Xinrui Li

and 6 more

Climate oscillations may drive the divergence of ancestral species through habitat isolation, species distribution patterns, and the cessation of gene flow. However, traditional ecological niche models lack the consideration for the genetic adaptation of species, thus it’s difficult to understand how climate oscillations affect species divergence by changing their climatic suitability and historical demography. We analyzed the impact of climate change on the divergence of two langur species, François’ langur and White-headed langur, using Maxent, Genotype–Environment Association (GEA) models and genomic data. Our results indicate that 1) Climatic suitability for François’ langur and White-headed langur has separated from the Last Interglacial (LIG, 120,000-140,000 years ago) to the Last Glacial Maximum (LGM); 2) Although the effective population size for both species decreased between the LIG and the LGM, the effective population size of François’ langur increased more quickly than that of White-headed langur from the LGM to the present; 3) Historical patterns of climate change have resulted in periods of expanded and contracted climatic suitability, with each species experiencing periods of interspecific genetic isolation and periods of interspecific genetic exchange; and 4) Human activities and future climate change have contracted the range of François’ langur (in China) and White-headed langur. Climate oscillation, population isolation, and in situ evolution in refugia from the LIG to the LGM appear to have played a critical role in langur speciation and adaptive evolution. Overall, our results demonstrate how climatic oscillations and historical demography drive speciation, providing a new perspective on species divergence and conservation.

Zi-Min Hu

and 10 more

Seagrasses play a vital role in structuring coastal marine ecosystems, but their distributional range and genetic diversity have declined rapidly over the past decades. In order to improve conservation of seagrass species, it is important to predict how climate change may impact their ranges. Such predictions are typically made with correlative species distribution models (SDMs), which can estimate a species’ potential distribution under present and future climatic scenarios given species’ presence data and climatic predictor variables. However, these models are typically constructed with species-level data, and thus ignore intraspecific genetic variability of populations that potentially have adaptations to heterogeneous climatic conditions. Here, we explore the link between intraspecific adaptation and niche differentiation in Thalassia hemprichii, a seagrass broadly distributed in the tropical Indo-Pacific Ocean and a crucial provider of habitat for numerous marine species. Using microsatellite-based genotyping, we identified two distinct phylogeographical lineages within the nominal species and found an intermediate level of differentiation in their multidimensional environmental niches, suggesting the possibility for local adaptation. We then compared projections of the species’ habitat suitability under climate change scenarios using species-level and lineage-level SDMs. In the Central Tropical Indo-Pacific region, both models predicted considerable range contraction in the future, but the lineage-level model predicted more severe habitat loss. The two modelling approaches predicted opposite pattern in habitat change in the Western Tropical Indo-Pacific region. Our results highlight the necessity of conserving distinct populations and genetic pools under climate change and have important implications for guiding future management of seagrasses.

Zhiqiang Han

and 6 more

Knowledge about the genetic adaptations of various organisms to heterogeneous environments in the Northwestern Pacific remains poorly understood. The mechanism by which organisms adapt to temperature in response to climate change must be determined. We sequenced the whole genomes of Sillago japonica individuals collected from different latitudinal locations along the coastal waters of China and Japan to detect the possible thermal adaptations. A total of 5.48 million single nucleotide polymorphisms (SNPs) from five populations revealed a complete genetic break between the China and Japan groups. This genetic structure was partly attributed to geographic distance and local adaptation. Although parallel evolution within species is comparatively rare at the DNA level, the shared natural selection genes between two isolated populations (Zhoushan and Ise Bay/Tokyo Bay) indicated possible parallel evolution at the genetic level induced by temperature. Our result proved that the process of temperature selection on isolated populations is repeatable. Additionally, the candidate genes were functionally related to membrane fluidity in cold environments and the cytoskeleton in high-temperature environments. These results advance our understanding of the genetic mechanisms underlying the rapid adaptations of fish species. Projections of species distribution models suggested that China and Japan groups may have different responses to future climate changes: the former could expand, whereas the latter may contract. The results of the present population genomic work expand our understanding of genetic differentiation and adaptation to changing environments.

Xin Wang

and 6 more

General theory predicts that ecological specialization should be rare in marine ecosystems, given that barriers to dispersal are less effective in the vastness of the sea compared to terrestrial settings. This paradigm, however, hardly fits with classical theories of local adaptation, leaving the question open of as to how marine diversity could originate at a restricted spatial scale. We tackled this so-called “Marine Speciation Paradox” by investigating how local specialization could arise in a widely distributed marine species, the seaweed pipefish Syngnathus schlegeli. We integrated morphological, genomic, and niche-based evidences to unravel geographical structuring in S. schlegeli populations. We revealed the existence of a north-to-south phenotypic gradient in eye size among S. schlegeli populations. This morphological differentiation was paralleled by genetic divergence, with South China Sea populations emerging as relatively independent. The north-to-south phylogeographical structuring was further corroborated by ecological analyses. We observed high niche differentiation among northern, central, and southern populations, resulting from both niche expansion and niche shift processes. Projected habitat suitability onto the Last Glacial Maximum revealed the existence of historical barriers to dispersal between the South and East China seas. We showed that the effect of this historical segregation, in concert with niche-driven ecological differentiation, lead to establishment of three distinct clades across the widely distributed marine pipefish. Ultimately, our study demonstrates that even the sea environment maintains the potential for adaptive radiation and ecological specialization, suggesting that ‘marine speciation’ may actually be far from being ‘paradoxical’.