïve occupancy as the response variable. Results We found that lowland species occur higher in elevation on two small mountains compared to Mt. Mulu. This result is inconsistent with the expectation that distributions of habitats are elevationally compressed on small mountains, but is consistent with the hypothesis that a reduction in competition (likely diffuse) on short mountains, which largely lack montane specialist species, allows lowland species to occur higher in elevation. The relative influence of competition changes with elevation, and the correlation between lower range limits of montane species and the distribution of their competitors was weaker than in lowland species. Main conclusions These findings provide support for the importance of biotic interactions in setting elevational range limits of tropical bird species, although abiotic gradients explain the majority of distribution patterns. Thus, models predicting range shifts under climate change scenarios must include not only climatic variables, as is currently most common, but also information on potentially resulting changes in species interactions, especially for lowland species.

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Section: Discussionmentioning

confidence: 61%

Biotic interactions help explain variation in elevational range limits of birds among Bornean mountains

Burner

Boyce

Bernasconi

et al. 2020

Journal of Biogeography

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“…; Moyle et al. ; among many others), including in Coccidioides . Nonetheless, few studies have identified haplotypes that have crossed the species boundaries.…”

Section: Discussionmentioning

confidence: 94%

“…Similar to other taxa, genomic data are revealing that hybridization and gene exchange seem to be common in fungi. Multilocus sequence typing and reduced representation sequencing have strongly suggested shared ancestry (e.g., Maroja et al 2015;Almeida et al 2017;Devier et al 2017;Moyle et al 2017; among many others), including in Coccidioides. Nonetheless, few studies have identified haplotypes that have crossed the species boundaries.…”

Section: Implications For Fungimentioning

confidence: 99%

Gene exchange between two divergent species of the fungal human pathogen,Coccidioides

et al. 2018

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The fungal genus Coccidioides is composed of two species, Coccidioides immitis and Coccidioides posadasii. These two species are the causal agents of coccidioidomycosis, a pulmonary disease also known as valley fever. The two species are thought to have shared genetic material due to gene exchange in spite of their long divergence. To quantify the magnitude of shared ancestry between them, we analyzed the genomes of a population sample from each species. Next, we inferred what is the expected size of shared haplotypes that might be inherited from the last common ancestor of the two species and find a cutoff to find what haplotypes have conclusively been exchanged between species. Finally, we precisely identified the breakpoints of the haplotypes that have crossed the species boundary and measure the allele frequency of each introgression in this sample. We find that introgressions are not uniformly distributed across the genome. Most, but not all, of the introgressions segregate at low frequency. Our results show that divergent species can share alleles, that species boundaries can be porous, and highlight the need for a systematic exploration of gene exchange in fungal species.

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“…Tropical elevational gradients have high levels of temporally stable thermal stratification (Janzen, 1967) that has been linked to selection for narrow thermal physiologies (Sheldon et al, 2018), reduced upslope or downslope dispersal (Polato et al, 2018), and high beta diversity (Jankowski et al, 2009). As a result, they have frequently been studied as a stage for this process (Mayr, 1942;Cadena et al, 2012;Funk et al, 2016;Arteaga et al, 2016;Caro et al, 2013;Moyle et al, 2017). Yet previous comparative phylogenetic studies have overwhelmingly supported models of divergence in allopatry followed by secondary contact and range displacement, particularly in vertebrates (Arteaga et al, 2016;Caro et al, 2013;Moyle et al, 2017).…”

Section: Discussionmentioning

confidence: 99%

“…As a result, they have frequently been studied as a stage for this process (Mayr, 1942;Cadena et al, 2012;Funk et al, 2016;Arteaga et al, 2016;Caro et al, 2013;Moyle et al, 2017). Yet previous comparative phylogenetic studies have overwhelmingly supported models of divergence in allopatry followed by secondary contact and range displacement, particularly in vertebrates (Arteaga et al, 2016;Caro et al, 2013;Moyle et al, 2017). Our finding of well-defined genotypic and phenotypic clusters (Figure 1) in the face of extensive historical and contemporary introgression (Figure 2) suggests that selection across elevational gradients is sufficient to maintain species boundaries with little evidence of strong postzygotic isolation.…”

Section: Discussionmentioning

confidence: 99%

Speciation and gene flow across an elevational gradient in New Guinea kingfishers

Linck

Freeman

Dumbacher

2019

Preprint

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Theory suggests speciation without geographic isolation is plausible if divergent natural selection is strong enough to counteract gene flow. Tropical mountains provide strong and temporally stable environmental gradients that can promote local adaptation and population genetic structure. Pairs of closely related species with adjacent but divergent elevational ranges are common in these environments, a pattern that suggests parapatric speciation (i.e., speciation with moderate gene flow), but evidence for this process is scarce.Here we use genomic data from modern and historical museum specimens to investigate speciation in a pair of New Guinea kingfishers that segregate ranges by elevation. We find that the lowland species Syma torotoro and montane species S. megarhyncha form discrete genotypic clusters with bimodal variance in phenotypic traits. Phylogenetic relationships among lineages are discordant between mitochondrial and nuclear genomes, which D-tests and demographic inference indicate is partly driven by interspecific gene flow over long time periods. Summary statistics reveal differentiation is concentrated in a handful of small regions of the genome. These data are consistent with ecological speciation driven by adaptation to abiotic or biotic factors varying with elevation. More broadly, they suggest selection across elevational gradients can maintain species boundaries without intrinsic reproductive isolation, a mechanism contributing to high tropical biodiversity.

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A genome-wide assessment of stages of elevational parapatry in Bornean passerine birds reveals no introgression: implications for processes and patterns of speciation

Cited by 23 publications

References 52 publications

Biotic interactions help explain variation in elevational range limits of birds among Bornean mountains

Biotic interactions help explain variation in elevational range limits of birds among Bornean mountains

Gene exchange between two divergent species of the fungal human pathogen,Coccidioides

Speciation and gene flow across an elevational gradient in New Guinea kingfishers

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